individualized-reconstitution-human-milk-microbiota-feasible-approach

Individualized Reconstitution of Human Milk Microbiota: A Feasible Approach in Real-World Settings

Mother&#39;s own milk (MOM) is the most complete nutritional resource for newborns. In cases where mothers are unable to produce sufficient milk or cannot ...

Federal University of Santa Catarina

Neisseria elongata is part of the commensal microbiota of the oropharynx. Although it is not considered pathogenic to humans, N. elongata has been implicated in several cases of infective endocarditis (IE). Here, we report a case of IE caused by N. elongata subsp. nitroreducens (Nel_M001) and compare its genome with 17 N. elongata genomes available in GenBank. We also evaluated resistance and virulence profiles with Comprehensive Antibiotic Resistance and Virulence Finder databases. The results showed a wide diversity among N. elongata isolates. Based on the pangenome cumulative curve, we demonstrate that N. elongata has an open pangenome. We found several different resistance genes, mainly associated with antibiotic efflux pumps. A wide range of virulence genes was observed, predominantly pilus formation genes. Nel_M001 was the only isolate to present two copies of some pilus genes and not present nspA gene. Together, our results provide insights into how this commensal microorganism can cause IE and may assist further biological investigations on nonpathogenic Neisseria spp. Case reporting and pangenome analyses are critical for enhancing our understanding of IE pathogenesis, as well as for alerting physicians and microbiologists to enable rapid identification and treatment to avoid unfavorable outcomes.

Genomic analysis of Neisseria elongata isolate from a patient with infective endocarditis.

Antimicrobial resistance is a major threat to public health. Antimicrobial use in animal husbandry is a major concern since it can favor an increase in antimicrobial resistance among farms. Herein, we aim to better understand and characterize the main resistome profiles in microbial communities found in pig farms. Sampling of swine manure was performed in two different timepoints (October 2019 and January 2020) in each of the 14 different swine farms, located in the mesoregion of Western Santa Catarina state in Brazil, a pole of swine product production of worldwide importance. Samples were divided into three groups: farms with the opened regimen and no usage of antimicrobials (F1; n = 10), farms with the closed regimen and usage of antimicrobials (F2; n = 16), and farms with the closed regimen and no usage of antimicrobials (F3; n = 2). The metagenomic evaluation was performed to obtain and identify genetic elements related to antimicrobial resistance using nanopore sequencing. We used ResistoXplorer software to perform composition, alpha and beta diversity, and clustering analysis. In addition, PCR reactions were performed to confirm the presence or absence of seven different beta-lactamase family genes and five phosphoethanolamine transferase gene variants clinically relevant. Our findings based on the identification of resistance genes at the mechanism level showed a prevalence of alteration of the drug target (72.3%) profile, followed by drug inactivation (17.5%) and drug efflux (10.1%). We identified predominantly aminoglycosides (45.3%), tetracyclines (15.9%), and multiclass (11,2%) resistance genes. PCoA analysis indicates differences between F1 and F2 profiles. F2 samples showed increased diversity when compared to the F1 group. In addition, herein we first report the identification of  in a slurry sample (C1F1.1) in Santa Catarina State. In general, our findings reinforce that many factors on the practices of animal husbandry are involved in the resistome profile at the mechanism and class levels. Further studies to better understand microbiome and mobilome aspects of these elements are necessary to elucidate transmission pathways between different bacteria and environments.

Different Swine Production Systems Can Shape Slurry Resistome at Mechanism and Class Levels Based on Swine Manure Evaluation.

This study aimed to implement a targeted multiple reaction monitoring (MRM) screening strategy using liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) for the initial detection of 165 compounds of emerging concern (CECs) in water, sediment, and fish samples. Following the screening, confirmatory and quantitative analyses were conducted using analytical standards for the detected compounds. Qualitative results were confirmed using high-resolution mass spectrometry (HRMS) for those CECs without available standards. Ecotoxicological and human health risk assessments were performed for the quantified CECs. The analysis identified 35 suspect CECs (12 quantified with analytical standards), including parent compounds and metabolites of anti-inflammatories, antibiotics, antidepressants, sedatives, stimulants, and illicit drugs. High concentrations of these CECs were particularly evident near a Wastewater Treatment Plant (WWTP), where notable levels of compounds such as caffeine (4.02-15.03 ng L), ciprofloxacin (6.05 ng L), clindamycin (6.04-7.01 ng L), and diclofenac (1.36-2.20 ng L) were detected. Sediment samples exhibited the highest incidence of CECs, with caffeine reaching the highest concentration (55.89 μg kg). Ciprofloxacin (2.94 to 4.18 μg kg) was the sole CEC detected in biota samples. The ecotoxicological risk assessment indicated that the concentrations of all detected compounds posed significant ecotoxicity risks to the aquatic environment. In particular, caffeine and diclofenac presented considerable acute and chronic toxic risks to aquatic organisms, including algae, crustaceans, and fish. The Hazard Index (HI) values (3.65 to 8.06) suggest that ingesting ciprofloxacin at the concentrations found in fish does not represent a significant risk to human health. However, due to the reported risks to estuarine biota, it is crucial to continuously monitor the accumulation of these compounds in food widely consumed by the local population to assess potential impacts on human health.

Suspect screening and quantitative analysis of 165 contaminants of emerging concern in water, sediments, and biota using LC-MS/MS: Ecotoxicological and human health risk assessment.

Antimicrobial resistance (AMR) poses a significant threat to global public health. The One Health approach, which integrates human, animal, and environmental health, highlights the roles of agricultural and hospital settings in the propagation of AMR. This study aimed to analyze the resistome and gut microbiome composition of individuals from a high-intensity animal husbandry area in the western region of Santa Catarina, Southern Brazil, who were subsequently admitted to the University Hospital in the city of Florianopolis, located in the eastern part of the same state.

Evaluation of the resistome and gut microbiome composition of hospitalized patients in a health unit of southern Brazil coming from a high animal husbandry production region.

Article	Year
Genomic analysis of Neisseria elongata isolate from a patient with infective endocarditis. FEBS open bio\| PubMed ID: 34038628	2021
Different Swine Production Systems Can Shape Slurry Resistome at Mechanism and Class Levels Based on Swine Manure Evaluation. Frontiers in cellular and infection microbiology\| PubMed ID: 35860383	2022
Suspect screening and quantitative analysis of 165 contaminants of emerging concern in water, sediments, and biota using LC-MS/MS: Ecotoxicological and human health risk assessment. The Science of the total environment\| PubMed ID: 39826219	2025
Evaluation of the resistome and gut microbiome composition of hospitalized patients in a health unit of southern Brazil coming from a high animal husbandry production region. Frontiers in antibiotics\| PubMed ID: 39896720	2024

Jussara Kasuko Palmeiro

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