Microbiology spectrum最新文献

{"title":"Evaluating methods for identifying and quantifying <i>Streptococcus pneumoniae</i> co-colonization using next-generation sequencing data.","authors":"Jada Hackman, Martin L Hibberd, Todd D Swarthout, Jason Hinds, James Ashall, Carmen Sheppard, Gerry Tonkin-Hill, Kate Gould, Comfort Brown, Jacquline Msefula, Andrew A Mataya, Michiko Toizumi, Lay-Myint Yoshida, Neil French, Robert S Heyderman, Stefan Flasche, Brenda Kwambana, Stéphane Hué","doi":"10.1128/spectrum.03643-23","DOIUrl":"https://doi.org/10.1128/spectrum.03643-23","url":null,"abstract":"<p><p>Detection of multiple pneumococcal serotype carriage can enhance monitoring of pneumococcal vaccine impact, particularly among high-burden childhood populations. We assessed methods for identifying co-carriage of pneumococcal serotypes from whole-genome sequences. Twenty-four nasopharyngeal samples were collected during community carriage surveillance from healthy children in Blantyre, Malawi, which were then serotyped by microarray. Pneumococcal DNA from culture plate sweeps were sequenced using Illumina MiSeq, and genomic serotyping was carried out using SeroCall and PneumoKITy. Their sensitivity was calculated in reference to the microarray data. Local maxima in the single-nucleotide polymorphism (SNP) density distributions were assessed for their correspondence to the relative abundance of serotypes. Across the 24 individuals, the microarray detected 77 non-unique serotypes, of which 42 occurred at high relative abundance (>10%) (per individual, median, 3; range, 1-6 serotypes). The average sequencing depth was 57X (range: 21X-88X). The sensitivity of SeroCall for identifying high-abundance serotypes was 98% (95% CI, 0.87-1.00), 20% (0.08-0.36) for low abundance (<10%), and 62% (0.50-0.72) overall. PneumoKITy's sensitivity was 86% (0.72-0.95), 20% (0.06-0.32), and 56% (0.42-0.65), respectively. Local maxima in the SNP frequency distribution were highly correlated with the relative abundance of high-abundance serotypes. Six samples were resequenced, and the pooled runs had an average fourfold increase in sequencing depth. This allowed genomic serotyping of two of the previously undetectable seven low-abundance serotypes. Genomic serotyping is highly sensitive for the detection of high-abundance serotypes in samples with co-carriage. Serotype-associated reads may be identified through SNP frequency, and increased read depth can increase sensitivity for low-abundance serotype detection.IMPORTANCEPneumococcal carriage is a prerequisite for invasive pneumococcal disease, which is a leading cause of childhood pneumonia. Multiple carriage of unique pneumococcal serotypes at a single time point is prevalent among high-burden childhood populations. This study assessed the sensitivity of different genomic serotyping methods for identifying pneumococcal serotypes during co-carriage. These methods were evaluated against the current gold standard for co-carriage detection. The results showed that genomic serotyping methods have high sensitivity for detecting high-abundance serotypes in samples with co-carriage, and increasing sequencing depth can increase sensitivity for low-abundance serotypes. These results are important for monitoring vaccine impact, which aims to reduce the prevalence of specific pneumococcal serotypes. By accurately detecting and identifying multiple pneumococcal serotypes in carrier populations, we can better evaluate the effectiveness of vaccination programs.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0364323"},"PeriodicalIF":3.7,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142583160","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"ITSxpress version 2: software to rapidly trim internal transcribed spacer sequences with quality scores for amplicon sequencing.","authors":"Sveinn V Einarsson, Adam R Rivers","doi":"10.1128/spectrum.00601-24","DOIUrl":"https://doi.org/10.1128/spectrum.00601-24","url":null,"abstract":"<p><p>The nuclear ribosomal RNA (rRNA) internal transcribed spacer (ITS) regions are commonly used to identify fungi and other eukaryotic taxa in amplicon sequencing. The highly conserved rRNA regions flanking the ITS are often trimmed before being used for taxonomic assignment. The Python software package ITSxpress rapidly trims single-end or paired-end sequences in FASTQ format for use in amplicon sequence variant clustering methods like DADA2. This new major release of ITSxpress improves the paired-end merging method, simplifies installation of the QIIME 2 ITSxpress plugin, removes major dependencies, adds use cases, and is compatible with newer compression formats. This article discusses the modifications to ITSxpress that improve the output and user experience, leading to a major version increase.IMPORTANCEITSxpress is a sequence trimming method applied to internal transcribed spacer (ITS) amplicon sequences before calling amplicon sequence variants (ASVs). The ITS region is used to understand the composition of eukaryotic microbial communities. ITS sequences provide good taxonomic resolution due to their hypervariability, but are flanked by conserved regions that allow their primers to be more universal. Amplicons generated with such primers contain regions with different evolutionary rates, and trimming these conserved regions results in better taxonomic classification and a more valid set of ASVs. This package can be used for most amplicon sequencing methods including for newer long-read sequencing formats, such as PacBio. ITSxpress can be installed from Bioconda, used as a Docker image, or installed from source code. The package works well with high-performance computing clusters or laptops due to its low-resource requirements.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0060124"},"PeriodicalIF":3.7,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142583254","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Assessment of resistance to colicinogenic synthetic phage antimicrobial system.","authors":"Meghan McGillin, Jeffrey I Tokman, Ella Hsu, Samuel D Alcaine","doi":"10.1128/spectrum.00793-24","DOIUrl":"10.1128/spectrum.00793-24","url":null,"abstract":"&lt;p&gt;&lt;p&gt;This work presents a multi-hurdle approach that addresses antimicrobial resistance by minimizing the selective pressure of antimicrobials using a novel colicinogenic-phage system. We have created two synthetic T7 phages (T7-E1 and T7-M) by inserting the gene of colicin E1 (Cea) or colicin M (Cma) into the genome of the T7 phage, thereby adding an additional colicin-based hurdle to the T7 lytic cycle. The colicin-phages' efficacy in suppressing the outgrowth of a T7-resistant sub-population within a mixed culture of &lt;i&gt;Escherichia coli&lt;/i&gt; was demonstrated using a challenge matrix design under planktonic and structured conditions. When T7-resistant cells were present at 1% of the total planktonic population, T7-E1 delayed the outgrowth. At 0.1% resistance, T7-M delayed resistant outgrowth, whereas T7-E1 suppressed the resistant sub-population. When T7-E1 and T7-M were combined into a triple-hurdle treatment, the T7-E1/T7-M cocktail completely suppressed a mixed planktonic population of 50% resistance cell concentrations. In structured environments, the colicin-phage treatments formed clear and confluent plaque-like zones of clearing in the mixed populations of 50% resistant cells with a lawn density of 1 × 10&lt;sup&gt;6&lt;/sup&gt; CFU/mL. Reducing the lawn density to 1 × 10&lt;sup&gt;5&lt;/sup&gt; CFU/mL diminished the multi-hurdle treatments' effectiveness, as demonstrated by localized zones of clearing within turbid bacterial lawns, highlighting the relationship between bacterial lawn density and phage effectiveness in structured environments. Fluctuation assays revealed persistence as the predominant mechanism for overcoming the treatments by T7-sensitive &lt;i&gt;E. coli&lt;/i&gt;. Results indicate that T7-M treatment significantly reduces persister formation compared to WT-T7, while T7-E1 unexpectedly increases persister formation significantly. This suggests a complex relationship between antimicrobial stress and persister formation.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Importance: &lt;/strong&gt;Antimicrobial resistance (AMR) poses a significant challenge in treating bacterial infections. To address this, we present a multi-hurdle approach that combines the power of different antimicrobials to target resistance. We have weaponized the natural predator of &lt;i&gt;Escherichia coli&lt;/i&gt;, the T7-phage, by engineering it to produce toxins called colicins, resulting in a colicin-phage antimicrobial. This multi-hurdled approach aims to decrease resistance risk because survival requires different tactics to overcome the phage and colicin activity, thus adding a hurdle in a bacterium's pathway to resistance. In cases of pre-existing resistance, the colicin effectively controlled the sub-population resistant to the phage. When investigating the emergence of resistance, we discovered that antimicrobial persistence was the predominant survival strategy. These findings reveal an essential slice of the AMR pie by emphasizing bacterial survival tactics that are not based on resistance genes. By expanding our AMR lens","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0079324"},"PeriodicalIF":3.7,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11537092/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142470025","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Continental-scale insights into the sugarbeet diffusion juice microbiomes.","authors":"Malick Bill, John D Eide, Karen K Fugate, Melvin D Bolton, Hari P Kandel, Shyam L Kandel","doi":"10.1128/spectrum.01093-24","DOIUrl":"10.1128/spectrum.01093-24","url":null,"abstract":"<p><p>Bacterial contamination of raw diffusion juice poses unique challenges during the sugar extraction process. This study profiled bacterial communities by using full-length 16S rRNA amplicon sequencing and quantified the carbohydrate concentrations in raw diffusion juice samples received from sugar factory regions across the USA and Canada. Juice samples were collected at four time points during the 2021 and 2022 processing campaigns. <i>Firmicutes</i> was the dominant phylum from the raw diffusion juice samples collected during both campaigns and comprised 85.5% of total bacterial abundance. Lactic acid bacteria such as <i>Leuconostoc</i> and <i>Lactobacillus</i> were among the core genera which also dominated the bacterial community in raw diffusion juice. Positive correlations in the abundance of functionally and taxonomically related bacterial communities were identified. During the 2021 campaign, 44 bacterial genera were differentially abundant in raw diffusion juice extracted from sugarbeet roots in Periods 1 to 4. This number declined sixfold during the 2022 campaign to three genera. The concentration of raffinose in raw diffusion juice positively correlated to the relative abundance of <i>Leuconostoc</i>. Furthermore, an <i>in vitro</i> assay was performed to assess the growth dynamics of <i>Leuconostoc mesenteroides</i> in sucrose or raffinose-rich medium and observed the rapid consumption of both carbohydrates by this bacterium. This finding is important for deciphering microbial growth dynamics in raw diffusion juice that can be useful in minimizing sugar loss during the factory processing.IMPORTANCEFindings additionally provide baseline information that can be used to develop mitigation strategies that reduce losses due to microbial contamination of sucrose processing streams.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0109324"},"PeriodicalIF":3.7,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11537105/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142291335","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Guanabenz acetate, an antihypertensive drug repurposed as an inhibitor of <i>Escherichia coli</i> biofilm.","authors":"Arakkaveettil Kabeer Farha, Olivier Habimana, Harold Corke","doi":"10.1128/spectrum.00738-24","DOIUrl":"10.1128/spectrum.00738-24","url":null,"abstract":"<p><p>Biofilms formed by <i>Escherichia coli</i> are composed of amyloid curli and cellulose and have been shown to be linked to pathogenicity, antibiotic resistance, and chronic infections. Guanabenz acetate (GABE), an antihypertensive drug, was identified as a potential strategic repurposing drug due to its biofilm inhibitory properties following an extensive antimicrobial screening assay of 2,202 Food and Drug Administration-approved non-antibiotic agents. The results of this study provide insights into the effectiveness of GABE as a therapeutic alternative against <i>E. coli</i> biofilm-associated infectious diseases.</p><p><strong>Importance: </strong>Biofilm-associated bacterial infections are one of the major problems in medical settings. There are currently limited biofilm inhibitors available for clinical use. Guanabenz acetate, a drug used to treat high blood pressure, was found to be an effective anti-biofilm agent against <i>Escherichia coli</i>. Our results show that this drug can inhibit the production of cellulose and curli amyloid protein, which are the two main components of <i>E. coli</i> biofilms. Our findings highlight the possibility of repurposing a drug to prevent <i>E. coli</i> biofilm formation.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0073824"},"PeriodicalIF":3.7,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11537090/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142291377","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cefepime-taniborbactam demonstrates potent <i>in vitro</i> activity vs <i>Enterobacterales</i> with <i>bla</i>_OXA-48.","authors":"Maria F Mojica, Elise T Zeiser, Scott A Becka, David A Six, Greg Moeck, Krisztina M Papp-Wallace","doi":"10.1128/spectrum.01144-24","DOIUrl":"10.1128/spectrum.01144-24","url":null,"abstract":"<p><p>Taniborbactam (formerly VNRX-5133) is a novel, investigational boronic acid β-lactamase inhibitor. The combination of cefepime (FEP) with taniborbactam is active against <i>Enterobacterales</i> carrying class A, B, C, and/or D enzymes. We assessed the activity of FEP-taniborbactam against <i>Enterobacterales</i> clinical strains carrying <i>bla</i>_OXA-48 (<i>N</i> = 50, 100%), of which 78% harbored at least one extended-spectrum β-lactamase (ESBL). CLSI-based agar dilution susceptibility testing was conducted using FEP-taniborbactam and comparators FEP, meropenem-vaborbactam (MVB), and ceftazidime-avibactam (CZA). The addition of taniborbactam lowered FEP MICs to the provisionally susceptible range of ≤16 µg/mL; the MIC₉₀ value decreased from ≥64 µg/mL for FEP to 4 µg/mL for FEP-taniborbactam. Notably, FEP-taniborbactam MIC₅₀/MIC₉₀ values (0.5/4 µg/mL) were lower than those for MVB (1/16 µg/mL) and comparable to those for CZA (0.5/1 µg/mL). Time-kill assays with <i>E. coli</i> clinical strains DOV (<i>bla</i>_OXA-48, <i>bla</i>_CTX-M-15, <i>bla</i>_TEM-1, and <i>bla</i>_OXA-1) and MLI (<i>bla</i>_OXA-48, <i>bla</i>_VEB, <i>bla</i>_TEM-1, and <i>bla</i>_CMY-2) revealed that FEP-taniborbactam at concentrations 1×, 2×, and 4× MIC displayed time-dependent reductions in the number of CFU/mL from 0 to 6 h, and at 4× MIC demonstrated bactericidal activity (3 log₁₀ reduction in CFU/mL at 24 h). Therefore, taniborbactam in combination with FEP was highly active against this diverse panel of <i>Enterobacterales</i> with <i>bla</i>_OXA-48 and represents a potential addition to our antibiotic arsenal.IMPORTANCEOXA-48-like β-lactamases are class D carbapenemases widespread in <i>Klebsiella pneumoniae</i> and other <i>Enterobacterales</i> and are associated with carbapenem treatment failures. As up to 80% of OXA-48-like positive isolates coproduce extended-spectrum β-lactamases, a combination of β-lactams with broad-spectrum β-lactamase inhibitors is required to counteract all OXA-48-producing strains effectively. Herein, we evaluated the activity of cefepime-taniborbactam against 50 clinical strains producing OXA-48. We report that adding taniborbactam shifted the minimum inhibitory concentration (MIC) toward cefepime's susceptible range, restoring its antimicrobial activity. Notably, cefepime-taniborbactam MIC₅₀/MIC₉₀ values (0.5/4 µg/mL) were comparable to ceftazidime-avibactam (0.5/1 µg/mL). Finally, time-kill assays revealed sustained bactericidal activity of cefepime-taniborbactam for up to 24 h. In conclusion, cefepime-taniborbactam will be a welcome addition to the antibiotic arsenal to combat <i>Enterobacterales</i> producing OXA-48.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0114424"},"PeriodicalIF":3.7,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11537129/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142308141","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transmission of multidrug-resistant tuberculosis in Jiangxi, China, and associated risk factors.","authors":"Jiahuan Zhan, Wei Wang, Dong Luo, Qiang Chen, Shengming Yu, Liang Yan, Kaisen Chen","doi":"10.1128/spectrum.03555-23","DOIUrl":"10.1128/spectrum.03555-23","url":null,"abstract":"<p><p>In order to effectively combat the urgent threat of multidrug-resistant tuberculosis (MDR-TB), it is imperative to gain a comprehensive understanding of the drug-resistant profiles, transmission dynamics, and associated risk factors. Our study encompassed a population-based retrospective analysis with 130 MDR-TB patients from 2018 to 2021. The research methodology incorporated whole-genome sequencing, drug susceptibility testing , and logistic regression analysis to discern the risk factors of genomic clustering linked to recent transmission. The findings from phenotypic drug resistance assessments revealed notable resistance rates: ethambutol at 62.3% (81/130), streptomycin at 72.3% (94/130), levofloxacin at 51.5% (67/130), and moxifloxacin at 50.0% (65/130). Furthermore, among all patients, 38 individuals (29.23%, 38/130) were found to be part of 17 clusters, indicating instances of recent MDR-TB transmission. The genomic clustering patients were deeply investigated. Lineage 2.2.1 was established as the primary sub-lineage (86.15%, 112/130), followed by lineage 4 (9.23%, 12/130). Moreover, the logistic regression analysis underscored that unemployment, farming occupations, and prior TB treatment were identified as significant risk factors for recent transmission.</p><p><strong>Importance: </strong>The high prevalence of multidrug-resistant tuberculosis (MDR-TB) in Jiangxi Province highlights the importance of understanding the genetic background and drug resistance patterns of these strains. This knowledge is crucial for developing effective control methods. Furthermore, in light of the significance of preventing transmission among tuberculosis patients, whole-genome sequencing was utilized to investigate the recent transmission of MDR-TB and identify associated risk factors. The findings revealed that individuals in the farming sector, those who are unemployed, and patients with a history of tuberculosis treatment are at elevated risk. Consequently, targeted public interventions for these at-risk groups are imperative.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0355523"},"PeriodicalIF":3.7,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11537056/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142361780","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unraveling the benefits of <i>Bacillus subtilis</i> DSM 29784 poultry probiotic through its secreted metabolites: an <i>in vitro</i> approach.","authors":"Nuria Vieco-Saiz, Damien P Prévéraud, Eric Pinloche, Aurélien Morat, Pauline Govindin, Hervé M Blottière, Elliot Matthieu, Estelle Devillard, Jessika Consuegra","doi":"10.1128/spectrum.00177-24","DOIUrl":"10.1128/spectrum.00177-24","url":null,"abstract":"<p><p>The probiotic <i>Bacillus subtilis</i> 29784 (Bs29784) sustains chicken's intestinal health, enhancing animal resilience and performance through the production of the bioactive metabolites hypoxanthine (HPX), niacin (NIA), and pantothenate (PTH). Here, using enterocyte <i>in vitro</i> models, we determine the functional link between these metabolites and the three pillars of intestinal resilience: immune response, intestinal barrier, and microbiota. We evaluated <i>in vitro</i> the capacity of Bs29784 vegetative cells, spores, and metabolites to modulate global immune regulators (using HT-29-NF-κB and HT-29-AP-1 reporter cells), intestinal integrity (HT-29-MUC2 reporter cells and Caco-2 cells), and cytokine production (Caco-2 cells). Finally, we simulated intestinal fermentations using chicken's intestinal contents as inocula to determine the effect of Bs29784 metabolites on the microbiota and their fermentation profile. Bs29784 vegetative cells reduced the inflammatory response more effectively than spores, indicating that their benefit is linked to metabolic activity. To assess this hypothesis, we studied Bs29784 metabolites individually. The results showed that each metabolite had different beneficial effects. PTH and NIA reduced the activation of the pro-inflammatory pathways AP-1 and NF-κB. HPX upregulated mucin production by enhancing MUC2 expression. HPX, NIA, and PTH increased cell proliferation. PTH and HPX increased epithelial resilience to an inflammatory challenge by limiting permeability increase. In cecal fermentations, NIA increased acetate, HPX increased butyrate, whereas PTH increased acetate, butyrate, and propionate. In ileal fermentations, PTH increased butyrate. All molecules modulated microbiota, explaining the different fermentation patterns. Altogether, we show that Bs29784 influences intestinal health by acting on the three lines of resilience via its secreted metabolites.</p><p><strong>Importance: </strong>Probiotics provide beneficial metabolites to its host. Here, we describe the mode of action of a commonly used probiotic in poultry, Bs29784. By using <i>in vitro</i> cellular techniques and simulated chickens' intestinal model, we show the functional link between Bs29784 metabolites and the three lines of animal resilience. Indeed, both Bs29784 vegetative cells and its metabolites stimulate cellular anti-inflammatory responses, strengthen intestinal barrier, and positively modulate microbiota composition and fermentative profile. Taken together, these results strengthen our understanding of the effect of Bs29784 on its host and explain, at least partly, its positive effects on animal health, resilience, and performance.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0017724"},"PeriodicalIF":3.7,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11537077/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142291322","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Patterns of microbiome composition in tsetse fly <i>Glossina palpalis palpalis</i> during vector control using Tiny Targets in Campo, South Cameroon.","authors":"Calmes Ursain Bouaka Tsakeng, Tito Tresor Melachio Tanekou, François Sougal Ngambia Freitas, Inaki Tirados, Jean Marc Tsagmo Ngoune, Jude Daiga Bigoga, Flobert Njiokou, Charles Sinclair Wondji","doi":"10.1128/spectrum.00935-24","DOIUrl":"10.1128/spectrum.00935-24","url":null,"abstract":"<p><p>Novel vector control tools against African trypanosomiases require a deep understanding of the factors driving tsetse vector fitness or population resilience in their ecosystems. Following evidence of microbiota-mediated host fitness or traits shaping, including insecticide resistance in arthropod populations, we undertook a comparative study of the microbiota in wild-caught tsetse flies during vector control with deltamethrin-impregnated traps called Tiny Targets. The bacterial microbiome composition of tsetse flies collected before and after 6, 12, and 18 months of vector control were characterized using high-throughput sequencing of the V3-V4 hypervariable region of the bacterial 16S rRNA gene and compared. Overall, 48 bacterial genera and five phyla were identified. The primary symbiont <i>Wigglesworthia</i> dominated almost all the samples with an overall relative abundance of 71.76%. A significant increase was observed in microbiome diversities over the vector control with new taxa identified. Interestingly, few genera, like <i>Curvibacter</i> for instance, displayed a regularly increasing abundance, from 0.57% to 0.65%, 4.73%, and 8.57% after 6, 12, and 18 months of tsetse control, respectively. This study provided preliminary for further investigation into the role and mechanism of action of microbiota in tsetse fly fitness under selective pressure like insecticides.IMPORTANCEThe interest in vector control in the fight against African trypanosomiases has been reinforced in recent years, with the development of small insecticide-impregnated screens, known as \"Tiny Targets\". As some tsetse biotopes are difficult to access for their installation, other tools are under consideration that involve using bacteria harbored by the tsetse vector to block the development of trypanosomes or impair the tsetse's fitness in its natural environment. Several bacterial symbionts were previously described as important for tsetse fly development, and some like <i>Burkholderia</i> and <i>Citrobacter</i> also found in tsetse flies were found associated with insecticide tolerance in other arthropods. In this research, we found the bacterial genera, <i>Curvibacter</i> and <i>Acinetobacter,</i> increased in abundance in tsetse flies during vector control. These bacteria deserve further attention to determine if they can interfere with insecticides used to control tsetse fly populations.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0093524"},"PeriodicalIF":3.7,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11540164/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142291387","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A novel method for the preparation of reproducible, stable, and non-infectious quality control materials for <i>Chlamydia trachomatis</i> nucleic acid detection.","authors":"Jing Li, Kuo Zhang, Yanxi Han, Rongxue Peng, Lin Li, Jinming Li, Guigao Lin","doi":"10.1128/spectrum.00837-24","DOIUrl":"10.1128/spectrum.00837-24","url":null,"abstract":"<p><p><i>Chlamydia trachomatis</i> (CT) is a significant sexually transmitted pathogen known to evoke severe complications, including infertility. Nucleic acid amplification tests (NAATs) are recommended by the World Health Organization to detect CT infection. Furthermore, the establishment of methods, performance validation, internal quality control, and external quality assessment for CT NAATs necessitate the utilization of quality control materials (QCs). QCs are specimens or solutions that are analyzed for quality control purposes in a test system. In this study, we established a novel cell line that stably integrates CT amplification target sequences for producing QCs for CT NAATs. Utilizing clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 technology, we integrated the CT plasmid-mediated sequence (comprising the full length of the cryptic plasmid and the major outer membrane protein gene, 9,136 bp) into the <i>MUC4</i> gene of HEK293T cells. Positive clones were screened through flow cytometric sorting, single-cell culture, and PCR-based identification, followed by the establishment of stable cell lines. These cells were then processed using optimized cell preservation procedures to prepare QCs. The sequence insertion copy number was confirmed by real-time quantitative PCR. This novel CT QCs demonstrate excellent clinical applicability, non-infectiousness, quantifiability, and stability. With an integrated sequence exceeding 9 kb in length, it offers exceptional flexibility for adapting to new kit developments. Furthermore, maintaining a well-defined copy number and stable shelf life, the QCs closely aligns with the quality control requirements of CT NAATs. This study presents an innovative method for preparing QCs for CT nucleic acid detection, making a valuable contribution to improving the performance of CT NAATs.IMPORTANCEUntreated CT infections impose significant burdens on individuals and communities, underscoring the importance of early and accurate testing via CT NAATs for disease control. QCs are instrumental in identifying testing process issues. Hence, we developed a cell line integrating CT-amplified target sequences as readily accessible non-infectious QCs. These QCs boast several advantages: the integration of over 9 kb of CT sequence allows for broad applicability, allowing flexible adaptation to the development of new kits. Confirming the CT sequence copy number provides a reliable basis for QC concentration preparation and kit detection limit evaluation. Optimized preservation protocol enhances QC stability during storage, facilitating convenient shipment to clinical laboratories at ambient temperatures. In summary, our novel CT QCs offer a powerful tool for improving CT NAAT performance and present a fresh perspective on QC preparation for detecting nucleic acids from intracellular parasitic pathogens.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0083724"},"PeriodicalIF":3.7,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11536990/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142381169","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}