FEMS microbes最新文献

The urinary tract is a hydrodynamically challenging microenvironment and uropathogenic Escherichia coli (UPEC) must overcome several physiological challenges in order to adhere and establish a urinary tract infection. Our previous work in vivo revealed a synergy between different UPEC adhesion organelles, which facilitated effective colonization of the renal proximal tubule. To allow high-resolution real-time analysis of this colonization behavior, we established a biomimetic proximal-tubule-on-chip (PToC). The PToC allowed for single-cell resolution analysis of the first stages of bacterial interaction with host epithelial cells, under physiological flow. Time-lapse microscopy and single-cell trajectory analysis in the PToC revealed that while the majority of UPEC moved directly through the system, a minority population initiated heterogeneous adhesion, identified as either rolling or bound. Adhesion was predominantly transient and mediated by P pili at the earliest time-points. These bound bacteria initiated a founder population which rapidly divided, leading to 3D microcolonies. Within the first hours, the microcolonies did not express extracellular curli matrix, but rather were dependent on Type 1 fimbriae as the key element in the microcolony structure. Collectively, our results show the application of Organ-on-chip technology to address bacterial adhesion behaviors, demonstrating a well-orchestrated interplay and redundancy between adhesion organelles that enables UPEC to form microcolonies and persist under physiological shear stress.

The widespread occurrence of clinically relevant antibiotic resistance within humans, animals, and environment motivates the development of sensitive and accurate detection and quantification methods. Metagenomics and quantitative PCR (qPCR) are amongst the most used approaches. In this study, we aimed to evaluate and compare the performance of these methods to screen antibiotic resistance genes in animal faecal, wastewater, and water samples. Water and wastewater samples were from hospital effluent, different treatment stages of two treatment plants, and of the receiving river at the discharge point. The animal samples were from pig and chicken faeces. Antibiotic resistance gene coverage, sensitivity, and usefulness of the quantitative information were analyzed and discussed. While both methods were able to distinguish the resistome profiles and detect gradient stepwise mixtures of pig and chicken faeces, qPCR presented higher sensitivity for the detection of a few antibiotic resistance genes in water/wastewater. In addition, the comparison of predicted and observed antibiotic resistance gene quantifications unveiled the higher accuracy of qPCR. Metagenomics analyses, while less sensitive, provided a markedly higher coverage of antibiotic resistance genes compared to qPCR. The complementarity of both methods and the importance of selecting the best method according to the study purpose are discussed.

Determination of the effect of water stress on the surface properties of bacteria is crucial to study bacterial induced soil water repellency. Changes in the environmental conditions may affect several properties of bacteria such as the cell hydrophobicity and morphology. Here, we study the influence of adaptation to hypertonic stress on cell wettability, shape, adhesion, and surface chemical composition of Pseudomonas fluorescens. From this we aim to discover possible relations between the changes in wettability of bacterial films studied by contact angle and single cells studied by atomic and chemical force microscopy (AFM, CFM), which is still lacking. We show that by stress the adhesion forces of the cell surfaces towards hydrophobic functionalized probes increase while they decrease towards hydrophilic functionalized tips. This is consistent with the contact angle results. Further, cell size shrunk and protein content increased upon stress. The results suggest two possible mechanisms: Cell shrinkage is accompanied by the release of outer membrane vesicles by which the protein to lipid ratio increases. The higher protein content increases the rigidity and the number of hydrophobic nano-domains per surface area.

The search for antimicrobials in propolis presents a new dimension for addressing the problem of antimicrobial drug resistance. The aim of this study was to determine the antimicrobial activity of extracts of crude propolis collected from different regions in Ghana and their active fractions. The antimicrobial activity of the extracts, as well as that of the chloroform, ethyl acetate, and petroleum ether fractions of the active samples were determined using the agar well diffusion method. The minimum inhibitory concentration (MIC) and the minimum bactericidal concentration (MBC) of the most active fractions were determined. The various crude propolis extracts frequently produced zones of inhibition against Staphylococcus aureus (17/20) than Pseudomonas aeruginosa (16/20), and Escherichia coli (1/20) test isolates. Chloroform and ethyl acetate solvents produced fractions possessing greater antimicrobial activity than the petroleum ether fraction. The mean MIC range of the most active fractions was greatest for S. aureus (76.0 ± 34.8-48.0 ± 33.0 mg/ml) than for P. aeruginosa (40.8 ± 33.3-30.4 ± 6.7 mg/ml) and E. coli, as was the mean MBC. Propolis has antimicrobial potential, and hence should be exploited as an alternative for the treatment of bacterial infections.

The activity of the microbiome of fish mucosae provides functions related to immune response, digestion, or metabolism. Several biotic and abiotic factors help maintaining microbial homeostasis, with disruptions leading to dysbiosis. Diseases and antibiotic administration are known to cause dysbiosis in farmed fish. Pathogen infections greatly affect the production of gilthead seabream, and antibiotic treatment is still frequently required. Here, we employed a 16S rRNA high-throughput metataxonomics approach to characterize changes in the gut, skin, and gill microbiomes occurring due to infection with Photobacterium damselae subsp. piscicida and subsequent antibiotic treatment with oxytetracycline (OTC), as well as during recovery. Although microbiota response differed between studied tissues, overall changes in composition, diversity, structure, and predicted function were observed in all mucosae. The skin and gill microbiomes of diseased fish became largely dominated by taxa that have been frequently linked to secondary infections, whereas in the gut the genus Vibrio, known to include pathogenic bacteria, increased with OTC treatment. The study highlights the negative impacts of disease and antibiotic treatment on the microbiome of farmed fish. Our results also suggest that fish transportation operations may have profound effects on the fish microbiome, but further studies are needed to accurately evaluate their impact.

The expression of biosynthetic genes in bacterial hosts can enable access to high-value compounds, for which appropriate molecular genetic tools are essential. Therefore, we developed a toolbox of modular vectors, which facilitate chromosomal gene integration and expression in Pseudomonas putida KT2440. To this end, we designed an integrative sequence, allowing customisation regarding the modes of integration (random, at attTn7, or into the 16S rRNA gene), promoters, antibiotic resistance markers as well as fluorescent proteins and enzymes as transcription reporters. We thus established a toolbox of vectors carrying integrative sequences, designated as pYT series, of which we present 27 ready-to-use variants along with a set of strains equipped with unique 'landing pads' for directing a pYT interposon into one specific copy of the 16S rRNA gene. We used genes of the well-described violacein biosynthesis as reporter to showcase random Tn5-based chromosomal integration leading to constitutive expression and production of violacein and deoxyviolacein. Deoxyviolacein was likewise produced after gene integration into the 16S rRNA gene of rrn operons. Integration in the attTn7 site was used to characterise the suitability of different inducible promoters and successive strain development for the metabolically challenging production of mono-rhamnolipids. Finally, to establish arcyriaflavin A production in P. putida for the first time, we compared different integration and expression modes, revealing integration at attTn7 and expression with NagR/P_nagAa to be most suitable. In summary, the new toolbox can be utilised for the rapid generation of various types of P. putida expression and production strains.

Background: Infections with respiratory viruses [e.g. influenza and respiratory syncytial virus (RSV)] can increase the risk of severe pneumococcal infections. Likewise, pneumococcal coinfection is associated with poorer outcomes in viral respiratory infection. However, there are limited data describing the frequency of pneumococcus and SARS-CoV-2 coinfection and the role of coinfection in influencing COVID-19 severity. We, therefore, investigated the detection of pneumococcus in COVID-19 inpatients during the early pandemic period.

Methods: The study included patients aged 18 years and older, admitted to the Yale-New Haven Hospital who were symptomatic for respiratory infection and tested positive for SARS-CoV-2 during March-August 2020. Patients were tested for pneumococcus through culture-enrichment of saliva followed by RT-qPCR (to identify carriage) and serotype-specific urine antigen detection (UAD) assays (to identify presumed lower respiratory tract pneumococcal disease).

Results: Among 148 subjects, the median age was 65 years; 54.7% were male; 50.7% had an ICU stay; 64.9% received antibiotics; and 14.9% died while admitted. Pneumococcal carriage was detected in 3/96 (3.1%) individuals tested by saliva RT-qPCR. Additionally, pneumococcus was detected in 14/127 (11.0%) individuals tested by UAD, and more commonly in severe than moderate COVID-19 [OR: 2.20; 95% CI: (0.72, 7.48)]; however, the numbers were small with a high degree of uncertainty. None of the UAD-positive individuals died.

Conclusions: Pneumococcal lower respiratory tract infection (LRTI), as detected by positive UAD, occurred in patients hospitalized with COVID-19. Moreover, pneumococcal LRTI was more common in those with more serious COVID-19 outcomes. Future studies should assess how pneumococcus and SARS-CoV-2 interact to influence COVID-19 severity in hospitalized patients.

Pathogen surveillance within wastewater rapidly progressed during the SARS-CoV-2 pandemic and informed public health management. In addition to the successful monitoring of entire sewer catchment basins at the treatment facility scale, subcatchment or building-level monitoring enabled targeted support of resource deployment. However, optimizing the temporal and spatial resolution of these monitoring programs remains complex due to population dynamics and within-sewer physical, chemical, and biological processes. To address these limitations, this study explores the advancement of the building-scale network that monitored the on-campus residential population at the University of Colorado Boulder between August 2020 and May 2021 through a daily SARS-CoV-2 surveillance campaign. During the study period, SARS-CoV-2 infection prevalence transitioned from robust community spread in Fall 2020 to sporadic infections in Spring 2021. Temporally, these distinct phases enabled investigating the effectiveness of resource commitment by exploring subsets of the original daily sampling data. Spatially, select sampling sites were installed along the flow path of the pipe network, enabling the exploration of the conservation of viral concentrations within the wastewater. Infection prevalence and resource commitment for informed action displayed an inverted relationship: higher temporal and spatial resolution surveillance is more imperative during sporadic infection phases than during high prevalence periods. This relationship was reinforced when norovirus (two minor clusters) and influenza (primarily absent) were additionally surveilled at a weekly frequency. Overall, resource commitment should scale to meet the objectives of the monitoring campaign-providing a general prevalence estimate requires fewer resources than an early-warning and targeted-action monitoring framework.

Secondary bacterial infections increase influenza-related morbidity and mortality, particularly if acquired after 5-7 d from the viral onset. Synergistic host responses and direct pathogen-pathogen interactions are thought to lead to a state of hyperinflammation, but the kinetics of the lung pathology have not yet been detailed, and identifying the contribution of different mechanisms to disease is difficult because these may change over time. To address this gap, we examined host-pathogen and lung pathology dynamics following a secondary bacterial infection initiated at different time points after influenza within a murine model. We then used a mathematical approach to quantify the increased virus dissemination in the lung, coinfection time-dependent bacterial kinetics, and virus-mediated and postbacterial depletion of alveolar macrophages. The data showed that viral loads increase regardless of coinfection timing, which our mathematical model predicted and histomorphometry data confirmed was due to a robust increase in the number of infected cells. Bacterial loads were dependent on the time of coinfection and corresponded to the level of IAV-induced alveolar macrophage depletion. Our mathematical model suggested that the additional depletion of these cells following the bacterial invasion was mediated primarily by the virus. Contrary to current belief, inflammation was not enhanced and did not correlate with neutrophilia. The enhanced disease severity was correlated to inflammation, but this was due to a nonlinearity in this correlation. This study highlights the importance of dissecting nonlinearities during complex infections and demonstrated the increased dissemination of virus within the lung during bacterial coinfection and simultaneous modulation of immune responses during influenza-associated bacterial pneumonia.

Wastewater surveillance is a cost-effective way to monitor pathogen prevalence and transmission patterns in the entire community. Here, we compare 24-hour composite and grab samples collected during September 2020 from several municipalities in New York State to detect SARS-CoV-2. A total of 45 paired samples (90 total samples) from three counties and 14 wastewater treatment plants were available for analysis. The categorical comparison (SARS-CoV-2 genetic material detected and quantifiable, genetic material detected but below the limits of quantification, and genetic material not detected) between the grab and composite samples was quite strong, with 91.1% agreement (kappa P-value < .001). The correlations among the quantifiable grab and composite samples were statistically significant yet modest for SARS2-CoV RNA (Pearson correlation = 0.44, P = .02), crAssphage cDNA (Pearson correlation = 0.36, P = .02), and crAssphage DNA (Pearson correlation = 0.46, P = .002). We found good comparison between grab and 24-hour composite samples for detecting SARS-CoV-2 RNA from municipal wastewater treatment plants. Grab sampling is an efficient and cost-effective method to monitor for the presence of SARS-CoV-2 in the entire community.