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Phylograms of concatenated sequences of seven housekeeping genes of S. enterica subsp. I (A) and E. coli/Shigella (B). The housekeeping genes used in MLST were selected for analysis. The Salmonella genes were aroC (chorismate synthase), dnaN (DNA polymerase III, β-subunit), hemD (uroporphyrinogen III synthase), hisD (histidinal dehydrogenase), purE (phosphoribosylaminoimidazole carboxylase), sucA (2-oxoglutarate dehydrogenase decarboxylase), and thrA (aspartokinase I). The E. coli genes were adk (adenylate kinase), fumC (fumarate hydratase class II), gyrB (DNA gyrase subunit B), icd (isocitrate dehydrogenase), mdh (malate dehydrogenase), purA (adenylosuccinate synthetase), and recA (recombinase A). Serovars and host specificity ranges were shown for the Salmonella strains, while pathotypes were mentioned for the E. coli strains. EAEC, ExPEC, EHEC, ETEC, and EPEC stand for enteroaggregative, extraintestinal pathogenic, enterohemorrhagic, enterotoxigenic, and enteropathogenic E. coli, respectively.
Source publication
One of the strongest signals of adaptive molecular evolution of proteins is the occurrence of convergent hot spot mutations:
repeated changes in the same amino acid positions. We performed a comparative genome-wide analysis of mutation-driven evolution
of core (omnipresent) genes in 17 strains of Salmonella enterica subspecies I and 22 strains of E...
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Citations
... On the one hand, most serotypes are polyphyletic, deriving from multiple independent ancestors [2]. On the other hand, homologous recombination and chromosomal mutations have resulted in genotypically and phenotypically diverse subtypes evolved from the same serovars [3]. Furthermore, serotyping has been traditionally performed by serological tests. ...
Salmonella enterica subspecies enterica is one of the most important foodborne pathogens and the causative agent of salmonellosis, which affects both humans and animals producing numerous infections every year. The study and understanding of its epidemiology are key to monitoring and controlling these bacteria. With the development of whole-genome sequencing (WGS) technologies, surveillance based on traditional serotyping and phenotypic tests of resistance is being replaced by genomic surveillance. To introduce WGS as a routine methodology for the surveillance of food-borne Salmonella in the region, we applied this technology to analyze a set of 141 S. enterica isolates obtained from various food sources between 2010 and 2017 in the Comunitat Valenciana (Spain). For this, we performed an evaluation of the most relevant Salmonella typing methods, serotyping and sequence typing, using both traditional and in silico approaches. We extended the use of WGS to detect antimicrobial resistance determinants and predicted minimum inhibitory concentrations (MICs). Finally, to understand possible contaminant sources in this region and their relationship to antimicrobial resistance (AMR), we performed cluster detection combining single-nucleotide polymorphism (SNP) pairwise distances and phylogenetic and epidemiological data. The results of in silico serotyping with WGS data were highly congruent with those of serological analyses (98.5% concordance). Multi-locus sequence typing (MLST) profiles obtained with WGS information were also highly congruent with the sequence type (ST) assignment based on Sanger sequencing (91.9% coincidence). In silico identification of antimicrobial resistance determinants and minimum inhibitory concentrations revealed a high number of resistance genes and possible resistant isolates. A combined phylogenetic and epidemiological analysis with complete genome sequences revealed relationships among isolates indicative of possible common sources for isolates with separate sampling in time and space that had not been detected from epidemiological information. As a result, we demonstrate the usefulness of WGS and in silico methods to obtain an improved characterization of S. enterica enterica isolates, allowing better surveillance of the pathogen in food products and in potential environmental and clinical samples of related interest.
... Remaining sequences were searched against all other remaining sequences using the "-usearch-global" function in VSEARCH v.2.14.2 with a minimal percentage identity stringency score of 0.97 (97%), self-hits were excluded, and, with the exception of Escherichia, Shigella, and Salmonella (ESS), top-hit pairs where sequences were observed to be from different genera were discarded. The ESS species were excluded from further filtration during this step due to the close evolutionary relatedness of these clinically relevant genera [38,43,91]. Finally, exact duplicates of 16S rRNA genes were removed resulting in a database of 68,724 16S rRNA genes from 21,928 species from 37 definite phyla and 70 candidate phyla/divisions (107 in total). ...
Background
The broiler gastrointestinal microbiome is a potent flock performance modulator yet may also serve as a reservoir for pathogen entry into the food chain. The goal of this project was to characterise the effect of mannan rich fraction (MRF) supplementation on microbiome diversity and composition of the intestinum tenue and cecum of commercial broilers. This study also aimed to address some of the intrinsic biases that exist in microbiome studies which arise due to the extensive disparity in 16S rRNA gene copy numbers between bacterial species and due to large intersample variation.
Results
We observed a divergent yet rich microbiome structure between different anatomical sites and observed the explicit effect MRF supplementation had on community structure, diversity, and pathogen modulation. Birds supplemented with MRF displayed significantly higher species richness in the cecum and significantly different bacterial community composition in each gastrointestinal (GI) tract section. Supplemented birds had lower levels of the zoonotic pathogens Escherichia coli and Clostridioides difficile across all three intestinum tenue sites highlighting the potential of MRF supplementation in maintaining food chain integrity. Higher levels of probiotic genera ( eg. Lactobacillus and Blautia ) were also noted in the MRF supplemented birds. Following MRF supplementation, the cecum displayed higher relative abundances of both short chain fatty acid (SFCA) synthesising bacteria and SCFA concentrations.
Conclusions
Mannan rich fraction addition has been observed to reduce the bioburden of pathogens in broilers and to promote greater intestinal tract microbial biodiversity. This study is the first, to our knowledge, to investigate the effect of mannan-rich fraction supplementation on the microbiome associated with different GI tract anatomical geographies. In addition to this novelty, this study also exploited machine learning and biostatistical techniques to correct the intrinsic biases associated with microbiome community studies to enable a more robust understanding of community structure.
... Two systemically invasive human-restricted serovars of Salmonella enterica subspecies I, Salmonella enterica serovar Typhi and Salmonella enterica serovar Paratyphi A, represent a good model to study pseudogene formation and gene deletion in comparison with several self-limiting gastroenteritis-causing serovars, such as Salmonella enterica serovar Typhimurium, which are adapted to a broad range of hosts (18,19). Typhi and Paratyphi A, as expected for their adaptation to the same niche with similar modes of pathogenesis, have been shown to undergo adaptive convergent evolution through both recombinational and mutational processes (20,21). Previous work has also showed the formation of pseudogenes to converge in the course of evolution of these two serovars (22). ...
... However, as mentioned earlier, gene inactivation is a major mode of adaptive evolution in bacteria, and one common way for a gene to be inactivated is via accumulation of premature stop codons, i.e., truncation mutations. On the other hand, the repeated amino acid mutations that occur independently (i.e., in a phylogenetically unlinked way) at a particular position are known to happen under potential positive selection pressures, suggesting fitness advantage of such mutant variants, and are called convergent mutations (CM) (21,(25)(26)(27)(28)(29)(30). While such mutational convergence suggests adaptive evolution, it is highly likely that many such convergent mutations are inactivating amino acid changes, thereby offering the same result as that of truncation mutations, as shown earlier for multiple Salmonella serovars (30). ...
... Microbiology Spectrum tricks to adapt to similar environmental conditions (31,32). This resulted in convergent adaptive evolution in these two serovars, as demonstrated earlier to happen via both recombination and mutation (20,21). Therefore, we next analyzed the overlap of TnM genes in Typhi and Paratyphi A. Any significant overlap, interestingly, could be explained through two possible mechanisms. ...
ABSTRACT Gene inactivation through the accumulation of truncation (or premature stop codon) mutations is a common mode of evolution in bacteria. It is frequently believed to result from reductive evolutionary processes allowing purging of superfluous traits. However, several works have demonstrated that, similar to the occurrences of inactivating nonsynonymous (i.e., amino acid replacement) mutations under positive selection pressures, truncation mutations can also be adaptive where specific traits deleterious in particular environmental conditions need to be inactivated for survival. Here, we performed a comparative analysis of genome-wide accumulation of truncation mutations in Salmonella enterica serovar Typhi and Salmonella enterica serovar Paratyphi A. Considering the known convergent evolutionary trajectories in these two serovars, we expected a strong overlap of truncated genes in S. Typhi and S. Paratyphi A, emerging through either reductive or adaptive dynamics. However, we detected a distinct set of core truncated genes encoding different overrepresented functional clusters in each serovar. In 54% and 28% truncated genes in S. Typhi and S. Paratyphi A, respectively, inactivating mutations were acquired by only different subsets of isolates, instead of all isolates analyzed for that serovar. Importantly, 62% truncated genes (P
... The fact that the host range improvement in the ε 2 -phages of E. coli is not as large could be related to the fact that E. coli strains are more diverse. The core genome of E. coli comprises only up to 25% of the genes, while the remaining are considered as accessory genomes [50][51][52]. In contrast, approximately 75% of S. aureus genes were classified into the core genome [53]. ...
Alternative treatments for Escherichia coli infections are urgently needed, and phage therapy is a promising option where antibiotics fail, especially for urinary tract infections (UTI). We used wastewater-isolated phages to test their lytic activity against a panel of 47 E. coli strains reflecting the diversity of strains found in UTI, including sequence type 131, 73 and 69. The plaquing host range (PHR) was between 13 and 63%. In contrast, the kinetic host range (KHR), describing the percentage of strains for which growth in suspension was suppressed for 24 h, was between 0% and 19%, substantially lower than the PHR. To improve the phage host range and their efficacy, we bred the phages by mixing and propagating cocktails on a subset of E. coli strains. The bred phages, which we termed evolution-squared ε2-phages, of a mixture of Myoviridae have KHRs up to 23% broader compared to their ancestors. Furthermore, using constant phage concentrations, Myoviridae ε2-phages suppressed the growth of higher bacterial inocula than their ancestors did. Thus, the ε2-phages were more virulent compared to their ancestors. Analysis of the genetic sequences of the ε2-phages with the broadest host range reveals that they are mosaic intercrossings of 2–3 ancestor phages. The recombination sites are distributed over the whole length of the genome. All ε2-phages are devoid of genes conferring lysogeny, antibiotic resistance, or virulence. Overall, this study shows that ε2-phages are remarkably more suitable than the wild-type phages for phage therapy.
... On the one hand, site-specific recombination circulated through mobile genetic elements and gene gain-loss events are associated with the flexible or accessory genes and thereby offer genomic and metabolic diversity in a population; the core genomic part, on the other hand, is linked with vertical transmission and homologous recombination, providing a stable genomic and metabolic backbone for the population. As the core clusters embody a set of highly conserved genes, phylogenetic analysis on the basis of core gene clusters provides information on the evolutionary history of its constituent organisms (Lefébure and Stanhope, 2007;Chattopadhyay et al., 2012a;Freschi et al., 2019). Thus, comparative pan-genomic study coupled with evolutionary analyses could be used as a framework to investigate the genome diversification associated with life under extreme conditions. ...
Sulfolobaceae family, comprising diverse thermoacidophilic and aerobic sulfur-metabolizing Archaea from various geographical locations, offers an ideal opportunity to infer the evolutionary dynamics across the members of this family. Comparative pan-genomics coupled with evolutionary analyses has revealed asymmetric genome evolution within the Sulfolobaceae family. The trend of genome streamlining followed by periods of differential gene gains resulted in an overall genome expansion in some species of this family, whereas there was reduction in others. Among the core genes, both Sulfolobus islandicus and Saccharolobus solfataricus showed a considerable fraction of positively selected genes and also higher frequencies of gene acquisition. In contrast, Sulfolobus acidocaldarius genomes experienced substantial amount of gene loss and strong purifying selection as manifested by relatively lower genome size and higher genome conservation. Central carbohydrate metabolism and sulfur metabolism coevolved with the genome diversification pattern of this archaeal family. The autotrophic CO 2 fixation with three significant positively selected enzymes from S. islandicus and S. solfataricus was found to be more imperative than heterotrophic CO 2 fixation for Sulfolobaceae. Overall, our analysis provides an insight into the interplay of various genomic adaptation strategies including gene gain-loss, mutation, and selection influencing genome diversification of Sulfolobaceae at various taxonomic levels and geographical locations.
... In these cases, the excess of beneficial mutations produced by the mutator clones drives them to a high frequency within the population, and the presence of a mutator allele can therefore be considered a signature of sustained adaptation. (iii) Genomic studies of epidemic bacterial clones and experimentally evolved laboratory strains (11) have revealed convergence at a molecular level (12,13) that can be seen as a hallmark of adaptation. Among all the possible mutations that may occur, finding mutations with comparable effects reflects the filtering action of natural selection. ...
Little is known about the dynamics of adaptation in acute bacterial infections. By sequencing multiple isolates from monoclonal extraintestinal
Escherichia coli
... However the technique is laborious, time consuming, requires more than 250 different typing antisera and even lead to imprecise results [8]. On the other hand microevolutions within Salmonella serovars by considerable homologous recombination and chromosomal mutations have resulted in genotypically and phenotypically diverse subtypes evolved from same serovars [9]. Most of the Salmonella serotypes are polyphyletic or homologous in origin with distinct pathogenic lineage. ...
Traditional serotyping based on the phenotypic variation of O-and H-antigen remains as the gold-standard for the identification and classification of Salmonella isolates for last 70 years. Although this classification is a globally recognized nomenclature, huge diversity of Salmonella serotypes have made the serovar identification to be very complex. Seven gene multilocus sequence typing (MLST) on the other hand can provide serovar prediction as well as the evolutionary origin between the serovars. In this study non typhoidal Salmonella (NTS) strains (n = 45) isolated from clinical samples (blood, faeces and pus) were identified by traditional phenotypic serotyping and biochemical testing. All the tested Salmonella isolates were designated as serovar Typhimurium based on phenotyping. However, by MLST 60% (27/45) of the isolates were S. Typhimurium, 35.5% (16/45) were S. Agona (ST13), 2.2% (1/45) were S. Kentucky (ST198) and 2.2% (1/45) were S. Saintpaul (ST27). MLST analysis assigned S. Typhimurium isolates as ST36 (18/127), ST19 (7/27) and ST313 (2/27). Mismatches in serovar designation between MLST database and phenotypic serotyping can be due to the misinterpretation of phenotypic serotyping as the antigenic structures of S. Typhimurium, S. Agona differs by a surface antigen. MLST based phylogeny of study isolates showed clustering according to sequence types. Concordance between MLST based sequence type and phenotypic serotype is important to provide insights into genetic population structure of Salmonella.
... Furthermore, strong purifying selection may prevail in species inhabiting diverse geographical locations, as reported for several wild varieties of South American tomatoes (Tellier et al., 2011). Importantly, the genomes of enteric bacteria such as Escherichia coli and Salmonella enterica that reside in similar habitats exhibit strong positive selection (Chattopadhyay et al., 2012). Exploiting the environmental situations and sustaining large effective population sizes by maintaining the functional sequences in the genome may have promoted adaptive diversification among various Polynucleobacter spp. ...
Polynucleobacter asymbioticus strain QLW-P1DMWA-1T represents a group of highly successful heterotrophic ultramicrobacteria that is frequently very abundant (up to 70% of total bacterioplankton) in freshwater habitats across all seven continents. This strain was originally isolated from a shallow Alpine pond characterized by rapid changes in water temperature and elevated UV radiation due to its location at an altitude of 1300 m. To elucidate the strain’s adjustment to fluctuating environmental conditions, we recorded changes occurring in its transcriptomic and proteomic profiles under contrasting experimental conditions by simulating thermal conditions in winter and summer as well as high UV irradiation. To analyze the potential connection between gene expression and regulation via methyl group modification of the genome, we also analyzed its methylome. The methylation pattern differed between the three treatments, pointing to its potential role in differential gene expression. An adaptive process due to evolutionary pressure in the genus was deduced by calculating the ratios of non-synonymous to synonymous substitution rates for 20 Polynucleobacter spp. genomes obtained from geographically diverse isolates. The results indicate purifying selection.
... Interestingly, we found that the STM ΔyjiY sup effectively inhibited E. coli bio lm. Although Salmonella had diverged from E. coli by acquiring virulence-associated genes, they share many evolutionarily conserved cellular pathways 39,40,41 . Therefore this observation reiterates that the inhibitory effects are more profound among closely related species. ...
Salmonella is a genus of widely spread Gram negative, facultative anaerobic bacteria, which is known to cause ¼th of the diarrhoeal morbidity and mortality globally. It causes typhoid fever and gastroenteritis by gaining access to the host gut through contaminated food and water. Salmonella utilizes its biofilm lifestyle to strongly resist antibiotics and persist in the host. Although the biofilm removal or dispersal have been studied widely, the inhibition of initiation Salmonella biofilm has not been studied much. This study was conducted to determine the anti-biofilm property of the cell-free supernatant obtained from a carbon-starvation inducible proline peptide transporter mutant ( ΔyjiY ) strain. Our study shows that Salmonella ΔyjiY culture supernatant inhibits biofilm initiation by regulating biofilm associated transcriptional network. This work demonstrates that highly abundant proteases like ecotin, HslV and GrpE cleave the protein aggregates, whereas global transcription regulators H-NS, FlgM regulate expression of SPIs and flagellar genes. Relatively low abundance of flavoredoxin, glutaredoxin, thiol peroxidase etc. leads to accumulation of ROS within the biofilm, and subsequent toxicity. This work further suggests that targeting these oxidative stress relieving proteins might be a good druggable choice to reduce Salmonella biofilm.
... Loss of key metabolic functions has specifically been observed in many host-restricted serotypes, such as S. Typhi and S. Paratyphi A (human), and S. Gallinarum (fowl) [14][15][16]. Besides gene acquisition and deletion, positive selection and homologous recombination have been shown to play important roles in the serotype divergence and adaptive evolution in Salmonella as well [15,17,18]. For example, a total of 41 Salmonella genes reported by [15] showed evidence for positive selection, including genes likely contributing to virulence. ...
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.
