Bacterial Species Research Articles

Oral Microbiota Alterations in Subjects with SARS-CoV-2 Displaying Prevalence of the Opportunistic Fungal Pathogen Candida albicans.

The oral cavity remains an underappreciated site for SARS-CoV-2 infection despite the myriad of oral conditions in COVID-19 patients. Recently, SARS-CoV-2 was shown to replicate in the salivary gland cells causing tissue inflammation. Given the established association between inflammation and microbiome disruption, we comparatively profiled oral microbial differences at a metagenomic level in a cohort of hospitalized COVID-19 patients and matched healthy controls. Specifically, we aimed to evaluate colonization by the opportunistic fungal pathogen Candida albicans, the etiologic agent of oral candidiasis. Comprehensive shotgun metagenomic analysis indicated that, overall, COVID-19 patients exhibited significantly reduced bacterial and viral diversity/richness; we identified 12 differentially abundant bacterial species to be negatively associated with COVID-19, and the functional pathways of certain bacteria to be highly associated with COVID-19 status. Strikingly, C. albicans was recovered from approximately half of the COVID-19 subjects but not from any of the healthy controls. The prevalence of Candida is likely linked to immune hypo-dysregulation caused by COVID-19 favoring Candida proliferation, warranting investigations into the interplay between Candida and SARS-CoV2 and potential therapeutic approaches directed toward oral candidiasis. Collectively, our findings prompt a reassessment of oral opportunistic infection risks during COVID-19 disease and their potential long-term impacts on oral health.

Enteric Populations of Escherichia coli are Likely to be Resistant to Phages Due to O Antigen Expression.

Bioinformatic data shows that bacteriophages are ubiquitous in the gut, however little is known about the role these bacterial viruses play in shaping the bacterial species and strain composition in the human gut microbiome or how they are maintained over time in this dynamic environment. Here we show that Escherichia coli isolated from fecal samples are likely to be resistant to their co-existing phages due to production of the O antigen. Based on these results, we postulate that bacteriophages are likely playing little role of shaping the abundance and diversity of bacteria in the human gut microbiome in healthy individuals.

A Comparative Study of Human Leptospirosis between Mayotte and Reunion Islands Highlights Distinct Clinical and Microbial Features Arising from Distinct Inter-Island Bacterial Ecology.

Leptospirosis is a neglected zoonosis for which investigations assessing host-pathogen interaction are scarce. The aim of this study was to compare the severity and bacterial species involved in human cases of leptospirosis on Reunion and Mayotte islands, territories located in the southwest Indian Ocean that have recorded high human leptospirosis incidence but display fairly distinct epidemiological situations. A retrospective multicentric study including all patients over 18 years of age from Mayotte or Reunion with proven leptospirosis was conducted from January 2018 to April 2020. This study collected demographic, geographical, clinical, and biological data. Overall, 490 patients were included, 222 on Mayotte and 268 on Reunion. More patients were hospitalized on Reunion (n = 215, 80%) compared with Mayotte (n = 102, 46%). Severe disease was more common on Reunion (n = 75, 28%) than on Mayotte (n = 22, 10%). The dominant Leptospira species on Reunion was Leptospira interrogans (79%) followed by Leptospira borgpetersenii (21%), contrasting with the epidemiological situation on Mayotte where L. interrogans was found in only a minority of patients (10%). The high frequency of severe cases on Reunion could be explained not only by higher comorbidities but also by the higher occurrence of L. interrogans infections compared with Mayotte. Finally, the distribution of cases linked to L. borgpetersenii was found almost exclusively on the west coast of Reunion, raising the potential role of a ruminant reservoir.

Investigating the Bacterial Profiles of Lactobacillus, Bifidobacterium, Actinobacteria, Fusobacterium, Firmicutes, and Bacteroides in Stool Samples from Patients with Severe Depression and Healthy Individuals

Depression is a multifaceted mental health disorder with complex etiology and significant global burden. Recent research indicates that the gut microbiota plays a role in the pathophysiology of depression, highlighting the potential role of specific bacterial species in influencing mood and cognitive function. In this study, we aimed to investigate the presence, copy numbers, and Ct values of selected bacterial species in stool samples from depressed patients (n=50) compared to control subjects (n=50). Our findings revealed significant differences in the abundance of Fusobacterium spp., Bifidobacterium spp., Lactobacillus spp., Bacteroidetes phylum, Firmicutes phylum, and Actinobacteria spp. between the two groups. Dysregulation of the gut microbiota, characterized by decreased presence of beneficial bacteria (e.g., Bifidobacterium spp., Lactobacillus spp.) and altered abundance of potentially pathogenic bacteria (e.g., Fusobacterium spp.), may contribute to the development or exacerbation of depression. These findings support the emerging concept of the gut-brain axis and its role in mental health. However, further research is needed to better understand the underlying mechanisms and explore the therapeutic potential of microbiota-targeted interventions for depression. Understanding the intricate interplay between the gut microbiota and depression could pave the way for novel treatment strategies and personalized approaches in mental health care.

Innovative bis-dihydrazothiazolone derivatives with a 1,4-xylenyl spacer: Design, antimicrobial prospective and construction of several transition metal chelates with iron, cobalt and zinc

Several new xylenyl-spaced bis-dihydrazothiazoles 6a-e and bis-dihydrazothiazolones 9a-e were synthesized by the simple reaction between bis-thiosemicarbazone 3 as a common synthetic scaffold, with two series of hydrazonoyl halides derivatives 4a-e and 7a-d. The chelation ability of these novel bis-dihydrazothiazole derivatives to perform as neutral tridentate ligands and coordinate to transition metal ions; Fe(III), Co(II), or Zn(II) through azomethine-N, thiazole-S, and azo-N atoms to form metal complexes with a metal/ligand ratio of 2:1 was elucidated. Diffused reflectance, magnetic moment, 1HNMR, FT-IR, TGA, and molar conductivity, were used to interpret the structures of all new xylenyl-spaced bis-heterocyclic compounds and their metal chelates. In-vitro, antibacterial and antiviral screening of these innovative xylenyl-spaced bis-dihydrazothiazole derivatives, as well as a selected group of their transition metal chelate complexes [M2L], were inspected, and the data was evaluated in comparison to those of Ketoconazole and Gentamycin as antimicrobial control standards using the agar well diffusion assay protocol against a selected group of fungal and bacterial species. Several compounds displayed respectable to great antimicrobial behavior against the examined microbial species. Bis-dihydrazothiazole 6c, particularly, showed exceptional inhibition of both C. albicans and E. coli. However, bis-dihydrazothiazolone 9b showed excellent inhibition of A. fumigatus. Additionally, amongst the three synthesized metal complexes [M2L], only the zinc complex, [Zn2L] showed remarkable inhibition of both C. albicans and S. typhimurium and was even more potent than the free ligand, 9a itself.

In vitro conjugation of IncB/O-plasmid: Minimum inhibitory concentration of β-lactams increases 16-fold in Salmonella enterica compared with Escherichia coli.

The use of antimicrobials in poultry leaves residues in the litter, favoring the emergence of antimicrobial-resistant pathogens and making it a source of contamination. An in vitro 4 × 4 factorial trial was performed to investigate the influence of four treatments, consisting of antimicrobial sub-concentrations, on the transference of IncB/O-plasmid through conjugation in four groups. Each group was composed of one plasmid donor bacterium (Escherichia coli H2332) and a recipient bacterium (Escherichia coli J62 or Salmonella enterica serovars, Enteritidis, Typhimurium, or Heidelberg). Our results showed a little decrease in the conjugation frequency in almost all treatments between the two bacterial species, which varied according to each strain. The MIC test revealed an increase of up to 4096-fold in resistance to beta-lactams in Salmonella serovars after plasmid acquisition. This finding suggests that some genetic apparatus may be involved in increased antimicrobial resistance in Salmonella serovars after the acquisition of primary resistance determinants.

The role of cell surface sulfhydryl and amine binding sites in the removal of Cr(VI) from solution by Bacillus subtilis bacterial cells

A range of bacterial species are known to be capable of reducing soluble Cr(VI) to Cr(III), causing the precipitation of Cr(III) phases from solution, but the mechanism responsible for the initial interaction between anionic aqueous Cr(VI) and the negatively charged cell surface has not been identified. Our study examines Cr(VI) removal from solution by the Gram-positive soil bacterial species Bacillus subtilis. We measured the kinetics of Cr(VI) removal as a function of pH in B. subtilis suspensions with different Cr(VI):cell ratios, and we measured the effect of pH on the extent of Cr(VI) removal at a fixed time in experiments with B. subtilis biomass (cells plus exudates) and in experiments involving B. subtilis exudates alone. The roles of sulfhydryl and amine binding sites in Cr(VI) removal were constrained using site–specific blocking molecules, and the impact of the site blocking on Cr(VI) removal was studied as a function of pH. Our results indicate that Cr(VI) removal by B. subtilis cells under the experimental conditions is at least partially non-reversible and is dependent on binding site concentration, pH, and metal loading. Our results are consistent with a two step removal process: Cr(VI) first adsorbs reversibly onto a cell wall binding site, followed by Cr(VI) reduction to Cr(III) likely via electron transfer from cell wall electron transport chain molecules. B. subtilis exudates are capable of removing a relatively small fraction of Cr(VI) from solution, and hence our results indicate that the dominant mechanism of Cr(VI) removal requires interaction with bacterial biomass. The presence of either the sulfhydryl-specific blocking molecule or the amine-specific blocking molecule or both in the experimental systems dramatically reduces the extent of Cr(VI) reduction, especially under circumneutral pH conditions, strongly suggesting that both sulfhydryl and amine binding site types participate in the initial attachment of Cr(VI) onto the cell surface. The experiments with either sulfhydryl or amine sites blocked both exhibited a similar reduction in Cr(VI) removal to the experiments with both types of sites blocked, strongly suggesting that both types of sites are involved simultaneously in binding Cr(VI) species to the cell surface. For example, these sites could both be involved in forming a bidentate bond with Cr(VI) species, or the positive charge of an amine site in close proximity to a sulfhydryl site could be necessary in order to enable the Cr(VI) species to approach the cell wall and to bind to a sulfhydryl site. The results of this study are the first to propose a viable mechanism that can explain the binding of anionic Cr(VI) onto an overall negatively charged cell surface as a first step in the reduction to Cr(III) and subsequent removal of Cr from solution.

Safety and efficacy of a feed additive consisting of Lactococcus lactisDSM 34262 as a silage additive for all animal species (Lactosan GmbH & Co.KG).

Following a request from the European Commission, EFSA was asked to deliver a scientific opinion on Lactococcus lactis DSM 34262 when used as a technological additive to improve ensiling of fresh plant material. The additive is intended for use in easy and moderately difficult to ensile fresh plant material for all animal species at a proposed minimum concentration of 1 × 108 colony forming units (CFU)/kg fresh plant material. The bacterial species L. lactis is considered by EFSA to be suitable for the qualified presumption of safety approach to safety assessment. The identity of the strain was established and no acquired antimicrobial resistance genes of concern were detected. Therefore, the FEEDAP Panel concluded that the use of the strain as a silage additive is considered safe for all the animal species, for consumers of products from animals fed the treated silage and for the environment. Regarding user safety, the additive containing Lactococcus lactis DSM 34262 should be considered as a potential skin and respiratory sensitiser, and any exposure through skin and respiratory tract is considered a risk. One preparation was shown not to be irritant to skin or eyes. However, the Panel cannot assess the irritation potential of other possible preparations. The FEEDAP Panel concluded that Lactococcus lactis DSM 34262 has the potential to improve the fermentation of the silage prepared from fresh plant material with a DM range of 30-35% at a minimum concentration of 1 × 108 CFU/kg fresh material.

Phenotypic and genotypic characterization of extended-spectrum beta-lactamase-producing Enterobacteriaceae in a Moroccan hospital.

Extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-E) is a major public health problem in hospitals and in the community. The objective of this work was to describe the epidemiology of ESBL-E, to study their resistance profile and to determine the genes encoding the ESBL phenotype. This is a retrospective study conducted in the bacteriology laboratory of the Mohamed V Military Training Hospital in Rabat, and covering all isolates of Enterobacteriaceae from 1 January 2018 to 31 December 2020. The molecular study of ESBL genes involved a representative sample of all ESBL isolates. The overall prevalence of ESBLs in isolated Enterobacteriaceae (1402/10268) is 13.65 %. The urinary tract was the main site of isolation of ESBL (61 %). The bacterial species most concerned are Escherichia coli (41.9 %), Klebsiella pneumoniae (42.2 %) and Enterobacter cloacae (11.9 %). The study of antibiotic susceptibility showed a resistant profile marked mainly by 100 % resistance to first generation cephalosporins (1GC) and third generation cephalosporins (3GC), 55 % to piperacillin-tazobactam, 16 % to imipenem, and 87 % to fluoroquinolones. Molecular typing of ESBL strains showed a prevalence of CTX-M (95 %), SHV (50 %) and TEM (56 %). The CTX-M-1 and the CTX-M-9 groups were the most common (96.19 % and 7.62 % respectively), and CTX-M15 was found in 78.10 % of CTX-M-1 ESBL positive isolates. Most strains had more than two coexisting resistance genes. The prevalence rate of ESBL-E is critical, and preventive action at different levels (prescriber, biologist, hospital, patient, etc.) are necessary in order to limit their spread and to manage a better therapeutic strategy.

Mapping the Escherichia coli DnaA-binding landscape reveals a preference for binding pairs of closely spaced DNA sites.

DnaA is a widely conserved DNA-binding protein that is essential for the initiation of DNA replication in many bacterial species, including Escherichia coli. Cooperative binding of ATP-bound DnaA to multiple 9mer sites ('DnaA boxes') at the origin of replication results in local unwinding of the DNA and recruitment of the replication machinery. DnaA also functions as a transcription regulator by binding to DNA sites upstream of target genes. Previous studies have identified many sites of direct positive and negative regulation by E. coli DnaA. Here, we use a ChIP-seq to map the E. coli DnaA-binding landscape. Our data reveal a compact regulon for DnaA that coordinates the initiation of DNA replication with expression of genes associated with nucleotide synthesis, replication, DNA repair and RNA metabolism. We also show that DnaA binds preferentially to pairs of DnaA boxes spaced 2 or 3 bp apart. Mutation of either the upstream or downstream site in a pair disrupts DnaA binding, as does altering the spacing between sites. We conclude that binding of DnaA at almost all target sites requires a dimer of DnaA, with each subunit making critical contacts with a DnaA box.

The Effect of Mouthwash in Oral Microbiome: A Literature Review

The oral microbiome contains over seven hundred bacterial species as well as fungi, viruses, archaea, and protozoa. The complex equilibrium between resident species in the oral cavity is responsible for the maintenance of a healthy state or a state associated with disease. Mouthwash has also been shown to reduce plaque and gingivitis. The purpose of this article is to update our current knowledge of the effect of mouthwash in oral microbiome and to discuss the impact of mouthwash on changes in the oral microbiome. The article was conducted of two databases and were limited to period January 2019 to May 2024 with combination of the following keywords: “oral microbiome” associated by the Boolean operator AND. The results obtained were 11 articles found at the beginning of the search in both databases, and the 6 full text articles were selected for further review and discussion. Commensal, gingivitis and halitosis associated species were significantly reduced by twice daily use of LCM (Listerine Cool Mint) or ACPM (alcohol-containing prototype mouthrinse). The AFPM (alcohol-free prototype mouthrinse) group showed no statistically significant reductions. Its microbiological action is not due to selective killing of pathogenic bacteria but rather via a reset mechanism, in which the plaque microbiome composition is shifted to a healthier state after repeated use. CHX (Chlorhexidine) led to an increase in the abundance of some genera such as Neisseria, Streptococcus and Granulicatella, and lowered the abundance of Actinomyces, but did not affect the abundance of Veillonella. The effect of mouthwash in oral microbiome are short-term and long-term impacts on supragingival plaque microbiome, return from dysbiosis to healthier levels, increasing abundance of common oral opportunistic bacteria, reduce the oral pathogenic microbial load in healthy subjects.

Phylogenetically diverse bacterial species produce histamine

Histamine is an important biogenic amine known to impact a variety of patho-physiological processes ranging from allergic reactions, gut-mediated anti-inflammatory responses, and neurotransmitter activity. Histamine is found both endogenously within specialized host cells and exogenously in microbes. Exogenous histamine is produced through the decarboxylation of the amino acid L-histidine by bacterial-derived histidine decarboxylase enzymes. To investigate how widespread histamine production is across bacterial species, we examined 102,018 annotated genomes in the Integrated Microbial Genomes Database and identified 3,679 bacterial genomes (3.6 %) which possess the enzymatic machinery to generate histamine. These bacteria belonged to 10 phyla: Bacillota, Bacteroidota, Actinomycetota, Pseudomonadota, Lentisphaerota, Fusobacteriota, Armatimonadota, Cyanobacteriota, Thermodesulfobacteriota, and Verrucomicrobiota. The majority of the identified bacteria were terrestrial or aquatic in origin, although several bacteria originated in the human gut microbiota. We used liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based targeted metabolomics to confirm our genome discoveries correlated with L-histidine-to-histamine conversion in a chemically defined bacterial growth medium by a cohort of select environmental and human gut bacteria. We found that environmental microbes Vibrio harveyi, Pseudomonas fluorescens and Streptomyces griseus generated considerable levels of histamine (788 – 8,730 ng/mL). Interestingly, we found higher concentrations of histamine produced by gut-associated Fusobacterium varium, Clostridium perfringens, Limosilactobacillus reuteri and Morganella morganii (8,510––82,400 ng/mL). This work expands our knowledge of histamine production by diverse microbes.

Development of a multiplex PCR assay and quantification of microbial markers by ddPCR for identification of saliva and vaginal fluid

The identification of biological fluids at crime scenes contributes to crime scene reconstruction and provides investigative leads. Traditional methods for body fluid identification are limited in terms of sensitivity and are mostly presumptive. Emerging methods based on mRNA and DNA methylation require high quality template source. An exploitable characteristic of body fluids is their distinct microbial profiles allowing for the discrimination of body fluids based on microbiome content. Microbial DNA is highly abundant within the body, robust and stable and can persist in the environment long after human DNA has degraded. 16S rRNA sequencing is the gold standard for microbial analysis; however, NGS is costly, and requires intricate workflows and interpretation. Also, species level resolution is not always achievable. Based on the current challenges, the first objective of this study was to develop a multiplex conventional PCR assay to identify vaginal fluid and saliva by targeting species-specific 16S rRNA microbial markers. The second objective was to employ droplet digital PCR (ddPCR) as a novel approach to quantify bacterial species alone and in a mixture of body fluids. Lactobacillus crispatus and Streptococcus salivarius were selected because of high abundance within vaginal fluid and saliva respectively. While Fusobacterium nucleatum and Gardnerella vaginalis, though present in healthy humans, are also frequently found in oral and vaginal infections, respectively. The multiplex PCR assay detected L. crispatus and G. vaginalis in vaginal fluid while F. nucleatum and S. salivarius was detected in saliva. Multiplex PCR detected F. nucleatum, S. salivarius and L. crispatus in mixed body fluid samples while, G. vaginalis was undetected in mixtures containing vaginal fluid. For samples exposed at room temperature for 65 days, L. crispatus and G. vaginalis were detected in vaginal swabs while only S. salivarius was detected in saliva swabs. The limit of detection was 0.06 copies/µl for F. nucleatum (2.5 ×10-9ng/µl) and S. salivarius (2.5 ×10-6ng/µl). L. crispatus and G. vaginalis had detection limits of 0.16 copies/µl (2.5 ×10-4ng/µl) and 0.48 copies/µl (2.5 ×10-7ng/µl). All 4 bacterial species were detected in mixtures and aged samples by ddPCR.No significant differences were observed in quantity of bacterial markers in saliva and vaginal fluid. The present research reports for the first time the combination of the above four bacterial markers for the detection of saliva and vaginal fluid and highlights the sensitivity of ddPCR for bacterial quantification in pure and mixed body fluids.

Advancements in inhibitors of crucial enzymes in the cysteine biosynthetic pathway: Serine acetyltransferase and O-acetylserine sulfhydrylase.

Infectious diseases have been jeopardized problem that threaten public health over a long period of time. The growing prevalence of drug-resistant pathogens and infectious cases have led to a decrease in the number of effective antibiotics, which highlights the urgent need for the development of new antibacterial agents. Serine acetyltransferase (SAT), also known as CysE in certain bacterial species, and O-acetylserine sulfhydrylase (OASS), also known as CysK in select bacteria, are indispensable enzymes within the cysteine biosynthesis pathway of various pathogenic microorganisms. These enzymes play a crucial role in the survival of these pathogens, making SAT and OASS promising targets for the development of novel anti-infective agents. In this comprehensive review, we present an introduction to the structure and function of SAT and OASS, along with an overview of existing inhibitors for SAT and OASS as potential antibacterial agents. Our primary focus is on elucidating the inhibitory activities, structure-activity relationships, and mechanisms of action of these inhibitors. Through this exploration, we aim to provide insights into promising strategies and prospects in the development of antibacterial agents that target these essential enzymes.

Safety and efficacy of a feed additive consisting of Lactiplantibacillus plantarumDSM 34271 as a silage additive for all animal species (Lactosan GmbH & Co.KG).

Following a request from the European Commission, EFSA was asked to deliver a scientific opinion on Lactiplantibacillus plantarum DSM 34271 when used as a technological additive to improve ensiling of fresh plant material. The additive is intended for use in easy and moderately difficult to ensile fresh plant material for all animal species at a proposed minimum concentration of 1 × 108 colony forming units (CFU)/kg fresh plant material. The bacterial species L. plantarum is considered by EFSA to be suitable for the qualified presumption of safety approach to safety assessment. The identity of the strain was established and no acquired antimicrobial resistance genes of concern were detected. Therefore, the FEEDAP Panel concluded that the use of the strain as a silage additive is considered safe for all the animal species, for consumers of products from animals fed the treated silage and for the environment. Regarding user safety, the additive containing Lactiplantibacillus plantarum DSM 34271 should be considered as a potential skin and respiratory sensitiser, and any exposure through skin and respiratory tract is considered a risk. One preparation was shown not to be irritant to skin or eyes. However, the Panel cannot assess the irritation potential of other possible preparations. The FEEDAP Panel concluded that Lactiplantibacillus plantarum DSM 34271 has the potential to improve the fermentation of the silage prepared from fresh plant material with a DM range of 30%-35% at a minimum concentration of 1 × 108 CFU/kg fresh material.

GWarrange: a pre- and post- genome-wide association studies pipeline for detecting phenotype-associated genome rearrangement events.

The use of k-mers to capture genetic variation in bacterial genome-wide association studies (bGWAS) has demonstrated its effectiveness in overcoming the plasticity of bacterial genomes by providing a comprehensive array of genetic variants in a genome set that is not confined to a single reference genome. However, little attempt has been made to interpret k-mers in the context of genome rearrangements, partly due to challenges in the exhaustive and high-throughput identification of genome structure and individual rearrangement events. Here, we present GWarrange, a pre- and post-bGWAS processing methodology that leverages the unique properties of k-mers to facilitate bGWAS for genome rearrangements. Repeat sequences are common instigators of genome rearrangements through intragenomic homologous recombination, and they are commonly found at rearrangement boundaries. Using whole-genome sequences, repeat sequences are replaced by short placeholder sequences, allowing the regions flanking repeats to be incorporated into relatively short k-mers. Then, locations of flanking regions in significant k-mers are mapped back to complete genome sequences to visualise genome rearrangements. Four case studies based on two bacterial species (Bordetella pertussis and Enterococcus faecium) and a simulated genome set are presented to demonstrate the ability to identify phenotype-associated rearrangements. GWarrange is available at https://github.com/DorothyTamYiLing/GWarrange.

Granular sludge characterization and microbial response in a hydroxyapatite (HAP)- anammox coupled process at different nitrogen loading rates

To enhance the treatment capacity and operational stability of the anammox process for nutrient-rich wastewater disposal, a hydroxyapatite (HAP)-anammox coupled process was developed in a granular sludge-based upflow bioreactor. The impact of nitrogen loading rate (NLR) on process performance was investigated by gradually increasing the NLR from 1 to 1.5, 3, and 5 kgN/m3/d for 264 days continuous operation. TN and TP removal rates of 82.51 ± 3.58 % and 60.49 ± 2.82 % were achieved at the NLR of 5 kgN/m3/d. The precipitation of Ca and phosphorus resulted in HAP crystals formation evidenced by sludge morphology and component analysis, which enhanced sludge settling properties and facilitated biomass enrichment. The HAP-anammox granular sludge was characterized by the outer layer HAP crystals formed on inner anammox granules, while highly mineralized granular sludge with higher density distributed at the bottom of the reactor is conducive to HAP-based phosphorus recovery. After a long-term accumulation, the abundance of Planctomycetota phylum gradually increased (from 7.7 % to 14.1 %), consisting of three species of anammox bacteria, namely Candidatus_Brocadia_sapporoensis, Candidatus_Brocadia_sinica and Candidatus_Kuenenia_stuttgartiensis. Nitrogen metabolic pathway analysis illustrated that denitrification was also present except the anammox reaction, synergistically contributing to superior nitrogen removal in the HAP-anammox process.

Comparative genomics of IncQ1 plasmids carrying blaGES variants from clinical and environmental sources in Brazil

IncQ-type plasmids have become important vectors in the dissemination of blaGES among different bacterial genera and species from different environments around the world, and studies estimating the occurrence of Guiana extended-spectrum (GES)-type β-lactamases are gaining prominence. We analyzed the genetic aspects of two IncQ1 plasmids harboring different blaGES variants from human and environmental sources. The blaGES variants were identified using polymerase chain reaction (PCR) in Aeromonas veronii isolated from hospital effluent and Klebsiella variicola isolated from a rectal swab of a patient admitted to the cardiovascular intensive care unit in a different hospital. Antimicrobial-susceptibility testing and transformation experiments were performed for phenotypic analysis. Whole-genome sequencing was performed using Illumina and Oxford Nanopore platforms. The comparative analysis of plasmids was performed using BLASTn, and the IncQ1 plasmids showed a high identity and similar size. A. veronii harbored blaGES-7 in a class 1 integron (In2061), recently described by our group, and K. variicola carried blaGES-5 in the known class 1 integron. Both integrons showed a fused gene cassette that encodes resistance to aminoglycosides and fluoroquinolones, with an IS6100 truncating the 3′-conserved segment. The fused genes are transcribed together, although the attC site is disrupted. These gene cassettes can no longer be mobilized. This study revealed a mobilome that may contribute to the dissemination of GES-type β-lactamases in Brazil. Class 1 integrons are hot spots for bacterial evolution, and their insertion into small IncQ-like plasmids displayed successful recombination, allowing the spread of blaGES variants in various environments. Therefore, they can become prevalent across clinically relevant pathogens.

Optimization and application of bacterial environmental DNA and RNA isolation for qualitative and quantitative studies

AbstractMolecular detection of environmental DNA (eDNA) and RNA (eRNA) allows highly sensitive qualitative (i.e., presence or absence) and quantitative (i.e., abundance) monitoring of aquatic bacteria. However, bacterial molecular diagnostics are limited by low positive predictive values. Protocols for bacterial eDNA and eRNA molecular monitoring have primarily focused on optimizing specimen collection, and the optimal method to purify bacterial nucleic material from postcollection aquatic specimens to maximize the analytical sensitivity of molecular diagnostics remains poorly defined. Accordingly, strategies to isolate bacterial eDNA and eRNA from fresh and saltwater were investigated. We evaluated two filtration and four nucleic acid purification systems as representative of current generation bacterial eDNA and eRNA isolation strategies for capacity to isolate bacterial eDNA and eRNA from prelysed (i.e., free‐nucleic acids) and viable (i.e., colony forming units, CFU) bacterial cells. We also compared the sensitivities of reverse transcription quantitative PCR (RT‐qPCR) and metagenomic shotgun microbiome sequencing. The optimal protocol used 0.7 μm borosilicate glass filters (Whatman plc) followed by extraction with the RNeasy PowerWater kit (Qiagen). The protocol had a very high analytical sensitivity (10−3–100 ng and 102–101 CFU detected in 500 mL) across multiple species of bacteria, when tested with either RTqPCR or metagenomic sequencing. Importantly, this study highlighted several limitations which are restrictive to both qualitative and quantitative bacterial eDNA and eRNA studies. First, a 12‐h time course between sampling and extraction revealed significant species‐specific changes in cell number and free‐nucleic acid concentrations can occur postspecimen collection. Second, we found Gram‐positive bacteria yielded less nucleic material compared to Gram‐negative bacteria suggesting bacterial eDNA and eRNA studies could be biased by microorganism genome stability and extraction efficiency. This study highlights the need to define the species‐specific diagnostic sensitivity of a protocol when monitoring aquatic bacterial eDNA and eRNA with molecular diagnostics.

Contribution of Streptococcus pseudopneumoniae and Streptococcus salivarius to vocal fold mucosal integrity and function.

Structural changes to the vocal fold (VF) epithelium, namely, loosened intercellular junctions, have been reported in VF benign lesions. The potential mechanisms responsible for the disruption of cell junctions do not address the contribution of resident microbial communities to this pathological phenomenon. In this study, we focused on determining the relationship between Streptococcus pseudopneumoniae (SP), a dominant bacterial species associated with benign lesions, and Streptococcus salivarius (SS), a commensal bacterium, with human VF epithelial cells in our three-dimensional model of the human VF mucosa. This experimental system enabled direct deposition of bacteria onto constructs at the air/liquid interface, allowing for the assessment of bacterium-host interactions at the cellular, molecular and ultrastructural levels. Our findings demonstrate that SP disrupts VF epithelial integrity and initiates inflammation via the exported products HtrA1 and pneumolysin. In contrast, SS attaches to the VF epithelium, reduces inflammation and induces Mmp2-mediated apical desquamation of infected cells to mitigate the impact of pathogens. In conclusion, this study highlights the complexity of microbial involvement in VF pathology and potential VF mucosal restoration in the presence of laryngeal commensals.