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PubMed2003

Predicting biogeochemical calcium precipitation in landfill leachate collection systems.

Clogging of leachate collection systems within municipal solid waste landfills can result in greater potential for contaminants to breach the landfill barrier system. The primary cause of clogging is calcium carbonate (CaCO3(s)) precipitation from leachate and its accumulation within the pore space of the drainage medium. CaCO3(s) precipitation is caused by the anaerobic fermentation of volatile fatty acids (VFAs), which adds carbonate to and raises the pH of the leachate. An important relationship in modeling clogging in leachate collections systems is a yield coefficient that relates microbial fermentation of VFAs to precipitation of calcium carbonate. This paper develops a new, mechanistically based yield coefficient, called the carbonic acid yield coefficient (Y(H)), which relates the carbonic acid (H2CO3) produced from microbial fermentation of acetate, propionate, and butyrate to calcium precipitation. The empirical values of Y(H) were computed from the changes in acetate, propionate, butyrate, and calcium concentrations in leachate as it permeated through gravel-size material. The theoretical and empirical results show that the primary driver of CaCO3(s) precipitation is acetate fermentation. Additionally, other non-calcium cations (e.g., iron and magnesium) precipitated with carbonate (CO3(2-)) when present in the leachate. A common yield between total cations bound to CO3(2-) and H2CO3 produced, called the calcium carbonate yield coefficient (Yc), can reconcile the empirical yield coefficient for synthetic and actual leachates.

Algorithms↗
PubMed2026

Unveiling microbial risks in Chinese household dust: a comprehensive analysis from absolute abundance to virulence unit.

BACKGROUND: People spend the majority of their lives indoors, yet the risk and virulence potential of household microbiota remain largely unexplored, particularly in developing countries. RESULTS: Here, we conducted a nationwide survey on both dust samples and health information across 118 Chinese households. The microbiota composition and its functional units were analyzed using absolute 16S rRNA/ITS sequencing, metagenomics, and metaproteomics. Cross-domain network analysis of the core microbial communities revealed robust co-occurrence patterns in household dust. The mean absolute abundance of potentially pathogenic bacteria and fungi in households was 2.39 × 105 and 2.83 × 106 DNA copies/g dust. The potentially pathogenic community was primarily influenced by latitude, relative humidity, and average temperature. Although total absolute abundance was substantially lower in urban areas, the relative abundance of potentially pathogenic bacteria was markedly higher compared to rural environments. While urban-rural differences existed, the underlying statistical drivers were the environmental variables. The absolute abundance of potential pathogens was significantly associated with the prevalence of rhinitis, wheeze, and dermatitis in 266 participants. Children were identified as the highest-risk group from inhalation exposure of average daily dose. A total of 170 bacterial, 223 fungal virulence factors (VFs), and 370 antibiotic resistance genes (ARGs) were detected in dust and dust extracellular vesicle (EV)-associated DNA. EV-associated cargoes contributed 47.13% to the bacterial VF profiles, 11.90% to fungal VF profiles, and 44.45% to ARG profiles. Metaproteomic analysis confirmed the presence of VF profiles in dust EVs, which was further verified by curated proteomics data from 35 household pathogens. CONCLUSIONS: This study provides a comprehensive, quantitative framework linking indoor microbial exposure to health risks, highlighting EVs as a non-negligible, novel, extracellular mechanistic pathway for health impact in household environments. Video Abstract.

Child↗
PubMedDate not supplied

Drug resistance among tuberculosis patients, New York City, 1991 and 1992.

The authors assessed drug susceptibility patterns among tuberculosis patients reported to the New York City Department of Health in the first quarters of 1991 and 1992. Resistance to one or more drugs was seen in 26 percent (137 divided by 520) in 1991 and 24 percent (122 divided by 517) in 1992. Resistance to isoniazid was seen in 22 percent and 19 percent of patients in 1991 and 1992, respectively; resistance to rifampin in 15 percent and 14 percent; and to both isoniazid and rifampin in 15 percent and 14 percent. Combined resistance to four first line drugs (isoniazid, rifampin, streptomycin, and ethambutol) was seen in 6 percent (1991) and 8 percent (1992). Patients with organisms resistant to both isoniazid and rifampin were as likely among U.S. born as among foreign born, and younger patients were more likely than older patients to have isoniazid and rifampin resistant organisms. These findings underscore the importance of obtaining susceptibility testing in all patients who have cultures positive for Mycobacterium tuberculosis.

Adolescent↗
PubMed2026

Heavy-metal stress shapes habitat-specific microbial survival strategies in estuarine environments.

Estuarine ecosystems face increasing heavy metal pollution from rapid urbanization and industrialization, yet the microbial adaptive strategies to multiple metal stressors across different habitats remain poorly understood. This study investigated the diversity and composition of bacterial and fungal communities across free-living (FL), particle-attached (PA), and sediment (SE) fractions from three estuaries with varying heavy metal contamination, and further investigated functional adaptations of bacterial communities. High-throughput amplicon sequencing revealed habitat-specific communities, with SE hosting the highest alpha diversity and enrichment of metal-resistant genera such as Woeseia and Sva1033. Environmental filtering, particularly by Zn, was the dominant driver shaping bacterial assemblages across all habitats, whereas fungal communities displayed greater stochastic assembly patterns. Analysis of 44 high-quality bacterial metagenome-assembled genomes (MAGs) revealed diverse metal resistance genes (cusA, znuB, and zntA), along with enriched metabolic pathways for carbon, nitrogen, and sulfur cycling. Notably, both active efflux/oxidative stress defense and indirect immobilization mechanisms were observed across all habitats, but their relative importance differed: FL and PA communities exhibited a greater reliance on active metal efflux (czcAB) and oxidative stress defense (trxAB) to maintain intracellular homeostasis, whereas SE communities displayed a stronger genomic potential for sulfate reduction (dsrAB) that may contribute to metal immobilization through sulfide precipitation. This metabolic partitioning highlights the complementary roles of different habitats in mediating metal toxicity and biogeochemical cycling, providing new insights into microbial resilience in polluted estuaries and underscoring the urgency of addressing heavy-metal contamination in these critical ecosystems.

Estuaries↗
PubMed2005

Antibacterial drivers of resistance.

Increased levels of antibacterial resistance among community-acquired pathogens have been influenced by various factors. Among the antibacterial-related drivers of resistance, the inappropriate and excessive use of antibacterials has been identified. A large number of antibacterial prescriptions can be attributed to syndromes of viral etiology; given that antibacterials provide no clinical benefit, this represents an important target for decreasing unnecessary antibacterial use. Notably, therapeutic exposure of bacteria to antibacterials exerts a continuous selection pressure on pathogens as well as on normal flora. This selection pressure may favor and/or enable resistance development through various mechanisms. The development of resistance may be reduced by avoiding subtherapeutic antibacterial exposure and prolonged treatment durations. Potency, or the product of in vitro antibacterial activity and the ability of an antibacterial to achieve adequate concentrations at the site of infection, is also a critical consideration. In general, the more potent an antibacterial, the less likely it is to propagate resistant isolates. Antibacterial resistance is unavoidable. However, consideration of the drivers of resistance and concerted efforts to avoid these effects will help to better control the development of resistance.

Anti-Bacterial Agents↗
PubMed2006

Process hydraulics, distributed bacterial states, and biological phosphorus removal from wastewater.

Hydraulic characteristics of biological wastewater treatment systems were shown to affect bacterial state distributions and system performance through mathematical simulations. The term "state" is used here to mean the microbial storage product and biomass content of a bacterium. The traditional approach to simulating biological treatment processes assumes "lumped" (average) states, rather than accounting for variable states across bacterial populations. Distributed states were previously suggested as critical to enhanced biological phosphorus removal (EBPR), but the factors that cause distributed states were not evaluated. A primary driver for distributed state development is variable hydraulic experiences of bacteria as they cycle through completely mixed reactors, and so process characteristics that affect hydraulics were hypothesized to affect state distributions. Two design characteristics affecting system hydraulics were evaluated using a new distributed state simulation program (DisSimulator 1.0): total hydraulic residence time (HRT) and numbers of reactors in series. Distributed predictions consistently predicted worse EBPR performance than did the lumped approach. Increasing HRTs (with constant solids retention times) tended to increase state distributions, to increase the differences between lumped and distributed simulation predictions, and to decrease predicted EBPR performance. As the numbers of reactors in series increased, distributed predictions tended to converge with lumped simulation predictions. Distributed simulations tended to predict a greater benefit to using reactors in series than did lumped simulations. This work provides guidance for new strategies to improve EBPR by minimizing state distributions. The targeted hydraulic characteristics may be more important to EBPR than previously recognized due to their effects on distributed states.

Bacteria↗
PubMed2006

Microbial community dynamics in a humic lake: differential persistence of common freshwater phylotypes.

In an effort to better understand the factors contributing to patterns in freshwater bacterioplankton community composition and diversity, we coupled automated ribosomal intergenic spacer analysis (ARISA) to analysis of 16S ribosomal RNA (rRNA) gene sequences to follow the persistence patterns of 46 individual phylotypes over 3 years in Crystal Bog Lake. Additionally, we sought to identify linkages between the observed phylotype variations and known chemical and biological drivers. Sequencing of 16S rRNA genes obtained from the water column indicated the presence of phylotypes associated with the Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria, TM7 and Verrucomicrobia phyla, as well as phylotypes with unknown affiliation. Employment of the 16S rRNA gene/ARISA method revealed that specific phylotypes varied independently of the entire bacterial community dynamics. Actinobacteria, which were present on greater than 95% of sampling dates, did not share the large temporal variability of the other identified phyla. Examination of phylotype relative abundance patterns (inferred using ARISA fragment relative fluorescence) revealed a strong correlation between the dominant phytoplankton succession and the relative abundance patterns of the majority of individual phylotypes. Further analysis revealed covariation among unique phylotypes, which formed several distinct bacterial assemblages correlated with particular phytoplankton communities. These data indicate the existence of unique persistence patterns for different common freshwater phylotypes, which may be linked to the presence of dominant phytoplankton species.

Bacteria↗
PubMed2026

Beyond borders: plasmids drive a shared antibiotic resistome in European urban water systems.

BACKGROUND: Urban wastewater systems (UWSs) act as reservoirs and conduits for the dissemination of antibiotic resistance genes (ARGs), with plasmids playing a central role in their spread. Despite their significance, the diversity and persistence of plasmids in UWSs remain underexplored. RESULTS: This study applies a multi-omics approach, including metagenomic and direct plasmidome sequencing, high-throughput qPCR array, and whole genome sequencing of plasmid isolates, to comprehensively profile the microbial plasmidome and resistome on 78 samples across UWSs in Denmark, Spain, and the UK. We successfully uncovered an extensive plasmid and ARG diversity that could not be fully captured by a single method, especially identified 78,574 plasmids, including 20,925 plasmids previously unreported. We also observed that plasmids carried a disproportionate share of clinically relevant ARGs, particularly beta-lactamase resistance genes; most importantly, they were preferentially located on transmissible plasmids. Furtherly, plasmids harbor ARG can enhance their persistence in wastewater ecosystems, especially harboring multiple types of ARGs. Moreover, Bacteroides emerged as a unique persistent ARG reservoir not only for harboring and disseminating diverse resistance genes especially in residential-relevant areas, but also emerged as a major driver of antimicrobial resistance dynamics across different wastewater treatment processes. CONCLUSIONS: Overall, this work provides the first attempt at a holistic description of the UWSs' resistome, its structure, dynamics, and mobility and significantly expands the current knowledge. Video Abstract.

Plasmids↗
PubMed1993

Antiviral activity of a phosphorothioate oligonucleotide complementary to RNA of the human cytomegalovirus major immediate-early region.

Phosphorothioate oligonucleotides complementary to mRNA of the human cytomegalovirus (HCMV) DNA polymerase gene or to RNA transcripts of the major immediate-early regions 1 and 2 (IE1 and IE2) of HCMV were evaluated for antiviral activity in a 96-well immunoassay with primary human dermal fibroblasts as host cells. Oligonucleotides complementary to RNA of the IE2 region exhibited the most potent antiviral activity. One of these oligonucleotides, ISIS 2922, was at least 30-fold more potent than the nucleoside analog, ganciclovir, with a 50% effective concentration of 0.37 microM in the 96-well immunoassay. In an infectious virus yield reduction assay, ISIS 2922 and ganciclovir reduced production of infectious virus by 2 log units at concentrations of 2.2 and 36 microM, respectively. A control oligonucleotide showed no inhibition of virus production at concentrations as high as 3 microM. ISIS 2922 reduced IE protein synthesis in HCMV-infected cells in a dose-dependent manner which correlated with antiviral activity. The antiviral activity of ISIS 2922 was not due to oligonucleotide-induced cytotoxicity since effects on cell viability or proliferation were observed only at concentrations well in excess of effective antiviral concentrations. The specificity and potency of ISIS 2922 suggest that it may be useful for the treatment of cytomegalovirus disease in humans.

Antiviral Agents↗
PubMed2025

Discrepancies in isoniazid susceptibility profiles: Bactec MGIT 960-resistant but GenoType MTBDRplus-susceptible Mycobacterium tuberculosis strains in Hunan, China.

UNLABELLED: Discordant drug susceptibility testing (DST) results between the Bactec MGIT 960 system (MGIT) and the GenoType MTBDRplus assay (MTBDRplus) for isoniazid (INH) complicate clinical decision-making. In this study, we performed minimum inhibitory concentration (MIC) assays and whole-genome sequencing (WGS) on 53 Mycobacterium tuberculosis strains identified as INH-resistant by MGIT but INH-susceptible by MTBDRplus. The variants conferring INH resistance were evaluated by the WHO mutation catalogue. Our results showed that only five strains carried variants classified as "associated with resistance" (Group 1/2), including katG Trp39STOP, katG Ser315Asn, inhA -154G>A, and inhA Ser94Ala. In addition, 44 strains carried 70 variants classified as "Group 3: Uncertain significance" across nine genes, including katG, ahpC, inhA, Rv0010c, Rv1129c, Rv2752c, mshA, dnaA, and Rv1258c. The remaining four strains carried no variants (Groups 1-3) linked to INH resistance. No significant difference in the prevalence of high-level INH resistance was observed between lineage 2 and lineage 4 strains (χ² = 0.232, P = 0.630). Our findings indicate that the variants classified as "uncertain significance" may be the main genetic determinants causing discordant results, highlighting their associations with INH resistance that need to be further investigated. IMPORTANCE: This study addresses a critical challenge in drug susceptibility testing (DST): the discrepancies in DST results for isoniazid (INH) between the Bactec MGIT 960 system and the GenoType MTBDRplus assay. These discordant results significantly complicate treatment decisions, potentially leading to suboptimal patient outcomes. Using MIC assays and WGS on 53 clinical Mycobacterium tuberculosis strains, we provide valuable insights into the genetic basis of INH resistance. Our findings showed that only a small fraction of strains carried variants definitively linked to INH resistance, while a larger number harbored variants of uncertain significance across multiple genes, underscoring the complexity of INH resistance mechanisms. This study highlights the urgent need to refine our understanding of these "Group 3: uncertain significance" variants, as they appear to be a primary driver of the discrepancies. Additionally, this study emphasizes the importance of integrating advanced sequencing tools into DST to improve the accuracy of INH resistance detection.

Isoniazid↗
PubMed2026

Whole genome sequencing reveals a specific microbiota in subglottic stenosis C. acnes may contribute to inflammation.

PURPOSE: Subglottic stenosis (SGS) progressively reduces the airway below the vocal folds. The cause is not known and there is a recurrent need of surgical treatment. Including all phenotypes, SGS affects 1/400 000/yr, with a female dominance. Previous studies have revealed a possible role of the Mycobacterium complex in SGS development. Our hypothesis is that microbiota is associated with the inflammation in SGS, if true it might affect the prevailing treatment options. METHODS: This prospective cross-sectional study included biopsies from 34 patients with subglottic stenosis, collected between 2020 and 2023. Nucleic acids were extracted from the tissue samples and analysed using whole genome sequencing. Microbial composition was characterized using taxonomic profiling of sequencing data. Species with sufficient read counts were selected for further validation using sequence alignment methods to ensure accuracy of identification. RESULTS: Using the most comprehensive form of genomic testing currently in clinical use, we present curated and stable data on the presence of Cutibacterium acnes in 28 out of the 34 cases. CONCLUSION: Cutibacterium acnes may serve as a driver of the inflammation characterizing SGS and should be considered in therapeutically oriented future studies.

Cutibacterium acnes↗
PubMed2026

How the microbiome shapes epigenetic trained memory in neuroinflammation: Implications for neurodegenerative diseases.

Neurodegenerative diseases are increasingly recognized as disorders involving immune dysregulation. However, the mechanisms underlying this dysfunction remain poorly characterized. Trained immunity has recently emerged as a potential contributor to immune dysregulation, particularly in neuroinflammation and neurodegenerative diseases, where trained immunity is the epigenetic reprogramming of innate immune responses following an initial inflammatory stimulus, which increases responses to subsequent exposures. In parallel, although the brain has traditionally been viewed as an immune-privileged organ, growing evidence indicates that peripheral immune activity exerts significant influence on neuroinflammation in the brain. A major driver of peripheral immunity is the microbiome. Therefore, this perspective aims to present a conceptual framework for a relationship between the microbiome, trained immunity, and neurodegenerative diseases. We first summarize evidence of trained immunity in the brain and its role in neurodegeneration. Next, we highlight the role of the microbiome in peripheral immune modulation and in trained immunity. Finally, we propose potential mechanisms through which the microbiome may induce or modulate trained immunity in the brain. These include: 1) immunogenic microbial metabolites that cross the blood-brain barrier and alter host cell epigenetics; 2) migration of peripherally trained myeloid cells into the brain; 3) viral infection-induced trained immunity that may predispose to neurodegeneration. Together, this perspective suggests that microbiome-induced trained immunity offers a novel mechanism linking peripheral immune regulation with neuroinflammation and neurodegeneration with implications for therapeutic targeting of epigenetic modification as a molecular prevention strategy for progression of neurodegeneration.

Humans↗
PubMed2005

Preventive measures to reduce bioaerosol exposure during refuse collection: results of field studies in the real-life situation.

The aim of the present research project was to investigate and evaluate technical and organisational measures targeted at bioaerosol reduction during the refuse collection and to determine the exposure of refuse collectors to dust, fungi and endotoxins in an on-the-job situation with different vehicle technologies and states of hygiene. The following technical factors were found to influence the bioaerosol concentration at the refuse collector's workplace: compaction method, lifting device control, rave rail height, hopper depth, design of intake area and dust interception. For instance, notably higher total fungal counts were recorded with rotating drum compaction than with packer plate compaction. A hinged lid closure at the lifting device in conjunction with a suction unit induced a positive effect. In addition, the automatic lifting system had a positive influence on rear-end loaders, as did loading operation control from the closed driver's cab on side loaders. Regular internal and external high-pressure cleaning of the lifting device at intervals of not more than 14 days is recommended as a basic rule for vehicle hygiene.

Aerosols↗
PubMed2026

Yeast Strain Development and Process Intensification in High-Gravity Fermentation.

High- and very-high-gravity (HG/VHG) fermentation increases substrate loading and product titers, thereby improving fermenter utilisation and potentially reducing water use and downstream processing requirements. Initially developed for brewing and fuel ethanol production, these approaches are now applied more broadly in food, beverage, and bioproduct manufacturing. This MiniReview summarises operational definitions and industrial drivers of HG/VHG fermentation and examines the associated constraints in rheology, mass and heat transfer, osmotic and ethanol stress, nutrient availability, and oxidative damage. Yeast improvement strategies are reviewed, including adaptive laboratory evolution, mutagenesis, genome shuffling, multiplex genome editing, non-conventional yeasts, and multi-omics-guided selection. Process developments such as no-cook simultaneous liquefaction, saccharification and fermentation (SLSF), enzyme formulation, nutrient management, and in situ product recovery are considered together with applications in alcoholic beverages, organic acids, microbial lipids, and other value-added products. The review also discusses coproduct valorisation and the need to integrate strain development with process design. Current evidence supports HG/VHG fermentation as a useful process-intensification platform, although performance and sustainability depend strongly on feedstock, operating conditions, product requirements, and the basis used to report fermentation outcomes.

circular bioeconomy↗
PubMed1997

Investigation and remediation of diesel converted trolley buses associated with extensive fungal growth and health complaints.

Fifteen bus drivers, operating diesel converted trolley buses, experienced symptoms including watery and itchy eyes, rhinorrhea, and headaches. A total of 49 buses were labeled as "problem buses" and operators refused to drive them. An investigation identified high fungal counts in some problem buses (> 70,000 colony forming units [CFU]/m3; n = 3) compared with control buses (< 220 CFU/m3; n = 4). The predominant species were Penicillium and Cladosporium (1/1). Remedial measures, including washing with a 0.17% solution of sodium hypochlorite and an ozone treatment, were not successful. Because fungal species are heat sensitive, two buses were subjected to a heat treatment of 55 degrees C for 4 hours. In one bus the fungal spores of Cladosporium appeared to be more heat sensitive than the spores of Penicillium. At this point the interior of one bus was completely renewed and another was given a formaldehyde treatment followed by heat treatments. Both strategies reduced fungal counts to 190 from > 107,000 CFU/m3 for the former and to 270 from > 71,000 CFU/m3 for the latter. Only the interior of the most heavily contaminated buses were refurbished prior to the heat treatment, which was done on all problem buses. All buses are still in active service 5 years later. The most frequent health symptoms reported by 88 exposed bus drivers were headache (36%), blocked/runny/itchy nose (26%), nausea (26%), and dry irritated throat (25%). No chronic health effects have been reported after 5 years, although some of these common fungal species are known to be opportunistic pathogens.

Adult↗
PubMed2026

Genomic determinants of fluoroquinolone resistance in Escherichia coli in Nigeria: dominance of QRDR mutations and limited contribution of PMQR in a cross-sectional study.

BACKGROUND: Fluoroquinolone-resistant&#xa0;Escherichia coli&#xa0;is a major global clinical threat, particularly in low- and middle-income countries like Nigeria. However, the full genomic landscape, including the relative contributions of chromosomal mutations, plasmid-mediated resistance, and the role of high-risk clones, remains poorly characterized in this setting. This study aimed to define the genomic mechanisms, clonal distribution, and genotype-phenotype relationships of fluoroquinolone resistance in clinical&#xa0;E. coli&#xa0;isolates from Nigeria. METHODS: A cross-sectional study of 107 clinical&#xa0;E. coli&#xa0;isolates was conducted. Phenotypic susceptibility to ciprofloxacin and nalidixic acid was determined using VITEK 2 and broth microdilution. Whole-genome sequencing was performed, and analysis included detection of quinolone resistance determining region (QRDR) mutations (gyrA, parC, parE) and plasmid-mediated quinolone resistance (PMQR) genes, multilocus sequence typing (MLST), and phylogenetic analysis. Statistical associations were evaluated using chi-squared tests or Fisher's exact tests. RESULTS: Ciprofloxacin non-susceptibility was high at 86.0%. Resistance was primarily driven by a conserved chromosomal mutation profile; the combination of&#xa0;gyrA&#xa0;S83L,&#xa0;gyrA&#xa0;D87N, and&#xa0;parC&#xa0;S80I was present in 85 isolates and was associated with ciprofloxacin non-susceptibility in all affected isolates in this cohort. Isolates with only&#xa0;gyrA&#xa0;mutations were resistant to nalidixic acid but susceptible to ciprofloxacin, consistent with a stepwise resistance pathway. In this cohort, the triple QRDR signature (gyrA S83L&#x2009;+&#x2009;gyrA D87N/Y&#x2009;+&#x2009;parC S80I) was a perfect positive predictor of ciprofloxacin non-susceptibility (85/85; 100%). The ST131 lineage dominated, accounting for 21.5% of isolates and universally carrying the complete triple QRDR profile; notably, no ST131 isolate carried a PMQR determinant. Plasmid-mediated quinolone resistance (PMQR) genes were detected in 15.0% of isolates but were not independently associated with ciprofloxacin non-susceptibility in this cohort in the absence of concomitant QRDR mutations. Efflux pump genes were ubiquitous and non-predictive. Notably, six isolates, all from urine, were non-susceptible (R/I) despite lacking all known QRDR and PMQR determinants, pointing to uncharacterized mechanisms. In a multivariable logistic regression model that included ST131 status, PMQR carriage, and parE mutation status, ST131 was associated with ciprofloxacin non-susceptibility (adjusted OR 5.96, 95% CI 1.21-29.4, p&#x2009;=&#x2009;0.028), whereas PMQR carriage was not (adjusted OR 0.94, 95% CI 0.18-4.85, p&#x2009;=&#x2009;0.94). The triple QRDR signature was not included in this model because it perfectly predicted ciprofloxacin non-susceptibility in this cohort. Resistance patterns varied by clinical source, with the highest burden in bloodstream and wound infections. This stepwise hierarchy from first-step gyrA mutations to the classic triple QRDR profile is summarised in the graphical abstract, Fig.&#xa0;1. CONCLUSIONS: Fluoroquinolone resistance in Nigerian clinical&#xa0;E. coli&#xa0;is predominantly driven by chromosomal QRDR mutations within successful clones like ST131. PMQR genes and efflux pumps appeared to play a supplementary role rather than being independent drivers of ciprofloxacin resistance in this cohort. These data support prioritising key QRDR mutations in genomic reporting and local stewardship decisions, while the QRDR-negative resistant urine isolates require further investigation.

Escherichia coli↗
PubMed2005

Significance of instream autotrophs in trophic dynamics of the Upper Mississippi River.

Trophic dynamics of large river-floodplain ecosystems are still not well understood despite development of several conceptual models over the last 25 years. To help resolve questions about the relative contribution of algal and detrital organic matter to food webs in the Upper Mississippi River, we (1) separated living and detrital components of ultrafine and fine transported organic matter (UTOM and FTOM, respectively) by colloidal silica centrifugation; (2) identified stable isotope signatures (delta(13)C and delta(15)N) for these two portions of transported organic matter and other potential organic matter sources; and (3) employed a multiple source, dual-isotope mixing model to determine the relative contribution of major energy sources to primary consumers and the potential contribution of basal sources to the biomass of secondary consumers. The delta(13)C and delta(15)N of living and detrital fractions of UTOM and FTOM were distinct, indicating clear differences in isotopic composition of the algal and detrital fractions of transported organic matter. Living and detrital transported organic matter also differed from other potential organic matter sources by either delta(13)C or delta(15)N. A six-source mixing model using both delta(13)C and delta(15)N indicated that algal transported organic matter was the major resource assimilated by primary consumers. The contribution of detrital transported organic matter was small in most cases, but there were a small number of taxa for which it could potentially contribute to more than half the assimilated diet. Colloidal dissolved organic matter, which includes heterotrophic bacteria, accounted for only a small fraction of the organic matter assimilated by most primary consumers, indicating that coupling between microbial processes and metazoan production is minimal. Terrestrial C(3) litter from the floodplain forest floor and aquatic macrophytes were also relatively unimportant to the assimilated diet of primary consumers. Application of the mixing model to compare basal source isotopic ratios to secondary consumers revealed that most organic matter moving from primary to secondary consumers originated from algal TOM. Our findings indicate that autochthonous organic matter is the major energy source supporting metazoan production in the main channel of this large river, at least during the summer. This study joins a number of other investigations performed globally that indicate organic matter originating from instream production of sestonic and benthic microalgae is a major driver in the trophic dynamics of large river ecosystems.

Animals↗