Search Results (115)

Three pathogenic species of the genus Yersinia, including Plague-associated Yersinia pestis, Yersinia pseudotuberculosis, and Yersinia enterocolitica, are commonly associated with human infection. Current qPCR detection methods are mainly limited to the identification of one or two Yersinia species in a single reaction tube, while multiplex assays for multiple genera have been more commonly reported. Therefore, the present study aimed to establish a multiplex TaqMan qPCR assay for the simultaneous detection of these three pathogenic Yersinia species. Primer and probe sets were designed based on the inv gene for Y. pseudotuberculosis, the caf1 gene for Y. pestis, and the foxA gene for Y. enterocolitica. Under the optimized reaction conditions, the standard curve slopes for the caf1, inv, and foxA genes were −3.046, −2.968, and −2.948, respectively. The correlation coefficients (R²) ranged from 0.993 to 0.996, while the amplification efficiencies ranged from 109% to 115%. The limits of detection (LOD) were determined to be 5 × 10² copies/μL for inv (FAM), 1 × 10¹ copies/μL for caf1 (ROX), and 1 × 10¹ copies/μL for foxA (CY5). The sensitivity of the multiplex qPCR assay was 10- to 100-fold higher than that of conventional PCR, depending on the target. Specificity experiments demonstrated that no cross-reactivity was observed with non-target bacteria, including Francisella tularensis, Brucella spp., Vibrio cholerae, Salmonella Typhi, and Shigella spp. The intra-assay coefficients of variation (CVs) ranged from 0.13% to 0.79%, whereas the inter-assay CVs ranged from 0.62% to 2.61%. Among 173 spleen samples collected from wild rodents, no positive signal for Y. pestis or Y. pseudotuberculosis was detected. In contrast, Y. enterocolitica was detected in three samples (1.73%, 3/173). In conclusion, the multiplex qPCR assay developed in this study provides a sensitive and specific tool for the simultaneous detection of three pathogenic Yersinia species and has the potential to improve detection efficiency in clinical and epidemiological investigations. Full article

Based on phylogenetic analysis of whole-genome sequencing of Yersinia pestis 2.MED1 strains of the medieval biovar, combined with epizootic, epidemiological, and climatic data over a 100-year period, we have reconstructed the most probable directions of distribution of plague in Eastern Europe and Central Asia (EECA) in the 20th and 21st centuries. The data suggest the important role of three great lakes—the Caspian, Aral, and Balkhash—in the circulation and preservation of Y. pestis 2.MED1 in EECA. Three main directions of Y. pestis 2.MED1 expansion have been identified: Caspian (Caspian Sea region foci, 1912–1945; Caucasus, 1953–1986), North Aral (Northern Aral Sea region foci, 1945–1959; Caspian Sea region foci, 1945–2015; Pre-Caucasus, 1999–2003; Karakum, 1949–1965) and Central Asian (Kyzylkum, 1924, 1983–2020; Balkhash foci, 1939–2020; Northern Aral Sea region foci, 1967–2020; Eastern Caspian Sea region foci, 1968–1985). Favorable climatic conditions in the Caspian Sea region, the Northern Aral Sea region, and the Balkhash region in the 20th and 21st centuries contributed to the rapid formation of stable natural plague foci and the long-term persistence of Y. pestis 2.MED1 strains of the medieval biovar, with their further introduction into other foci of EECA. Periodic introductions of the pathogen are one of the reasons for the plague re-emergence and activation of plague foci in the EECA region. Full article

This review provides a comprehensive overview of the genetic diversity and epidemiological potential of Yersinia pestis in Kazakhstan’s natural plague foci, emphasizing the link between genotypic variation and outbreak capacity. Integrating historical epidemiological records with contemporary microbiological and genomic data (including PCR, VNTR/MLVA, SNP analysis, and whole-genome sequencing), we evaluate core and accessory genome variations. The data reveal substantial regional heterogeneity. High-risk desert foci (Caspian and Aral regions) are dominated by the Medievalis biovar, including atypical genovariants lacking canonical markers. Conversely, high-mountain foci (Sarydzhaz, Talas) harbor the Antiqua and Talas biovars, primarily linked to enzootic circulation. Notably, the Ili River focus exhibits extreme genomic variability, featuring strains with plesiomorphic traits. Furthermore, the widespread distribution of mobile elements like the cryptic plasmid pCKF suggests significant horizontal transfer contributing to pathogen adaptation. Ultimately, Central Asian plague dynamics are driven by complex evolutionary and ecological interactions. Given climate change and expanding human–wildlife interfaces, continuous genomic and ecological surveillance is essential for the early detection of high-risk Y. pestis genovariants and improving public health preparedness. Full article

The plague, caused by Yersinia pestis, has resulted in significant mortality over the past century. Despite advances in antimicrobial therapy, plague remains a re-emerging infectious disease with ongoing outbreaks and increasing concerns regarding antimicrobial resistance. Today, plague cases are still being reported, and the loss of effectiveness of treatment methods remains a major challenge. Therefore, effective treatment strategies are needed. In this study, we aimed to develop aptamers specific to Yersinia outer protein M (YopM), a key immunosuppressive protein that is essential for virulence. Our goal was to develop an aptamer that binds to YopM and inhibits its interaction with the human DEAD-box helicase 3 (DDX3) protein. YopM-DDX3 protein interaction was targeted because of its key role in nucleocytoplasmic shuttling of YopM. To achieve this, we developed the YopM16 aptamer using magnetic bead-based (Systematic Evolution of Ligands by Exponential Enrichment) (SELEX). The selected YopM16 aptamer exhibited a half-maximal inhibitory concentration(IC₅₀) value of 103.3 ± 2 nM and effectively inhibited the interaction between YopM and DDX3. The inhibitory effect of the aptamer on protein interaction was confirmed using a pull-down assay and colorimetric test. Given that protein–protein interaction surfaces are considered undruggable, YopM16 is a promising inhibitor with the potential to serve as a molecular tool to investigate the virulence mechanism of YopM, as well as a novel antibacterial agent upon validation of its inhibition in cellular models. Full article

The Third Plague Pandemic originated in 19th-century Yunnan, China, yet the confluence of factors that enabled the pandemic strain Yersinia pestis 1.ORI to emerge and spread globally remains unclear. Using a One Health framework, this study investigates how human-driven ecological and socioeconomic changes disrupted zoonotic barriers in Yunnan. We conduct an interdisciplinary historical analysis, triangulating evidence from Qing dynasty gazetteers, environmental reconstructions, and biological data on plague ecology, including host–vector dynamics, to model conditions for spillover and spread and to build a convergent, validated case. The analysis identifies a mid-19th-century convergence that created a high-risk interface: widespread deforestation from mining and agriculture, rapid population growth, increased synanthropic rat densities, and the turmoil of the Panthay Rebellion. Socioeconomic stressors—labour migration into mining valleys, currency devaluation undermining food security, and comorbidities such as malnutrition, heavy metal contamination, and opium use—may have further increased host susceptibility. This socio-ecological context catalysed spillover and establishment of the 1.ORI strain in commensal rat populations. The findings show the pandemic’s origin reflects spatiotemporal convergence rather than a single cause, while noting uncertainty in quantifying historical ecological and health parameters; the case offers a framework for assessing contemporary pandemic risks. It underscores how layered pressures operate across timescales. Full article

Yersinia pestis is the etiological agent of plague, a severe and often fatal disease in humans when left untreated. Because of the high genetic clonality of Y. pestis, high-resolution genotyping assays are necessary to differentiate between individual strains. Here, we report on the development and validation of a robust and reproducible core-genome multilocus sequence typing (cgMLST) assay for Y. pestis comprising 3139 gene targets, enabling high-resolution typing at the strain level. The assay was validated using 222 publicly available Y. pestis genomes, including 45 recently sequenced outbreak isolates from Madagascar and 21 isolates from Mongolia. The cgMLST analysis revealed primary clustering aligned with known biovar-associated branches and sub-branches. Additional geographically structured sub-clusters illustrate its application for regional diversification analysis. Yersinia pestis strains from different geographic regions were clearly distinguished, consistent with spatial clustering. Within the analyzed dataset, closely related or epidemiologically linked strains differed by zero to three alleles, suggesting this range as an operational reference for identifying highly similar isolates. The cgMLST showed clustering patterns concordant with previously described single-nucleotide polymorphism (SNP) assays. It therefore provides a standardized high-resolution typing approach, with demonstrated applicability for outbreak investigations, source tracking, and comparative genomic surveillance of Y. pestis. Full article

Yersinia pestis and Francisella tularensis are Tier-1 pathogens with high interest for biodefense and public health. Evaluating the antibacterial activity of repurposed drugs against these high-priority pathogens is a key element in the ongoing effort to develop diversified antimicrobial strategies. Drug repurposing offers a cost-effective and time-efficient approach to address antibiotic resistance by identifying new applications for existing therapeutics. In this study, we demonstrate in vitro antibacterial effect of the antifungal agent ciclopirox and offer this drug as a potential antibacterial treatment. Ciclopirox in vitro activity was previously reported against various Gram-negative bacteria, including resistant strains, primarily through iron chelation that disrupts key metabolic pathways and virulence mechanisms. Additionally, it exhibits antibiofilm activity and can potentiate the efficacy of certain antibiotics. Our findings reveal that ciclopirox effectively inhibits the in vitro growth of fully virulent strains of Y. pestis and F. tularensis, as well as avirulent isolates, including avirulent mutants that their wild-type susceptibility was reduced through selection to MIC levels defining them as “nonsusceptible” to ciprofloxacin (Y. pestis Kim53Δ70Δ10 and F. tularensis LVS) and doxycycline (LVS), or resistant to doxycycline (Kim53Δ70Δ10) according to CLSI interpretive criteria. Additionally, prolonged exposure of Y. pestis and F. tularensis to sub-MIC and MIC concentrations of ciclopirox did not lead to an increase in observed MIC during the study period. These results highlight ciclopirox as a potential candidate for treatment alternative, combined with other antibiotic substances or repurposed drugs against these bacterial threats. Full article

Yersinia pestis caused the three plague pandemics that claimed more than two hundred million human lives. There is still no vaccine that meets all WHO requirements, and many researchers continue to develop plague vaccines using various technological platforms. For example, researchers led by Roy Curtiss 3rd have developed a new approach to achieve controlled, delayed attenuation of bacterial pathogens. Mutants generated using this method were superior in protecting Y. pestis-infected mice immunized with strains generated using traditional gene knockout. However, further studies are needed to determine the safety and efficacy of these delayed-attenuated strains in other mammalian species in order to extrapolate on humans the data obtained in accordance with the FDA Animal Rule. Three Y. pestis strains, a Δcrp mutant, a mutant with arabinose-dependent regulated crp expression (araC P_BAD crp) or an araC P_BAD crp mutant cured of plasmid pPst were derived from virulent wild-type strain 231. To evaluate the safety, outbred mice or guinea pigs were immunized subcutaneously with serial tenfold dilutions of mutated strains. For vaccine studies, immunized animals were subcutaneously challenged with 200 LD₁₀₀ (lethal dose in all exposed subjects) of the wild-type Y. pestis strain. The challenge caused the death of 100% of naïve animals in controls. The Y. pestis strain 231Δcrp was nonlethal in mice at a dose of 10⁷ CFs. The LD₅₀ of the 231Δcrp strain in guinea pigs increased by at least 10⁷-fold compared to that of the wild-type strain. The LD₅₀s of the 231P_BAD-crp mutant in mice and guinea pigs were approximately 10⁴-fold and 10⁷-fold higher than those of Y. pestis 231, respectively. The 231P_BAD-crp(pPst¯) strain did not cause death in mice (LD₅₀ > 10⁷ CFU) and guinea pigs (LD₅₀ > 10⁹ CFU) when administered subcutaneously and was capable of inducing intense protective immunity in both species of laboratory animals. Our research has shown once again the necessity of balance between safety and effectiveness demonstrating the feasibility of further investigation of crp mutants as promising candidate plague vaccines. Full article

Three episodes of sylvatic plague occurred in Yunnan from April to November 2022, and nine Yersinia pestis strains were isolated. Whole-genome sequencing was performed on these isolates, and phylogenetic analysis based on SNP comparisons included 234 publicly available genomes from NCBI. All nine 2022 strains clustered within the 1.IN5 lineage, together with historical isolates from the Lijiang wild rodent plague focus. The Heqing strain HQ1 was most closely related to previous Heqing isolates, while seven Lijiang 2022 strains formed a monophyletic cluster with historical Lijiang strains; the remaining strain LJ4 was the closest relative to this cluster. Whole-genome comparison of HQ1 with historical Heqing strains revealed six SNPs and two indels. Of these, one nonsynonymous SNP and both indels—one being a deletion in the flagellin gene flgF—were located in coding regions. Comparison of the Lijiang strain 2022YL002 with historical local isolates identified ten SNPs and three indels. Five nonsynonymous SNPs were found in coding regions, including one at position 1566343 causing an amino acid change in the iron uptake regulator Fur, a virulence-associated mutation. All three indels were in coding regions. These findings confirm that the 2022 outbreaks originated from local plague reservoirs, while genetic differences indicate ongoing bacterial evolution. The results underscore the persistent activity of sylvatic plague in the Lijiang area and highlight the need for continued surveillance to prevent human spillover. Full article

As promising biological tools, bacteriophages offer broad potential applications in disease diagnosis, treatment, and food safety. This study is the first to isolate a novel bacteriophage, designated vB_YpP_JC53 (abbreviated JC53), from the soil of wild rodent nests in plague-endemic areas of Yunnan Province. This bacteriophage is a T7-like phage that has the broadest host range among all T7-like phages discovered to date and remains stable under varying temperature and pH conditions. Comparative genomic analysis through NCBI revealed that the nucleotide sequence of phage JC53 shares 94.98% homology (95% coverage) with phage PSTCR2, a member of the Solymavirus genus, while exhibiting substantially lower similarity to known Yersinia phages. Further phylogenetic and collinearity analyses demonstrate that JC53 represents an evolutionarily distinct lineage, clearly diverging from Yersinia-infecting, T7-like, and Shigella phages, suggesting the emergence of a novel evolutionary branch. Its low ANI values relative to Yersinia phages and mosaic genome organization indicate a complex evolutionary origin, reflecting the extensive diversity of environmental phage populations. Collectively, these findings support the designation of JC53 as a novel Yersinia phage. Genome sequencing revealed that JC53 has a genome size of 39,415 bp, with a total of 52 predicted open reading frames. The broad bacteriophage spectrum of JC53 challenges the long-standing perception that T4-like bacteriophages primarily depend on a wide host range. These findings suggest that, within plague foci, JC53 may maintain ecological fitness by targeting other bacteria rather than strictly relying on Yersinia pestis. As a result, JC53 holds potential as an ecological control agent with the potential to suppress plague transmission by regulating the microbial community structure within foci. Full article

This review summarizes the interactions between three major bacterial groups, Rickettsia sp., Bartonella sp. and Yersinia pestis, the flea vectors and the diverse gut microbiota of fleas and highlights open questions. The focus is on the plague pathogen, Y. pestis, which adapted to transmission by fleas several thousand years ago. This caused one of the deadliest infectious diseases known to mankind, and the three pandemics resulted in an estimated 200 million deaths. In the vector, Y. pestis resists the adverse conditions, like other numerous bacterial species. Rickettsia sp. and Bartonella sp. as well as Y. pestis induce specific changes in the microbiota. The presence of bacteria in the ingested blood activates the production of antimicrobial proteins and reactive oxygen species, which normally have no effect on the development of Y. pestis. This bacterium infects mammals by different modes, first by an early-phase transmission and then by biofilm-mediated blockage of the foregut. Both interfere with blood ingestion and lead to reflux or regurgitation of intestinal contents containing Y. pestis into the bite site. Blockage of the gut leads to more attempts to ingest blood, increasing the risk of transmission. The lifespan of the fleas is also reduced. As Y. pestis is still endemic in wildlife in many regions of the world and human infections continue to occur in limited areas, studies of the interactions are needed to find new ways to control the disease. Full article

Yersinia pestis, the causative agent of plague, is arguably the most devastating pathogen in human history. Paleogenomic studies indicate its presence as early as the Neolithic era. It evolved from Yersinia pseudotuberculosis, with divergence estimates ranging from 1500 to 20,000 years ago, most often placed around 5000 years ago. Its natural reservoirs are wild mammals, particularly rodents, with fleas serving as vectors, while humans are incidental hosts. Over time, Y. pestis has acquired multiple virulence factors that disrupt immune responses and can lead to rapid, often fatal disease. Because the bacterium is maintained in wildlife cycles and can spill over to domestic animals, eradication is difficult, if not impossible. Nevertheless, mitigation is achievable using a One Health approach integrating human health, animal health, and the health of the environment. Neither vaccines nor monoclonal antibodies are currently licensed in most Western countries, thus, antibiotics remain the mainstay of therapy. Timely administration, ideally within 24 h of symptom onset, is critical, particularly in pneumonic forms. Phage therapy is under investigation as a potential treatment. Though often neglected in high-income settings, plague remains endemic in several regions, with the highest burden reported in Madagascar and the Democratic Republic of the Congo. Full article

Microbial forensics involves analyzing biological evidence to evaluate weaponized microorganisms or their toxins. This study aimed to detect and type Yersinia pestis from four simulated forensic samples—human plasma diluted in phosphate-buffered saline (#24-2), tomato juice (#24-5), grape juice (#24-8), and a surgical mask (#24-10). Notably, samples #24-10 may have contained live bacteria other than Y. pestis. A real-time polymerase chain reaction confirmed the presence of Y. pestis in all samples; however, whole-genome sequencing (WGS) coverage of the Y. pestis chromosome ranged from 0.46% to 97.1%, largely due to host DNA interference and low abundance. To address these limitations and enable strain-level identification, we designed a hybridization-based target enrichment approach focused on multilocus variable number tandem repeat analysis (MLVA). Next-generation sequencing (NGS) using whole-genome amplification revealed that the accuracy of the 25 MLVA profiles of Y. pestis for samples #24-2, #24-5, #24-8, and #24-10 was 4%, 100%, 52%, and 0%, respectively. However, all samples showed 100% accuracy with target-enriched NGS, confirming they all belong to the same strain. These findings demonstrate that a targeted enrichment strategy for MLVA loci can overcome common obstacles in microbial forensics, particularly when working with trace or degraded samples where conventional WGS proves challenging. Full article

While pathogenic microbes, such as Yersinia pestis, Mycobacterium tuberculosis, Clostridium tetani, influenza A virus, and many others, have historically been the focus of scientific attention due to their role in causing severe diseases, beneficial microorganisms are being increasingly recognized for their essential contributions to human, animal, and plant health within the One Health framework, as well as their contributions to nutrition and the stability of ecosystems [...] Full article

Yersinia pestis, the causative agent of plague, has triggered multiple pandemics throughout human history, yet its long-term evolutionary patterns and reservoir dynamics remain poorly understood. Here, we present a global phylogenomic analysis of ancient and modern Y. pestis strains spanning from the Neolithic and Bronze Age to the present day. We show that pandemic-causing lineages did not arise from a single ancestral strain but instead emerged independently along deep branches of the Y. pestis phylogeny. Pandemic-associated Y. pestis strains were recovered exclusively from human remains and display clear local temporal divergence, indicating evolution driven by human transmission during outbreaks. These findings support the hypothesis that plague emergence is driven by complex, regionally rooted reservoirs, with recurrent spillovers into human populations across millennia. Our work highlights the need to view plague not as a series of isolated outbreaks but as a long-standing zoonotic threat shaped by deep evolutionary history, host ecology, and human societal structures. Full article