Microbiology spectrum最新文献

Coronavirus disease 2019 (COVID-19) has complicated the management of acute respiratory infections and impacted antibiotic use. We assessed the relationship between nirmatrelvir/ritonavir (NMV/r) receipt and outpatient antibiotic prescribing among patients with COVID-19 in a large national health system. We conducted a retrospective cohort study among outpatients enrolled in the Veterans Affairs Healthcare System who had a positive severe acute respiratory syndrome coronavirus 2 test or COVID-19 diagnosis and were eligible for NMV/r treatment between 1 April 2022 and 31 March 2024. NMV/r-treated patients were compared with those who did not receive NMV/r and were considered unexposed until NMV/r was dispensed. We assessed the relationship between NMV/r receipt and being prescribed an outpatient antibiotic in the 30 days after a COVID-19 diagnosis using adjusted Cox proportional hazards regression. We included 302,600 NMV/r-eligible outpatients with COVID-19, of whom 67,649 received NMV/r and 234,951 did not receive NMV/r. NMV/r-treated patients were less likely to receive outpatient antibiotics compared to those who did not receive NMV/r (7.2% [4,901/67,649] vs 9.2% [21,533/234,951], respectively; adjusted hazard ratio [HR] 0.65, 95% CI: 0.63‒0.68). After excluding patients who received an antibiotic prescription upon COVID-19 diagnosis (i.e., likely empiric therapy), this relationship was attenuated (HR: 0.91, 95% CI: 0.87‒0.95). NMV/r-eligible patients with COVID-19 who received NMV/r were 35% less likely to be prescribed outpatient antibiotics compared to patients who did not receive NMV/r, possibly driven by a diminished perceived need for empiric antibiotic therapy. Treatment with NMV/r may reduce unnecessary outpatient antibiotic use. Antibiotics should be reserved for patients with a high suspicion of bacterial co-infection.IMPORTANCEAntimicrobial resistance, driven by the overuse of antibiotics, is a major global health threat. The coronavirus disease 2019 (COVID-19) pandemic has complicated this issue, with antibiotics often prescribed to patients with COVID-19 despite being ineffective against viruses. These practices, typically aimed at preventing or empirically treating rare bacterial co-infections, have raised concerns about accelerating resistance. The antiviral nirmatrelvir/ritonavir (NMV/r), widely used in high-risk patients with COVID-19 to prevent severe illness, offers an opportunity to reassess antibiotic use in patients with respiratory infections. Our study of over 300,000 patients in a national healthcare system found that those treated with NMV/r for COVID-19 were 35% less likely to receive antibiotics than those who did not receive the antiviral. Lower antibiotic use among patients treated with NMV/r may reflect a reduction in unnecessary outpatient antibiotic use. These findings highlight the potential role of antivirals in supporting antibiotic stewardship and addressing a critical public health challenge.

Streptococcus mutans is a primary cariogenic pathogen involved in dental biofilm formation, a major virulence factor in the development of dental caries. In S. mutans, the competence-stimulating peptide (CSP), encoded by comC, plays a critical role in environmental stress response, growth regulation, and virulence expression. In this study, we performed transcriptome analysis to investigate the role of SMU.1147, a unique core gene in S. mutans, in biological pathways related to transport, defense responses, and environmental sensing. The deletion of SMU.1147 led to the upregulation of genes involved in carbohydrate uptake and metabolism, particularly phosphotransferase system (PTS) transporters, thereby enhancing the sugar transport capacity. However, despite increased sugar uptake, the mutant strain did not show significant changes in growth rate or ATP production and displayed slightly reduced organic acid production. Additionally, the mutant exhibited significantly reduced cell viability after an 8-h incubation compared to the parental strain. Notably, genes associated with CSP-dependent signal transduction and stress defense, such as comX, comR, htrA, scnRK, and ciaRH, were downregulated in the mutant strain. Furthermore, stress-related genes, including spxA2, clpP, and clpX, were significantly downregulated, suggesting compromised protein quality control and oxidative stress responses. Our findings suggest that SMU.1147 plays a critical role in regulating peptide-mediated signaling, metabolic coordination, and environmental adaptation in S. mutans, positioning it as a key integrator of the metabolic and stress response networks that are essential for pathogenicity and survival.

Importance: Understanding the regulatory mechanisms that govern virulence and environmental adaptation in Streptococcus mutans is essential for developing strategies to mitigate dental caries. This study reveals the critical role of the SMU.1147 gene in S. mutans in metabolic regulation, stress response, and cell viability. Our results demonstrate how the deletion of this gene affects sugar uptake and organic acid production, leading to imbalances in carbon metabolism and reduced long-term survival. These findings provide valuable insights into the ability of S. mutans to adapt to stressed conditions and highlight the role of SMU.1147 in modulating biofilm formation and virulence, contributing to our understanding of regulatory pathways in dental pathogens.

The efficient carbon source utilization in dynamic environments, including anoxic subsurface contaminated by aromatic compounds, is a challenge for anaerobic bacteria such as Geotalea daltonii strain FRC-32. The aim of this study was to elucidate the metabolic pathways employed by G. daltonii FRC-32 during anaerobic benzoate oxidation in the presence of acetate, a key intermediate in anaerobic organic matter degradation, to predict carbon source transport and utilization strategies. Simultaneous carbon source oxidation and monoauxic growth were observed in G. daltonii FRC-32 cultures grown on 1 mM benzoate + 5 mM acetate, 1 mM benzoate + 2 mM acetate, and 2 mM acetate spiked with 1 mM benzoate. Sequential carbon source oxidation and diauxic growth were observed only in cultures grown on 5 mM acetate spiked with 1 mM benzoate. Benzoate accumulation in G. daltonii FRC-32 whole cell lysates indicated that intracellular benzoate transport occurred during benzoate oxidation in the presence of acetate. Expression analyses of putative benzoate transporter BenK and protein-ligand binding affinity prediction suggested BenK's specificity for transporting benzoate. Relative expression levels for the gene benK, encoding BenK, and the genes bamNOPQ, involved in the benzoyl-CoA pathway, were significantly higher in cultures grown on both benzoate and acetate than in cultures grown on acetate as sole carbon source, indicating that intracellular benzoate accumulation facilitated the regulation of bamNOPQ. Our results demonstrated that G. daltonii FRC-32 can perform differential benzoate oxidation in the presence of acetate, by either simultaneous or sequential carbon source oxidation, which indicated the metabolic plasticity of G. daltonii FRC-32 in response to varying carbon source availability.IMPORTANCEThe contamination of anaerobic subsurface environments by crude oil derivatives including aromatic compounds is a global concern due to the persistence and toxicity of these pollutants. Anaerobic bacteria play a crucial role in the degradation of aromatic hydrocarbons under anoxic conditions; however, the potential mechanisms involved in metabolic regulation of aromatic degradation pathways are not well understood. This study contributed to elucidating how G. daltonii strain FRC-32 efficiently utilizes benzoate as a carbon source in the presence of acetate. Findings of intracellular benzoate accumulation and regulation of key genes associated with benzoate oxidation contributed to the understanding of G. daltonii FRC-32's aromatic degradation pathways, provided significant insights into potential mechanisms that modulate anaerobic benzoate oxidation in the presence of the energetically favorable carbon source acetate, and indicated metabolic strategies of G. daltonii FRC-32 in response to dynamic environmental conditions.

Amazonian soil microbial communities are known to be altered by land-use change. However, attempts to understand these impacts have focused on broader community alterations or the response of specific microbial groups. Here, we recovered and characterized 69 soil bacterial and archaeal metagenome-assembled genomes (MAGs) from three forests and three pastures of the Eastern Brazilian Amazon and evaluated the impacts of land conversion on their genomic features. Pasture MAGs had significantly higher GC content (64.9% vs 60.2%), genome size (4.0 vs 3.1 Mbp), and number of coding sequences (4,058 vs 3,306) compared to forest genomes. Taxonomically, MAGs belonged to eight phyla; however, most (90%) had low similarity to previously known species, indicating potentially novel taxa at multiple levels. We also observed that the functional profiles associated with biogeochemical cycling and carbohydrate-active enzyme genes were impacted by forest conversion, with pasture MAGs exhibiting a notably higher number of both gene groups. Together, these data constitute the largest single-sourced genomic data set from upland soils of the Brazilian Amazon to date and increase the known MAG richness in these soils by 78%. Our data, therefore, not only add to a neglected yet emerging field but, importantly, highlight that land-use change has drastic impacts on the genomic characteristics and functional traits of dominant soil microbes.IMPORTANCEThe Brazilian Amazon is facing unprecedented threats, including increasing deforestation and degradation, which together impact half of the original forest area. Soil microorganisms are sensitive indicators of land-use change, linked to a rise in microbial methane emissions and antibiotic-resistance genes in the Amazon. However, most Amazonian soil microbes remain unknown, and little attention has been given to their genomes. Using sequencing and bioinformatics, we recovered and characterized 69 soil bacterial and archaeal genomes (metagenome-assembled genomes). These abundant members of the microbial communities diverged across forests and pastures in terms of taxonomic and functional traits. Forest conversion favors organisms with specific genomic features - increased GC content, genome size, and gene number - selecting for microorganisms that can thrive under altered conditions. Our paper helps us understand the intricate relationships between microbes and the environment, which are crucial pieces of information for comprehensive soil health assessments and future policy formulation.

Viability testing for anaerobes is a time-consuming and expensive process, posing challenges for research and public health settings. Here, we present a rapid, economical, and reliable method for testing anaerobe viability using the Geometric Viability Assay (GVA) with Clostridium perfringens as our model, a bacterium known for causing toxin-related systemic and enteric diseases. This method is efficient and cost-effective, requiring one pipette tip per sample, and is compatible with the economical anaerobic jar system. The results align with traditional plate-based assays in terms of colony-forming unit (CFU) measurements. Anaerobic GVA has low technical bias and a dynamic range extending over 5 orders of magnitude. In addition, our method determined the bactericidal activity of antibiotics in a dose-dependent manner, when an antibiotic sensitivity testing (AST) was performed with a panel of four antibiotics (ampicillin, gentamicin, meropenem, and tetracycline). Furthermore, the minimum concentrations for complete bactericidal activity (MBC) of four clinical isolates were determined and the MBC concentration for tetracycline was up to 8× higher than the concentration for complete growth inhibition (MIC). Additional tests involving Clostridium bifermentans and Clostridium sporogenes demonstrated the generality of our method for other anaerobic species. Beyond viability testing, the GVA measured spore concentrations of various Clostridium perfringens isolates, showing consistency with classical plating methods. Our study confirms that the anaerobic GVA is a valuable tool for rapid, accurate viability screening in anaerobic settings and is compatible with routine assays, such as AST and spore screening. This method enhances the scalability and utility of anaerobic viability-based assays.

Importance: The routine assessment for the viability of anaerobes is based on bacterial plating, but so far, it has been limited in throughput by the long preparation steps and the tedious anaerobic culturing. Thus, comparatively little is known about the susceptibility pattern, and the sporulation of anaerobes because of the absence of the proper method. Here, we show GVA can quantify the anaerobic Clostridiums colonies accurately by utilizing an anaerobic jar to measure viable cells and spores in high throughput with minimal volumes of reagents and at a comparable time to the traditional viability testing practice. Furthermore, this method enabled high-throughput detection of the bactericidal activity of the antibiotics against anaerobes and allowed for the quantification of hetero-tolerant/resistant subpopulation, which was previously unattainable. Our approach is rapid and easy to use, making it ideal for various applications where high-throughput capabilities can drive innovation, including drug-microbe interactions, host-microbe interactions, and microbe-microbe interactions.

Post-chikungunya viral arthritis may persist for months to years after infection and is characterized by relapsing and remitting symptoms. This study investigates the relationship between autoantibodies and chikungunya arthritis severity, providing insights into arthritis pathogenesis. We assessed arthritis measures in a cohort of serologically confirmed chikungunya cases from Colombia between 2019 and 2021 (n = 144). We measured arthritis disease severity, flare intensity, pain, and disability, then plasma antibody levels of rheumatoid factor IgM, anti-cyclic citrullinated peptide (CCP), anti-citrullinated α-enolase peptide 1 (CEP-1), anti-nuclear antibody (ANA), anti-citrullinated vimentin (Sa), and immunoglobulins produced in response to chikungunya, Zika and Mayaro. Finally, we examined the correlation between the arthritis measures with the titers of antibodies hypothesized to play a potential role in arthritis pathogenesis. Cases were characterized by moderate disease severity (Disease Activity Score-28 mean, 3.66 ± 1.23) in current arthritis flare with moderate intensity (Flare Score, 25.42 ± 12.38), moderate pain (61.47 ± 27.23 on visual analog scale 0-100), and some disability (Health Assessment Questionnaire 0.77 ± 0.58). After Bonferroni adjustment, there were no statistically significant correlations between the levels of antibodies and arthritis measures. Weak correlations between rheumatoid factor IgM with arthritis severity and pain (P < 0.01) and anti-CEP1 with disability (P < 0.05) were observed when unadjusted for multiple comparisons. The data suggest that autoantibodies, such as RF, anti-CCP, and anti-CEP-1, do not correlate with post-chikungunya arthritis disease severity, thus unlikely to significantly contribute to pathogenesis. Exposure to other arboviral infections was not related to worse post-chikungunya arthritis. This suggests that other pathways for arthritis disease pathogenesis should be examined.IMPORTANCEThis cohort study describes the correlation between levels of autoantibodies, viral antibodies, and arthritis outcomes, suggesting that autoantibodies known to play an important role in other autoimmune diseases do not correlate with chikungunya arthritis relapse disease severity and are unlikely to contribute significantly to arthritis pathogenesis. This suggests that other pathways for arthritis disease pathogenesis should be examined to identify diagnostic and prognostic markers of alphaviral arthritis.

The identification of Helicobacter pylori infection from gastric biopsy samples requires PCR or bacterial cultures. However, it is difficult to culture H. pylori because it is a fragile bacterium. Next-generation sequencing (NGS) allows direct assessment of the resistome and virulome. Here we describe a new NGS method for studying the resistome and virulome of H. pylori directly from gastric biopsies, based on enrichment analyses and targeted sequencing of H. pylori DNA. In all, 19 DNA samples from human gastric biopsies that tested positive for H. pylori were analyzed. The Agilent SureSelectXT target-enrichment protocol was used with a custom bait library prior to sequencing using the Agilent MagnisDx NGS Library Prep System. NGS sequencing was performed on the Illumina iSeq 100 sequencer using RNA probes for virulence, resistance, and molecular typing genes. The method yielded significant results with a limit of detection of around 1.8e⁵ CFU per mL H. pylori. Mutations in the 23S rDNA sequence associated with macrolide resistance and in the quinolone resistance-determining region of gyrase A associated with levofloxacin resistance were correctly identified. The results of MLST phylogeny analyses performed after target-enrichment were consistent with those obtained via conventional Sanger sequencing. Among the cagA-positive isolates, the gene was detected correctly, and the vacA genotype was determined. In conclusion, our enrichment method enables rapid assessment of the resistome and virulome of H. pylori directly from fresh gastric biopsies.IMPORTANCEHelicobacter pylori, a bacterium that infects at least 50% of the world population, is often treated by probabilistic antimicrobial therapies due to the lack of antimicrobial resistance data provided by clinical laboratories to clinicians. However, targeted antimicrobial therapies are increasingly recommended to achieve efficient eradication with a limited impact on the gut microbiota and with fewer adverse events for the patient. Recent advancements in next-generation sequencing strategies have opened new opportunities in the diagnosis of H. pylori infection. The significance of our research is the development of a novel next-generation sequencing strategy based on target-enrichment. This approach enables the identification of the resistome and the virulome of H. pylori directly from gastric biopsies, providing clinicians with a broad overview of therapeutic options.

The microbiome inhabiting animal skin plays a crucial role in host fitness by influencing both the composition and function of microbial communities. Environmental factors, including climate, significantly impact microbial diversity and the functional attributes of these communities. However, it remains unclear how specific climatic factors affect amphibian skin microbial composition, community function, and the relationship between these two aspects. Understanding these effects is particularly important because amphibians are poikilotherms and, thus, more susceptible to temperature fluctuations. Here, we investigated the skin microbiome of the rhacophorid tree frog Polypedates megacephalus across different climatic regimes using 16S rRNA gene sequencing. Skin swab samples were collected from nine populations of P. megacephalus adults in the Guangxi region, China. The majority of the core microbiota were found to belong to the genus Pseudomonas. Our findings indicate that microbial community diversity, composition, and function are associated with changes in climatic conditions. Specifically, the taxonomic and functional diversity of the skin microbiome increased in response to higher climate variability, particularly in temperature fluctuations. Additionally, the functional traits of microbial communities changed in parallel with shifts in community diversity and composition. The significant correlations of the functional redundancy index with climatic factors suggest that environmental filtering driven by climate change impacts microbial community functional stability. These results highlight the critical influence of climatic factors on amphibian skin microbiomes and offer new insights into how microbial composition and function contribute to host adaptation in varying environmental conditions.IMPORTANCEThis study is important in understanding the association between climate variability, microbial diversity, and host adaptation in amphibians, which are particularly vulnerable to environmental changes due to their poikilothermic nature. Amphibians rely on their skin microbiome for key functions like disease resistance, yet little is known about how climate fluctuations impact these microbial communities. By analyzing the microbiome of Polypedates megacephalus across different climatic regimes, our analysis reveals that warmer climates could reduce the microbial diversity and community functional redundancy, indicating the functional stability of skin microbiome could be susceptible to climate variability, particularly in hosts adapted to relatively cooler conditions. These findings highlight the potential ecological consequences of climate change and emphasize the need to integrate microbiome health into amphibian conservation strategies.

We aim to define the optimal white cell count threshold that correlates with a clinically significant urinary tract infection, as there is insufficient data exploring this in the adult population. We conducted a retrospective cohort study at the Royal Melbourne Hospital analyzing urine samples collected over 6 months in 2022. Urinary tract infection (UTI) was defined as the presence of symptoms (dysuria, urgency, frequency, flank pain, or loin to groin pain) and isolation of a uropathogen with colony counts greater than 10⁷ CFU/L. The relationship between urinary white cell count, growth of uropathogen, and likelihood of UTI was estimated using locally weighted scatterplot smoothing. Of the 6,328 samples included, at a urinary white cell count of less than 10 per microliter, 38% grew a microorganism, while 7% of the total grew a uropathogen. For our sub-analysis part C, at the same WBC count, 2% of samples fulfilled our criteria for UTI. The optimal WBC range for identifying a UTI was 30-50 WBC/µL, demonstrating the most pragmatic balance of sensitivity (92.3%-94.9%, 95% CI 85.9-98.1) and specificity (41.6-47.2, 95% CI 38.6%-50.3%) for a UTI. A lower-than-expected number of UTIs were confirmed in our study, likely due to inappropriate indications for culture collection and the types of urine specimens collected. However, the optimal white cell cutoff for identifying a UTI was higher than the defined pyuria cutoff of 10 WBC/µL. Utilizing a higher urinary WBC cutoff could improve urine culture processing protocols.

Importance: The importance of this study is that it explores the optimal range of white cell count that defines a clinically significant urinary tract infection. The traditional cutoff of more than 10 white blood cells per microliter is often used; however, we now recognize that using this cutoff may not accurately represent true urinary infections, especially in certain populations such as young women. The uncertainty in the optimal white cell count cutoff has widespread implications. For the clinician, it may lead to unnecessary prescribing of antibiotics for patients who do not have a Urinary tract infection, such as asymptomatic bacteriuria. For the microbiology laboratory, it may lead to unnecessary workup and culture of urine samples that are not clinically relevant. Many studies to date have attempted to define an optimal value for urinary white cell count; however, not many have incorporated relevant clinical data, which this study has.

Solid organ transplant recipients (SOTRs) suffer more frequent and more severe infections due to their compromised immune responses resulting from immunosuppressive treatments designed to prevent organ rejection. Pharmacological immunosuppression can adversely affect immune responses to vaccination. A cohort of kidney transplant recipients (KTRs) received their third dose of ancestral, monovalent COVID-19 vaccine in the context of a clinical trial and antibody responses to the vaccine strain, as well as two Omicron variants BA.1 and BA.5 were investigated and compared with healthy controls who also received a third dose of mRNA vaccine (HCs). Total IgG and live virus neutralizing antibody titers were reduced in KTRs compared with controls for all variants. KTRs displayed altered IgG subclass switching, with significantly lower IgG3 antibodies. Responses in KTRs were also very heterogeneous, with some individuals showing strong responses but a significant number showing no Omicron-specific neutralizing antibodies. Taken together, immune responses after COVID-19 vaccination in KTRs were not only lower than HCs but highly variable, indicating that simply increasing the number of vaccine doses alone may not be sufficient to provide greater protection in this population. These findings underscore the need for tailored vaccination strategies for immunosuppressed populations, such as KTRs. Alternative formulations and doses of COVID-19 vaccines should be considered for people with severely compromised immune systems, as more frequent vaccinations may not significantly improve the response, especially regarding neutralizing antibodies.IMPORTANCEThis study addresses the challenges faced by kidney transplant recipients (KTRs) in mounting effective immune responses against COVID-19. By evaluating the antibody responses to a third dose of monovalent mRNA COVID-19 vaccine and its effectiveness against Omicron subvariants (BA.1 and BA.5), this study reveals significant reductions in both binding and neutralizing antibodies in KTRs compared with healthy controls. The research highlights altered IgG subclass switching and heterogeneous responses within the KTR population. Reduced recognition of variants, coupled with differences in IgG subclasses, decreases both the quality and quantity of protective antibodies after vaccination in KTRs. These findings underscore the need for tailored vaccination strategies for immunosuppressed populations, such as KTRs. Alternative formulations and doses of COVID-19 vaccines should be considered for people with severely compromised immune systems, as more frequent vaccinations may not significantly improve the response, especially regarding neutralizing antibodies.