Review

Authors: Thomas A Russo, Candace M Marr

Hypervirulent (hvKp) is an evolving pathotype that is more virulent than classical (cKp). hvKp usually infects individuals from the community, who are often healthy. Infections are more common in the Asian Pacific Rim but are occurring globally. hvKp infection frequently presents at multiple sites or subsequently metastatically spreads, often requiring source control. hvKp has an increased ability to cause central nervous system infection and endophthalmitis, which require rapid recognition and site-specific treatment. The genetic factors that confer hvKp's hypervirulent phenotype are present on a large virulence plasmid and perhaps integrative conjugal elements. Increased capsule production and aerobactin production are established hvKp-specific virulence factors. Similar to cKp, hvKp strains are becoming increasingly resistant to antimicrobials via acquisition of mobile elements carrying resistance determinants, and new hvKp strains emerge when extensively drug-resistant cKp strains acquire hvKp-specific virulence determinants, resulting in nosocomial infection. Presently, clinical laboratories are unable to differentiate cKp from hvKp, but recently, several biomarkers and quantitative siderophore production have been shown to accurately predict hvKp strains, which could lead to the development of a diagnostic test for use by clinical laboratories for optimal patient care and for use in epidemiologic surveillance and research studies.

Topics: Anti-Bacterial Agents; Bacterial Typing Techniques; Humans; Klebsiella Infections; Klebsiella pneumoniae; Virulence

PubMed: 31092506
DOI: 10.1128/CMR.00001-19

Authors: Jing Yang, Mohammed Eslami, Yi-Pei Chen...

Bacterial pathogen identification, which is critical for human health, has historically relied on culturing organisms from clinical specimens. More recently, the application of machine learning (ML) to whole-genome sequences (WGSs) has facilitated pathogen identification. However, relying solely on genetic information to identify emerging or new pathogens is fundamentally constrained, especially if novel virulence factors exist. In addition, even WGSs with ML pipelines are unable to discern phenotypes associated with cryptic genetic loci linked to virulence. Here, we set out to determine if ML using phenotypic hallmarks of pathogenesis could assess potential pathogenic threat without using any sequence-based analysis. This approach successfully classified potential pathogenetic threat associated with previously machine-observed and unobserved bacteria with 99% and 85% accuracy, respectively. This work establishes a phenotype-based pipeline for potential pathogenic threat assessment, which we term PathEngine, and offers strategies for the identification of bacterial pathogens.

Topics: Bacteria; Genome, Bacterial; Machine Learning; Phenotype; Virulence; Virulence Factors; Whole Genome Sequencing

PubMed: 35363569
DOI: 10.1073/pnas.2112886119

Authors: Lavanya Gunamalai, Danielle Duanis-Assaf, Tom Sharir...

attacks over 500 plant species and is an important pathogen of tropical and subtropical fruit. Due to global warming and climate change, the incidence of disease associated with is rising. Virulence tests performed on avocado and mango branches and fruit showed a large diversity of virulence of different isolates. Genome sequencing was performed for two isolates, representing more virulent (Avo62) and less-virulent (Man7) strains, to determine the cause of their variation. Comparative genomics, including orthologous and single-nucleotide polymorphism (SNP) analyses, identified SNPs in the less-virulent strain in genes related to secreted cell wall-degrading enzymes, stress, transporters, sucrose, and proline metabolism, genes in secondary metabolic clusters, effectors, genes involved in the cell cycle, and genes belonging to transcription factors that may contribute to the virulence of . Moreover, carbohydrate-active enzyme analysis revealed a minor increase in gene counts of cutinases and pectinases and the absence of a few glycoside hydrolases in the less-virulent isolate. Changes in gene-copy numbers might explain the morphological differences found in the in-vitro experiments. The more virulent Avo62 grew faster on glucose, sucrose, or starch as a single carbon source. It also grew faster under stress conditions, such as osmotic stress, alkaline pH, and relatively high temperature. Furthermore, the more virulent isolate secreted more ammonia than the less-virulent one both in vitro and in vivo. These study results describe genome-based variability related to virulence, which might prove useful for the mitigation of postharvest stem-end rot. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Topics: Virulence; Ascomycota; Polygalacturonase

PubMed: 37147768
DOI: 10.1094/MPMI-11-22-0234-R

Review

Authors: Belgin Sırıken

Salmonella species are facultative intracellular pathogenic bacteria. They can invade macrophages, dendritic and epithelial cells. The responsible virulence genes for invasion, survival, and extraintestinal spread are located in Salmonella pathogenicity islands (SPIs). SPIs are thought to be acquired by horizontal gene transfer. Some of the SPIs are conserved throughout the Salmonella genus, and some of them are specific for certain serovars. There are differences between Salmonella serotypes in terms of adaptation to host cell, virulence factors and the resulting infection according to SPA presence and characteristics. The most important Salmonella virulence gene clusters are located in 12 pathogenicity islands. Virulence genes that are involved in the intestinal phase of infection are located in SPI-1 and SPI-2 and the remaining SPIs are required for intracellular survival, fimbrial expression, magnesium and iron uptake, multiple antibiotic resistance and the development of systemic infections. In addition SPIs, Sigma ss (RpoS) factors and adaptive acid tolerance response (ATR) are the other two important virulence factors. RpoS and ATR found in virulent Salmonella strains help the bacteria to survive under inappropriate conditions such as gastric acidity, bile salts, inadequate oxygen concentration, lack of nutrients, antimicrobial peptides, mucus and natural microbiota and also to live in phagosomes or phagolysosomes. This review article summarizes the data related to pathogenicity islands in Salmonella serotypes and some factors which play role in the regulation of virulence genes.

Topics: Genomic Islands; Salmonella; Salmonella Infections; Virulence; Virulence Factors

PubMed: 23390917
DOI: 10.5578/mb.4138

Review

Authors: Annick Gauthier, Nikhil A Thomas, B Brett Finlay...

Topics: Bacteria; Bacterial Physiological Phenomena; Genes, Bacterial; Models, Biological; Virulence

PubMed: 12759358
DOI: 10.1074/jbc.R300012200

Review

Authors: J Ruiz, I Castro, E Calabuig...

The abuse and uncontrolled use of antibiotics has resulted in the emergence and spread of resistant bacteria. The utility of conventional antibiotics for the treatment of bacterial infections has become increasingly strained due to increased rates of resistance coupled with reduced rates of development of new agents. As a result, multidrug-resistant, extensively drug-resistant, and pan-drug-resistant bacterial strains are now frequently encountered. This has led to fears of a "post-antibiotic era" in which many bacterial infections could be untreatable. Alternative non-antibiotic treatment strategies need to be explored to ensure that a robust pipeline of effective therapies is available to clinicians. The new therapeutic approaches for bacterial infections (beyond antibiotics) may provide a way to extend the usefulness of current antibiotics in an era of multidrug-resistant (MDR) bacterial infections.

Topics: Bacteria; Bacteriophages; Humans; Infections; Microbiota; Vaccines; Virulence

PubMed: 28882020
DOI: No ID Found

Authors: Mark S Thomas, Sivaramesh Wigneshweraraj

Topics: Bacteria; Gene Expression; Gene Expression Regulation, Bacterial; Virulence; Virulence Factors

PubMed: 25603428
DOI: 10.1080/21505594.2014.995573

Review

Authors: Annika Flint, James Butcher, Alain Stintzi...

Invading pathogens are exposed to a multitude of harmful conditions imposed by the host gastrointestinal tract and immune system. Bacterial defenses against these physical and chemical stresses are pivotal for successful host colonization and pathogenesis. Enteric pathogens, which are encountered due to the ingestion of or contact with contaminated foods or materials, are highly successful at surviving harsh conditions to colonize and cause the onset of host illness and disease. Pathogens such as Campylobacter, Helicobacter, Salmonella, Listeria, and virulent strains of Escherichia have evolved elaborate defense mechanisms to adapt to the diverse range of stresses present along the gastrointestinal tract. Furthermore, these pathogens contain a multitude of defenses to help survive and escape from immune cells such as neutrophils and macrophages. This chapter focuses on characterized bacterial defenses against pH, osmotic, oxidative, and nitrosative stresses with emphasis on both the direct and indirect mechanisms that contribute to the survival of each respective stress response.

Topics: Adaptation, Physiological; Animals; Bacteria; Bacterial Physiological Phenomena; Defense Mechanisms; Gastrointestinal Tract; Humans; Microbial Viability; Stress, Physiological; Virulence

PubMed: 27227312
DOI: 10.1128/microbiolspec.VMBF-0007-2015

Authors: Ziyi Yin, Xinyu Liu, Jie Huang...

Topics: Fungi; Virulence; Plants

PubMed: 37065206
DOI: 10.3389/fcimb.2023.1168148

Review

Authors: Pierre-Olivier Méthot, Samuel Alizon

Until quite recently and since the late 19(th) century, medical microbiology has been based on the assumption that some micro-organisms are pathogens and others are not. This binary view is now strongly criticized and is even becoming untenable. We first provide a historical overview of the changing nature of host-parasite interactions, in which we argue that large-scale sequencing not only shows that identifying the roots of pathogenesis is much more complicated than previously thought, but also forces us to reconsider what a pathogen is. To address the challenge of defining a pathogen in post-genomic science, we present and discuss recent results that embrace the microbial genetic diversity (both within- and between-host) and underline the relevance of microbial ecology and evolution. By analyzing and extending earlier work on the concept of pathogen, we propose pathogenicity (or virulence) should be viewed as a dynamical feature of an interaction between a host and microbes.

Topics: Animals; Bacteria; Biological Evolution; Fungi; Genetic Variation; Host-Parasite Interactions; Host-Pathogen Interactions; Humans; Virulence; Viruses

PubMed: 25483864
DOI: 10.4161/21505594.2014.960726