Grow now, pay later: When should a bacterium go into debt?

Microbes grow in a wide variety of environments and must balance growth and stress resistance. Despite the prevalence of such trade-offs, understanding of their role in nonsteady environments is limited. In this study, we introduce a mathematical model of "growth debt," where microbes grow rapidly initially, paying later with slower growth or heightened mortality. We first compare our model to a classical chemostat experiment, validating our proposed dynamics and quantifying Escherichia coli's stress resistance dynamics. Extending the chemostat theory to include serial-dilution cultures, we derive phase diagrams for the persistence of "debtor" microbes. We find that debtors cannot coexist with nondebtors if "payment" is increased mortality but can coexist if it lowers enzyme affinity. Surprisingly, weak noise considerably extends the persistence of resistance elements, pertinent for antibiotic resistance management. Our microbial debt theory, broadly applicable across many environments, bridges the gap between chemostat and serial dilution systems.

The underappreciated diversity of bile acid modifications

The repertoire of modifications to bile acids and related steroidal lipids by host and microbial metabolism remains incompletely characterized. To address this knowledge gap, we created a reusable resource of tandem mass spectrometry (MS/MS) spectra by filtering 1.2 billion publicly available MS/MS spectra for bile-acid-selective ion patterns. Thousands of modifications are distributed throughout animal and human bodies as well as microbial cultures. We employed this MS/MS library to identify polyamine bile amidates, prevalent in carnivores. They are present in humans, and their levels alter with a diet change from a Mediterranean to a typical American diet. This work highlights the existence of many more bile acid modifications than previously recognized and the value of leveraging public large-scale untargeted metabolomics data to discover metabolites. The availability of a modification-centric bile acid MS/MS library will inform future studies investigating bile acid roles in health and disease.

In situ community transcriptomics illuminates CO2-fixation potentials and supporting roles of phagotrophy and proton pump in plankton in a subtropical marginal sea

Lineage-wise physiological activities of plankton communities in the ocean are important but challenging to characterize. Here, we conducted whole-assemblage metatranscriptomic profiling at continental shelf and slope sites in the South China Sea to investigate carbon fixation potential in different lineages. RuBisCO expression, the proxy of Calvin carbon fixation (CCF) potential, was mainly contributed by Bacillariophyta, Chlorophyta, Cyanobacteria, and Haptophyta, which was differentially affected by environmental factors among lineages. CCF potential exhibited positive or negative correlations with phagotrophy gene expression, suggesting phagotrophy possibly enhances or complements CCF. Our data also reveal significant non-Calvin carbon fixation (NCF) potential, as indicated by the active expression of genes in all five currently recognized NCF pathways, mainly contributed by Flavobacteriales, Alteromonadales, and Oceanospirillales. Furthermore, in Flavobacteriales, Alteromonadales, Pelagibacterales, and Rhodobacterales, NCF potential was positively correlated with proton-pump rhodopsin (PPR) expression, suggesting that NCF might be energetically supported by PPR. The novel insights into the lineage-differential potential of carbon fixation, widespread mixotrophy, and PPR as an energy source for NCF lay a methodological and informational foundation for further research to understand carbon fixation and the trophic landscape in the ocean.IMPORTANCEMarine plankton plays an important role in global carbon cycling and climate regulation. Phytoplankton and cyanobacteria fix CO2 to produce organic compounds using solar energy and mainly by the Calvin cycle, whereas autotrophic bacteria and archaea may fix CO2 by non-Calvin cycle carbon fixation pathways. How active individual lineages are in carbon fixation and mixotrophy, and what energy source bacteria may employ in non-Calvin carbon fixation, in a natural plankton assemblage are poorly understood and underexplored. Using metatranscriptomics, we studied carbon fixation in marine plankton with lineage resolution in tropical marginal shelf and slope areas. Based on the sequencing results, we characterized the carbon fixation potential of different lineages and assessed Calvin- and non-Calvin- carbon fixation activities and energy sources. Data revealed a high number of unigenes (4.4 million), lineage-dependent differential potentials of Calvin carbon fixation and responses to environmental conditions, major contributors of non-Calvin carbon fixation, and their potential energy source.

The views of parents and carers on managing acute otitis media in urban Aboriginal and Torres Strait Islander children: a qualitative study

OBJECTIVES

To explore the views of parents and carers regarding the management of acute otitis media in urban Aboriginal and Torres Strait Islander children who are at low risk of complications living in urban communities.

STUDY DESIGN

Qualitative study; semi-structured interviews and short telephone survey.

SETTING, PARTICIPANTS

Interviews: purposive sample of parents and carers of urban Aboriginal and Torres Strait Islander children (18 months - 16 years old) screened in Aboriginal medical services in Queensland, New South Wales, and Canberra for the WATCH study, a randomised controlled trial that compared immediate antibiotic therapy with watchful waiting for Aboriginal and Torres Strait Islander children with acute otitis media.

SURVEY

parents and carers recruited for the WATCH trial who had completed week two WATCH surveys.

RESULTS

We interviewed twenty-two parents and carers, including ten who had declined participation in or whose children were ineligible for the WATCH trial. Some interviewees preferred antibiotics for managing acute otitis media, others preferred watchful waiting, expressing concerns about side effects and reduced efficacy with overuse of antibiotics. Factors that influenced this preference included the severity, duration, and recurrence of infection, and knowledge about management gained during the trial and from personal and often multigenerational experience of ear disease. Participants highlighted the importance of shared decision making by parents and carers and their doctors. Parents and carers of 165 of 262 WATCH participants completed telephone surveys (63%); 81 were undecided about whether antibiotics should always be used for treating acute otitis media. Open-ended responses indicated that antibiotic use should be determined by clinical need, support for general practitioners' decisions, and the view that some general practitioners prescribed antibiotics too often.

CONCLUSIONS

Parents and carers are key partners in managing acute otitis media in urban Aboriginal and Torres Strait Islander children. Our findings support shared decision making informed by the experience of parents and carers, which could also lead to reduced antibiotic use for managing acute otitis media.

Detection of boldenone in the urine of female horses-ex vivo formation versus administration

Boldenone is an anabolic-androgenic steroid (AAS) that is prohibited in equine sports. However, in certain situations, it is endogenous, potentially formed by the microbes in urine. An approach to the differentiation based on the detection of the biomarkers Δ1-progesterone, 20(S)-hydroxy-Δ1-progesterone and 20(S)-hydroxyprogesterone was assessed, and their concentrations were monitored in the urine of untreated female horses (n = 291) alongside boldenone, boldienone, testosterone and androstenedione. Using an ultra-sensitive analytical method, boldenone (256 ± 236 pg/mL, n = 290) and the biomarkers (Δ1-progesterone up to 57.6 pg/mL, n = 8; 20(S)-hydroxy-Δ1-progesterone 85.3 ± 181 pg/mL, n = 130; 20(S)-hydroxyprogesterone 43.5 ± 92.1 pg/mL, n = 158) were detected at low concentrations. The ex vivo production of Δ1-steroids was artificially induced following the storage of urine samples at room temperature for 7 days in order to assess the concentrations and ratios of the monitored steroids. The administration of inappropriately stored feed source also resulted in an increase in 20(S)-hydroxy-Δ1-progesterone concentrations and the biomarker ratios. Using the results from different datasets, an approach to differentiation was developed. In situations where the presence of boldenone exceeds a proposed action limit of 5 ng/mL, the presence of the biomarkers would be investigated. If Δ1-progesterone is above 50 pg/mL or if 20(S)-hydroxy-Δ1-progesterone is above 100 pg/mL with the ratio of 20(S)-hydroxy-Δ1-progesterone:20(S)-hydroxyprogesterone greater than 5:1, then this would indicate ex vivo transformation or consumption of altered feed rather than steroid administration. There remains a (small) possibility of a false negative result, but the model increases confidence that adverse analytical findings reported in female horses are caused by AAS administrations.

A proof of concept: Clinical anti-aging efficacy and safety of Lactiplantibacillus plantarum LB244R® applied topically in a double-blinded placebo-controlled study

BACKGROUND

With the increasing age of the westernized population, there is also increasing economic and aesthetic interest in reducing the signs of skin aging. Additionally, the physical aspect of aging can be displeasing and have detrimental effects psychologically in individuals. Probiotics have shown potential as anti-aging agents, albeit proper studies are needed to confirm their potential.

AIMS

Proving that Lactiplantibacillus plantarum LB244R® could alleviate aging signs relative to its placebo vehicle.

PATIENTS/METHODS

In total, 46 subjects were randomly assigned either the ointment with live bacteria, L. plantarum LB244R® or its vehicle ointment, and had to use the assigned ointment twice daily for 56 days. On Day 0, Day 28, and Day 56 subepidermal low echogenic band (SLEB) thickness, dermal density, skin firmness and elasticity, skin hydration, transepidermal water loss (TEWL), skin pH, collagen fiber visualization using confocal microscopy, Crow's feet, spot score, skin smoothness, and complexion radiance were assessed by dermatologists.

RESULTS

All parameters except TEWL improved relative to their baseline (D0) for the active group. L. plantarum LB244R® improved SLEB thickness, dermal density, skin elasticity, skin hydration, and Crow's feet wrinkle score relative to the placebo vehicle ointment.

CONCLUSION

The study demonstrates an anti-aging effect of L. plantarum LB244R® for topical skin use in the first double-blinded, vehicle-ointment placebo-controlled clinical study.

Multidrug-Resistant Sepsis: A Critical Healthcare Challenge

Sepsis globally accounts for an alarming annual toll of 48.9 million cases, resulting in 11 million deaths, and inflicts an economic burden of approximately USD 38 billion on the United States healthcare system. The rise of multidrug-resistant organisms (MDROs) has elevated the urgency surrounding the management of multidrug-resistant (MDR) sepsis, evolving into a critical global health concern. This review aims to provide a comprehensive overview of the current epidemiology of (MDR) sepsis and its associated healthcare challenges, particularly in critically ill hospitalized patients. Highlighted findings demonstrated the complex nature of (MDR) sepsis pathophysiology and the resulting immune responses, which significantly hinder sepsis treatment. Studies also revealed that aging, antibiotic overuse or abuse, inadequate empiric antibiotic therapy, and underlying comorbidities contribute significantly to recurrent sepsis, thereby leading to septic shock, multi-organ failure, and ultimately immune paralysis, which all contribute to high mortality rates among sepsis patients. Moreover, studies confirmed a correlation between elevated readmission rates and an increased risk of cognitive and organ dysfunction among sepsis patients, amplifying hospital-associated costs. To mitigate the impact of sepsis burden, researchers have directed their efforts towards innovative diagnostic methods like point-of-care testing (POCT) devices for rapid, accurate, and particularly bedside detection of sepsis; however, these methods are currently limited to detecting only a few resistance biomarkers, thus warranting further exploration. Numerous interventions have also been introduced to treat MDR sepsis, including combination therapy with antibiotics from two different classes and precision therapy, which involves personalized treatment strategies tailored to individual needs. Finally, addressing MDR-associated healthcare challenges at regional levels based on local pathogen resistance patterns emerges as a critical strategy for effective sepsis treatment and minimizing adverse effects.

The Dynamics of OXA-23 β-Lactamase from Acinetobacter baumannii

Antibiotic resistance is a pressing topic, which also affects β-lactam antibiotic molecules. Until a few years ago, it was considered no more than an interesting species from an academic point of view, Acinetobacter baumanii is today one of the most serious threats to public health, so much so that it has been declared one of the species for which the search for new antibiotics, or new ways to avoid its resistance, is an absolute priority according to WHO. Although there are several molecular mechanisms that are responsible for the extreme resistance of A. baumanii to antibiotics, a class D β-lactamase is the main cause for the clinical concern of this bacterial species. In this work, we analyzed the A. baumanii OXA-23 protein via molecular dynamics. The results obtained show that this protein is able to assume different conformations, especially in some regions around the active site. Part of the OXA-23 protein has considerable conformational motility, while the rest is less mobile. The importance of these observations for understanding the functioning mechanism of the enzyme as well as for designing new effective molecules for the treatment of A. baumanii is discussed.

Barriers and Facilitators in Pricing and Funding Policies of European Countries That Impact the Use of Point-of-Care Diagnostics for Acute Respiratory Tract Infections in Outpatient Practices

Antimicrobial resistance is a major global health threat, which is increased by the irrational use of antibiotics, for example, in the treatment of respiratory tract infections in community care. By using rapid point-of-care diagnostics, overuse can be avoided. However, the diagnostic tests are rarely used in most European countries. We mapped potential barriers and facilitators in health technology assessment (HTA), pricing, and funding policies related to the use of rapid diagnostics in patients with community-acquired acute respiratory tract infections. Expert interviews were conducted with representatives of public authorities from five European case study countries: Austria, Estonia, France, Poland, and Sweden. Barriers to the HTA process include the lack of evidence and limited transferability of methods established for medicines to diagnostics. There was no price regulation for the studied diagnostics in the case study countries, but prices were usually indirectly determined via procurement. The lack of price regulation and weak purchasing power due to regional procurement processes were mentioned as pricing-related barriers. Regarding funding, coverage (reimbursement) of the diagnostic tests and the optimized remuneration of physicians in their use were mentioned as facilitators. There is potential to strengthen peri-launch policies, as optimized policies may promote the uptake of POCT.

Ability of three dairy feed evaluation systems to predict postruminal outflows of nitrogenous compounds in dairy cows: A meta-analysis

Adequate prediction of postruminal outflow of protein fractions is the starting point for the determination of metabolizable protein supply in dairy cows. The objective of this meta-analysis was to compare the performance of 3 dairy feed evaluation systems (National Research Council [NRC], Cornell Net Protein and Carbohydrate System [CNCPS], and National Academies of Sciences, Engineering and Medicine [NASEM]) to predict outflows (g/d) of nonammonia nitrogren (NAN), microbial N (MiN), and nonammonia nonmicrobial N (NANMN). Predictions of rumen degradabilities (% of nutrient) of protein (RDP), NDF, and starch were also evaluated. The data set included 1,294 treatment means from 312 digesta flow studies. The 3 feed evaluation systems were compared using the concordance correlation coefficient (CCC), the ratio of root mean square prediction error (RMSPE) on standard deviation of observed values (RSR), and the slope between observed and predicted values. Mean and linear biases were deemed biologically relevant and are discussed if higher than a threshold of 5% of the mean of observed values. The comparisons were done on observed values adjusted or not for the study effect; the adjustment had a small effect on the mean bias but the linear bias reflected a response to a dietary change rather than absolute predictions. For the absolute predictions of NAN and MiN, CNCPS had the best-fit statistics (8% greater CCC; 6% lower RMSPE) without any bias; NRC and NASEM underpredicted NAN and MiN, and NASEM had an additional linear bias indicating that the underprediction of MiN increased at increased predictions. For NANMN, fit statistics were similar among the 3 feed evaluation systems with no mean bias; however, the linear bias with NRC and CNCPS indicated underprediction at low predictions and overprediction at elevated predictions. On average, the CCC were smaller and RSR ratios were greater for MiN versus NAN indicating increased prediction errors for MiN. For NAN responses to a dietary change, CNCPS also had the best predictions, although the mean bias with NASEM was not biologically relevant and the 3 feed evaluation systems did not present a linear bias. However, CNCPS, but not the 2 other feed evaluation systems, presented a linear bias for MiN, with responses being overpredicted at increased predictions. For NANMN, responses were overpredicted at increased predictions for the 3 feed evaluation systems, but to a lesser extent with NASEM. The site of sampling had an effect on the mean bias of MiN and NANMN in the 3 feed evaluation systems. The mean bias of MiN was higher in omasal than duodenal studies in the 3 feed evaluation systems (from 55 to 61 g/d) and this mean bias was twice as large when 15N labeling was used as a microbial marker compared with purines. Such a difference was not observed for duodenal studies. The reasons underlying these systematic differences are not clear as the type of measurements used in the current meta-analysis does not allow to delineate if one site or one microbial marker is yielding the "true" postruminal N outflows. Rumen degradabilities of protein was underpredicted with CNCPS, and RDP responses to a dietary change was underpredicted by the 3 feed evaluation systems with increased RDP predictions. Rumen degradability of NDF was underpredicted and had poor fit statistics for NASEM compared with CNCPS. Fit statistics were similar between CNCPS and NASEM for rumen degradability of starch, but with an underprediction of the response with NASEM and absolute values being overpredicted with CNCPS. Multivariate regression analyses showed that diet characteristics were correlated with prediction errors of N outflows in each feed evaluation system. Globally, compared with NAN and NANMN, residuals of MiN were correlated with several moderators in the 3 feed evaluation systems reflecting the complexity to measure and model this outflow. In addition, residuals of NANMN were correlated positively with RDP suggesting an overestimation of this parameter. In conclusion, although progress is still to be made to improve equations predicting postruminal N outflows, the current feed evaluation systems provide sufficient precision and accuracy to predict postruminal outflows of N fractions.

Update of antimicrobial resistance in level III and IV health institutions in Colombia between January 2018 and December 2021

Introduction

Antimicrobial resistance surveillance is a fundamental tool for the development, improvement, and adjustment of antimicrobial stewardship programs, therapeutic guidelines, and universal precautions to limit the cross-transmission of resistant bacteria between patients. Since the beginning of 2020, the SARS-CoV-2 pandemic profoundly challenged the health system and, according to some reports, increased the rates of antimicrobial resistance.

Objective

To describe the behavior of antimicrobial resistance of the most frequent bacterial pathogens in twenty Colombian hospitals from January 2018 to December 2021.

Materials and methods

We conducted a descriptive study based on the microbiological information recorded from January 2018 to December 2021 in twenty levels III and IV health institutions in twelve Colombian cities. We identified the species of the ten most frequent bacteria along with their resistance profile to the antibiotic markers after analyzing the data through WHONET.

Results

We found no statistically significant changes in most pathogens’ resistance profiles from January 2018 to December 2021. Only Pseudomonas aeruginosa had a statistically significant increase in its resistance profile, particularly to piperacillin/tazobactam and carbapenems.

Conclusions

The changes in antimicrobial resistance in these four years were not statistically significant except for P. aeruginosa to piperacillin/tazobactam and carbapenems.

Seq' and ARMS shall find: DNA (meta)barcoding of Autonomous Reef Monitoring Structures across the tree of life uncovers hidden cryptobiome of tropical urban coral reefs

Coral reefs are among the richest marine ecosystems on Earth, but there remains much diversity hidden within cavities of complex reef structures awaiting discovery. While the abundance of corals and other macroinvertebrates are known to influence the diversity of other reef-associated organisms, much remains unknown on the drivers of cryptobenthic diversity. A combination of standardized sampling with 12 units of the Autonomous Reef Monitoring Structure (ARMS) and high-throughput sequencing was utilized to uncover reef cryptobiome diversity across the equatorial reefs in Singapore. DNA barcoding and metabarcoding of mitochondrial cytochrome c oxidase subunit I, nuclear 18S and bacterial 16S rRNA genes revealed the taxonomic composition of the reef cryptobiome, comprising 15,356 microbial ASVs from over 50 bacterial phyla, and 971 MOTUs across 15 metazoan and 19 non-metazoan eukaryote phyla. Environmental factors across different sites were tested for relationships with ARMS diversity. Differences among reefs in diversity patterns of metazoans and other eukaryotes, but not microbial communities, were associated with biotic (coral cover) and abiotic (distance, temperature and sediment) environmental variables. In particular, ARMS deployed at reefs with higher coral cover had greater metazoan diversity and encrusting plate cover, with larger-sized non-coral invertebrates influencing spatial patterns among sites. Our study showed that DNA barcoding and metabarcoding of ARMS constitute a valuable tool for quantifying cryptobenthic diversity patterns and can provide critical information for the effective management of coral reef ecosystems.

Non-prescription antibiotics dispensing by community pharmacies: implications for antimicrobial resistance

Introduction

The non-prescription antibiotics dispensing (NPAD) from pharmacies is on the rise in low- and middle-income countries, which contributes to the emergence of antimicrobial resistance (AMR). This study was conducted with the objective to determine the community pharmacy personnel's perspectives on NPAD and its implications for AMR.

Methods

A questionnaire-based cross-sectional survey was conducted in Pakistan among 336 pharmacies. The data were analyzed using SPSS v21 and MedCalc for Windows v12.3.0. Modified Bloom's cut-off point was utilized to categorize the participants' overall knowledge, attitude, and practice. For univariable logistic regression analyses, odds ratio (OR) was calculated at 95% confidence interval (CI). For multivariable logistic regression analyses, adjusted OR was calculated at 95% CI. Spearman's rank correlation coefficient test was used to assess the relationships among knowledge, attitude, and/or practice scores.

Results

The majority of the respondents were staff pharmacists (45.5%). About four-fifths (78.9%) and half (50.9%) of the participants demonstrated moderate to good knowledge and practice, respectively. However, about only one-third (33.1%) had a moderate to good attitude. Staff pharmacists had higher odds of moderate to good knowledge (OR: 2.4, 95% CI: 1.2-4.7) and practice (OR: 2.3, 95% CI: 1.4-3.8). Total knowledge and practice (Spearman's ρ: 0.280; P <0.001) and total attitude and practice (Spearman's ρ: 0.299; P <0.001) scores were significantly correlated.

Conclusion

The qualified pharmacists had satisfactory knowledge, attitude, and practices toward antibiotics. However, non-pharmacist staff lacked knowledge and had probable NPAD practice, which has a negative impact on public health. Regular refresher training, seminars, and strict enforcement of rules and regulations are essential.

A Randomized Controlled Trial of Animal-assisted Activities for Pediatric Oncology Patients: Psychosocial and Microbial Outcomes

INTRODUCTION

Evidence about the effectiveness and safety of dog visits in pediatric oncology is limited.

METHOD

We conducted a randomized controlled trial (n=26) of dog visits versus usual care among pediatric oncology inpatients. Psychological functioning and microbial load from hand wash samples were evaluated. Parental anxiety was a secondary outcome.

RESULTS

We did not observe a difference in the adjusted mean present functioning score (-3.0; 95% confidence interval [CI], -12.4 to 6.4). The difference in microbial load on intervention versus control hands was -0.04 (95% CI, -0.60 to 0.52) log10 CFU/mL, with an upper 95% CI limit below the prespecified noninferiority margin. Anxiety was lower in parents of intervention versus control patients.

DISCUSSION

We did not detect an effect of dog visits on functioning; however, our study was underpowered by low recruitment. Visits improved parental anxiety. With hand sanitization, visits did not increase hand microbial levels.

CLINICAL TRIAL REGISTRATION

Clinicaltrials.gov NCT03471221.

Synergistic Responses of Tibetan Sheep Rumen Microbiota, Metabolites, and the Host to the Plateau Environment

Plateau adaptation in animals involves genetic mechanisms as well as coevolutionary mechanisms of the microbiota and metabolome of the animal. Therefore, the characteristics of the rumen microbiome and metabolome, transcriptome, and serum metabolome of Tibetan sheep at different altitudes (4500 m, 3500 m, and 2500 m) were analyzed. The results showed that the rumen differential metabolites at 3500 m and 4500 m were mainly enriched in amino acid metabolism, lipid metabolism, and carbohydrate metabolism, and there was a significant correlation with microbiota. The differentially expressed genes and metabolites at middle and high altitudes were coenriched in asthma, arachidonic acid metabolism, and butanoate and propanoate metabolism. In addition, the serum differential metabolites at 3500 m and 4500 m were mainly enriched in amino acid metabolism, lipid metabolism, and metabolism of xenobiotics by cytochrome P450, and they were also related to microbiota. Further analysis revealed that rumen metabolites accounted for 7.65% of serum metabolites. These common metabolites were mainly enriched in metabolic pathways and were significantly correlated with host genes (p < 0.05). This study found that microbiota, metabolites, and epithelial genes were coenriched in pathways related to lipid metabolism, energy metabolism, and immune metabolism, which may be involved in the regulation of Tibetan sheep adaptation to plateau environmental changes.

Evaluation of a clinical pharmacist-led antimicrobial stewardship program in a neurosurgical intensive care unit: a pre-and post-intervention cohort study

Background: Antimicrobial resistance poses a significant challenge in neurosurgical intensive care units (ICU). The excessive use of broad-spectrum antibiotics is closely linked to the emergence and dissemination of drug-resistant bacteria within neurosurgical ICUs. This study assessed the effects of implementing a comprehensive Antimicrobial Stewardship (AMS) program in a neurosurgical ICU setting. Methods: From April 2022 to September 2022, an AMS program was implemented in the neurosurgical ICU. The program involved the regular presence of a pharmacist and an infectious disease physician who conducted prospective audits and provided feedback. To assess the impact of the AMS program, the outcome measures were compared between the AMS period and the 6 months before AMS implementation (pre-AMS period). The primary outcome was the use of antibacterial agents, including anti-pseudomonal beta-lactams (APBLs), polymyxin, and tigecycline. Additionally, the study evaluated the appropriateness of antimicrobial de-escalation and the susceptibility of Gram-negative bacilli to antimicrobial agents. Results: A total of 526 were included during the AMS period, while 487 patients were included in the pre-AMS period. The two groups had no significant differences in disease severity and mortality rates. During the AMS period, there was a notable decrease in the use of APBLs as empiric treatment (43.92% vs. 60.99%, p < 0.001). Multi-drug resistant organism (MDRO) infections decrease significantly during AMS period (11.03% vs. 18.48%, p < 0.001). The number of prescription adjustment increased significantly in all patients (0 item vs. 0 item, p < 0.001) and MDRO-positive patients (3 items vs. 2 items, p < 0.001) during the AMS period. Additionally, appropriate antimicrobial de-escalation for patients with MDRO showed improvement during the AMS period (39.66% vs. 20%, p = 0.001). Polymyxin utilization also decreased during the AMS period (15.52% vs. 31.11%, p = 0.034). Furthermore, the susceptibility of Gram-negative Bacilli isolates to APBLs was significantly higher during the AMS period. Conclusion: Implementing a comprehensive pharmacist-led AMS program led to a decrease in the use of antibacterial agents. This reduction in usage is significant because it can potentially delay the emergence of bacterial resistance.

Bibliometric Analysis of Global Research Output on Antimicrobial Resistance among Pneumonia Pathogens (2013-2023)

Antimicrobial resistance (AMR) is a pressing global concern, posing significant challenges to the effective treatment of infections, including pneumonia. This bibliometric analysis aims to investigate the research output on AMR among pneumonia pathogens from 2013 to 2023. Data were extracted from the Web of Science Core Collection (WOS-CC) using an inclusive search strategy. The analysis included 152 relevant studies published in 99 different sources, involving 988 authors and yielding an average of 16.33 citations per document over the past decade. The findings reveal a notable increase in research on AMR among pneumonia pathogens, indicating a growing awareness of this critical issue. Collaborative studies were prevalent, with the majority of authors engaging in joint research efforts. Bradford's Law identified twelve core journals that were instrumental in disseminating research in this field, with "Medicine" emerging as the most prolific journal. The USA and China emerged as the leading contributors, while Germany displayed a strong inclination towards collaborative research. Intermountain Medical Center, Saitama Medical University, and Udice-French Research Universities were the most productive institutions, and Yayan J. and Rasche K. were the top authors. Furthermore, the analysis identified commonly encountered microorganisms such as Acinetobacter baumanii and Klebsiella pneumoniae in the context of AMR. Time-based analysis of keywords highlighted the significance of terms like "community-acquired pneumonia" and "ventilator-associated pneumonia". Overall, this comprehensive study sheds light on the global research landscape of AMR among pneumonia pathogens. The insights gained from this analysis are essential for guiding future research priorities and collaborative efforts to combat AMR effectively and improve treatment outcomes for pneumonia and related infections. As the frequency of reports concerning resistance among pneumonia pathogens, notably A. baumannii and K. pneumoniae, continues to rise, there is an immediate requirement for pharmaceutical manufacturers and healthcare providers to respond proactively and ready themselves for the forthcoming implications of this matter. It also underscores the importance of knowledge dissemination and evidence-based interventions to address this growing public health challenge. However, the study acknowledges the limitations associated with using a single publication database and encourages the inclusion of data from other sources in future research.

Organic-rich bimineralic ooids record biological processes in Shark Bay, Western Australia

Marine ooids have formed in microbially colonized environments for billions of years, but the microbial contributions to mineral formation in ooids continue to be debated. Here we provide evidence of these contributions in ooids from Carbla Beach, Shark Bay, Western Australia. Dark 100-240 μm diameter ooids from Carbla Beach contain two different carbonate minerals. These ooids have 50-100 μm-diameter dark nuclei that contain aragonite, amorphous iron sulfide, detrital aluminosilicate grains and organic matter, and 10-20 μm-thick layers of high-Mg calcite that separate nuclei from aragonitic outer cortices. Raman spectroscopy indicates organic enrichments in the nuclei and high-Mg calcite layers. Synchrotron-based microfocused X-ray fluorescence mapping reveals high-Mg calcite layers and the presence of iron sulfides and detrital grains in the peloidal nuclei. Iron sulfide grains within the nuclei indicate past sulfate reduction in the presence of iron. The preservation of organic signals in and around high-Mg calcite layers and the absence of iron sulfide suggest that organics stabilized high-Mg calcite under less sulfidic conditions. Aragonitic cortices that surround the nuclei and Mg-calcite layers do not preserve microporosity, iron sulfide minerals nor organic enrichments, indicating growth under more oxidizing conditions. These morphological, compositional, and mineralogical signals of microbial processes in dark ooids from Shark Bay, Western Australia, record the formation of ooid nuclei and the accretion of magnesium-rich cortical layers in benthic, reducing, microbially colonized areas.

Urinary Plasmids Reduce Permissivity to Coliphage Infection

The microbial community of the urinary tract (urinary microbiota or urobiota) has been associated with human health. Bacteriophages (phages) and plasmids present in the urinary tract, like in other niches, may shape urinary bacterial dynamics. While urinary Escherichia coli strains associated with urinary tract infection (UTI) and their phages have been catalogued for the urobiome, bacterium-plasmid-phage interactions have yet to be explored. In this study, we characterized urinary E. coli plasmids and their ability to decrease permissivity to E. coli phage (coliphage) infection. Putative F plasmids were predicted in 47 of 67 urinary E. coli isolates, and most of these plasmids carried genes that encode toxin-antitoxin (TA) modules, antibiotic resistance, and/or virulence. Urinary E. coli plasmids, from urinary microbiota strains UMB0928 and UMB1284, were conjugated into E. coli K-12 strains. These transconjugants included genes for antibiotic resistance and virulence, and they decreased permissivity to coliphage infection by the laboratory phage P1vir and the urinary phages Greed and Lust. Plasmids in one transconjugant were maintained in E. coli K-12 for up to 10 days in the absence of antibiotic resistance selection; this included the maintenance of the antibiotic resistance phenotype and decreased permissivity to phage. Finally, we discuss how F plasmids present in urinary E. coli strains could play a role in coliphage dynamics and the maintenance of antibiotic resistance in urinary E. coli. IMPORTANCE The urinary tract contains a resident microbial community called the urinary microbiota or urobiota. Evidence exists that it is associated with human health. Bacteriophages (phages) and plasmids present in the urinary tract, like in other niches, may shape urinary bacterial dynamics. Bacterium-plasmid-phage interactions have been studied primarily in laboratory settings and are yet to be thoroughly tested in complex communities. This is especially true of the urinary tract, where the bacterial genetic determinants of phage infection are not well understood. In this study, we characterized urinary E. coli plasmids and their ability to decrease permissivity to E. coli phage (coliphage) infection. Urinary E. coli plasmids, encoding antibiotic resistance and transferred by conjugation into naive laboratory E. coli K-12 strains, decreased permissivity to coliphage infection. We propose a model by which urinary plasmids present in urinary E. coli strains could help to decrease phage infection susceptibility and maintain the antibiotic resistance of urinary E. coli. This has consequences for phage therapy, which could inadvertently select for plasmids that encode antibiotic resistance.

Regulations on the Use of Antibiotics in Livestock Production in South America: A Comparative Literature Analysis

As a global health problem, antimicrobial resistance (AMR) crosses national borders, leading UN (United Nations) multilateral agencies to call for all countries to improve the stewardship of antibiotics in humans and animals. South American countries have changed their regulations regarding antibiotic use in livestock production. This literature review examines how far the five largest meat-producing countries in South America (Argentina, Brazil, Chile, Colombia, and Uruguay) have come in terms of the relevant legislation. Rules on market entry (marketing authorization and official distribution systems) are already set in all countries examined. Four countries do not allow growth promoters based on critically important antibiotics, and countries have also begun to set guidelines and minimum welfare and biosecurity requirements to reduce the therapeutic demand for antibiotics. Nonetheless, there are aspects related to the distribution, use, and disposal of antibiotics that need to be developed further. In conclusion, legislation in South American countries is moving towards the goals set by UN multilateral agencies, but more can be done. Differences between countries' rules and the gold standards set by the World Organization for Animal Health (OIE), World Health Organization (WHO), and Food and Agriculture Organization of the United Nations (FAO) reveal possible adaptations to the countries' realities. Further studies must examine compliance with the legislation already set and investigate other tools that can be used alongside legislation as a driving force to change stakeholder behaviour.

SARS-CoV-2 Papain-like Protease Responsive ZnO/Daclatasvir-Loaded Chitosan/Gelatin Nanofibers as Smart Antimicrobial Medical Textiles: In Silico, In Vitro and Cell Studies

A significant number of deaths are reported annually worldwide due to microbial and viral infections. The development of protective medical textiles for patients and healthcare professionals has attracted many researchers' attention. Therefore, this study aims to develop smart drug-eluting nanofibrous matrices to be used as a basic material for medical textile fabrication. First, chitosan/gelatin nanofibers were selected as the basic material owing to the wide antimicrobial activity of chitosan and the capability of gelatin to be hydrolyzed in the abundance of the papain-like protease (PLpro) enzyme secreted by SARS-CoV-2. Daclatasvir (DAC), an NS5A inhibitor, was selected as the model drug based on in silico studies where it showed high anti-SARS-CoV-2 potential compared to FDA-approved references. Due to their reported antimicrobial and antiviral activities, ZnO NPs were successfully prepared and incorporated with daclatasvir in chitosan/gelatin nanofibrous matrices through electrospinning. Afterward, an in vitro release study in a simulated buffer revealed the controlled release of DAC over 21 days from the nanofibers compared to only 6 h for free DAC. On the other hand, the abundance of PLpro induced the complete release of DAC from the nanofibers in only 4-8 h. Finally, the nanofibers demonstrated a wide antimicrobial activity against S. aureus, E. coli, and C. albicans.

Impact of gamma irradiation and guava leaf extract on the quality and storage stability of chicken patties

The current investigation was carried out to evaluate the impact of gamma irradiation and guava leaf extract (GLE) on chicken meat patties. The effects of treatments on chicken meat patties were determined by physicochemical, stability (oxidative and microbial), and antioxidant status during different packaging (aerobic and vacuum) at storage intervals (0, 5, and 10 days). The changes in physicochemical parameters of chicken patties were observed on various treatments, storage intervals, and different packaging. The TBARS and POV were found to increase significantly (p < .05) on 2 kGy and with the passage of storage time. The results of microbial load in samples were found to decrease on gamma irradiation with and without GLE. The antioxidant profile in chicken patties was with respect to control. Slight changes were seen in sensory parameters on different treatments at storage intervals. It is concluded that gamma irradiation eliminated the microbes and different concentrations of GLE improve the stability and antioxidant profile of chicken patties.

Antimicrobial stewardship: Prescribing across the primary care health professions

We examined the patterns of antibiotic prescribing by medical and non-medical prescribers (dentists, nurse practitioners, and midwives) in Australia. We explored trends in the dispensed use of antibiotics (scripts and defined daily dose [DDD] per 1000 population/day) by Australian prescribers over the 12-year period, 2005-2016. We obtained data on dispensed prescriptions of antibiotics from registered health professionals subsidized on the Pharmaceutical Benefits Scheme (PBS). There were 216.2 million medical and 7.1 million non-medical dispensed prescriptions for antibiotics over 12 years. The top four antibiotics for medical prescribers were doxycycline; amoxicillin, amoxicillin plus clavulanic acid, and cefalexin, constituting 80% of top 10 use in 2005 and 2016; the top three for non-medical were amoxicillin, amoxicillin plus clavulanic acid and metronidazole (84% of top 10 use in 2016). The proportional increase in antibiotic use was higher for non-medical than medical prescribers. While medical prescribers preferentially prescribed broad-spectrum and non-medical prescribers moderate-spectrum antibiotics, there was a large increase in the use of broad-spectrum antibiotics over time by all prescribers. One in four medical prescriptions were repeats. Overprescribing of broad-spectrum antibiotics conflicts with national antimicrobial stewardship initiatives and guidelines. The proportional higher increase in antibiotic use by non-medical prescribers is a concern. To reduce inappropriate use of antibiotics and antimicrobial resistance, educational strategies targeted at all medical and non-medical prescribers are needed to align prescribing with current best practice within the scope of practice of respective prescribers.

[The evolution of Brazilian human health policies for the prevention and control of antimicrobial resistance: a scoping reviewEvolución de las políticas de prevención y control de la resistencia a los antimicrobianos desde la perspectiva de la salud humana en Brasil: revisión exploratoria]

Objective

To map the policies related to the prevention and control of antimicrobial resistance from a human health perspective in Brazil and systematize the historical course of these policies.

Method

A scoping review was performed following Joana Briggs Institute and PRISMA guidelines. A literature search was performed in December 2020 in the LILACS, PubMed and EMBASE databases. The terms "antimicrobial resistance" AND "Brazil" as well as their synonyms were used. Using the same keywords, Brazilian government websites were searched for documents published until December 2021. Studies of all designs were included, with no language or date restrictions. Clinical documents, reviews and epidemiological studies that did not focus on antimicrobial resistance management policies in Brazil were excluded. Categories based on World Health Organization documents were used for data systematization and analysis.

Results

In Brazil, policies related to antimicrobial resistance such as the National Immunization Program and hospital infection control programs can be traced back to before the creation of the Unified Health System. In the late 1990s and 2000s, the first specific policies on antimicrobial resistance (surveillance networks and programs) and education strategies were established; especially noteworthy is The National Action Plan for the Prevention and Control of Antimicrobial Resistance in the Single Health Scope (PAN-BR) of 2018.

Conclusions

Despite the long history of policies related to antimicrobial resistance in Brazil, gaps were identified, particularly in monitoring the use of antimicrobials and surveillance of antimicrobial resistance. The PAN-BR, the first government document prepared from a One Health perspective, represents an important milestone.

Effectiveness and safety of multidrug therapy containing clofazimine for paucibacillary leprosy and clarithromycin for rifampicin-resistant leprosy: a systematic review and meta-analysis

Introduction

The present study aimed to evaluate leprosy cure and relapse rates as primary outcomes related to two additional strategies for leprosy treatment: clofazimine for paucibacillary (PB) leprosy patients and clarithromycin for patients with rifampicin-resistant leprosy.

Methods

We conducted two systematic reviews (protocols CRD42022308272 and CRD42022308260). We searched the PubMed, EMBASE, Web of Science, Scopus, LILACS, Virtual Health Library and Cochrane Library databases, registers of clinical trial databases and gray literature. We included clinical trials evaluating the addition of clofazimine to PB leprosy treatment and the use of clarithromycin for treating patients with rifampicin-resistant leprosy. Risk of bias (RoB) in randomized clinical trials was assessed by the RoB 2 tool and that in non-randomized clinical trials was assessed by the ROBINS-I tool; and the certainty of the evidence was assessed by the Grading of Recommendations Assessment, Development and Evaluation (GRADE) system. A meta-analysis of dichotomous outcomes was performed.

Results

For clofazimine, four studies were included. Cure and relapse rates were not different with the addition of clofazimine to PB leprosy treatment and demonstrated very low certainty of evidence. For clarithromycin, six studies were included. Considerable heterogeneity resulted from the difference between comparators, and studies showed no difference in the assessed outcomes with the addition of clarithromycin to rifampicin-resistant leprosy treatment. Mild adverse events were reported for both drugs but did not significantly impact treatment.

Discussion

The effectiveness of both drugs still needs to be determined. Adding clofazimine to PB leprosy treatment may reduce the repercussions of an incorrect operational classification with no apparent relevant side effects.

Systematic review registration

https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42022308272; https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42022308260, identifier: CRD42022308272; CRD42022308260.

The Comprehensive Effects of Carassius auratus Complex Formula against Lipid Accumulation, Hepatocarcinogenesis, and COVID-19 Pathogenesis via Stabilized G-Quadruplex and Reduced Cell Senescence

Carassius auratus complex formula (CACF) is a traditional Chinese medicine known for its antidiabetic effects. Hepatocellular carcinoma (HCC) is a major cause of cancer-related deaths worldwide, and there are currently no effective therapies for advanced HCC. This study explores the comprehensive effects and possible mechanisms of CACF on HCC. The results show that CACF reduces the viability of hepatoma cells in vitro, while benefiting normal hepatocytes. In addition, CACF inhibits hepatoma cell growth in a zebrafish xenotransplantation model and decreases lipid accumulation, represses inflammation and cell proliferation markers in fatty acid translocase (CD36) transgenic zebrafish, and inhibits the expression of cell proliferation and β-catenin downstream targets in telomerase (tert) transgenic zebrafish models. Ingenuity Pathway Analysis reveals that CACF exerts multiple functions, including reduction of inflammation and inhibition of lipid transporter and PPAR signaling pathway. Surprisingly, CACF also regulates the expression of genes and reduces coronavirus infection and pathogenesis in a zebrafish model. CACF treatment is validated to regulate the expression of genes for anti-coronavirus activity. Mechanistically, CACF stabilizes G-quadruplex and reduces cell senescence associated β-galactosidase activity. In summary, CACF may be a promising therapeutic agent with multiple functions including anticancer, anti-inflammation, and anti-microorganisms in a zebrafish model.

Geography shapes the microbial community in Heliconius butterflies

Heliconius butterflies are an ideal organism for studying ecology, behavior, adaptation, and speciation. These butterflies can be found in various locations and habitats in Central and South America, where they encounter and interact with different sources of pollen, nectar, and host plants. However, there is limited knowledge on how geographic and habitat variations affect the microbiota of these insects, and whether microbial associates play a role in their ability to exploit different habitats. To date, research on the microbial communities associated with Heliconius has mainly focused on host phylogenetic signal in microbiomes or microbiome characterization in specific communities of butterflies. In this study we characterized the microbiomes of several species and populations of Heliconius from distant locations that represent contrasting environments. We found that the microbiota of different Heliconius species is taxonomically similar but vary in abundance. Notably, this variation is associated with a major geographic barrier-the Central Cordillera of Colombia. Additionally, we confirmed that this microbiota is not associated with pollen-feeding. Therefore, it seems likely that geography shapes the abundance of microbiota that the butterfly carries, but not the taxonomic diversity of the microbial community. Based on the current evidence, the bacterial microbiota associated with Heliconius does not appear to play a beneficial role for these butterflies.

Genomic Features Predict Bacterial Life History Strategies in Soil, as Identified by Metagenomic Stable Isotope Probing

Bacteria catalyze the formation and destruction of soil organic matter, but the bacterial dynamics in soil that govern carbon (C) cycling are not well understood. Life history strategies explain the complex dynamics of bacterial populations and activities based on trade-offs in energy allocation to growth, resource acquisition, and survival. Such trade-offs influence the fate of soil C, but their genomic basis remains poorly characterized. We used multisubstrate metagenomic DNA stable isotope probing to link genomic features of bacteria to their C acquisition and growth dynamics. We identify several genomic features associated with patterns of bacterial C acquisition and growth, notably genomic investment in resource acquisition and regulatory flexibility. Moreover, we identify genomic trade-offs defined by numbers of transcription factors, membrane transporters, and secreted products, which match predictions from life history theory. We further show that genomic investment in resource acquisition and regulatory flexibility can predict bacterial ecological strategies in soil. IMPORTANCE Soil microbes are major players in the global carbon cycle, yet we still have little understanding of how the carbon cycle operates in soil communities. A major limitation is that carbon metabolism lacks discrete functional genes that define carbon transformations. Instead, carbon transformations are governed by anabolic processes associated with growth, resource acquisition, and survival. We use metagenomic stable isotope probing to link genome information to microbial growth and carbon assimilation dynamics as they occur in soil. From these data, we identify genomic traits that can predict bacterial ecological strategies which define bacterial interactions with soil carbon.

Impact of different structures of biochar on decreasing methane emissions from sewage sludge composting

Methane (CH₄) emissions from sewage sludge composting can be reduced by using biochar more effectively. This study investigates the impact of different structure of biochar on CH₄ emissions during sewage sludge composting. Corncob biochar (CB, pore size = 35.3990 nm), rice husk biochar (RB, pore size = 3.4242 nm) and wood biochar (WB, pore size = 1.6691 nm) were applied to the composting. The results showed that biochar decreased CH₄ emissions, mainly through the indirect effect of improving the pile environment. Compared with the control group (CK), the biochars with smaller pore structures, WB and RB, reduced CH₄ emissions by 41.83% and 33.59%, respectively, compared to only 8.20% for CB, which has a larger pore structure. In addition, RB and WB increased the free air space (FAS) by more than 10% and CB improved the microbial diversity. Methanothermobacter was reported in WB and RB, with an abundance of 45.45% in WB. Redundancy analysis (RDA) showed that pore size was positively correlated with the CH₄ emission rate. The results of this study can provide a theoretical reference for CH₄ reduction from biochar co-composting of sewage sludge.

Knowns and unknowns of the soil fungal necrobiome

Dead microbial cells, commonly referred to as necromass, are increasingly recognized as an important source of both persistent carbon as well as nutrient availability in soils. Studies of the microbial communities associated with decomposing fungal necromass have accumulated rapidly in recent years across a range of different terrestrial ecosystems. Here we identify the primary ecological patterns regarding the structure and dynamics of the fungal necrobiome as well as highlight new research frontiers that will likely be key to gaining a full understanding of fungal necrobiome composition and its associated role in soil biogeochemical cycling. Because many members of the fungal necrobiome are culturable, combining laboratory functional assays with field-based surveys and experiments will allow ongoing studies of the fungal necrobiome to move from largely descriptive to increasingly predictive.

Molecular and Clinical Data of Antimicrobial Resistance in Microorganisms Producing Bacteremia in a Multicentric Cohort of Patients with Cancer in a Latin American Country

Patients with cancer have a higher risk of severe bacterial infections. This study aims to determine the frequency, susceptibility profiles, and resistance genes of bacterial species involved in bacteremia, as well as risk factors associated with mortality in cancer patients in Colombia. In this prospective multicenter cohort study of adult patients with cancer and bacteremia, susceptibility testing was performed and selected resistance genes were identified. A multivariate regression analysis was carried out for the identification of risk factors for mortality. In 195 patients, 206 microorganisms were isolated. Gram-negative bacteria were more frequently found, in 142 cases (68.9%): 67 Escherichia coli (32.5%), 36 Klebsiella pneumoniae (17.4%), and 21 Pseudomonas aeruginosa (10.1%), and 18 other Gram-negative isolates (8.7%). Staphylococcus aureus represented 12.4% (n = 25). Among the isolates, resistance to at least one antibiotic was identified in 63% of them. Genes coding for extended-spectrum beta-lactamases and carbapenemases, blaCTX-M and blaKPC, respectively, were commonly found. Mortality rate was 25.6% and it was lower in those with adequate empirical antibiotic treatment (22.0% vs. 45.2%, OR: 0.26, 95% CI: 0.1-0.63, in the multivariate model). In Colombia, in patients with cancer and bacteremia, bacteria have a high resistance profile to beta-lactams, with a high incidence of extended-spectrum beta-lactamases and carbapenemases. Adequate empirical treatment diminishes mortality, and empirical selection of treatment in this environment of high resistance is of key importance.

Differentiating methicillin resistant and susceptible Staphylococcus aureus from ocular infections using photoacoustic labeling

Introduction

Antibiotic resistance in bacterial species constitutes a growing problem in the clinical management of infections. Not only does it limit therapeutic options, but application of ineffective antibiotics allows resistant species to progress prior to prescribing more effective treatment to patients. Methicillin resistance in Staphylococcus aureus is a major problem in clinical infections as it is the most common hospital acquired infection.

Methods

We developed a photoacoustic flow cytometer using engineered bacteriophage as probes for rapid determination of methicillin resistance in Staphylococcus aureus with thirteen clinical samples obtained from keratitis patients. This method irradiates cells under flow with 532 nm laser light and selectively generates acoustic waves in labeled bacterial cells, thus enabling detection and enumeration of them. Staphylococcus aureus isolates were classified from culture isolation as either methicillin resistant or susceptible using cefoxitin disk diffusion testing. The photoacoustic method enumerates bacterial cells before and after treatment with antibiotics. Decreasing counts of bacteria after treatment indicate susceptible strains. We quantified the bacterial cells in the treated and untreated samples.

Results

Using k-means clustering on the data, we achieved 100% concordance with the classification of Staphylococcus aureus resistance using culture.

Discussion

Photoacoustics can be used to differentiate methicillin resistant and susceptible strains of bacteria from ocular infections. This method may be generalized to other bacterial species using appropriate bacteriophages and testing for resistance using other antibiotics.

Bacteriophage Therapy for Pan-Drug-Resistant Pseudomonas aeruginosa in Two Persons With Cystic Fibrosis

Cystic fibrosis (CF) is an important monogenic disease that affects more than 70 000 people worldwide. Defects of the CF transmembrane conductance regulator gene lead to dehydrated viscous secretions that result in chronic bacterial colonization. This leads to frequent recurrent lung infections called pulmonary exacerbations, lung inflammation, and resulting structural lung damage called bronchiectasis. Pseudomonas aeruginosa in particular is a common pathogen in persons with CF associated with increased pulmonary exacerbations, long-term lung function decline, and reduced survival. In addition, P. aeruginosa commonly develops antibiotic resistance and forms biofilms, making it difficult to treat. Here, we report the details of two patients with CF with pan-drug-resistant P. aeruginosa who were treated with a novel therapeutic strategy, bacteriophages. These cases highlight the need for further research and development of this treatment modality, including pediatric clinical trials.

State of Knowledge on the Acquisition, Diversity, Interspecies Attribution and Spread of Antimicrobial Resistance between Humans, Animals and the Environment: A Systematic Review

Resistance to antibiotics is considered one of the most urgent global public health concerns. It has considerable impacts on health and the economy, being responsible for the failure to treat infectious diseases, higher morbidity and mortality rates, and rising health costs. In spite of the joint research efforts between different humans, animals and the environment, the key directions and dynamics of the spread of antimicrobial resistance (AMR) still remain unclear. The aim of this systematic review is to examine the current knowledge of AMR acquisition, diversity and the interspecies spread of disease between humans, animals and the environment. Using a systematic literature review, based on a One Health approach, we examined articles investigating AMR bacteria acquisition, diversity, and the interspecies spread between humans, animals and the environment. Water was the environmental sector most often represented. Samples were derived from 51 defined animal species and/or their products A large majority of studies investigated clinical samples of the human population. A large variety of 15 different bacteria genera in three phyla (Proteobacteria, Firmicutes and Actinobacteria) were investigated. The majority of the publications compared the prevalence of pheno- and/or genotypic antibiotic resistance within the different compartments. There is evidence for a certain host or compartment specificity, regarding the occurrence of ARGs/AMR bacteria. This could indicate the rather limited AMR spread between different compartments. Altogether, there remains a very fragmented and incomplete understanding of AMR acquisition, diversity, and the interspecies spread between humans, animals and the environment. Stringent One Health epidemiological study designs are necessary for elucidating the principal routes and dynamics of the spread of AMR bacteria between humans, animals and the environment. This knowledge is an important prerequisite to develop effective public health measures to tackle the alarming AMR situation.

Antimicrobial Resistance and Mortality in Hospitalized Patients with Bacteremia in the Greater Paris Area from 2016 to 2019

PURPOSE

Antibiotic-resistant bacteremia is a leading global cause of infectious disease morbidity and mortality. Clinical data warehouses (CDWs) allow for the secure, real-time coupling of diverse data sources from real-world clinical settings, including care-based medical-administrative data and laboratory-based microbiological data. The main purpose of this study was to assess the contribution of CDWs in the epidemiological study of antibiotic resistance by constructing a database of bacteremia patients, BactHub, and describing their main clinico-microbiological features and outcomes.

PATIENTS AND METHODS

Adult patients with bacteremia hospitalized between January 1, 2016 and December 31, 2019 in 14 acute care university hospitals from the Greater Paris area were identified; their first bacteremia episode was included. Data describing patients, episodes of bacteremia, bacterial isolates, and antimicrobial resistance were structured.

RESULTS

Among 29,228 patients with bacteremia, 41% of episodes were community-onset (CO) and 59% were hospital-acquired (HA). Thirty-day and ninety-day mortality rates were 15% and 20% in CO episodes, and 18% and 36% in HA episodes. Overall resistance rates were high, including third-generation cephalosporin resistance among Klebsiella pneumoniae (CO 21%, HA 37%) and Escherichia coli (CO 13%, HA 17%), and methicillin resistance among Staphylococcus aureus (CO 11%, HA 14%). Annual incidence rates increased significantly from 2017 to 2019, from 20.0 to 20.9 to 22.1 stays with bacteremia per 1000 stays (p < 0.0001).

CONCLUSION

The Bacthub database provides accurate clinico-microbiological data describing bacteremia across France's largest hospital group. Data from Bacthub may inform surveillance and the clinical decision-making process for bacteremia patients, including choice of antimicrobial therapy. The database also offers opportunities for research, including analysis of hospital care pathways and significant patient outcomes such as mortality and recurrence of infection.

Molecular mimicry among human proteinase 3 and bacterial antigens: implications for development of c-ANCA associated vasculitis

Wegener's granulomatosis is an autoimmune disease where autoantibodies target human autoantigen PR3, a serine protease locates on the neutrophil membrane. This disease affects blood small vessels and could be deadly. The origin of these autoantibodies is unknown, but infections have been implicated with autoimmune disease. In this study, we explored potential molecular mimicry between human PR3 and homologous pathogens through in silico analysis. Thirteen serine proteases from human pathogens (Klebsiella pneumoniae, Acinetobacter baumannii, Salmonella sp., Streptococcus suis, Vibrio parahaemolyticus, Bacteroides fragilis, Enterobacter ludwigii, Vibrio alginolyticus, Staphylococcus haemolyticus, Enterobacter cloacae, Escherichia coli and Pseudomonas aeruginosa) shared structural homology and amino acid sequence identity with human PR3. Epitope prediction found an only conserved epitope IVGG, located between residues 59-74. However, multiple alignments showed conserved regions that could be involved in cross-reactivity between human and pathogens serine proteases (90-98, 101-108, 162-169, 267 and 262 residues positions). In conclusion, this is the first report providing in silico evidence about the existence of molecular mimicry between human and pathogens serine proteases, that could explain the origins of autoantibodies found in patients suffering from Wegener's granulomatosis.

Haemophilus influenzae drug resistance in France from 2017 to 2021: consideration for treatment of otitis media

OBJECTIVES

Haemophilus influenzae is a prevalent agent of respiratory infections, including acute otitis media (AOM), that lead to high antibiotic prescription and may contribute to the development of bacterial resistance to antibiotics. The objective of this work was to describe and analyse antibiotic resistance of H. influenzae from 2017 to 2021 in France.

METHODS

We characterized H. influenzae isolates transmitted to the French national reference centre for H. influenzae between 2017 and 2021. We included all the 608 non-invasive respiratory isolates. Resistance rates to the main antibiotics were described. The relationship between resistance rate, age, and sex of patients and germ serotype was investigated.

RESULTS

Isolates were mainly from alveolar lavage (29.3%), expectoration (22.9%), or sputum (15%). Resistance to amoxicillin (61.4%), amoxicillin/clavulanic acid (47.4%), and cefotaxime (39.3%) was high and correlated with the presence of β-lactamase and/or modifications of the ftsI gene encoding penicillin-binding protein 3. Resistance to sulfamethoxazole/trimethoprim (33.2%) was more moderate. There were no significant differences according to serotype, age, or gender.

CONCLUSIONS

The benefit/risk balance of first choice use of amoxicillin and even of amoxicillin/clavulanic acid in AOM is questionable in view of the significant resistance to H. influenzae. The use of sulfamethoxazole/trimethoprim could be an alternative but may still need further evaluation.

Gene expression profiles of ERG11, MDR1 and AFR1 in Cryptococcus neoformans var.grubbi from HIV patients

Introduction: Fluconazole is the most used antifungal drug for prevention and treatment of Cryptococcus spp. infections, the etiological agent of cryptococcosis. Resistance to fluconazole among Cryptococcus neoformans isolates can lead to treatment failure and generate relapses. Objective: To evaluate the expression profiles of the AFR1, MDR1 and ERG11 genes in C. neoformans var. grubii clinical isolates during the in vitro response to fluconazole induction. Materials and methods: Fourteen C. neoformans var. grubii isolates recovered from HIV patients were studied, in which 6 showed sensitivities to fluconazole and 8 decreased sensitivity. The expression levels of ERG11, AFR1 and MDR1 genes were determined by real-time PCR from extracted mRNA. Results: AFR1 and MDR1 genes from C. neoformans var. grubii were overexpressed in fluconazole resistant isolates, whereas ERG11 maintains homogeneous expression in all the evaluated resistance phenotypes of C. neoformans var. grubii isolates. Conclusions: The overexpression of AFR1 and MDR1 genes, which codify for efflux pumps, contributes to fluconazole resistance in the studied isolates. However, the resistance patterns in this fungus and the relapse cases in HIV patients cannot be attributed solely to the exposure to the drug. Heteroresistance and the emerging resistance (resistance through other ERG genes), might be other mechanisms involved in this phenomenon, which must be studied in these isolations.

Microbial warfare and the evolution of symbiosis

Cooperative symbionts enable their hosts to exploit a diversity of environments. A low genetic diversity (high relatedness) between the symbionts within a host is thought to favour cooperation by reducing conflict within the host. However, hosts will not be favoured to transmit their symbionts (or commensals) in costly ways that increase relatedness, unless this also provides an immediate fitness benefit to the host. We suggest that conditionally expressed costly competitive traits, such as antimicrobial warfare with bacteriocins, could provide a relatively universal reason for why hosts would gain an immediate benefit from increasing the relatedness between symbionts. We theoretically test this hypothesis with a simple illustrative model that examines whether hosts should manipulate relatedness, and an individual-based simulation, where host control evolves in a structured population. We find that hosts can be favoured to manipulate relatedness, to reduce conflict between commensals via this immediate reduction in warfare. Furthermore, this manipulation evolves to extremes of high or low vertical transmission and only in a narrow range is partly vertical transmission stable.

The Use of Medicinal Plant-Derived Metallic Nanoparticles in Theranostics

In the quest to effectively diagnose and treat the diseases that afflict mankind, the development of a tool capable of simultaneous detection and treatment would provide a significant cornerstone for the survival and control of these diseases. Theranostics denotes a portmanteau of therapeutics and diagnostics which simultaneously detect and treat ailments. Research advances have initiated the advent of theranostics in modern medicine. Overall, theranostics are drug delivery systems with molecular or targeted imaging agents integrated into their structure. The application of theranostics is rising exponentially due to the urgent need for treatments that can be utilized for diagnostic imaging as an aid in precision and personalised medicine. Subsequently, the emergence of nanobiotechnology and the green synthesis of metallic nanoparticles (MNPs) has provided one such avenue for nanoscale development and research. Of interest is the drastic rise in the use of medicinal plants in the synthesis of MNPs which have been reported to be potentially effective in the diagnosis and treatment of diseases. At present, medicinal plant-derived MNPs have been cited to have broad pharmacological applications and have been studied for their potential use in the treatment and management of cancer, malaria, microbial and cardiovascular diseases. The subject of this article regards the role of medicinal plants in the synthesis of MNPs and the potential role of MNPs in the field of theranostics.

Therapeutic and Metagenomic Potential of the Biomolecular Therapies against Periodontitis and the Oral Microbiome: Current Evidence and Future Perspectives

The principles of periodontal therapy are based on the control of microbial pathogens and host factors that contribute to biofilm dysbiosis, with the aim of modulating the progression of periodontitis and periodontal tissue destruction. It is currently known how differently each individual responds to periodontal treatment, depending on both the bacterial subtypes that make up the dysbiotic biofilm and interindividual variations in the host inflammatory response. This has allowed the current variety of approaches for the management of periodontitis to be updated by defining the goals of target strategies, which consist of reducing the periodontopathogenic microbial flora and/or modulating the host-mediated response. Therefore, this review aims to update the current variety of approaches for the management of periodontitis based on recent target therapies. Recently, encouraging results have been obtained from several studies exploring the effects of some targeted therapies in the medium- and long-term. Among the most promising target therapies analyzed and explored in this review include: cell-based periodontal regeneration, mediators against bone resorption, emdogain (EMD), platelet-rich plasma, and growth factors. The reviewed evidence supports the hypothesis that the therapeutic combination of epigenetic modifications of periodontal tissues, interacting with the dysbiotic biofilm, is a key step in significantly reducing the development and progression of disease in periodontal patients and improving the therapeutic response of periodontal patients. However, although studies indicate promising results, these need to be further expanded and studied to truly realize the benefits that targeted therapies could bring in the treatment of periodontitis.

A quarterly Survey of antibiotic prescribing in small animal and equine practices-Minnesota and North Dakota, 2020

Antimicrobials are critical for medicine, but the problem of antimicrobial resistance (AMR) threatens the effectiveness of these valuable drugs. In USA, there are no national- or state-level programs or policies in place to track antibiotic use (AU) in dogs, cats, and horses, despite acknowledgement of this sector's importance to both the AMR problem and its solution. AU measurement is a key part of antibiotic stewardship and AMR prevention. This study aimed to fill existing gaps in the veterinary professions' knowledge of antibiotic prescribing in small animals and horses. To address this aim, medical record data were collected on a single day per quarter for 1 year from 19 Minnesota and North Dakota small animal and equine practices, totaling 1,899 veterinarian consults of dogs, cats, and horses. Overall, 25.8% of all canine, feline, and equine consults involved an antibiotic prescription. Third-generation cephalosporins were the most commonly prescribed systemic antibiotic drug class, and the long-acting injectable drug, cefovecin, was the most commonly prescribed antibiotic for cats (34.5%). Topical antibiotic preparations were prescribed frequently, especially in dogs (42.5% of canine prescriptions), though systemic antibiotics were often prescribed concurrently. Common general indications, based on problem or diagnosis recorded in the medical record, for antibiotics in all species combined were skin conditions (24.4%), otitis (22.1%), ophthalmic (9.4%), gastrointestinal (8.3%), respiratory (8.3%), and urinary tract (7.6%) diseases. While 44.2% of patients for which antibiotics were prescribed had cytology performed, only 3.9% had bacterial culture and susceptibility performed. In a pre-study survey, veterinarians' recommendations for AU differed from actual prescribing, suggesting collection of AU data provides more accurate assessments of veterinary prescribing behaviour than surveys. This study shows feasibility of AU measurement in small animals and horses. The data collection tool and standard operating procedures described prove suitable for national AU data collection.

Anti-microbial efficacy of root canal preparation in deciduous teeth with manual and rotary files: A randomized clinical trial

BACKGROUND

In a pulpectomy, the eradication of microbes from the primary root canal is accomplished through biomechanical preparation, which could be carried out with either manual or rotary instruments.

AIMS

The objective of this clinical trial was to evaluate the efficiency of manual K-files, H-files, and Kedo-S Square rotary files in reducing microbial flora after canal preparation in primary molars.

MATERIALS AND METHODS

This randomized clinical trial consisted of 45 primary molars requiring pulpectomy. The teeth were randomly allocated to one of the three groups: Group I: Manual K-files, Group II: Manual H-files, and Group III: Kedo-S Square rotary files, based on the type of instrumentation. Pre-and Post-instrumentation sampling was performed using clean absorbent paper points and kept in a clean Eppendorf tube having thioglycolate broth as the transport medium. Culturing was performed on agar media from which both aerobic and anaerobic microbial counts were estimated. Collected data were statistically analyzed using one-way analysis of variance (ANOVA) and Wilcoxon signed-rank test. Following root canal preparation, 87-89% reduction of the aerobic and anaerobic microbial load was noted in group I, whereas it was an 89-92% reduction in group II and a 93-95% reduction in group III.

RESULTS

Biomechanical preparation with Kedo-S Square rotary file showed higher efficacy in microbial reduction compared to manual instrumentation.

CONCLUSION

Manual and rotary files were equally effective in removing root canal microbes. Biomechanical preparation with a KedoS Square rotary file resulted in greater microbial efficacy. Hence In children, effective root canal cleaning in a short period of time is a major consideration.

Chloramine Prevents Manganese Accumulation in Drinking Water Pipes Compared to Free Chlorine by Simultaneously Inhibiting Abiotic and Biotic Mn(II) Oxidation

The oxidation of residual Mn(II) in finished water can lead to MnO_x deposit formation in drinking water pipes. Previous work has illustrated that microbes readily cause Mn deposit build-up in nondisinfected pipes. Here, we investigated how disinfectant type and dose affected Mn(II) oxidation and MnO_x accumulation through long-term pipe experiments using water produced by a full-scale water treatment plant. The results showed that Mn(II) oxidation initiated quickly in the new pipes chlorinated with 1.0 mg/L free chlorine. After 130 days of MnO_x accumulation, 100 μg/L Mn(II) in water could drop to 1.0 μg/L within 1.5 h, resulting from autocatalytic Mn(II) oxidation and Mn(II) adsorption by MnO_x deposits accumulated on pipe walls. In contrast to chlorination, chloramination (1.0 mg/L Cl₂) caused almost no MnO_x accumulation during the entire study period. The underlying mechanism was probably that monochloramine inhibited microbial Mn(II) oxidation without causing significant abiotic Mn(II) oxidation like free chlorine. A low free chlorine dose (0.3 mg/L) also reduced Mn deposit formation by mass but to a lesser extent than chloramination. After disinfection (chlorination or chloramination) was discontinued for days, biotic Mn(II) oxidation occurred, and this process was inhibited again once disinfection was resumed. In addition, Fe(III) of 200 μg/L enhanced the stability of MnO_x accumulated on pipe surfaces, while humic acid induced MnO_x deposit resuspension. Overall, this study highlighted the regulating role of disinfectants in MnO_x formation and provided insights into developing appropriate disinfection strategies for Mn deposit control.

Rapid evolution allows coexistence of highly divergent lineages within the same niche

Marine microbial communities are extremely complex and diverse. The number of locally coexisting species often vastly exceeds the number of identifiable niches, and taxonomic composition often appears decoupled from local environmental conditions. This is contrary to the view that environmental conditions should select for a few locally well-adapted species. Here we use an individual-based eco-evolutionary model to show that virtually unlimited taxonomic diversity can be supported in highly evolving assemblages, even in the absence of niche separation. With a steady stream of heritable changes to phenotype, competitive exclusion may be weakened, allowing sustained coexistence of nearly neutral phenotypes with highly divergent lineages. This behaviour is robust even to abrupt environmental perturbations that might be expected to cause strong selection pressure and an associated loss of diversity. We, therefore, suggest that rapid evolution and individual-level variability are key drivers of species coexistence and maintenance of microbial biodiversity.

Pneumococcal genetic variability in age-dependent bacterial carriage

The characteristics of pneumococcal carriage vary between infants and adults. Host immune factors have been shown to contribute to these age-specific differences, but the role of pathogen sequence variation is currently less well-known. Identification of age-associated pathogen genetic factors could leadto improved vaccine formulations. We therefore performed genome sequencing in a large carriage cohort of children and adults and combined this with data from an existing age-stratified carriage study. We compiled a dictionary of pathogen genetic variation, including serotype, strain, sequence elements, single-nucleotide polymorphisms (SNPs), and clusters of orthologous genes (COGs) for each cohort - all of which were used in a genome-wide association with host age. Age-dependent colonization showed weak evidence of being heritable in the first cohort (h2 = 0.10, 95% CI 0.00-0.69) and stronger evidence in the second cohort (h2 = 0.56, 95% CI 0.23-0.87). We found that serotypes and genetic background (strain) explained a proportion of the heritability in the first cohort (h2serotype = 0.07, 95% CI 0.04-0.14 and h2GPSC = 0.06, 95% CI 0.03-0.13) and the second cohort (h2serotype = 0.11, 95% CI 0.05-0.21 and h2GPSC = 0.20, 95% CI 0.12-0.31). In a meta-analysis of these cohorts, we found one candidate association (p=1.2 × 10-9) upstream of an accessory Sec-dependent serine-rich glycoprotein adhesin. Overall, while we did find a small effect of pathogen genome variation on pneumococcal carriage between child and adult hosts, this was variable between populations and does not appear to be caused by strong effects of individual genes. This supports proposals for adaptive future vaccination strategies that are primarily targeted at dominant circulating serotypes and tailored to the composition of the pathogen populations.

Integrating 16S rRNA gene sequencing and metabolomics to evaluate the association between gut microbiota and serum metabolites in patients with myositis

AIMS

Gut microbiota and metabolites have a profound impact on the maintenance of body health. In this study, we assessed the association between gut microbiota and serum metabolite changes in myositis using 16S rRNA gene sequencing and metabolomics to provide new ideas for screening and treating myositis.

METHODS AND RESULTS

Blood and fecal samples were collected from twenty myositis patients and twenty healthy control subjects. Then, 16S rRNA gene sequencing, enzyme-linked immunosorbent assays, and untargeted metabolomics study were performed to evaluate the relationship between gut microbiota and serum metabolites in patients with myositis. Compared to healthy control subjects, the blood samples from the patients with myositis had elevated levels of interleukin-4 (IL-4), tumor necrosis factor-α (TNF-α), and malondialdehyde (MDA), and decreased superoxide dismutase (SOD) levels. The increase in Bacteroidota (including Bacteroides and Parabacteroides, but not Prevotella) and the decrease in Firmicutes in the patients were accompanied by functional changes in amino acid and lipid metabolism. The gut microbiota (Bacteroides and Parabacteroides) were negatively correlated with the differential serum metabolites (glutamate and taurine). The differential serum metabolites (glutamate, pyrrolidonecarboxylic acid, and taurine) were also correlated with inflammatory factors (IL-4 and TNF-α) and oxidative stress indexes (MDA and SOD).

CONCLUSION

Dysbiosis of gut microbiota in patients with myositis was accompanied by changes in inflammatory factors, oxidative stress indexes, and small molecule metabolites in serum.

SIGNIFICANCE AND IMPACT OF STUDY

Blood and fecal biomarkers could be used for screening myositis.