Microbiology spectrum最新文献

Most human pathogens, while originating from animals, have crossed species barriers to infect humans, often leading to outbreaks of new infectious diseases. Despite significant efforts, the mechanisms, timing, and locations of these emerging diseases remain largely uncertain. Here, using a viral metagenomic approach, we discovered a novel canine-associated parvovirus in human oropharyngeal secretions. Molecular screening revealed the presence of this parvovirus in different canine tissues, including 24 of 108 pharyngeal lymph node samples. Further molecular investigation showed that the virus was detected in the oropharyngeal secretions of pet dogs and in human samples that were not linked to these animals. This parvovirus was therefore named human-canine associated parvovirus 1 (HCAPV-1). Nine complete genomes of HCAPV-1 were acquired through next-generation sequencing, combining Sanger sequencing. Genomic and phylogenetic analyses indicate that these nine strains of HCAPV-1 belong to the genus Protoparvovirus and form a distinct clade, with their closest relatives being newlaviruses from foxes. Amino acid substitutions have been characterized in the capsid proteins of the variants of HCAPV-1, which potentially alter their infection patterns. Potential genomic recombination was also observed in HCAPV-1. Taken together, our findings reveal the presence of a novel parvovirus in both canine and human samples, highlighting the need to investigate its host range and transmission dynamics.IMPORTANCEThis study identified a novel parvovirus, human-canine associated parvovirus 1 (HCAPV-1), which was detected in human oropharyngeal secretions and various canine tissues, suggesting that its host range may extend beyond a single species. Phylogenetic analysis revealed that HCAPV-1 forms a distinct clade within the genus Protoparvovirus, closely related to newlaviruses from foxes. Amino acid substitutions observed in the capsid proteins of HCAPV-1 variants indicate genetic divergence, warranting further investigation into their potential implications for host interactions. Recombination events may have contributed to its emergence. This finding highlights the importance of continued surveillance in settings where humans and companion animals coexist and underscores the need for further research to clarify the ecological and host-range characteristics of such viruses.

The coordinated post-natal development of the gut microbiome and metabolome is essential for preterm infant health, yet its disruption is increasingly linked to adverse outcomes such as bronchopulmonary dysplasia (BPD). In this study, we performed an integrated multiomics analysis of fecal samples collected from preterm infants to characterize temporal changes in gut microbial and metabolic profiles and explore their potential associations with BPD development. This study observed a distinct trajectory of the phylum Bacteroidota as a hallmark of normal gut maturation, with its abundance progressively declining across non-BPD infants. In contrast, infants who later developed BPD exhibited early depletion followed by irregular enrichment of Bacteroidota. Correlation analysis revealed that Streptococcus abundance was positively associated with elevated cysteic acid, a metabolite linked to oxidative stress. Together, these findings suggest that altered Bacteroidota succession and Streptococcus-associated oxidative imbalance may reflect early microbial-metabolic perturbations in infants at risk of BPD. This work provides preliminary, hypothesis-generating insights into gut-associated signatures potentially relevant to BPD pathogenesis.

Importance: Bronchopulmonary dysplasia (BPD) remains a leading cause of morbidity in preterm infants, yet early biomarkers and targeted preventive strategies are limited. By integrating microbiome and metabolome data from a pilot cohort, this study identified patterns of disrupted Bacteroidota succession and Streptococcus-associated oxidative stress that are associated with BPD risk. These findings highlight the gut as a potential extrapulmonary contributor to disease susceptibility and support early risk assessment and guide future microbiome-targeted interventions in preterm infants.

Campylobacteriosis and salmonellosis are the leading bacterial zoonoses in Europe, with poultry meat being the primary source of human contamination. Although both Campylobacter and Salmonella bacteria can coexist asymptomatically in chickens, their reciprocal impact remains underexplored. An in vitro study showed that Campylobacter jejuni survival was positively affected by the presence of Salmonella, but no data are available on this interaction in the animal gut. In this study, an in vivo investigation was carried out to explore the dynamics between Campylobacter and Salmonella colonization in chickens. The results revealed that both Salmonella and Campylobacter maintained significantly higher levels of colonization in the ceca throughout the experiment when co-inoculated compared to when inoculated alone. Additionally, changes in the microbiota were associated with each pathogen inoculated alone, but the simultaneous presence of Campylobacter and Salmonella induced specific modulations that could possibly explain this phenomenon. Significant differences were found in the serum metabolome of the contaminated groups, and partial least squares discriminant analysis models enabled the discrimination of contaminated animals from controls using these metabolic signals. Furthermore, possible links between variations in the microbiota and variations in the metabolome were identified.IMPORTANCEThis study demonstrates a synergistic effect between Salmonella and Campylobacter jejuni in the gut during co-infection in chickens, leading to an increased presence of both pathogens, as well as unique microbiota and metabolome changes. These findings underscore the importance of considering co-infection in poultry control measures and highlight the complex interplay between pathogens, microbiota, and metabolism.

Saxifraga stolonifera Meeb is widely used as a traditional Chinese medicine for the treatment of infections. This study aims to evaluate the antibacterial properties and suppression of virulence by Saxifraga stolonifera Meeb extracts on Pseudomonas aeruginosa. Following extraction of Saxifraga stolonifera Meeb with petroleum ether, ethyl acetate, n-butyl alcohol, and water, the n-butyl alcohol extract had the strongest activity against P. aeruginosa PAO1 and P. aeruginosa ATCC27853, with minimum inhibitory concentration (MIC) values of 10 and 5 mg/mL, respectively. In the presence of the n-butyl alcohol (n-BuOH) extract at 1/4MIC, genes lasI, lasR, rhlI, phzA1, phzA2, and pilG were decreased to levels ranging from 13% (lasI) to 43% (phzA2). Both biofilm formation and pyocyanin production of PAO1 were inhibited by the n-BuOH extract at sub-inhibitory concentrations. N-butyl alcohol extract analyzed by HPLC-Q-TOF-MS/MS showed more than 11 compounds. Overall, our results suggest that the n-BuOH extract from Saxifraga stolonifera Meeb may be used as a new anti-virulence agent for P. aeruginosa infection.

Importance: Pseudomonas aeruginosa infections pose severe challenges to clinical treatment, and anti-virulence therapy has emerged as a novel therapeutic strategy. This study demonstrates that the n-butanol extract of Saxifraga stolonifera exerts anti-virulence effects by downregulating virulence-related genes, inhibiting quorum-sensing systems, and biofilm formation. Moreover, its multiple bioactive components also possess antibacterial and anti-virulence properties. S. stolonifera is thus promising to be developed into a novel anti-virulence inhibitor against P. aeruginosa for the prevention and treatment of clinically relevant infections.

Marek's disease, a highly contagious avian immunosuppressive disorder caused by the α-herpesvirus MDV-1, poses a significant threat to poultry health. The development of rapid visual detection methods capable of distinguishing epidemic MDV-1 strains from vaccine strains is crucial for early disease warning, vaccine efficacy evaluation, and precise disease control. We developed a novel isothermal detection system that integrates recombinase polymerase amplification (RPA) with CRISPR/Cas14a technology for the visual identification of epidemic MDV-1 strains. This method operates at a constant temperature of 37°C and allows for either real-time analysis or endpoint visual readout without the need for complex instrumentation. Our results showed no cross-reactivity with Newcastle disease virus, infectious bursal disease virus, MDV-1 vaccine strains, or herpesvirus of turkeys. Plasmid DNA standards were used to determine the sensitivity of the assay, and the detection limit was 24.6 copies/μL. Clinical evaluation using 24 field samples confirmed that the method successfully identified all Marek's disease virus-positive cases, demonstrating its diagnostic reliability. In conclusion, we have developed a rapid, highly specific nucleic acid detection platform for MDV-1 that enables visual readout without complex instrumentation by combining the sensitivity of RPA with the specificity of CRISPR/Cas14a technology, offering promising potential for field-based diagnostics and disease surveillance.IMPORTANCEMarek's disease virus (MDV-1) is a highly contagious and economically important avian pathogen. Existing diagnostic methods are unable to reliably distinguish between epidemic and vaccine strains in field settings, which hampers effective surveillance and evaluation of vaccination programs. To address this challenge, we developed a portable isothermal detection assay that combines recombinase polymerase amplification with CRISPR/Cas14a technology. This approach enables highly sensitive (24.6 copies/μL) and specific visual detection of epidemic MDV-1 strains without cross-reactivity with vaccine strains or related viruses. The assay demonstrated 100% agreement with reference methods when evaluated using clinical samples. As a cost-effective method that avoids the need for complex detection instruments, it offers a practical solution for rapid on-site diagnosis, facilitating enhanced outbreak control and improved poultry health management globally.

To evaluate the performance of the iFIND INH/FQ, a low-complexity molecular assay, for the rapid and simultaneous detection of resistance to isoniazid (INH) and fluoroquinolones (FQs) in Mycobacterium tuberculosis. Frozen sputum specimens stored at the Chengde Center for Disease Control and Prevention laboratory were used. Phenotypic drug susceptibility testing (pDST) and DNA sequencing served as reference standards. The limit of detection (LOD) was determined using probit regression with spiked samples. The assay's ability to detect resistance-conferring mutations in katG, inhA, and gyrA genes was assessed using genotypically characterized strains. Diagnostic accuracy was evaluated against pDST. The LOD was 20.79 CFU/mL for INH and 9.34 CFU/mL for FQs. The assay detected all targeted mutations except ahpC c.-6 associated with INH resistance. Compared to pDST, the iFIND INH/FQ assay demonstrated a sensitivity of 97.59% (95% confidence interval [CI]: 91.63-99.34%) and specificity of 98.10% (95% CI: 94.57-99.35%) for INH resistance. For FQ resistance, sensitivity was 92.16% (95% CI: 81.50-96.91%) for levofloxacin and 92.00% (95% CI: 81.16-96.85%) for moxifloxacin, with specificities of 97.33% (95% CI: 93.89-98.85%) and 96.81% (95% CI: 93.21-98.53%), respectively. Sequencing confirmed iFIND results in the majority of discrepant cases (100% for INH and 55.65% for FQs). The iFIND INH/FQ LC-aNAAT is a highly accurate and rapid molecular assay for simultaneous detection of INH and FQ resistance. It is a promising tool for scaling up rapid drug susceptibility testing in clinical and peripheral laboratory settings.

Importance: As a low-complexity automated nucleic acid amplification test, the iFIND assay achieves the goal of simultaneously detecting isoniazid and fluoroquinolone resistance in approximately 90 min, perfectly meeting the TPP's core requirements for "rapid" and "simple operation." Its fully integrated system minimizes manual steps and contamination risk, making it highly suitable for use in resource-limited, lower-biosafety-level primary laboratories.

Targeting cell death pathways, including pyroptosis and necroptosis, has been shown to mitigate influenza virus infection severity. Here, we examined whether pyroptosis specifically driven by the pore-forming protein gasdermin E (GSDME) is involved in regulating influenza virus infection outcomes. We found that Gsdme^-/- mice showed similar weight loss and survival in severe A/PR/8/34 (H1N1) virus infections compared to WT counterparts. Likewise, lung dysfunction, histopathological damage, viral titers, and inflammatory cytokine levels were similar in the two groups. Global transcriptomic analysis also revealed similar inflammatory and antiviral gene expression programs in WT versus Gsdme^-/- mouse lungs at baseline and in response to infection. To confirm the generality of these findings, we infected mice with minimally mouse-adapted 2009 pandemic H1N1 virus and again observed similar weight loss, lung dysfunction, and mortality in WT and Gsdme^-/- mice. Our results overall demonstrate that GSDME contributes negligibly to the host response against H1N1 influenza virus, refining our understanding of cell death pathways in influenza pathogenesis.

Importance: Influenza virus infection activates multiple cell death pathways that shape disease outcomes. Here, we demonstrate that gasdermin E (GSDME)-mediated pyroptotic cell death does not significantly affect lung pathology or survival during severe H1N1 influenza virus infection. This finding contrasts with prior reports showing that GSDME worsens disease caused by H3N2 or H7N9 strains, as well as studies implicating gasdermin D in exacerbating H1N1 pathology. Thus, our data clarify that gasdermin family members contribute to influenza pathogenesis in a context-specific manner, underscoring the importance of considering viral diversity when evaluating the therapeutic potential of targeting cell death pathways.

The potable water dispenser (PWD) system plays a critical role as a source of drinking water for astronauts on the International Space Station (ISS). In this study, we examined the bioburden in the potable water produced by the PWD. The amount of extracellular polymeric substances (EPSs) in the PWD water was approximately 19 or 55 times greater than the bacterial count, and the EPS biomass accounted for approximately 24% or 86% of the bacterial biomass. Ralstonia pickettii consistently comprised approximately 70% or 80% of the bacteria for 3 years. Under simulated microgravity conditions, the isolated R. pickettii strains exhibited higher cell and EPS concentrations and higher total volume concentrations (average volume multiplied by concentration) of cell and EPS than under 1G conditions, whereas the average cell volume was smaller and the average EPS volume was larger. The ISS isolates showed higher EPS production and biofilm-formation abilities than terrestrial strains under nutrient-rich conditions and possessed high biofilm-formation ability comparable to those of terrestrial strains under nutrient-poor conditions. The ability of R. pickettii to produce EPS may play a crucial role in its adaptation to the water environment on the ISS.IMPORTANCEIn space habitation environments, the use of recycled water is indispensable, and ensuring its microbiological safety is essential. In this study, we elucidated the microbiological characteristics of water from the potable water dispenser (PWD) on the International Space Station (ISS). Our findings revealed that bacteria of the Ralstonia pickettii are the predominant species in PWD water and that extracellular polymeric substances (EPSs) constitute a large proportion of the biomass. Furthermore, the isolated R. pickettii was shown to possess high EPS production ability and strong biofilm-forming capacity. Since EPS plays a crucial role in biofilm formation, these abilities may be important factors enabling R. pickettii to adapt to the water environment of the ISS.

Although contact lens wear is widespread and known to affect the ocular surface, its impact on the ocular surface microbiome (OSM) remains poorly understood, with existing studies reporting conflicting findings. Additionally, the relationship between contact lens wear, tear proteome, and dry eye disease (DED) is unclear. In this study, we aimed to characterize the OSM (via whole-metagenome shotgun sequencing) and the tear proteome of 25 contact lens wearers and 23 age- and sex-matched controls. The dominant phyla were Actinobacteria, Proteobacteria, and Firmicutes, with Cutibacterium acnes being the most abundant species. No significant differences in microbial composition, diversity, or tear proteome were observed between contact lens wearers and controls. DED parameters (tear breakup time, Schirmer's test, tear osmolarity, and Ocular Surface Disease Index [OSDI]) also showed no significant differences, although contact lens wearers reported a trend toward higher subjective symptoms (OSDI). Sex-stratified analysis revealed a marginal difference in microbial beta diversity between male contact lens wearers and male controls, along with increased tear production in male contact lens wearers. Female contact lens wearers reported a higher OSDI compared to female controls. These findings suggest that contact lens wear does not significantly alter the OSM or tear proteome in healthy individuals, although sex-specific responses may warrant further investigation.IMPORTANCEContact lenses are worn by millions of people, yet the scientific literature contains conflicting reports about their impact on the microbial communities that are naturally present on the eye surface. This study addresses these knowledge gaps by examining both the eye microbiome and tear proteins using advanced sequencing and linking them to dry eye symptoms. Understanding the relationship between contact lens wear, natural eye bacteria, and tear composition is essential for resolving contradictory findings in the field. Additionally, identifying potential sex-specific differences in how individuals respond to contact lens wear could lead to more personalized approaches to contact lens management.