Microbiology spectrum最新文献

Cholera, caused by Vibrio cholerae, remains a significant diarrheal disease, especially in coastal regions of developing countries. In Malaysia, cholera is largely non-endemic except in Sabah, which has had recurrent outbreaks accounting for ∼75% of national cases between 2004 and 2014. To understand the origin and transmission of the disease, we sequenced the genomes of clinical isolates of V. cholerae O1 collected during an outbreak in 2019 and 2020. Genotypic analyses revealed that all Sabah isolates were atypical El Tor biotype harboring Classical CTX prophage elements. In particular, the strains carried two tandem CTX prophage copies in chromosome 2 and three tandem RS1 sequences on chromosome 1, including a Classical type rstR, which is atypical for canonical El Tor. Genome comparisons revealed conserved seventh-pandemic genomic islands (VSP1 and VSP2) and variably arranged biotype-specific loci, suggesting pandemic-lineage markers and mobile elements linked to environmental adaptation. Phylogenetic reconstruction placed the Sabah strains within wave 2 of the seventh-pandemic clade, forming a distinct subclade with two genotypes, consistent with regional endemicity over the last few decades. Although wave 3 strains have largely replaced wave 2 globally, an established population of wave 2 strains in Southeast Asia suggests that they are more resilient than previously thought.IMPORTANCEThis study addresses a critical public health concern by investigating the genomic characteristics of Vibrio cholerae O1 strains responsible for recurrent cholera outbreaks in Sabah, Malaysia. Although cholera is largely non-endemic in most parts of Malaysia, Sabah remains an exception, contributing disproportionately to national case counts. By sequencing clinical isolations from the 2019 and 2020 outbreaks, this research provides essential insights into the origins, evolutionary dynamics, and transmission patterns of V. cholerae in a region with persistent endemicity. These findings underscore the importance of continuous genomic surveillance in geographically distinct settings and offer valuable data for informing public health strategies aimed at cholera control and prevention in Southeast Asia.

The tumor immune microenvironment and intratumoral microbiota play critical roles in cancer progression and immunotherapy response, yet their integrated functions in stomach adenocarcinoma (STAD) are not well understood. This study conducted a multi-omics analysis of transcriptomic and microbiome data from 348 patients with STAD. Using the ImmuCellAI algorithm, immune cell infiltration (ICI) was estimated, and non-negative matrix factorization classified samples into three immune subtypes (INC-1, INC-2, and INC-3). Differential expression analysis identified immune-related signature genes enriched in immune signaling pathways. Tumor mutational burden, microsatellite instability, immune checkpoint gene expression, and drug sensitivity were compared across subtypes. Microbiome clustering identified three subtypes (MC-1, MC-2, and MC-3), with associations to immune infiltration and microbial composition. The immune subtypes showed distinct patterns of ICI, clinical stage, and gene expression, with differentially expressed genes enriched in immune and tumor-related pathways. Microbiome subtypes exhibited unique diversity metrics and associations with the immune microenvironment. Integration of immune and microbial data improved immune checkpoint blockade (ICB) prediction, with genera like Staphylococcus and Ralstonia correlating with immune genes such as CD22, VIPR2, and FLT3. These findings provide insights into ICB response and support more precise immunotherapy strategies for STAD.IMPORTANCEDeciphering the interactions between the tumor immune microenvironment and the intratumoral microbiota is crucial for advancing precision immunotherapy in stomach adenocarcinoma (STAD). In this study, we present an integrative multi-omics framework that stratifies patients into distinct immune and microbial subtypes, uncovering their associations with immunogenomic profiles, immune cell infiltration patterns, and clinical features. Notably, we identify specific microbial genera correlated with immune-related gene expression and immune checkpoint blockade responsiveness. These findings provide novel insights into the immune-microbiome axis in STAD and underscore the potential of integrative multi-omics approaches to enhance patient stratification and guide more effective immunotherapeutic strategies.

Rhinoviruses (RVs) and enteroviruses (EVs) are important respiratory pathogens. Although numerous molecular assays have been developed for detection of RVs and EVs, their genetic similarities pose challenges for molecular differentiation. In this study, we described a real-time nested reverse transcription (RT)-PCR assay using SYBR green and RV- and EV-specific reverse primers to differentially detect RVs and EVs. The primers were designed so that the numbers and locations of mismatches should be the most adequate for objective viruses and the least adequate for opposite viruses using all EV and RV sequences in GenBank. The assay was validated using nasopharyngeal swab specimens from pediatric patients who have fever and/or respiratory symptoms at Keio University Hospital from November 2021 to January 2023 and tested positive for Human Rhinovirus/Enterovirus by the FilmArray Respiratory Panel 2.1. The species and serotypes were identified by analyzing sequences of PCR products using the BLAST program. The results of the present RT-PCR assay and the BLAST analysis were completely consistent with each other. Furthermore, the current assay revealed the cases of dual infections of RV and EV. No significant differences were observed in patient demographics or clinical courses among viral species. The assay presented here may be the most suitable for routine diagnosis and surveillance of RV and EV infections.

Importance: We describe a real-time nested reverse transcription-PCR assay that enables us to differentially detect rhinoviruses and enteroviruses. Differential diagnosis of rhinovirus and enterovirus infections has not been succeeded because of their genetic diversities and similarities. We resolved this problem by using specific PCR primers that were designed by in silico analysis of all rhinovirus and enterovirus sequences obtained from GenBank. The developed method was validated by applying to more than 100 nasopharyngeal swab specimens from pediatric patients in Keio University Hospital in Japan and analyzing with the BLAST algorithm. The assay may be suitable for routine diagnosis and surveillance of rhinovirus and enterovirus infections.

Interferon-γ release assays (IGRAs), such as the QuantiFERON-TB Gold Plus (QFTTB), are commonly used to detect past exposure to Mycobacterium tuberculosis complex (Mtb), the cause of tuberculosis (TB). IGRA-positive (IGRA+) asymptomatic individuals are diagnosed with presumptive latent tuberculosis infection (LTBI) and often offered therapy to prevent active disease. However, discordant results during serial testing pose challenges for interpretation and may lead to unnecessary treatment. We conducted a retrospective study of subjects who received QFTTB testing at Stony Brook Medicine between October 2020 and March 2024 to identify sociodemographic and clinical variables associated with quantitative QFTTB results. A total of 743 subjects were analyzed, including all 436 QFTTB-positive (QFTTB+) cases of 11,641 tests ordered (3.7%), of whom 16 were diagnosed with active TB during the 4-year study period within the context of a reported incidence rate of 3.4/100,000 persons per year in Suffolk County, a region of low TB incidence. A random sample of 307 age-sex-matched QFTTB-negative controls was included. Of 203 subjects undergoing serial QFTTB testing, 170 (83.7%) had concordant results, while 33 (16.3%) showed discordance-23 (69.7%) with reversion and 10 (30.3%) with conversion. Conversions occurred in significantly older subjects (mean age 51.1 ± 15.0 vs 37.0 ± 15.6, P = 0.025) and over longer intervals (415.1 vs 91.2 days, P = 0.026). Our findings reinforce the use of confirmatory or repeat testing before initiating LTBI therapy, particularly when testing intervals are short (<6 months) or results fall near the diagnostic cutoff (0.35 IU/mL).

Importance: Reliable interpretation of interferon-γ release assays (IGRAs) is critical for the diagnosis and management of latent tuberculosis infection (LTBI). However, variability in test performance during serial or confirmatory testing complicates clinical decision-making and may result in unnecessary treatment. Our study demonstrates that demographic factors, clinical comorbidities, and testing intervals contribute to discordant QuantiFERON-TB Gold Plus results. These findings underscore the need to integrate epidemiologic risk, pre-test probability of Mycobacterium tuberculosis complex exposure, clinical history, and repeat testing when appropriate before initiating LTBI therapy. Improved understanding of IGRA variability can strengthen both patient care and research applications, including tuberculosis vaccine and protective biomarker studies.

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.