mSphere最新文献

{"title":"Genomic and transcriptomic insights into vertebrate host-specific <i>Lactobacillus johnsonii</i> adaptation in the gastrointestinal tract.","authors":"Keerthikka Ravi, Nicole R Falkowski, Gary B Huffnagle","doi":"10.1128/msphere.00052-25","DOIUrl":"10.1128/msphere.00052-25","url":null,"abstract":"<p><p>We conducted a comparative genomic analysis of <i>Lactobacillus johnsonii</i> strains isolated from the gastrointestinal tract of diverse vertebrate hosts to explore the genetic basis of host specificity. We then utilized transcriptomics analysis to investigate the expression profile of identified rodent-specific genes in mouse isolate MR1 during <i>in vitro</i> and <i>in vivo</i> growth conditions. There was significant heterogeneity among strains, in both genome sequence and content, with phylogenetic clustering of strains into distinct clades associated with rodent or avian sources. There were not sufficient genomes to identify whether porcine isolates formed their own genetic clade. However, human isolates did not form a distinct clade. Functional enrichment analysis revealed significant enrichment of several genes, including surface proteins and accessory secretory pathway-related genes, as well as tyrosine decarboxylase genes in rodent isolates compared to avian isolates, including in mouse isolate MR1. A total of 40 genes were identified as rodent-associated, and all were transcriptionally active in <i>L. johnsonii</i> MR1. The global transcriptomic analysis of <i>L. johnsonii</i> MR1 was done using cells grown anaerobically, at 37˚C, under both the late-exponential phase and stationary phase, as well as during <i>in vivo</i> growth in the cecum of mono-colonized germ-free mice. Several of these genes were uniquely regulated during late exponential vs stationary phase growth and <i>in vivo</i> colonization in mice, highlighting their potential role in nutrient adaptation and host-microbe interactions.IMPORTANCE<i>Lactobacillus johnsonii</i> is a well-known probiotic species with health-beneficial properties, including host immunomodulation and pathogen inhibition. Its growing relevance in the medical industry highlights the need to understand its biology, particularly how it adapts to different host environments. In bacteria, niche adaptation is often accompanied by the loss or gain of coding sequences along with changes in the genome size. In this study, we explored the genetic diversity of <i>L. johnsonii</i> strains from the gastrointestinal tracts of various vertebrates such as rodents, birds, swine, and humans. We found associations between genome content and host species of origin and could conceptually demonstrate that these genes are being differentially transcribed under varying conditions. Several functions were associated with specific host groups, suggesting that <i>L. johnsonii</i> strains have adapted to their hosts over time.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0005225"},"PeriodicalIF":3.7,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12188725/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144009046","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 silver-ruthenium-based antimicrobial kills Gram-negative bacteria through oxidative stress-induced macromolecular damage.","authors":"Patrick Ofori Tawiah, Luca Finn Gaessler, Greg M Anderson, Emmanuel Parkay Oladokun, Jan-Ulrik Dahl","doi":"10.1128/msphere.00017-25","DOIUrl":"10.1128/msphere.00017-25","url":null,"abstract":"<p><p>Amplified by the decline in antibiotic discovery, the rise of antibiotic resistance has become a significant global challenge in infectious disease control. Extraintestinal <i>Escherichia coli</i> (ExPEC), known to be the most common instigators of urinary tract infections (UTIs), represents such a global threat. Novel strategies for more efficient treatments are therefore desperately needed. These include silver nanoparticles, which have been used as antimicrobial surface coatings on catheters to eliminate biofilm-forming uropathogens and reduce the risk of nosocomial infections. AGXX is a promising silver-ruthenium coating that presumably kills bacteria through the generation of reactive oxygen species (ROS). However, neither AGXX's mode of action is fully understood, nor have its effects on Gram-negative bacteria or bacterial response and defense mechanisms toward AGXX been studied in detail. Here, we report that the bactericidal effects of AGXX are primarily based on ROS formation, as supplementation of the media with a ROS scavenger completely abolished AGXX-induced killing. We further show that AGXX impairs the integrity of the bacterial cell envelope and causes substantial protein aggregation and DNA damage already at sublethal concentrations. ExPEC strains appear to be more resistant to the proteotoxic effects of AGXX compared to non-pathogenic <i>E. coli,</i> indicating improved defense capabilities of the uropathogen. Global transcriptomic studies of AGXX-stressed ExPEC revealed a strong oxidative stress response, perturbations in metal homeostasis, as well as the activation of heat shock and DNA damage responses. Finally, we present evidence that ExPEC counteracts AGXX damage through the production of the chaperone polyphosphate, protecting cells from protein aggregation.IMPORTANCEThe rise in drug-resistant bacteria, together with the decline in antibiotic development, requires new strategies for infectious disease control. Gram-negative pathogens are particularly challenging to combat due to their outer membrane. This study highlights the effectiveness of the silver-containing antimicrobial AGXX against the Gram-negative bacterium <i>Escherichia coli</i>. AGXX effectively reduces bacterial survival by interfering with the membrane integrity and causing DNA damage and protein aggregation, which is likely a consequence of uncontrolled generation of oxidative stress. Our findings emphasize AGXX's potential as an antimicrobial surface coating and shed light on potential targets to reduce bacterial resistance to AGXX.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0001725"},"PeriodicalIF":3.7,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12188735/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144187428","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":"The GATA-like transcription factor Gat201 determines alkaline-restricted growth in <i>Cryptococcus neoformans</i>.","authors":"Elizabeth S Hughes, Laura R Tuck, Zhenzhen He, Elizabeth R Ballou, Edward W J Wallace","doi":"10.1128/msphere.00191-25","DOIUrl":"10.1128/msphere.00191-25","url":null,"abstract":"<p><p>The fungus <i>Cryptococcus neoformans</i> is an opportunistic human pathogen that causes fatal meningitis through uncontrolled proliferation in host tissues. Evasion of host defenses relies on a protective polysaccharide capsule, regulated, in part, by the GATA-like transcription factor Gat201. Gat201 additionally contributes to virulence through capsule-independent mechanisms. Here, we show that Gat201 affects the proliferation of <i>C. neoformans</i>: in RPMI-1640 cell culture media at an alkaline pH that restricts wild-type cell growth, <i>gat201</i>∆ strains show increased budding, growth, and viability. RNA-seq analysis shows that Gat201 pathway genes, including co-factors <i>GAT204</i> and LIV3, are rapidly activated within minutes of inoculating <i>C. neoformans</i> in RPMI media, and strains mutated for <i>GAT204</i> and, to a lesser extent, <i>LIV3</i> also show improved growth. The effect of Gat201 on growth is pH-dependent: <i>gat201</i>∆ cells grow better than wild-type cells at high pH but worse than wild-type cells at neutral pH, in otherwise identical media. Together, this identifies the Gat201 pathway as an alkaline-responsive regulator of proliferation: Gat201 appears to govern an environment-dependent trade-off between proliferation and production of the defensive capsule. Furthermore, evolutionary analysis shows that Gat201 is in a subfamily of GATA-like transcription factors that is conserved within diverse fungi but absent in model yeasts. Together, our findings urge improved understanding of proliferation in diverse environmental niches in order to understand the mechanistic basis of fungal pathogenesis.IMPORTANCEInfectious microorganisms must adapt to differences between external and host environments in order to colonize and cause disease. <i>Cryptococcus neoformans</i> is an encapsulated fungal pathogen that can infect human airways and travel to the brain to cause life-threatening meningitis. The airway is a dynamic environment characterized by nutrient limitation, high temperature (37°C), CO₂, and transiently high pH (>8.5). In both the lung and brain, fungal proliferation through budding is a major driver of pathogenesis; however, the regulators of <i>Cryptococcus</i> proliferation are poorly understood and distinct from other model yeasts. In this work, we explore how <i>Cryptococcus</i> adapts to shifting environments and identify that the transcription factor Gat201, known to regulate capsule production, negatively regulates proliferation under alkaline conditions. Our findings highlight the need for improved understanding of proliferation/adaptation and its regulation in non-model systems.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0019125"},"PeriodicalIF":3.7,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12188746/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144216332","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":"The antibacterial activity and therapeutic potential of the amphibian-derived peptide TB_KKG6K.","authors":"Cristina Schöpf, Magdalena Knapp, Jakob Scheler, Débora C Coraça-Huber, Alessandra Romanelli, Peter Ladurner, Anna C Seybold, Ulrike Binder, Reinhard Würzner, Florentine Marx","doi":"10.1128/msphere.01016-24","DOIUrl":"10.1128/msphere.01016-24","url":null,"abstract":"<p><p>Antimicrobial peptides (AMPs) have great potential to be developed as topical treatments for microbial infections of the skin, including those caused by the gram-positive human pathogen <i>Staphylococcus aureus</i>. Among the AMPs, temporin B (TB) is of particular interest. This 13-amino-acid-long cationic peptide is secreted by the granular glands of the European frog <i>Rana temporaria</i> and represents a primary line of defense against invading pathogens. The objective of this study was to investigate the antibacterial efficacy and the mode of action of the synthetic TB analog, TB_KKG6K, in a drug-resistant clinical isolate of <i>S. aureus</i> and assess the peptide's tolerance and curative potential in an <i>in vitro</i> infection model using three-dimensional human epidermis equivalents (HEEs). The results revealed a high bactericidal efficacy of TB_KKG6K at low micromolar concentrations. The peptide perturbed the bacterial cell membrane integrity by permeabilization and depolarization. TB_KKG6K showed no toxicity in the invertebrate mini-host model <i>Galleria mellonella</i> and a high level of tolerance when topically applied in HEEs. Importantly, the therapeutic potential of TB_KKG6K was confirmed in HEEs infected with <i>S. aureus</i>. The topical application of TB_KKG6K significantly reduced the bacterial load and lowered the pro-inflammatory response in the infected HEEs. These findings reinforce the antibacterial potential and therapeutic efficacy of TB_KKG6K against <i>S. aureus</i> infection, particularly in the context of a cutaneous infection.IMPORTANCEThe emergence of multidrug-resistant bacteria has rendered the exploration of novel therapeutic treatment strategies a pivotal area of research. Among the most promising candidates are amphibian-derived antimicrobial peptides (AMPs), which are ideal for the development of novel drugs due to their multifaceted mode of action. Extensive studies have been conducted on these peptides over the last decade, resulting in the development of temporin B (TB) peptide analogs that have undergone modifications to their primary sequence. These modified analogs have demonstrated enhanced antibacterial and antifungal efficacy, while exhibiting reduced hemolytic activity. TB_KKG6K has the potential to be a promising candidate for topical treatments due to its small size and high antimicrobial activity against pathogens of the human skin. In particular, it demonstrated efficacy against <i>Staphylococcus aureus</i>, a skin commensal that can become an opportunistic pathogen, causing a range of infections from minor skin infections to life-threatening diseases such as bacteremia and sepsis.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0101624"},"PeriodicalIF":3.7,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12188738/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144094394","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":"Field expedient stool collection methods for gut microbiome analysis in deployed military environments.","authors":"Car Reen Kok, James B Thissen, Michele Cerroni, David R Tribble, Anthony Cancio, Sophia Tran, Christina Schofield, Rhonda E Colombo, Tom Troth, Christie Joya, Tahaniyat Lalani, Nicholas A Be","doi":"10.1128/msphere.00818-24","DOIUrl":"10.1128/msphere.00818-24","url":null,"abstract":"<p><p>Field expedient devices and protocols for the collection, storage, and shipment of stool samples in deployed settings are needed for the advancement of microbiome research in military health. Relevant assessments include the evaluation of microbiome signatures associated with susceptibility to travelers' diarrhea and recovery of gut function following infection. However, inherent biases in microbial measurements due to preservatives and sampling methods are unclear and should be assessed for an accurate evaluation of the microbiome. We performed shotgun metagenomic sequencing and compared the microbiome composition in paired fecal samples collected using Flinters Technology Associates (FTA) cards and OMNIgene (OG) Gut tubes, prior to and during international travel, from 49 adult participants, 39 of whom remained asymptomatic and 10 experienced travelers' diarrhea. Higher concentrations of nucleic acid and sequencing libraries were observed in OG samples. A majority of genera (82.9%) were detected with both methods, and detections of genera limited to one collection method were not highly prevalent across samples and were present in extremely low relative abundances (<0.01%). Differences in beta diversity were largely explained by inter-individuality of microbiome composition, followed by the effect of collection method and timepoint-disease states. Differential abundance analysis indicated that <i>Corynebacterium</i> and <i>Blautia</i> were consistently higher in abundance across all groups with FTA and OG collection, respectively. The observed differences in microbiome composition between methods suggest the need for consistent and standardized protocols within a study. Overall, the data presented here could help guide the future design of fecal microbiome study protocols in field and military deployment settings.IMPORTANCEThe assessment of field-deployable methods for fecal sample collection and storage is required to reliably capture samples collected in remote and austere locations. This study describes a comparative metagenomics analysis between samples collected by two different commercially available methods in a military-deployed setting. The results presented here are foundational for the future design of fecal microbiome study protocols in an operational context.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0081824"},"PeriodicalIF":3.7,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12188722/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144079233","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":"Defining neuronal responses to the neurotropic parasite <i>Toxoplasma gondii</i>.","authors":"Hannah J Johnson, Joshua A Kochanowsky, Sambamurthy Chandrasekaran, Christopher A Hunter, Daniel P Beiting, Anita A Koshy","doi":"10.1128/msphere.00216-25","DOIUrl":"10.1128/msphere.00216-25","url":null,"abstract":"<p><p>A select group of pathogens infects neurons in the brain. Prior dogma held that neurons were \"defenseless\" against infecting microbes, but many studies suggest that neurons can mount anti-microbial defenses. However, a knowledge gap in understanding how neurons respond <i>in vitro</i> and <i>in vivo</i> to different classes of microorganisms remains. To address this gap, we compared a transcriptional data set derived from primary neuron cultures (PNCs) infected with the neurotropic intracellular parasite <i>Toxoplasma gondii</i> with a data set derived from neurons injected with <i>T. gondii</i> protein <i>in vivo</i>. These curated responses were then compared to the transcriptional responses of PNCs infected with the single-stranded RNA viruses, West Nile virus or Zika virus. These analyses highlighted a conserved response to infection associated with chemokines (<i>Cxcl10, Ccl2</i>) and cytokines (interferon signaling). However, <i>T. gondii</i> had diminished IFN-α signaling <i>in vitro</i> compared to the viral data sets and was uniquely associated with a decrease in neuron-specific genes (<i>Snap25</i>, <i>Slc17a7</i>, <i>Prkcg</i>). These data underscore that neurons participate in infection-induced neuroinflammation and illustrate that neurons possess both pathogen-specific and pathogen-conserved responses.IMPORTANCEThough neurons are commonly the target of pathogens that infect the central nervous system (CNS), few data sets assess the neuronal response to infection. This paucity of data is likely because neurons are perceived to have diminished immune capabilities. However, to understand the role of neurons in neuroinflammation and their immune capabilities, their responses must be investigated. Here, we analyzed publicly accessible, neuron-specific data sets to compare neuron responses to a eukaryotic pathogen vs two Orthoflaviviruses. A better understanding of neuron responses to different infections will allow us to develop methods for inhibiting pathways that lead to neuron dysfunction, enhancing those that limit pathogen survival, and mitigating infection-induced damage to the CNS.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0021625"},"PeriodicalIF":3.7,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12188731/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144187429","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":"<i>Mycobacterium tuberculosis</i> bacillus induces pyroptosis in human lung fibroblasts.","authors":"Takemasa Takii, Hiroyuki Yamada, Chihiro Motozono, Sho Yamasaki, Jordi B Torrelles, Joanne Turner, Aoi Kimishima, Yukihiro Asami, Naoya Ohara, Shigeaki Hida, Hidetoshi Hayashi, Kikuo Onozaki","doi":"10.1128/msphere.00110-25","DOIUrl":"10.1128/msphere.00110-25","url":null,"abstract":"<p><p>We previously reported that live, but not dead, virulent <i>Mycobacterium tuberculosis</i> (<i>Mtb</i>) H37Rv bacilli induce cell death in human lung fibroblast cell lines, MRC-5, MRC-9, and TIG-1. Here, using two distinct <i>Mtb</i> strains from two different lineages (HN878 lineage 2 and H37Rv lineage 4), we confirmed cell death at day 2 after infection with a device that measures cell growth/cytotoxicity in real time (Maestro-Z [AXION]). <i>Mtb</i> bacilli uptake by the fibroblast was confirmed with a transmission electron microscope on day 2. Expressions of inflammatory cytokines and interleukin (IL)-1β, IL-6, and IL-8 were observed when exposed to live, but not dead bacteria. The cell death of fibroblasts induced by both <i>Mtb</i> strains tested was prevented by caspase-1/4 and NLRP3 inflammasome inhibitors, but not by caspase-3 and caspase-9 inhibitors. Therefore, we classified the fibroblast cell death by <i>Mtb</i> infection as pyroptosis. To investigate the biological and pathological relevance of fibroblast cell death by <i>Mtb</i> infection, we performed dual RNA-Seq analysis on <i>Mtb</i> within fibroblasts and <i>Mtb</i>-infected fibroblasts at day 2. In <i>Mtb</i> bacilli <i>tcrR</i>, <i>secE2</i>, <i>ahpD</i>, and <i>mazF8</i> genes were highly induced during infection. These genes play roles in survival in a hypoxic environment, production of a calcium-binding protein-inducing cytokine, and regulation of transcription in a toxin-antitoxin system. The gene expressions of IL-1β, IL-6, and IL-8, caspase-4, and NLRP3, but not of caspase-3 and caspase-9, were augmented in <i>Mtb</i> bacilli-infected fibroblasts. Taken together, our study suggests that <i>Mtb</i> bacilli attempt to survive in lung fibroblasts and that pyroptosis of the host fibroblasts activates the immune system against the infection.</p><p><strong>Importance: </strong>The role of \"non-classical immune cells,\" that is, fibroblasts, epithelial cells, adipocytes, etc., except for the \"classical immune cells,\" that is, macrophages and lymphoid cells, is not well known in the infection of Mtb bacilli. We have previously found that live, but not dead, Mtb bacilli induce cell death in human lung fibroblasts, except in human macrophages and monocytes. The present study reveals that fibroblasts ingest Mtb bacilli the same as macrophages and that <i>in vivo</i> Mtb bacilli within fibroblasts attempt to survive in the host cells, and pyroptosis, including the production of inflammatory cytokines, is induced in the Mtb-infected fibroblasts. Our results suggest that pyroptosis of the host fibroblasts activates the immune system against the infection.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0011025"},"PeriodicalIF":3.7,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12188705/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144094391","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":"Multiple perinatal characteristics affect the association between maternal diabetes status and early neonatal gut microbiota.","authors":"Cheng Liu, Wei Zheng, Jia Wang, Xianxian Yuan, Yuan Zhang, Yuanyuan Wang, Xu Ma, Guanghui Li","doi":"10.1128/msphere.00914-24","DOIUrl":"10.1128/msphere.00914-24","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Increasing evidence has suggested that maternal gestational diabetes mellitus (GDM) can influence the neonatal gut microbiota. However, the initial microbial colonization of neonates is still unclear. The discrepancy in results between studies may be due to many other prenatal characteristics. This study aimed to investigate whether perinatal characteristics affect the association between maternal GDM status and early neonatal gut microbiota. This nested case-control study was based on a cohort of mothers and children (2016YFC1000304). Meconium samples were collected from neonates of mothers with (&lt;i&gt;n&lt;/i&gt; = 114) and without GDM (&lt;i&gt;n&lt;/i&gt; = 133) within 24 h after birth, and then assessed via 16S rRNA gene amplicon sequencing. Differences in the diversity and composition of the neonatal gut microbiota were compared according to maternal GDM status and other perinatal characteristics. The gut microbiota of neonates born to mothers with GDM presented lower alpha diversity with the Chao1 index (&lt;i&gt;P&lt;/i&gt; = 0.0235). Principal coordinate analysis revealed that the meconium samples were clustered by maternal GDM status only with unweighted UniFrac distances (&lt;i&gt;R&lt;/i&gt;&lt;sup&gt;2&lt;/sup&gt; = 0.011, &lt;i&gt;P&lt;/i&gt; = 0.003). In other groups, such as maternal age ≥ 35 years old and maternal prepregnancy BMI ≥ 24 kg/m&lt;sup&gt;2&lt;/sup&gt;, meconium was not clustered by maternal GDM status. Linear discriminant analysis revealed that 81 taxa were significantly different between the GDM group and the control group. Based on delivery mode, there were 226 representative taxa in the control group, whereas in the GDM group, there were no representative taxa. In addition, based on neonatal sex, there were 79 representative taxa in the GDM group and seven in the control group. Other perinatal characteristics, such as maternal prepregnancy BMI, age, gestational weight gain, and birth weight also influenced the differential taxa of the neonatal gut microbiota between the two groups. In our cohort, newborns from mothers with GDM and without GDM had similar composition but different abundances of the gut microbiota. Maternal prepregnancy BMI, age, gestational weight gain, and neonatal delivery mode, sex, and birth weight had different influences on the diversity and differential taxa of the neonatal gut microbiota. The results of this study suggest that when studying the association between GDM and neonatal gut microbiota, it is necessary to consider the concomitant perinatal characteristics.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Importance: &lt;/strong&gt;This study uses 16S rRNA gene amplicon sequencing to analyze 247 meconium samples with or without maternal gestational diabetes mellitus (GDM) and make a multi-group comparison. We found that newborns from mothers with GDM and normoglycemic mothers had similar compositions but different abundances of the gut microbiota. Other than the maternal diabetes status, maternal body mass index, age, gestational weight gain, and neonatal delivery mode, gender and birth weight a","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0091424"},"PeriodicalIF":3.7,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12188708/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144079235","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":"Ceftazidime retains <i>in vivo</i> efficacy against strains of <i>Stenotrophomonas maltophilia</i> for which traditional testing predicts resistance.","authors":"Matthew C Phillips, Bosul Lee, Sarah L Miller, Jun Yan, Kristine Goy, Marlène Maeusli, Tina Lam, Catherine Spellberg, Michael Spellberg, Rosemary She, Brad Spellberg, Brian Luna","doi":"10.1128/msphere.00840-24","DOIUrl":"10.1128/msphere.00840-24","url":null,"abstract":"<p><p><i>Stenotrophomonas maltophilia</i> is responsible for a growing number of nosocomial infections and is difficult to treat owing to limited antibiotic susceptibilities. However, there are numerous recently published examples where traditional susceptibility testing methodology fails to accurately predict <i>in vivo</i> efficacy. We sought to determine if there were efficacious antibiotics against <i>S. maltophilia</i> that have been overlooked due to specious <i>in vivo</i> resistance determined by traditional <i>in vitro</i> methods. Antibiotic resistance testing was performed utilizing conventional and nutrient-limited media. Antibiotics with discordant minimum inhibitory concentrations (MICs) between the two media were selected for further experimentation. Metal ions were supplemented back into the nutrient-limited media to establish possible mechanisms. <i>In vivo</i> corroborations of <i>in vitro</i> MICs were done utilizing two infection models, <i>Galleria mellonella</i> and a neutropenic mouse oral aspiration pneumonia model. <i>S. maltophilia</i> MICs were significantly lower for ceftazidime in nutritionally deficient media that better corresponds to the <i>in vivo</i> environment than conventional rich media, resulting in a high percentage of strains determined resistant in traditional media being determined susceptible in nutritionally deficient media. The addition of zinc and manganese to the deficient media abrogated this difference, which was dependent on the L1 metallo-β-lactamase (MBL). Ceftazidime protected both <i>G. mellonella</i> and neutropenic mice against lethal infection caused by <i>S. maltophilia</i> that was predicted to be resistant in traditional media but susceptible in nutrient-deficient media. Ceftazidime may remain a viable therapeutic option for patients with <i>S. maltophilia</i> infection caused by strains predicted to be resistant by traditional susceptibility testing. Sequestration of trace metals in the host environment may prevent <i>S. maltophilia</i> MBL activity against ceftazidime.IMPORTANCEBreakpoint interpretation criteria for ceftazidime against <i>S. maltophilia</i> were recently removed by CLSI and the FDA. It was noted that clinical data were insufficient to validate the current breakpoints. Clinical data were mixed, with some studies reporting treatment success, but others reporting treatment failure. We believe that antimicrobial testing is suboptimal, and improved testing strategies, such as the use of zinc-limited media for culture, will better model the activity of ceftazidime <i>in vitro</i>. Improved susceptibility testing strategies may better discriminate against those isolates that are truly resistant from those that were previously falsely identified as being resistant using conventional testing methods.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0084024"},"PeriodicalIF":3.7,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12188716/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144120357","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":"Application of a high-resolution melt assay for monitoring SARS-CoV-2 variants in Burkina Faso and Kenya.","authors":"Caitlin Greenland-Bews, Sonal Shah, Morine Achieng, Emilie S Badoum, Yaya Bah, Hellen C Barsosio, Helena Brazal-Monzó, Jennifer Canizales, Anna Drabko, Alice J Fraser, Luke Hannan, Sheikh Jarju, Jean-Moise Kaboré, Mariama A Kujabi, Cristina Leggio, Maia Lesosky, Jarra Manneh, Tegwen Marlais, Julian Matthewman, Issa Nebié, Eric Onyango, Alphonse Ouedraogo, Kephas Otieno, Samuel S Serme, Sodiomon Sirima, Ben Soulama, Brian Tangara, Alfred Tiono, William Wu, Emily R Adams, Abdul Karim Sesay, Chris Drakeley, Feiko O Ter Kuile, Issiaka Soulama, Simon Kariuki, David J Allen, Thomas Edwards","doi":"10.1128/msphere.00027-25","DOIUrl":"10.1128/msphere.00027-25","url":null,"abstract":"<p><p>The rapid emergence and global dissemination of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) highlighted a need for robust, adaptable surveillance systems. However, financial and infrastructure requirements for whole-genome sequencing mean most surveillance data have come from higher-resource geographies, despite unprecedented investment in sequencing in low- and middle-income countries (LMICs). Consequently, the molecular epidemiology of SARS-CoV-2 in some LMICs is limited, and there is a need for more cost-accessible technologies to help close data gaps for surveillance of SARS-CoV-2 variants. To address this, we have developed two high-resolution melt (HRM) curve assays that target variant-defining mutations in the SARS-CoV-2 genome, which give unique signature profiles that define different SARS-CoV-2 variants of concern (VOCs). Extracted RNA from SARS-CoV-2-positive samples collected from 205 participants (112 in Burkina Faso, 93 in Kenya) enrolled in the MALCOV study (Malaria as a Risk Factor for COVID-19) between February 2021 and February 2022 were analyzed using our optimized HRM assays. With next-generation sequencing on Oxford Nanopore MinION as a reference, two HRM assays, HRM-VOC-1 and HRM-VOC-2, demonstrated sensitivity/specificity of 100%/99.29% and 92.86%/99.39%, respectively, for detecting Alpha, 90.08%/100% and 92.31%/100% for Delta, and 93.75%/100% and 100%/99.38% for Omicron BA.1. The assays described here provide a lower-cost approach to conducting molecular epidemiology, capable of high-throughput testing. We successfully scaled up the HRM-VOC-2 assay to screen a total of 506 samples from which we were able to show the replacement of Alpha with the introduction of Delta and the replacement of Delta by the Omicron variant in this community in Kisumu, Kenya.IMPORTANCEThe rapid evolution of the severe acute respiratory syndrome coronavirus 2 variants of concern (VOCs) demonstrated the need for accessible surveillance tools so all communities can conduct viral surveillance. Sequencing, the gold standard, is still a largely inaccessible methodology in low-resource settings. Here, we present a quick, low-cost tool to screen for the common VOCs, designed to support surveillance efforts in low-resource settings. This tool was used to screen samples from Burkina Faso and Western Kenya throughout the pandemic. We show through comparison to sequencing that our assay can generate highly similar data on the different variants circulating in a population, therefore showing the effectiveness of our tool. While not a replacement for sequencing, we present a method of screening and prioritizing samples for further investigation and reduce overburdening sequencing capacity. Our findings provide insight into one potential tool that could be further applied to pathogen screening in the absence of robust sequencing infrastructure.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0002725"},"PeriodicalIF":3.7,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12188703/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144173979","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}