The Salmonella enterica pan-genome

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.

Genome sequencing and analysis of Salmonella enterica subsp. enterica serotype Enteritidis PT4 578: insights into pathogenicity and virulence

Salmonella enterica serotype Enteritidis is a generalist serotype that adapts to different hosts and transmission niches. It has significant epidemiological relevance and is among the most prevalent serotypes distributed in several countries. Salmonella Enteritidis causes self-limited gastroenteritis in humans, which can progress to systemic infection in immunocompromised individuals. The Salmonella pathogenicity mechanism is multifactorial and complex, including the presence of virulence factors that are encoded by virulence genes. Poultry products are considered significant reservoirs of many Salmonella serotypes, and Salmonella Enteritidis infections are often related to the consumption of chicken meat and eggs. This study reports the whole-genome sequence of Salmonella Enteritidis PT4 strain 578. A total of 165 genes (3.66%) of the 4506 coding sequences (CDS) predicted in its genome are virulence factors associated with cell invasion, intestinal colonization, and intracellular survival. The genome harbours twelve Salmonella pathogenicity islands (SPIs), with the SPI-1 and SPI-2 genes encoding type III secretion systems (T3SS) showing high conservation. Six prophage-related sequences were found, with regions of intact prophages corresponding to Salmon_118970_sal3 and Gifsy-2. The genome also contains two CRISPR systems. Comparative genome analysis with Salmonella Enteritidis ATCC 13076, Salmonella Typhimurium ATCC 13311, and Salmonella Typhimurium ATCC 14028 demonstrates that most unshared genes are related to metabolism, membrane, and hypothetical proteins. Finally, the phenotypic characterization evidenced differences among Salmonella Enteritidis PT4 578 and the other three serotypes regarding the expression of the red, dry, and rough (rdar) morphotype and biofilm formation. Overall, the genomic characterization and phenotypic properties expand knowledge of the mechanisms of pathogenicity in Salmonella Enteritidis PT4 578.

Heterogeneity of Salmonella enterica lipopolysaccharide counteracts macrophage and antimicrobial peptide defenses

Salmonella enterica is comprised of over 2,500 serovars, in which non-typhoidal serovars (NTS), Enteritidis (SE), and Typhimurium (STM) are the most clinically associated with human infections. Although NTS have similar genetic elements to cause disease, phenotypic variation including differences in lipopolysaccharide (LPS) composition may control immune evasion. Here, we demonstrate that macrophage host defenses and LL-37 antimicrobial efficacy against SE and STM are substantially altered by LPS heterogeneity. We found that SE evades macrophage killing by inhibiting phagocytosis while STM survives better intracellularly post-phagocytosis. SE-infected macrophages failed to activate the inflammasomes and subsequently produced less interleukin-1β (IL-1β), IL-18, and interferon λ. Inactivation of LPS biosynthesis genes altered LPS composition, and the SE LPS-altered mutants could no longer inhibit phagocytosis, inflammasome activation, and type II interferon signaling. In addition, SE and STM showed differential susceptibility to the antimicrobials LL-37 and colistin, and alteration of LPS structure substantially increased susceptibility to these molecules. Collectively, our findings highlight that modification of LPS composition by Salmonella increases resistance to host defenses and antibiotics.

Unveiling a Comprehensive Multi-epitope Subunit Vaccine Strategy Against Salmonella subsp. enterica: Bridging Core, Subtractive Proteomics, and Immunoinformatics

Salmonella subsp. enterica (SE) presents a significant global health challenge in both developed and developing countries. Current SE vaccines have limitations, targeting specific strains and demonstrating moderate efficacy in adults, while also being unsuitable for young children and often unaffordable in regions with lower income levels where the disease is prevalent. To address these challenges, this study employed a computational approach integrating core proteomics, subtractive proteomics, and immunoinformatics to develop a universal SE vaccine and identify potential drug targets. Analysis of the core proteome of 185 SE strains revealed 1964 conserved proteins. Subtractive proteomics identified 9 proteins as potential vaccine candidates and 41 as novel drug targets. Using reverse vaccinology-based immunoinformatics, four multi-epitope-based subunit vaccine constructs (MESVCs) were designed, aiming to stimulate cytotoxic T lymphocyte, helper T lymphocyte, and linear B lymphocyte responses. These constructs underwent comprehensive evaluations for antigenicity, immunogenicity, toxicity, hydropathicity, and physicochemical properties. Predictive modeling, refinement, and validation were conducted to determine the secondary and tertiary structures of the SE-MESVCs, followed by docking studies with MHC-I, MHC-II, and TLR4 receptors. Molecular docking assessments showed favorable binding with all three receptors, with SE-MESVC-4 exhibiting the most promising binding energy. Molecular dynamics simulations confirmed the binding affinity and stability of SE-MESVC-4 with the TLR4/MD2 complex. Additionally, codon optimization and in silico cloning verified the efficient translation and successful expression of SE-MESVC-4 in Escherichia coli (E. coli) str. K12. Subsequent in silico immune simulation evaluated the efficacy of SE-MESVC-4 in triggering an effective immune response. These results suggest that SE-MESVC-4 may induce both humoral and cellular immune responses, making it a potential candidate for an effective SE vaccine. However, further experimental investigations are necessary to validate the immunogenicity and efficacy of SE-MESVC-4, bringing us closer to effectively combating SE infections.

Salmonella Hadar linked to two distinct transmission vehicles highlights challenges to enteric disease outbreak investigations

In 2020, an outbreak of Salmonella Hadar illnesses was linked to contact with non-commercial, privately owned (backyard) poultry including live chickens, turkeys, and ducks, resulting in 848 illnesses. From late 2020 to 2021, this Salmonella Hadar strain caused an outbreak that was linked to ground turkey consumption. Core genome multilocus sequence typing (cgMLST) analysis determined that the Salmonella Hadar isolates detected during the outbreak linked to backyard poultry and the outbreak linked to ground turkey were closely related genetically (within 0-16 alleles). Epidemiological and traceback investigations were unable to determine how Salmonella Hadar detected in backyard poultry and ground turkey were linked, despite this genetic relatedness. Enhanced molecular characterization methods, such as analysis of the pangenome of Salmonella isolates, might be necessary to understand the relationship between these two outbreaks. Similarly, enhanced data collection during outbreak investigations and further research could potentially aid in determining whether these transmission vehicles are truly linked by a common source and what reservoirs exist across the poultry industries that allow Salmonella Hadar to persist. Further work combining epidemiological data collection, more detailed traceback information, and genomic analysis tools will be important for monitoring and investigating future enteric disease outbreaks.

Diversification of gene content in the Mycobacterium tuberculosis complex is determined by phylogenetic and ecological signatures

We analyzed the pan-genome and gene content modulation of the most diverse genome data set of the Mycobacterium tuberculosis complex (MTBC) gathered to date. The closed pan-genome of the MTBC was characterized by reduced accessory and strain-specific genomes, compatible with its clonal nature. However, significantly fewer gene families were shared between MTBC genomes as their phylogenetic distance increased. This effect was only observed in inter-species comparisons, not within-species, which suggests that species-specific ecological characteristics are associated with changes in gene content. Gene loss, resulting from genomic deletions and pseudogenization, was found to drive the variation in gene content. This gene erosion differed among MTBC species and lineages, even within M. tuberculosis, where L2 showed more gene loss than L4. We also show that phylogenetic proximity is not always a good proxy for gene content relatedness in the MTBC, as the gene repertoire of Mycobacterium africanum L6 deviated from its expected phylogenetic niche conservatism. Gene disruptions of virulence factors, represented by pseudogene annotations, are mostly not conserved, being poor predictors of MTBC ecotypes. Each MTBC ecotype carries its own accessory genome, likely influenced by distinct selective pressures such as host and geography. It is important to investigate how gene loss confer new adaptive traits to MTBC strains; the detected heterogeneous gene loss poses a significant challenge in elucidating genetic factors responsible for the diverse phenotypes observed in the MTBC. By detailing specific gene losses, our study serves as a resource for researchers studying the MTBC phenotypes and their immune evasion strategies.IMPORTANCEIn this study, we analyzed the gene content of different ecotypes of the Mycobacterium tuberculosis complex (MTBC), the pathogens of tuberculosis. We found that changes in their gene content are associated with their ecological features, such as host preference. Gene loss was identified as the primary driver of these changes, which can vary even among different strains of the same ecotype. Our study also revealed that the gene content relatedness of these bacteria does not always mirror their evolutionary relationships. In addition, some genes of virulence can be variably lost among strains of the same MTBC ecotype, likely helping them to evade the immune system. Overall, our study highlights the importance of understanding how gene loss can lead to new adaptations in these bacteria and how different selective pressures may influence their genetic makeup.

The pangenome analysis of the environmental source Salmonella enterica highlights a diverse accessory genome and a distinct serotype clustering

Salmonella remains the leading cause of foodborne infections globally. Environmental reservoirs, particularly aquatic bodies, serve as conduits for the fecal-oral transmission of this pathogen. While the gastrointestinal tract is traditionally considered the primary habitat of Salmonella, mounting evidence suggests the bacterium's capacity for survival in external environments. The application of advanced technological platforms, such as next-generation sequencing, facilitates a comprehensive analysis of Salmonella's genomic features. This study aims to characterize the genomic composition of Salmonella isolates from river water, contributing to a potential paradigm shift and advancing public health protection. A total of 25 river water samples were collected and processed, followed by microbiological isolation of Salmonella strains, which were then sequenced. Genomic characterization revealed adaptive mechanisms, including gene duplication. Furthermore, an open pangenome, predisposed to incorporating foreign genetic material, was identified. Notably, antibiotic resistance genes were found to be part of the core genome, challenging previous reports that placed them in the accessory genome.

Step-by-Step Bacterial Genome Comparison

Thanks to advancements in genome sequencing and bioinformatics, thousands of bacterial genome sequences are available in public databases. This presents an opportunity to study bacterial diversity in unprecedented detail. This chapter describes a complete bioinformatics workflow for comparative genomics of bacterial genomes, including genome annotation, pangenome reconstruction and visualization, phylogenetic analysis, and identification of sequences of interest such as antimicrobial-resistance genes, virulence factors, and phage sequences. The workflow uses state-of-the-art, open-source tools. The workflow is presented by means of a comparative analysis of Salmonella enterica serovar Typhimurium genomes. The workflow is based on Linux commands and scripts, and result visualization relies on the R environment. The chapter provides a step-by-step protocol that researchers with basic expertise in bioinformatics can easily follow to conduct investigations on their own genome datasets.

For Someone, You Are the Whole World: Host-Specificity of Salmonella enterica

Salmonella enterica is a bacterial pathogen known to cause gastrointestinal infections in diverse hosts, including humans and animals. Despite extensive knowledge of virulence mechanisms, understanding the factors driving host specificity remains limited. In this study, we performed a comprehensive pangenome-wide analysis of S. enterica to identify potential loci determining preference towards certain hosts. We used a dataset of high-quality genome assemblies grouped into 300 reference clusters with a special focus on four host groups: humans, pigs, cattle, and birds. The reconstructed pangenome was shown to be open and enriched with the accessory component implying high genetic diversity. Notably, phylogenetic inferences did not correspond to the distribution of affected hosts, as large compact phylogenetic groups were absent. By performing a pangenome-wide association study, we identified potential host specificity determinants. These included multiple genes encoding proteins involved in distinct infection stages, e.g., secretion systems, surface structures, transporters, transcription regulators, etc. We also identified antibiotic resistance loci in host-adapted strains. Functional annotation corroborated the results obtained with significant enrichments related to stress response, antibiotic resistance, ion transport, and surface or extracellular localization. We suggested categorizing the revealed specificity factors into three main groups: pathogenesis, resistance to antibiotics, and propagation of mobile genetic elements (MGEs).

Role of lactoyl-glutathione lyase of Salmonella in the colonization of plants under salinity stress

Salmonella, a foodborne human pathogen, can colonize the members of the kingdom Plantae. However, the basis of the persistence of Salmonella in plants is largely unknown. Plants encounter various biotic and abiotic stress agents in soil. We conjectured that methylglyoxal (MG), one of the common metabolites that accumulate in plants during both biotic and abiotic stress, plays a role in regulating the plant-Salmonella interaction. The interaction of Salmonella Typhimurium with plants under salinity stress was investigated. It was observed that wild-type Salmonella Typhimurium can efficiently colonize the root, but mutant bacteria lacking MG detoxifying enzyme, lactoyl-glutathione lyase (Lgl), showed lower colonization in roots exclusively under salinity stress. This colonization defect is due to the poor viability of the mutated bacterial strains under these conditions. This is the first report to prove the role of MG-detoxification genes in the colonization of stressed plants and highlights the possible involvement of metabolic genes in the evolution of the plant-associated life of Salmonella.

Development of a novel machine learning-based weighted modeling approach to incorporate Salmonella enterica heterogeneity on a genetic scale in a dose-response modeling framework

Estimating microbial dose-response is an important aspect of a food safety risk assessment. In recent years, there has been considerable interest to advance these models with potential incorporation of gene expression data. The aim of this study was to develop a novel machine learning model that considers the weights of expression of Salmonella genes that could be associated with illness, given exposure, in hosts. Here, an elastic net-based weighted Poisson regression method was proposed to identify Salmonella enterica genes that could be significantly associated with the illness response, irrespective of serovar. The best-fit elastic net model was obtained by 10-fold cross-validation. The best-fit elastic net model identified 33 gene expression-dose interaction terms that added to the predictability of the model. Of these, nine genes associated with Salmonella metabolism and virulence were found to be significant by the best-fit Poisson regression model (p < 0.05). This method could improve or redefine dose-response relationships for illness from relative proportions of significant genes from a microbial genetic dataset, which would help in refining endpoint and risk estimations.

Computational biology: Role and scope in taming antimicrobial resistance

BACKGROUND

Infectious diseases pose many challenges due to increasing threat of antimicrobial resistance, which necessitates continuous research to develop novel strategies for development of new molecules with antibacterial activity. In the era of computational biology there are tools and techniques available to address and solve the disease management issues in the field of clinical microbiology. The sequencing techniques, structural biology and machine learning can be implemented collectively to tackle infectious diseases e.g. for the diagnosis, epidemiological typing, pathotyping, antimicrobial resistance detection as well as the discovery of novel drugs and vaccine biomarkers.

OBJECTIVES

The present review is a narrative review representing a comprehensive literature-based assessment regarding the use of whole genome sequencing, structural biology and machine learning for the diagnosis, molecular typing and antibacterial drug discovery.

CONTENT

Here, we seek to present an overview of molecular and structural basis of resistance to antibiotics, while focusing on the recent bioinformatics approaches in whole genome sequencing and structural biology. The application of next generation sequencing in management of bacterial infections focusing on investigation of microbial population diversity, genotypic resistance testing and scope for the identification of targets for novel drug and vaccine candidates, has been addressed along with the use of structural biophysics and artificial intelligence.

Pan-Genome Analysis of Transcriptional Regulation in Six Salmonella enterica Serovar Typhimurium Strains Reveals Their Different Regulatory Structures

Establishing transcriptional regulatory networks (TRNs) in bacteria has been limited to well-characterized model strains. Using machine learning methods, we established the transcriptional regulatory networks of six Salmonella enterica serovar Typhimurium strains from their transcriptomes. By decomposing a compendia of RNA sequencing (RNA-seq) data with independent component analysis, we obtained 400 independently modulated sets of genes, called iModulons. We (i) performed pan-genome analysis of the phylogroup structure of S. Typhimurium and analyzed the iModulons against this background, (ii) revealed different genetic signatures in pathogenicity islands that explained phenotypes, (iii) discovered three transport iModulons linked to antibiotic resistance, (iv) described concerted responses to cationic antimicrobial peptides, and (v) uncovered new regulons. Thus, by combining pan-genome and transcriptomic analytics, we revealed variations in TRNs across six strains of serovar Typhimurium. IMPORTANCE Salmonella enterica serovar Typhimurium is a pathogen involved in human nontyphoidal infections. Treating S. Typhimurium infections is difficult due to the species's dynamic adaptation to its environment, which is dictated by a complex transcriptional regulatory network (TRN) that is different across strains. In this study, we describe the use of independent component analysis to characterize the differential TRNs across the S. Typhimurium pan-genome using a compendium of high-quality RNA-seq data. This approach provided unprecedented insights into the differences between regulation of key cellular functions and pathogenicity in the different strains. The study provides an impetus to initiate a large-scale effort to reveal the TRN differences between the major phylogroups of the pathogenic bacteria, which could fundamentally impact personalizing treatments of bacterial pathogens.

Reverse engineering approach: a step towards a new era of vaccinology with special reference to Salmonella

INTRODUCTION

Salmonella is responsible for causing enteric fever, septicemia, and gastroenteritis in humans. Due to high disease burden and emergence of multi- and extensively drug-resistant Salmonella strains, it is becoming difficult to treat the infection with existing battery of antibiotics as we are not able to discover newer antibiotics at the same pace at which the pathogens are acquiring resistance. Though vaccines against Salmonella are available commercially, they have limited efficacy. Advancements in genome sequencing technologies and immunoinformatics approaches have solved the problem significantly by giving rise to a new era of vaccine designing, i.e. 'Reverse engineering.' Reverse engineering/vaccinology has expedited the vaccine identification process. Using this approach, multiple potential proteins/epitopes can be identified and constructed as a single entity to tackle enteric fever.

AREAS COVERED

This review provides details of reverse engineering approach and discusses various protein and epitope-based vaccine candidates identified using this approach against typhoidal Salmonella.

EXPERT OPINION

Reverse engineering approach holds great promise for developing strategies to tackle the pathogen(s) by overcoming the limitations posed by existing vaccines. Progressive advancements in the arena of reverse vaccinology, structural biology, and systems biology combined with an improved understanding of host-pathogen interactions are essential components to design new-generation vaccines.

Comparative Genomic Analysis Discloses Differential Distribution of Antibiotic Resistance Determinants between Worldwide Strains of the Emergent ST213 Genotype of Salmonella Typhimurium

Salmonella enterica constitutes a global public health concern as one of the main etiological agents of human gastroenteritis. The Typhimurium serotype is frequently isolated from human, animal, food, and environmental samples, with its sequence type 19 (ST19) being the most widely distributed around the world as well as the founder genotype. The replacement of the ST19 genotype with the ST213 genotype that has multiple antibiotic resistance (MAR) in human and food samples was first observed in Mexico. The number of available genomes of ST213 strains in public databases indicates its fast worldwide dispersion, but its public health relevance is unknown. A comparative genomic analysis conducted as part of this research identified the presence of 44 genes, 34 plasmids, and five point mutations associated with antibiotic resistance, distributed across 220 genomes of ST213 strains, indicating the MAR phenotype. In general, the grouping pattern in correspondence to the presence/absence of genes/plasmids that confer antibiotic resistance cluster the genomes according to the geographical origin where the strain was isolated. Genetic determinants of antibiotic resistance group the genomes of North America (Canada, Mexico, USA) strains, and suggest a dispersion route to reach the United Kingdom and, from there, the rest of Europe, then Asia and Oceania. The results obtained here highlight the worldwide public health relevance of the ST213 genotype, which contains a great diversity of genetic elements associated with MAR.

Exploring the predictive capability of advanced machine learning in identifying severe disease phenotype in Salmonella enterica

The past few years have seen a significant increase in availability of whole genome sequencing information, allowing for its incorporation in predictive modeling for foodborne pathogens to account for inter- and intra-species differences in their virulence. However, this is hindered by the inability of traditional statistical methods to analyze such large amounts of data compared to the number of observations/isolates. In this study, we have explored the applicability of machine learning (ML) models to predict the disease outcome, while identifying features that exert a significant effect on the prediction. This study was conducted on Salmonella enterica, a major foodborne pathogen with considerable inter- and intra-serovar variation. WGS of isolates obtained from various sources (i.e., human, chicken, and swine) were used as input in four machine learning models (logistic regression with ridge, random forest, support vector machine, and AdaBoost) to classify isolates based on disease severity (extraintestinal vs. gastrointestinal) in the host. The predictive performances of all models were tested with and without Elastic Net regularization to combat dimensionality issues. Elastic Net-regularized logistic regression model showed the best area under the receiver operating characteristic curve (AUC-ROC; 0.86) and outcome prediction accuracy (0.76). Additionally, genes coding for transcriptional regulation, acidic, oxidative, and anaerobic stress response, and antibiotic resistance were found to be significant predictors of disease severity. These genes, which were significantly associated with each outcome, could possibly be input in amended, gene-expression-specific predictive models to estimate virulence pattern-specific effect of Salmonella and other foodborne pathogens on human health.

Salmonella Genomics in Public Health and Food Safety

The species Salmonella enterica comprises over 2,600 serovars, many of which are known to be intracellular pathogens of mammals, birds, and reptiles. It is now apparent that Salmonella is a highly adapted environmental microbe and can readily persist in a number of environmental niches, including water, soil, and various plant (including produce) species. Much of what is known about the evolution and diversity of nontyphoidal Salmonella serovars (NTS) in the environment is the result of the rise of the genomics era in enteric microbiology. There are over 340,000 Salmonella genomes available in public databases. This extraordinary breadth of genomic diversity now available for the species, coupled with widespread availability and affordability of whole-genome sequencing (WGS) instrumentation, has transformed the way in which we detect, differentiate, and characterize Salmonella enterica strains in a timely way. Not only have WGS data afforded a detailed and global examination of the molecular epidemiological movement of Salmonella from diverse environmental reservoirs into human and animal hosts, but they have also allowed considerable consolidation of the diagnostic effort required to test for various phenotypes important to the characterization of Salmonella. For example, drug resistance, serovar, virulence determinants, and other genome-based attributes can all be discerned using a genome sequence. Finally, genomic analysis, in conjunction with functional and phenotypic approaches, is beginning to provide new insights into the precise adaptive changes that permit persistence of NTS in so many diverse and challenging environmental niches.

Developing Recombinant Antibodies by Phage Display Against Infectious Diseases and Toxins for Diagnostics and Therapy

Antibodies are essential molecules for diagnosis and treatment of diseases caused by pathogens and their toxins. Antibodies were integrated in our medical repertoire against infectious diseases more than hundred years ago by using animal sera to treat tetanus and diphtheria. In these days, most developed therapeutic antibodies target cancer or autoimmune diseases. The COVID-19 pandemic was a reminder about the importance of antibodies for therapy against infectious diseases. While monoclonal antibodies could be generated by hybridoma technology since the 70ies of the former century, nowadays antibody phage display, among other display technologies, is robustly established to discover new human monoclonal antibodies. Phage display is an in vitro technology which confers the potential for generating antibodies from universal libraries against any conceivable molecule of sufficient size and omits the limitations of the immune systems. If convalescent patients or immunized/infected animals are available, it is possible to construct immune phage display libraries to select in vivo affinity-matured antibodies. A further advantage is the availability of the DNA sequence encoding the phage displayed antibody fragment, which is packaged in the phage particles. Therefore, the selected antibody fragments can be rapidly further engineered in any needed antibody format according to the requirements of the final application. In this review, we present an overview of phage display derived recombinant antibodies against bacterial, viral and eukaryotic pathogens, as well as microbial toxins, intended for diagnostic and therapeutic applications.

Genomic Characterization of Salmonella enterica Isolates From Retail Meat in Beijing, China

Salmonella enterica remains one of the leading causes of foodborne bacterial disease. Retail meat is a major source of human salmonellosis. However, comparative genomic analyses of S. enterica isolates from retail meat from different sources in China are lacking. A total of 341 S. enterica strains were isolated from retail meat in sixteen districts of Beijing, China, at three different time points (January 1st, May 1st, and October 1st) in 2017. Comparative genomics was performed to investigate the genetic diversity, virulence and antimicrobial resistance gene (ARG) profiles of these isolates. The most common serotype was S. Enteritidis (203/341, 59.5%), which dominated among isolates from three different time points during the year. Laboratory retesting confirmed the accuracy of the serotyping results predicted by the Salmonella In Silico Typing Resource (SISTR) (96.5%). The pangenome of the 341 S. enterica isolates contained 13,931 genes, and the core genome contained 3,635 genes. Higher Salmonella phage 118970 sal3 (219/341, 64.2%) and Gifsy-2 (206/341, 60.4%) prevalence contributed to the diversity of the accessory genes, especially those with unknown functions. IncFII(S), IncX1, and IncFIB(S) plasmid replicons were more common in these isolates and were major sources of horizontally acquired foreign genes. The virulence gene profile showed fewer virulence genes associated with type III secretion systems in certain isolates from chicken. A total of 88 different ARGs were found in the 341 isolates. Three beta-lactamases, namely, bla_CTX–M–55 (n = 15), bla_CTX–M–14 (n = 11), and bla_CTX–M–65 (n = 11), were more prevalent in retail meats. The emergence of qnrE1 and bla_{CTX–M–123} indicated a potential increase in the prevalence of retail meats. After the prohibition of colistin in China, three and four isolates were positive for the colistin resistance genes mcr-1.1 and mcr-9, respectively. Thus, we explored the evolution and genomic features of S. enterica isolates from retail meats in Beijing, China. The diverse ARGs of these isolates compromise food security and are a clinical threat.

Genomic Analysis of Antimicrobial Resistance and Resistance Plasmids in Salmonella Serovars from Poultry in Nigeria

Antimicrobial resistance is a global public health concern, and resistance genes in Salmonella, especially those located on mobile genetic elements, are part of the problem. This study used phenotypic and genomic methods to identify antimicrobial resistance and resistance genes, as well as the plasmids that bear them, in Salmonella isolates obtained from poultry in Nigeria. Seventy-four isolates were tested for susceptibility to eleven commonly used antimicrobials. Plasmid reconstruction and identification of resistance and virulence genes were performed with a draft genome using in silico approaches in parallel with plasmid extraction. Phenotypic resistance to ciprofloxacin (50.0%), gentamicin (48.6%), nalidixic acid (79.7%), sulphonamides (71.6%) and tetracycline (59.5%) was the most observed. Antibiotic resistance genes (ARGs) detected in genomes corresponded well with these observations. Commonly observed ARGs included sul1, sul2, sul3, tet (A), tet (M), qnrS1, qnrB19 and a variety of aminoglycoside-modifying genes, in addition to point mutations in the gyrA and parC genes. Multiple ARGs were predicted to be located on IncN and IncQ1 plasmids of S. Schwarzengrund and S. Muenster, and most qnrB19 genes were carried by Col (pHAD28) plasmids. Seventy-two percent (19/24) of S. Kentucky strains carried multidrug ARGs located in two distinct variants of Salmonella genomic island I. The majority of strains carried full SPI-1 and SPI-2 islands, suggesting full virulence potential.

Genomic characterization and phylogenetic analysis of Salmonella enterica serovar Javiana

Salmonella enterica serovar Javiana is the fourth most reported serovar of laboratory-confirmed human Salmonella infections in the U.S. and in Tennessee (TN). Although Salmonella ser. Javiana is a common cause of human infection, the majority of cases are sporadic in nature rather than outbreak-associated. To better understand Salmonella ser. Javiana microbial population structure in TN, we completed a phylogenetic analysis of 111 Salmonella ser. Javiana clinical isolates from TN collected from Jan. 2017 to Oct. 2018. We identified mobile genetic elements and genes known to confer antibiotic resistance present in the isolates, and performed a pan-genome-wide association study (pan-GWAS) to compare gene content between clades identified in this study. The population structure of TN Salmonella ser. Javiana clinical isolates consisted of three genetic clades: TN clade I (n = 54), TN clade II (n = 4), and TN clade III (n = 48). Using a 5, 10, and 25 hqSNP distance threshold for cluster identification, nine, 12, and 10 potential epidemiologically-relevant clusters were identified, respectively. The majority of genes that were found to be over-represented in specific clades were located in mobile genetic element (MGE) regions, including genes encoding integrases and phage structures (91.5%). Additionally, a large portion of the over-represented genes from TN clade II (44.9%) were located on an 87.5 kb plasmid containing genes encoding a toxin/antitoxin system (ccdAB). Additionally, we completed phylogenetic analyses of global Salmonella ser. Javiana datasets to gain a broader insight into the population structure of this serovar. We found that the global phylogeny consisted of three major clades (one of which all of the TN isolates belonged to) and two cgMLST eBurstGroups (ceBGs) and that the branch length between the two Salmonella ser. Javiana ceBGs (1,423 allelic differences) was comparable to those from other serovars that have been reported as polyphyletic (929–2,850 allelic differences). This study demonstrates the population structure of TN and global Salmonella ser. Javiana isolates, a clinically important Salmonella serovar and can provide guidance for phylogenetic cluster analyses for public health surveillance and response.

Diverse lineages of multidrug resistant clinical Salmonella enterica and a cryptic outbreak in New Hampshire, USA revealed from a year-long genomic surveillance

Salmonella enterica, the causative agent of gastrointestinal diseases and typhoid fever, is a human and animal pathogen that causes significant mortality and morbidity worldwide. In this study, we examine the genomic diversity and phylogenetic relationships of 63 S. enterica isolates from human-derived clinical specimens submitted to the Department of Health and Human Services (DHHS) in the state of New Hampshire, USA in 2017. We found a remarkably large genomic, phylogenetic and serotype variation among the S. enterica isolates, dominated by serotypes Enteritidis (sequence type [ST] 11), Heidelberg (ST 15) and Typhimurium (ST 19). Analysis of the distribution of single nucleotide polymorphisms in the core genome suggests that the ST 15 cluster is likely a previously undetected or cryptic outbreak event that occurred in the south/southeastern part of New Hampshire in August-September. We found that nearly all of the clinical S. enterica isolates carried horizontally acquired genes that confer resistance to multiple classes of antimicrobials, most notably aminoglycosides, fluoroquinolones and macrolides. Majority of the isolates (76.2%) carry at least four resistance determinants per genome. We also detected the genes mdtK and mdsABC that encode multidrug efflux pumps and the gene sdiA that encodes a regulator for a third multidrug resistance pump. Our results indicate rapid microevolution and geographical dissemination of multidrug resistant lineages over a short time span. These findings are critical to aid the DHHS and similar public health laboratories in the development of effective disease control measures, epidemiological studies and treatment options for serious Salmonella infections.

From sequence to information

Today massive amounts of sequenced metagenomic and metatranscriptomic data from different ecological niches and environmental locations are available. Scientific progress depends critically on methods that allow extracting useful information from the various types of sequence data. Here, we will first discuss types of information contained in the various flavours of biological sequence data, and how this information can be interpreted to increase our scientific knowledge and understanding. We argue that a mechanistic understanding of biological systems analysed from different perspectives is required to consistently interpret experimental observations, and that this understanding is greatly facilitated by the generation and analysis of dynamic mathematical models. We conclude that, in order to construct mathematical models and to test mechanistic hypotheses, time-series data are of critical importance. We review diverse techniques to analyse time-series data and discuss various approaches by which time-series of biological sequence data have been successfully used to derive and test mechanistic hypotheses. Analysing the bottlenecks of current strategies in the extraction of knowledge and understanding from data, we conclude that combined experimental and theoretical efforts should be implemented as early as possible during the planning phase of individual experiments and scientific research projects.

This article is part of the theme issue ‘Integrative research perspectives on marine conservation’.

Pathogenicity of clinical Salmonella enterica serovar Typhimurium isolates from Thailand in a mouse colitis model

Salmonella enterica serovar Typhimurium (S. Typhimurium [STM]) is a leading cause of nontyphoidal salmonellosis (NTS) worldwide. The pathogenesis of NTS has been studied extensively using a streptomycin-pretreated mouse colitis model with the limited numbers of laboratory STM strains. However, the pathogenicity of the clinically isolated STM (STMC) strains endemic in Thailand in mice has not been explored. The aim of this study was to compare the pathogenicity of STMC strains collected from Northern Thailand with the laboratory STM (IR715) in mice. Five STMC isolates were obtained from the stool cultures of patients with acute NTS admitted to Maharaj Nakorn Chiang Mai Hospital in 2016 and 2017. Detection of virulence genes and sequence type (ST) of the strains was performed. Female C57BL/6 mice were pretreated with streptomycin sulfate 1 day prior to oral infection with STM. On Day 4 postinfection, mice were euthanized, and tissues were collected to analyze the bacterial numbers, tissue inflammation, and cecal histopathological score. We found that all five STMC strains are ST34 and conferred the same or reduced pathogenicity compared with that of IR715 in mice. A strain-specific effect of ST34 on mouse gut colonization was also observed. Thailand STM ST34 exhibited a significant attenuated systemic infection in mice possibly due to the lack of spvABC-containing virulence plasmid.

Antimicrobial Drug Resistance in Salmonella enteritidis Isolated From Edible Snakes With Pneumonia and Its Pathogenicity in Chickens

The growing consumption of snakes in China has led to a boom in edible snakes farming. Food producing reptiles, such as snakes can carry many pathogenic microbes and potentially infect humans. Here, we report the occurrence of multi drug resistant Salmonella enteritidis strains isolated from edible snakes in China. Our results showed that the isolated S. enteritidis was resistant to the majority of the tested drugs and sensitive to tetracycline and amikacin. Antimicrobial susceptibility test showed that the strains carried the blaTEM, qnrD, aadA₁, catA₁ o, sul I, and sul II genes. The pathogenicity testing of the S. enteritidis isolated strains showed that these strains were highly pathogenic (75% mortality, with LD₅₀ at 10^7.7 CFU/mL). The chickens in the high-dose groups developed acute septicemia and died within 24 h. Results of the dissection showed extensive abdominal bleeding and swelling in the high dose groups, as well as hyperemia edema in the livers, lungs, kidneys, cecum, and bursa of the chickens, with spotty bleeding. In addition, rod-shaped bacterial aggregation was also seen in the visual field. A total of 23 virulence genes, mainly associated with pathogenicity island were tested, of which 8 genes including avrA, iacP, prgK, ssrA, siiD (spi4D), siiE, spi4H, and pipC were found positive. Altogether, our results provide useful information regarding edible snakes contaminated with S. enteritidis, which may have public health implications.

Genomic analyses of multidrug-resistant Salmonella Indiana, Typhimurium, and Enteritidis isolates using MinION and MiSeq sequencing technologies

We sequenced 25 isolates of phenotypically multidrug-resistant Salmonella Indiana (n = 11), Typhimurium (n = 8), and Enteritidis (n = 6) using both MinION long-read [SQK-LSK109 and flow cell (R9.4.1)] and MiSeq short-read (Nextera XT and MiSeq Reagent Kit v2) sequencing technologies to determine the advantages of each approach in terms of the characteristics of genome structure, antimicrobial resistance (AMR), virulence potential, whole-genome phylogeny, and pan-genome. The MinION reads were base-called in real-time using MinKnow 3.4.8 integrated with Guppy 3.0.7. The long-read-only assembly, Illumina-only assembly, and hybrid assembly pipelines of Unicycler 0.4.8 were used to generate the MinION, MiSeq, and hybrid assemblies, respectively. The MinION assemblies were highly contiguous compared to the MiSeq assemblies but lacked accuracy, a deficiency that was mitigated by adding the MiSeq short reads through the Unicycler hybrid assembly which corrected erroneous single nucleotide polymorphisms (SNPs). The MinION assemblies provided similar predictions of AMR and virulence potential compared to the MiSeq and hybrid assemblies, although they produced more total false negatives of AMR genotypes, primarily due to failure in identifying tetracycline resistance genes in 11 of the 19 MinION assemblies of tetracycline-resistant isolates. The MinION assemblies displayed a large genetic distance from their corresponding MiSeq and hybrid assemblies on the whole-genome phylogenetic tree, indicating that the lower read accuracy of MinION sequencing caused incorrect clustering. The pan-genome of the MinION assemblies contained significantly more accessory genes and less core genes compared to the MiSeq and hybrid assemblies, suggesting that although these assemblies were more contiguous, their sequencing errors reduced accurate genome annotations. Our research demonstrates that MinION sequencing by itself provides an efficient assessment of the genome structure, antimicrobial resistance, and virulence potential of Salmonella; however, it is not sufficient for whole-genome phylogenetic and pan-genome analyses. MinION in combination with MiSeq facilitated the most accurate genomic analyses.

Genomic profiling of antimicrobial resistance genes in clinical isolates of Salmonella Typhi from patients infected with Typhoid fever in India

The development of multidrug resistance in Salmonella enterica serovar Typhi currently forms a major roadblock for the treatment of enteric fever. This poses a major health problem in endemic regions and extends to travellers returning from developing countries. The appearance of fluoroquinolone non-susceptible strains has resulted in use of ceftriaxone as drug of choice with azithromycin being recommended for uncomplicated cases of typhoid fever. A recent sporadic instance of decreased susceptibility to the latest drug regime has necessitated a detailed analysis of antimicrobial resistance genes and possible relationships with their phenotypes to facilitate selection of future treatment regimes. Whole genome sequencing (WGS) was conducted for 133 clinical isolates from typhoid patients. Sequence output files were processed for pan-genome analysis and prediction of antimicrobial resistance genes. The WGS analyses disclosed the existence of fluoroquinolone resistance conferring mutations in gyrA, gyrB, parC and parE genes of all strains. Acquired resistance determining mechanisms observed included catA1 genes for chloramphenicol resistance, dfrA7, dfrA15, sul1 and sul2 for trimethoprim-sulfamethoxazole and bla_TEM-116/bla_TEM-1B genes for amoxicillin. No resistance determinants were found for ceftriaxone and cefixime. The genotypes were further correlated with their respective phenotypes for chloramphenicol, ampicillin, co-trimoxazole, ciprofloxacin and ceftriaxone. A high correlation was observed between genotypes and phenotypes in isolates of S. Typhi. The pan-genome analysis revealed that core genes were enriched in metabolic functions and accessory genes were majorly implicated in pathogenesis and antimicrobial resistance. The pan-genome of S. Typhi appears to be closed (B_pan  =  0.09) as analysed by Heap’s law. Simpson’s diversity index of 0.51 showed a lower level of genetic diversity among isolates of S. Typhi. Overall, this study augments the present knowledge that WGS can help predict resistance genotypes and eventual correlation with phenotypes, enabling the chance to spot AMR determinants for fast diagnosis and prioritize antibiotic use directly from sequence.

Comprehensive Genome Analysis on the Novel Species Sphingomonas panacis DCY99T Reveals Insights into Iron Tolerance of Ginseng

Plant growth-promoting rhizobacteria play vital roles not only in plant growth, but also in reducing biotic/abiotic stress. Sphingomonas panacis DCY99T is isolated from soil and root of Panax ginseng with rusty root disease, characterized by raised reddish-brown root and this is seriously affects ginseng cultivation. To investigate the relationship between 159 sequenced Sphingomonas strains, pan-genome analysis was carried out, which suggested genomic diversity of the Sphingomonas genus. Comparative analysis of S. panacis DCY99T with Sphingomonas sp. LK11 revealed plant growth-promoting potential of S. panacis DCY99T through indole acetic acid production, phosphate solubilizing, and antifungal abilities. Detailed genomic analysis has shown that S. panacis DCY99T contain various heavy metals resistance genes in its genome and the plasmid. Functional analysis with Sphingomonas paucimobilis EPA505 predicted that S. panacis DCY99T possess genes for degradation of polyaromatic hydrocarbon and phenolic compounds in rusty-ginseng root. Interestingly, when primed ginseng with S. panacis DCY99T during high concentration of iron exposure, iron stress of ginseng was suppressed. In order to detect S. panacis DCY99T in soil, biomarker was designed using spt gene. This study brings new insights into the role of S. panacis DCY99T as a microbial inoculant to protect ginseng plants against rusty root disease.

Genome Sequence of an Emerging Salmonella enterica Serovar Infantis and Genomic Comparison with Other S. Infantis Strains

Salmonella enterica serovar Infantis (S. Infantis) is one of the dominant serovars of the bacterial pathogen S. enterica. In recent years, the number of human infections caused by S. Infantis has been increasing in many countries, and often the emerging population harbors a unique virulence-resistant megaplasmid called plasmid of emerging S. Infantis (pESI). Here, we report the complete gap-free genome sequence of the S. Infantis Israeli emerging clone and compare its chromosome and pESI sequences with other complete S. Infantis genomes. We show a conserved presence of the Salmonella pathogenicity islands 1-6, 9, 11, 12, and CS54 and a common integration of five bacteriophages in the S. Infantis chromosome. In contrast, we found variable presence of additionally three chromosomally integrated phages and eight modular regions in pESI, which contribute to the genetic and phenotypic diversity (including antimicrobial resistance) of this ubiquitous foodborne pathogen.

Salmonella from a Microtidal Estuary Are Capable of Invading Human Intestinal Cell Lines

Faecal contamination poses health risks for the recreational users of urban estuaries. However, our understanding of the potential pathogenicity of faecal microbes in these environments is limited. To this end, a study was conducted to understand the spatial and seasonal distribution of Salmonella in water and sediments of the Yarra River estuary, Melbourne, Australia. Among 210 samples in total, culturable Salmonella were recovered from 27%, 17%, and 19% of water, bank, and bed sediment samples, respectively. The combined detection increased from 15% in winter to 32% in summer (p < 0.05) indicating seasonal variation as potential part of public health risk assessments. Further, pathogenic potential of the Salmonella isolates was characterised via the quantification of attachment and invasion capacity using human epithelial colorectal cell line Caco-2 on a subset of isolates (n = 62). While all of these isolates could attach and invade Caco-2 cells, 52% and 13% of these showed greater attachment and invasiveness, respectively, than the corresponding mean values for S. Typhimurium ATCC14028 control. Isolates from winter were on average more invasive (seven out of eight isolates with the highest invasiveness recovered from the colder sampling period) than the isolates from summer, and Salmonella collected during summer showed lower invasion (p < 0.05) compared with the control. Similar low invasion compared with the same control was observed for isolates recovered from bank sediment (p < 0.05). While the higher prevalence in summer may imply higher risks during these peak recreational periods, it is essential that this information is used in combination with quantitative microbial risk assessments to fully understand the health risks posed by Salmonella in microtidal estuaries.

Pathogenicity island excision during an infection by Salmonella enterica serovar Enteritidis is required for crossing the intestinal epithelial barrier in mice to cause systemic infection

Pathogenicity island excision is a phenomenon that occurs in several Salmonella enterica serovars and other members of the family Enterobacteriaceae. ROD21 is an excisable pathogenicity island found in the chromosome of S. Enteritidis, S. Dublin and S. Typhi among others, which contain several genes encoding virulence-associated proteins. Excision of ROD21 may play a role in the ability of S. Enteritidis to cause a systemic infection in mice. Our previous studies have shown that Salmonella strains unable to excise ROD21 display a reduced ability to colonize the liver and spleen. In this work, we determined the kinetics of ROD21 excision in vivo in C57BL/6 mice and its effect on virulence. We quantified bacterial burden and excision frequency in different portions of the digestive tract and internal organs throughout the infection. We observed that the frequency of ROD21 excision was significantly increased in the bacterial population colonizing mesenteric lymph nodes at early stages of the infective cycle, before 48 hours post-infection. In contrast, excision frequency remained very low in the liver and spleen at these stages. Interestingly, excision increased drastically after 48 h post infection, when intestinal re-infection and mortality begun. Moreover, we observed that the inability to excise ROD21 had a negative effect on S. Enteritidis capacity to translocate from the intestine to deeper organs, which correlates with an abnormal transcription of invA in the S. Enteritidis strain unable to excise ROD21. These results suggest that excision of ROD21 is a genetic mechanism required by S. Enteritidis to produce a successful invasion of the intestinal epithelium, a step required to generate systemic infection in mice.

Salmonella is a bacterial genus that causes foodborne illnesses worldwide. The ability of Salmonella to cause disease is related to the presence of Pathogenicity Islands (PAIs), which are clusters of genes within the bacterial chromosome that are involved in virulence. Interestingly, some PAIs excise and re-integrate into the bacterial chromosome, which is a process probably involved in the capacity of Salmonella to cause infection in their hosts. Here we show that the excision of Region of Difference 21 (ROD21), one of the excisable PAIs within the genome of Salmonella enterica serovar Enteritidis, occurs with high frequency in the mesenteric lymph node at early stages of infection, suggesting that excision is required by S. Enteritidis to reach this organ from the intestinal tract. Accordingly, S. Enteritidis strains unable to excise ROD21 are unable to invade intestinal host cells, delaying the infective cycle and showing attenuated virulence. We propose that ROD21 excision in vivo is required by S. Enteritidis to cross the intestinal barrier, a fundamental step to further colonize deep organs, due to modulation of virulence genes transcription. Thus, ROD21 excision may play an important role in the capacity of the bacteria to cause a successful systemic infection in the mouse. Our data suggest that the excision of PAIs is a mechanism used by Salmonella and probably other Gram-negative enterobacteria to modulate the expression of virulence genes and may provide insights to design novel therapies to control the infection caused by these pathogens.

Genetic and metabolic signatures of Salmonella enterica subsp. enterica associated with animal sources at the pangenomic scale

BACKGROUND

Salmonella enterica subsp. enterica is a public health issue related to food safety, and its adaptation to animal sources remains poorly described at the pangenome scale. Firstly, serovars presenting potential mono- and multi-animal sources were selected from a curated and synthetized subset of Enterobase. The corresponding sequencing reads were downloaded from the European Nucleotide Archive (ENA) providing a balanced dataset of 440 Salmonella genomes in terms of serovars and sources (i). Secondly, the coregenome variants and accessory genes were detected (ii). Thirdly, single nucleotide polymorphisms and small insertions/deletions from the coregenome, as well as the accessory genes were associated to animal sources based on a microbial Genome Wide Association Study (GWAS) integrating an advanced correction of the population structure (iii). Lastly, a Gene Ontology Enrichment Analysis (GOEA) was applied to emphasize metabolic pathways mainly impacted by the pangenomic mutations associated to animal sources (iv).

RESULTS

Based on a genome dataset including Salmonella serovars from mono- and multi-animal sources (i), 19,130 accessory genes and 178,351 coregenome variants were identified (ii). Among these pangenomic mutations, 52 genomic signatures (iii) and 9 over-enriched metabolic signatures (iv) were associated to avian, bovine, swine and fish sources by GWAS and GOEA, respectively.

CONCLUSIONS

Our results suggest that the genetic and metabolic determinants of Salmonella adaptation to animal sources may have been driven by the natural feeding environment of the animal, distinct livestock diets modified by human, environmental stimuli, physiological properties of the animal itself, and work habits for health protection of livestock.

Genomic comparison of diverse Salmonella serovars isolated from swine

Food animals act as a reservoir for many foodborne pathogens. Salmonella enterica is one of the leading pathogens that cause food borne illness in a broad host range including animals and humans. They can also be associated with a single host species or a subset of hosts, due to genetic factors associated with colonization and infection. Adult swine are often asymptomatic carriers of a broad range of Salmonella servoars and can act as an important reservoir of infections for humans. In order to understand the genetic variations among different Salmonella serovars, Whole Genome Sequences (WGS) of fourteen Salmonella serovars from swine products were analyzed. More than 75% of the genes were part of the core genome in each isolate and the higher fraction of gene assign to different functional categories in dispensable genes indicated that these genes acquired for better adaptability and diversity. High concordance (97%) was detected between phenotypically confirmed antibiotic resistances and identified antibiotic resistance genes from WGS. The resistance determinants were mainly located on mobile genetic elements (MGE) on plasmids or integrated into the chromosome. Most of known and putative virulence genes were part of the core genome, but a small fraction were detected on MGE. Predicted integrated phage were highly diverse and many harbored virulence, metal resistance, or antibiotic resistance genes. CRISPR (Clustered regularly interspaced short palindromic repeats) patterns revealed the common ancestry or infection history among Salmonella serovars. Overall genomic analysis revealed a great deal of diversity among Salmonella serovars due to acquired genes that enable them to thrive and survive during infection.

First complete genome sequence and comparative analysis of Salmonella enterica subsp. diarizonae serovar 61:k:1,5,(7) indicates host adaptation traits to sheep

Background

The Salmonella enterica subsp. diarizonae serovar 61:k:1,5,(7) (SASd) has been found to be host-adapted to sheep, with a high prevalence in sheep herds worldwide. Infections are usually sub-clinical, however the serovar has the potential to cause diarrhea, abortions and chronic proliferative rhinitis. Although occurrence and significance of SASd infections in sheep have been extensively studied, the genetic mechanism underlying this unusual host-adaptation have remained unknown, due to a lack of (a) available high-quality genome sequence(s).

Results

We utilized Nanopore and Illumina sequencing technologies to generate a de novo assembly of the 4.88-Mbp complete genome sequence of the SASd strain 16-SA00356, isolated from the organs of a deceased sheep in 2016. We annotated and analyzed the genome sequence with the aim to gain a deeper understanding of the genome characteristics associated with its pathogenicity and host adaptation to sheep. Overall, we found a number of interesting genomic features such as several prophage regions, a VirB4/D4 plasmid and novel genomic islands. By comparing the genome of 16-SA00356 to other S. enterica serovars we found that SASd features an increased number of pseudogenes as well as a high level of genomic rearrangements, both known indicators of host-adaptation.

Conclusions

With this sequence, we provide the first complete and closed genome sequence of a SASd strain. With this study, we provide an important basis for an understanding of the genetic mechanism that underlie pathogenicity and host adaptation of SASd to sheep.

DNA enrichment and tagmentation method for species-level identification and strain-level differentiation using ON-rep-seq

Despite the massive developments within culture-independent methods for detection of microorganisms during the last decade, culture-based methods remain a cornerstone in microbiology. Yet, the problem of rapid, accurate and inexpensive identification of bacterial isolates down to species/strain level remains unresolved. We have developed a new method for bacterial DNA enrichment and tagmentation allowing fast (<24 h) and cost-effective species level identification and strain level differentiation using the MinION portable sequencing platform (ON-rep-seq). DNA library preparation for 96 isolates takes less than 5 h and ensures highly reproducible distribution of reads that can be used to generate strain level specific read length counts profiles (LCp). We have developed a pipeline that by correcting reads error within peaks of LCp generates a set of high quality (>99%) consensus reads. Whereas, the information from high quality reads is used to retrieve species level taxonomy, comparison of LCp allows for strain level differentiation.

Analysis of isolates from Bangladesh highlights multiple ways to carry resistance genes in Salmonella Typhi

Background

Typhoid fever, caused by Salmonella Typhi, follows a fecal-oral transmission route and is a major global public health concern, especially in developing countries like Bangladesh. Increasing emergence of antimicrobial resistance (AMR) is a serious issue; the list of treatments for typhoid fever is ever-decreasing. In addition to IncHI1-type plasmids, Salmonella genomic island (SGI) 11 has been reported to carry AMR genes. Although reports suggest a recent reduction in multidrug resistance (MDR) in the Indian subcontinent, the corresponding genomic changes in the background are unknown.

Results

Here, we assembled and annotated complete closed chromosomes and plasmids for 73 S. Typhi isolates using short-length Illumina reads. S. Typhi had an open pan-genome, and the core genome was smaller than previously reported. Considering AMR genes, we identified five variants of SGI11, including the previously reported reference sequence. Five plasmids were identified, including the new plasmids pK91 and pK43; pK43and pHCM2 were not related to AMR. The pHCM1, pPRJEB21992 and pK91 plasmids carried AMR genes and, along with the SGI11 variants, were responsible for resistance phenotypes. pK91 also contained qnr genes, conferred high ciprofloxacin resistance and was related to the H58-sublineage Bdq, which shows the same phenotype. The presence of plasmids (pHCM1 and pK91) and SGI11 were linked to two H58-lineages, Ia and Bd. Loss of plasmids and integration of resistance genes in genomic islands could contribute to the fitness advantage of lineage Ia isolates.

Conclusions

Such events may explain why lineage Ia is globally widespread, while the Bd lineage is locally restricted. Further studies are required to understand how these S. Typhi AMR elements spread and generate new variants. Preventive measures such as vaccination programs should also be considered in endemic countries; such initiatives could potentially reduce the spread of AMR.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5916-6) contains supplementary material, which is available to authorized users.

Serotype-specific evolutionary patterns of antimicrobial-resistant Salmonella enterica

Background

The emergence of antimicrobial-resistant (AMR) strains of the important human and animal pathogen Salmonella enterica poses a growing threat to public health. Here, we studied the genome-wide evolution of 90 S. enterica AMR isolates, representing one host adapted serotype (S. Dublin) and two broad host range serotypes (S. Newport and S. Typhimurium).

Results

AMR S. Typhimurium had a large effective population size, a large and diverse genome, AMR profiles with high diversity, and frequent positive selection and homologous recombination. AMR S. Newport showed a relatively low level of diversity and a relatively clonal population structure. AMR S. Dublin showed evidence for a recent population bottleneck, and the genomes were characterized by a larger number of genes and gene ontology terms specifically absent from this serotype and a significantly higher number of pseudogenes as compared to other two serotypes. Approximately 50% of accessory genes, including specific AMR and putative prophage genes, were significantly over- or under-represented in a given serotype. Approximately 65% of the core genes showed phylogenetic clustering by serotype, including the AMR gene aac (6′)-Iaa. While cell surface proteins were shown to be the main target of positive selection, some proteins with possible functions in AMR and virulence also showed evidence for positive selection. Homologous recombination mainly acted on prophage-associated proteins.

Conclusions

Our data indicates a strong association between genome content of S. enterica and serotype. Evolutionary patterns observed in S. Typhimurium are consistent with multiple emergence events of AMR strains and/or ecological success of this serotype in different hosts or habitats. Evolutionary patterns of S. Newport suggested that antimicrobial resistance emerged in one single lineage, Lineage IIC. A recent population bottleneck and genome decay observed in AMR S. Dublin are congruent with its narrow host range. Finally, our results suggest the potentially important role of positive selection in the evolution of antimicrobial resistance, host adaptation and serotype diversification in S. enterica.

Electronic supplementary material

The online version of this article (10.1186/s12862-019-1457-5) contains supplementary material, which is available to authorized users.

Optimal translational fidelity is critical for Salmonella virulence and host interactions

Translational fidelity is required for accurate flow of genetic information, but is frequently altered by genetic changes and environmental stresses. To date, little is known about how translational fidelity affects the virulence and host interactions of bacterial pathogens. Here we show that surprisingly, either decreasing or increasing translational fidelity impairs the interactions of the enteric pathogen Salmonella Typhimurium with host cells and its fitness in zebrafish. Host interactions are mediated by Salmonella pathogenicity island 1 (SPI-1). Our RNA sequencing and quantitative RT-PCR results demonstrate that SPI-1 genes are among the most down-regulated when translational fidelity is either increased or decreased. Further, this down-regulation of SPI-1 genes depends on the master regulator HilD, and altering translational fidelity destabilizes HilD protein via enhanced degradation by Lon protease. Our work thus reveals that optimal translational fidelity is pivotal for adaptation of Salmonella to the host environment, and provides important mechanistic insights into this process.

Comparative genome-scale modelling of the pathogenic Flavobacteriaceae species Riemerella anatipestifer in China

Riemerella anatipestifer (RA) is a gram-negative bacterium that has a high potential to infect waterfowl. Although more and more genomes of RA have been generated comparaed to genomic analysis of RA still remains at the level of individual species. In this study, we analysed the pan-genome of 27 RA virulent isolates to reveal the intraspecies genomic diversity from various aspects. The multi-locus sequence typing (MLST) analysis suggests that the geographic origin of R. anatipestifer is Guangdong province, China. Results of pan-genome analysis revealed an open pan-genome for all 27 species with the sizes of 2967 genes. We identified 387 genes among 555 unique genes originated by horizontal gene transfer. Further studies showed 204 strain-specific HGT genes were predicted as virulent proteins. Screening the 1113 core genes in RA through subtractive genomic approach, 70 putative vaccine targets out of 125 non-cytoplasmic proteins have been predicted. Further analysis of these non A. platyrhynchos homologous proteins predicted that 56 essential proteins as drug target with more interaction partners were involved in unique metabolic pathways of RA. In conclusion, the present study indicated the essence and the diversity of RA and also provides useful information for identification of vaccine and drugs candidates in future.

Evolutionary and Genomic Insights into Clostridioides difficile Sequence Type 11: a Diverse Zoonotic and Antimicrobial-Resistant Lineage of Global One Health Importance

Historically, Clostridioides difficile (Clostridium difficile) has been associated with life-threatening diarrhea in hospitalized patients. Increasing rates of C. difficile infection (CDI) in the community suggest exposure to C. difficile reservoirs outside the hospital, including animals, the environment, or food. C. difficile sequence type 11 (ST11) is known to infect/colonize livestock worldwide and comprises multiple ribotypes, many of which cause disease in humans, suggesting CDI may be a zoonosis. Using high-resolution genomics, we investigated the evolution and zoonotic potential of ST11 and a new closely related ST258 lineage sourced from diverse origins. We found multiple intra- and interspecies clonal transmission events in all ribotype sublineages. Clones were spread across multiple continents, often without any health care association, indicative of zoonotic/anthroponotic long-range dissemination in the community. ST11 possesses a massive pan-genome and numerous clinically important antimicrobial resistance elements and prophages, which likely contribute to the success of this globally disseminated lineage of One Health importance.

Clostridioides difficile (Clostridium difficile) sequence type 11 (ST11) is well established in production animal populations worldwide and contributes considerably to the global burden of C. difficile infection (CDI) in humans. Increasing evidence of shared ancestry and genetic overlap of PCR ribotype 078 (RT078), the most common ST11 sublineage, between human and animal populations suggests that CDI may be a zoonosis. We performed whole-genome sequencing (WGS) on a collection of 207 ST11 and closely related ST258 isolates of human and veterinary/environmental origin, comprising 16 RTs collected from Australia, Asia, Europe, and North America. Core genome single nucleotide variant (SNV) analysis identified multiple intraspecies and interspecies clonal groups (isolates separated by ≤2 core genome SNVs) in all the major RT sublineages: 078, 126, 127, 033, and 288. Clonal groups comprised isolates spread across different states, countries, and continents, indicative of reciprocal long-range dissemination and possible zoonotic/anthroponotic transmission. Antimicrobial resistance genotypes and phenotypes varied across host species, geographic regions, and RTs and included macrolide/lincosamide resistance (Tn6194 [ermB]), tetracycline resistance (Tn6190 [tetM] and Tn6164 [tet44]), and fluoroquinolone resistance (gyrA/B mutations), as well as numerous aminoglycoside resistance cassettes. The population was defined by a large “open” pan-genome (10,378 genes), a remarkably small core genome of 2,058 genes (only 19.8% of the gene pool), and an accessory genome containing a large and diverse collection of important prophages of the Siphoviridae and Myoviridae. This study provides novel insights into strain relatedness and genetic variability of C. difficile ST11, a lineage of global One Health importance.

Current strategy for local- to global-level molecular epidemiological characterisation of global antimicrobial resistance surveillance system pathogens

The prime goal of molecular epidemiology is to identify the origin and evolution of pathogens, which can potentially influence the public health worldwide. Traditional methods provide limited information which is not sufficient for outbreak investigation and studying transmission dynamics. The recent advancement of next-generation sequencing had a major impact on molecular epidemiological studies. Currently, whole-genome sequencing (WGS) has become the gold standard typing method, especially for clinically significant pathogens. Here, we aimed to describe the application of appropriate molecular typing methods for global antimicrobial resistance surveillance system pathogens based on the level of discrimination and epidemiological settings. This shows that sequence-based methods such as multi-locus sequence typing (MLST) are widely used due to cost-effectiveness and database accessibility. However, WGS is the only method of choice for studying Escherichia coli and Shigella spp. WGS is shown to have higher discrimination than other methods in typing Klebsiella pneumoniae, Acinetobacter baumannii and Salmonella spp. due to its changing accessory genome content. For Gram positives such as Streptococcus pneumoniae, WGS would be preferable to understand the evolution of the strains. Similarly, for Staphylococcus aureus, combination of MLST, staphylococcal protein A or SCCmec typing along with WGS could be the choice for epidemiological typing of hospital- and community-acquired strains. This review highlights that combinations of different typing methods should be used to get complete information since no one standalone method is sufficient to study the varying genome diversity.

Prediction of new vaccine targets in the core genome of Corynebacterium pseudotuberculosis through omics approaches and reverse vaccinology

Corynebacterium pseudotuberculosis is the etiologic agent of veterinary relevance diseases, such as caseous lymphadenitis, affecting different animal species causing damage to the global agribusiness. So far, there are no completely effective treatment methods to overcome the impacts caused by this pathogen. Several genomes of the species are deposited on public databases, allowing the execution of studies related to the pan-genomic approach. In this study, we used an integrated in silico workflow to prospect novel putative targets using the core genome, a set of shared genes among 65 C. pseudotuberculosis strains. Subsequently, through RNA-Seq data of the same abiotic stresses in two strains, we selected only induced genes to compose the reverse vaccinology workflow based in two different strategies. Our results predicted six probable antigens in both analysis, which indicates that they have a strong potential to be used in further studies as vaccine targets against this bacterium.

The Pseudomonas aeruginosa Pan-Genome Provides New Insights on Its Population Structure, Horizontal Gene Transfer, and Pathogenicity

The huge increase in the availability of bacterial genomes led us to a point in which we can investigate and query pan-genomes, for example, the full set of genes of a given bacterial species or clade. Here, we used a data set of 1,311 high-quality genomes from the human pathogen Pseudomonas aeruginosa, 619 of which were newly sequenced, to show that a pan-genomic approach can greatly refine the population structure of bacterial species, provide new insights to define species boundaries, and generate hypotheses on the evolution of pathogenicity. The 665-gene P. aeruginosa core genome presented here, which constitutes only 1% of the entire pan-genome, is the first to be in the same order of magnitude as the minimal bacterial genome and represents a conservative estimate of the actual core genome. Moreover, the phylogeny based on this core genome provides strong evidence for a five-group population structure that includes two previously undescribed groups of isolates. Comparative genomics focusing on antimicrobial resistance and virulence genes showed that variation among isolates was partly linked to this population structure. Finally, we hypothesized that horizontal gene transfer had an important role in this respect, and found a total of 3,010 putative complete and fragmented plasmids, 5% and 12% of which contained resistance or virulence genes, respectively. This work provides data and strategies to study the evolutionary trajectories of resistance and virulence in P. aeruginosa.

Protective effect of Lactobacillus reuteri KUB-AC5 against Salmonella Enteritidis challenge in chickens

Poultry is an important high-quality food and protein source for humans. However, chicken is considered a primary source of foodborne diseases, especially Salmonella Enteritidis infection. Reducing Salmonella contamination in live poultry will thus lower the risk to consumers. Our previous studies reported that Lactobacillus reuteri KUB-AC5 can produce a substance with antimicrobial activity against pathogenic bacteria, especially Salmonella. In vivo testing revealed that this strain greatly influenced the ileal microbiota by improving chicken gastrointestinal health and inhibiting certain pathogenic bacteria. However, its activity against Salmonella in chicken is unknown. This study investigated the effects of the probiotic L. reuteri KUB-AC5 at various concentrations against Salmonella and the microbiota status in the gastrointestinal tract of broiler chickens. Four treatments groups were used: negative-control group (no Salmonella challenge), positive-control group (Salmonella challenge), and 5 or 7 log cfu probiotic supplementation to Salmonella-challenged chickens. The resultant microbial diversities at the growing and finisher stages were not significantly different among the groups (P>0.05). However, a high dosage of KUB-AC5 maintained similar microbial diversity in Salmonella-challenged chickens as observed in the non-challenged group in the early stage. The exposure Salmonella can affect the microbial diversity that consequently contributes to the disease progression in chicken. Low and high dosages of KUB-AC5 eliminated S. Enteritidis from the ileum and caecum at 14, 21 and 35 days of age. A high-dose of KUB-AC5 also enhanced Lactobacillaceae levels in the growing stage in both the ileum and caecum and suppressed Enterobacteriaceae levels in the finisher stage on day 35, whereas these effects were not observed in the low dose of KUB-AC5 or control groups. These results support the potential value of high-dose L. reuteri KUB-AC5 supplementation for three days after hatching in preventing Salmonella infection in chickens.

Extensive genomic diversity among Mycobacterium marinum strains revealed by whole genome sequencing

Mycobacterium marinum is the causative agent for the tuberculosis-like disease mycobacteriosis in fish and skin lesions in humans. Ubiquitous in its geographical distribution, M. marinum is known to occupy diverse fish as hosts. However, information about its genomic diversity is limited. Here, we provide the genome sequences for 15 M. marinum strains isolated from infected humans and fish. Comparative genomic analysis of these and four available genomes of the M. marinum strains M, E11, MB2 and Europe reveal high genomic diversity among the strains, leading to the conclusion that M. marinum should be divided into two different clusters, the "M"- and the "Aronson"-type. We suggest that these two clusters should be considered to represent two M. marinum subspecies. Our data also show that the M. marinum pan-genome for both groups is open and expanding and we provide data showing high number of mutational hotspots in M. marinum relative to other mycobacteria such as Mycobacterium tuberculosis. This high genomic diversity might be related to the ability of M. marinum to occupy different ecological niches.

Whole genome sequencing reveals widespread distribution of typhoidal toxin genes and VirB/D4 plasmids in bovine-associated nontyphoidal Salmonella

Nontyphoidal Salmonella (NTS) is a common pathogen in food-producing animals and a public health concern worldwide. Various NTS serovars may be present in apparently healthy animals. This could result in carcass contamination during the slaughter process leading to human exposure. While most genomic research has focused on Salmonella pathogenesis, little is known on the factors associated with subclinical infections and environmental persistence. We report here the widespread distribution of typhoidal toxin genes (i. e. the cdtB islet, hlyE, taiA), among NTS strains from a beef slaughter operation (n = 39) and from epidemiologically unconnected ground beef (n = 20). These genes were present in 76% of the strains, regardless of serovar, isolation source or geographical location. Moreover, strains that predominated in the slaughterhouse carry plasmid-borne type IV secretion systems (T4SS), which have been linked to persistent infections in numerous pathogens. Population genomics supports clonal dissemination of NTS along the food production chain, highlighting its role as reservoir of genetic variability in the environment. Overall, the study provides a thorough characterization of serovar diversity and genomic features of beef-associated NTS in Mexico. Furthermore, it reveals how common genetic factors could partially explain the emergence and persistence of certain NTS serovars in the beef industry.