Microbiology spectrum最新文献

{"title":"Hyperpiliation, not loss of pilus retraction, reduces <i>Pseudomonas aeruginosa</i> pathogenicity.","authors":"Sara L N Kilmury, Katherine J Graham, Ryan P Lamers, Lesley T MacNeil, Lori L Burrows","doi":"10.1128/spectrum.02558-24","DOIUrl":"10.1128/spectrum.02558-24","url":null,"abstract":"<p><p>Type IVa pili (T4aP) are important virulence factors for many bacterial pathogens. Previous studies suggested that the retraction ATPase, PilT, modulates pathogenicity due to its critical role in pilus dynamics and twitching motility. Here we use a <i>Caenorhabditis elegans</i> slow-killing model to show that hyperpiliation, not loss of pilus retraction, reduces virulence of <i>Pseudomonas aeruginosa</i> strains PAK and PA14. Hyperactivating point mutations in the <i>P. aeruginosa</i> PilSR two-component system that controls transcription of the major pilin gene, <i>pilA</i>, increased levels of surface pili to the same extent as deleting <i>pilT</i>, without impairing twitching motility. These functionally hyperpiliated PilSR mutants had significant defects in pathogenicity that were rescued by deleting <i>pilA</i> or through disruption of hyperpiliation via deletion of the type III secretion system needle-length regulator, PscP. Hyperpiliated <i>pilT</i> deletion or <i>pilO</i> point mutants showed similar PilA-dependent impairments in virulence, validating the phenotype. Together, our data support a model where a surfeit of pili reduces virulence, potentially through the prevention of effective engagement of contact-dependent virulence factors. These findings suggest that the role of T4aP retraction in virulence should be revised.IMPORTANCE<i>Pseudomonas aeruginosa</i> is a major contributor to hospital-acquired infections and particularly problematic due to its intrinsic resistance to many front-line antibiotics. Strategies to combat this and other important pathogens include the development of anti-virulence therapeutics. We show that the pathogenicity of <i>P. aeruginosa</i> is impaired when the amount of T4aP expressed on the cell surface increases, independent of the bacteria's ability to twitch. We propose that having excess T4aP on the cell surface may physically interfere with productive engagement of the contact-dependent type III secretion toxin delivery system. A better understanding of how T4aP modulate interaction of bacteria with target cells will improve the design of therapeutics targeting components involved in the regulation of T4aP expression and function to reduce the clinical burden of <i>P. aeruginosa</i> and other T4aP-expressing bacteria.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0255824"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143492956","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":"GrcC1 mediates low-level resistance to multiple drugs in <i>M. marinum</i>, <i>M. abscessus,</i> and <i>M. smegmatis</i>.","authors":"Cuiting Fang, Han Zhang, Jing He, Xirong Tian, Sanshan Zeng, Xingli Han, Shuai Wang, Buhari Yusuf, Jinxing Hu, Nanshan Zhong, Yamin Gao, H M Adnan Hameed, Tianyu Zhang","doi":"10.1128/spectrum.02289-24","DOIUrl":"10.1128/spectrum.02289-24","url":null,"abstract":"<p><p>The escalating threat of mycobacterial infectious diseases, particularly those caused by nontuberculous mycobacteria (NTM), poses a serious challenge to public health. Linezolid (LZD), an oxazolidinone antimicrobial, exhibits potent activity against <i>Mycobacterium tuberculosis</i> and NTM. Generally, mutations in the <i>rrl</i> and <i>rplC</i> genes are widely associated with resistance to LZD. However, in this study, we screened <i>Mycobacterium marinum</i> strains lacking such mutations, indicating the presence of an alternative resistance mechanism. Notably, through whole-genome sequencing, we identified a novel mutation C395T in the <i>MMAR_0911</i> (<i>grcC1</i>) gene that has never been linked to drug resistance. This mutation leads to an A132V substitution in the encoded protein, a polyprenyl diphosphate synthase potentially involved in the synthesis of cell wall components and menaquinones. We found that the overexpression of <i>grcC1</i> caused resistance to multiple drugs including LZD, clarithromycin (CLR), vancomycin (VAN), clofazimine (CFZ), rifampicin (RIF), cefoxitin (CEF), levofloxacin (LEV), and moxifloxacin (MXF) and reduced cell wall permeability, while the silence and knockout of <i>grcC1</i> showed increased cell wall permeability and susceptibility to these drugs. Using CRISPR/Cpf1-assisted gene editing, we confirmed that the A132V mutation conferred low-level resistance to the aforementioned drugs in <i>Mycobacterium abscessus</i> and <i>Mycobacterium smegmatis</i>. Furthermore, thin-layer chromatography analysis indicated reduced glycolipid polarity in the <i>grcC1</i> mutant strains, suggesting an impact on the cell envelope integrity. Our findings suggest that GrcC1 contributes to low-level drug resistance in mycobacteria by potentially reducing cell wall permeability, highlighting its potential as a novel target for antimicrobial agents and as a diagnostic marker.IMPORTANCEOur study uncovers a novel drug resistance mechanism in mycobacteria, focusing on the previously uncharacterized <i>grcC1</i> gene. We identified a new mutation, A132V, in GrcC1, which is involved in cell wall component synthesis and menaquinone production. This mutation contributes to low-level resistance not only to linezolid but also to a broad range of drugs, including clarithromycin, vancomycin, and rifampicin. Through advanced techniques like CRISPR interference and gene editing, we demonstrated that GrcC1 plays a critical role in drug susceptibility and cell wall permeability across multiple <i>Mycobacterium</i> species. These findings represent the first connection between GrcC1 and drug resistance, offering new insights into combating infections caused by nontuberculous mycobacteria (NTM). Our work highlights the potential of GrcC1 as a target for novel therapeutic approaches and as a diagnostic marker for drug-resistant NTM infections.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0228924"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143516143","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":"Influence of bacterial morphotype on urine culture and molecular epidemiological differences in <i>Escherichia coli</i> harboring bacterial morphotype-induced urinary tract infections.","authors":"Yewei Fang, Shuan Tao, Huimin Chen, Yao Xu, Luyan Chen, Wei Liang","doi":"10.1128/spectrum.00980-24","DOIUrl":"10.1128/spectrum.00980-24","url":null,"abstract":"<p><p>Bacteria that adhere to epithelial cells, form intracellular bacterial communities (IBCs), or transition to filamentous forms are referred to as morphotype-positive bacteria. <i>Escherichia coli</i> (<i>E. coli</i>) with this morphotype plays a critical role in urinary tract infections (UTIs), yet its impact on urine culture outcomes and molecular epidemiological characteristics remains unclear. In this retrospective study, we assessed the effect of bacterial morphotype on urine culture results and investigated the molecular differences between <i>E. coli</i> strains with and without this morphotype, using PCR and whole genome sequencing (WGS). We observed that <i>E. coli</i> with the morphotype-positive phenotype frequently appeared in urine sediments, leading to fewer colony-forming units (CFUs) in culture and contributing to false-negative results. However, vortexing the urine samples significantly increased CFUs, improving culture sensitivity. Additionally, <i>E. coli</i> with the positive morphotype carried more adhesion-related virulence genes (VGs), with the majority belonging to phylogenetic group B2. Whole genome sequencing further revealed a broader array of virulence genes in these strains. Our findings demonstrate that vortexing is an effective method to enhance urine culture positivity by releasing intracellular bacteria, and that morphotype-positive <i>E. coli</i> harbors a diverse set of virulence factors, indicating their potential high pathogenicity. These results highlight the importance of detecting bacterial morphotypes in urine samples for accurate UTI diagnosis and emphasize the need for increased attention to these highly virulent strains.</p><p><strong>Importance: </strong>Uropathogenic <i>Escherichia coli</i> (UPEC) is widely acknowledged as the primary pathogen responsible for urinary tract infections (UTIs). Following adherence to the epithelium, UPEC undergoes periodic morphological changes, such as filamentation, which not only contribute to immune evasion but also lead to false-negative results. This study focuses on three transient stages of UPEC morphological changes: adherence to the epithelium, formation of intracellular bacterial communities (IBCs), and the presence of filamentous UPEC. Any one of these characteristics is acceptable to classify UPEC strains as morphotype-positive UPEC. This study reported the prevalence of UPEC with the bacterial morphotype and established a direct relationship between urine culture and bacterial morphotype. The molecular epidemiological distinctions were both revealed. These findings provide further evidence of the necessary for bacterial morphotype detection, and greater attention should be given to <i>E. coli</i> harboring this bacterial morphotype.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0098024"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143557237","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":"Altered gut microbiota and metabolite profiles in community-acquired pneumonia: a metagenomic and metabolomic study.","authors":"Fuxin Zhang, Jiahui Luan, Lijun Suo, Haiyan Wang, Yi Zhao, Tianyu Sun, Yawen Ni, Hongyun Cao, Xiaohui Zou, Bo Liu","doi":"10.1128/spectrum.02639-24","DOIUrl":"10.1128/spectrum.02639-24","url":null,"abstract":"<p><p>Emerging evidence suggests that altered gut microbiota is linked to community-acquired pneumonia (CAP), but the potential mechanisms by which gut microbiota and its metabolites contribute to the development of CAP remain unclear. Fecal samples from 32 CAP patients and 36 healthy controls were analyzed through metagenomic sequencing and metabolomic profiling. The gut microbiota composition in CAP patients showed significant differences and lower diversity compared to healthy controls. Genera involved in short-chain fatty acid (SCFA) production, such as <i>Faecalibacterium</i>, <i>Ruminococcus</i>, and <i>Eubacterium</i>, as well as species like <i>Faecalibacterium prausnitzii</i>, <i>Bifidobacterium adolescentis</i>, <i>Eubacterium rectale</i>, <i>Prevotella copri</i>, and <i>Ruminococcus bromii</i>, were significantly depleted in CAP patients. Bacterial co-occurrence network analysis revealed an over-representation of pro-inflammatory bacteria, which contributed to the core gut microbiome in CAP patients. Metabolomic analysis of fecal samples identified a distinct metabolic profile, with a notable increase in arachidonic acid, but a decrease in secondary bile acids, such as deoxycholic acid, lithocholic acid, and ursodeoxycholic acid, compared to healthy controls. Spearman correlation analysis between differential microbiota and bile acids showed that <i>Faecalibacterium prausnitzii</i>, <i>Bifidobacterium adolescentis</i>, <i>Eubacterium rectale</i>, and <i>Prevotella copri</i> were positively correlated with ursocholic acid, lithocholic acid, and ursodeoxycholic acid, respectively. Our results suggest that the reduction in secondary bile acids, insufficient production of SCFAs, and an overabundance of pro-inflammatory bacteria may contribute to metabolic inflammation in the body. These factors could play a key role in the pathogenesis of CAP, driven by gut microbiota alterations.</p><p><strong>Importance: </strong>This study presents a comprehensive metagenomic and metabolomic analysis of fecal samples from community-acquired pneumonia (CAP) patients, identifying key characteristics, such as decreased secondary bile acids, imbalanced short-chain fatty acid production, and increased pro-inflammatory bacteria. These findings provide valuable insights into the mechanisms linking gut microbiota alterations to CAP pathogenesis and suggest that targeting the gut microbiota could be a promising strategy for intervening in CAP.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0263924"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143586248","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":"Application of versatile reverse genetics system for feline coronavirus.","authors":"Izumi Kida, Tomokazu Tamura, Yudai Kuroda, Takasuke Fukuhara, Ken Maeda, Keita Matsuno","doi":"10.1128/spectrum.02692-24","DOIUrl":"10.1128/spectrum.02692-24","url":null,"abstract":"<p><p>Feline infectious peritonitis (FIP) is a fatal disease caused by feline coronavirus (FCoV). Although multiple gene mutations in FCoV likely account for FIP pathogenesis, molecular studies for FCoV have been limited due to the lack of a suitable reverse genetics system. In the present study, we established a rapid PCR-based system to generate recombinant FCoV using the circular polymerase extension reaction (CPER) method for both serotype 1 and 2 viruses. Recombinant FCoV was successfully rescued at sufficient titers to propagate the progeny viruses with high sequence accuracy. The growth kinetics of recombinant FCoV were comparable to those of the parental viruses. We successfully generated recombinants harboring the spike gene from a different FCoV strain or a reporter HiBiT tag using the CPER method. The chimeric virus demonstrated similar characteristics with the parental virus of the spike gene. The reporter tag stably expressed after five serial passages in the susceptible cells, and the reporter virus could be applied to evaluate the sensitivity of antiviral inhibitors using the luciferase assay system to detect HiBiT tag. Taken together, our versatile reverse genetics system for FCoV shown herein is a robust tool to characterize viral genes even without virus isolation and to investigate the molecular mechanisms of the proliferation and pathogenicity of FCoV.</p><p><strong>Importance: </strong>Feline infectious peritonitis is a highly fatal disease in cats caused by feline coronavirus variants that can infect systemically. Due to the lack of a versatile toolbox for manipulating the feline coronavirus genome, an efficient method is urgently needed to study the virus proteins responsible for the severe disease. Herein, we established a rapid reverse genetics system for the virus and demonstrated the capability of the recombinant viruses to be introduced with desired modifications or reporter genes without any negative impacts on virus characteristics in cell culture. Recombinant viruses are also useful to evaluate antiviral efficacy. Overall, our system can be a promising tool to reveal the molecular mechanisms of the viral life cycle of feline coronavirus and disease progression of feline infectious peritonitis.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0269224"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143586260","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":"The emergence of <i>E. coli</i> ST906 harboring the <i>bla</i>_NDM-21 gene in a maternity and infant hospital in Jiangsu, China.","authors":"Yuehua Gao, Yaozhi Qi, Yue Yang, Yuhan Sun, Yujie Zhu, Guoping Zhao, Fei Xia, Biao Tang","doi":"10.1128/spectrum.02927-24","DOIUrl":"10.1128/spectrum.02927-24","url":null,"abstract":"","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0292724"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143586294","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":"Experimental evolution of <i>Escherichia coli</i> on semi-dry silver, copper, stainless steel, and glass surfaces.","authors":"Merilin Rosenberg, Sandra Park, Sigrit Umerov, Angela Ivask","doi":"10.1128/spectrum.02173-24","DOIUrl":"10.1128/spectrum.02173-24","url":null,"abstract":"<p><p>To study bacterial adaptation to antimicrobial metal surfaces in application-relevant conditions, <i>Escherichia coli</i> was exposed to copper and silver surfaces for 30 exposure cycles in low-organic dry or high-organic humid conditions. The evolved populations demonstrated increased metal surface tolerance without concurrent increase in minimal biocidal concentration (MBC) and minimal inhibitory concentration (MIC) values of respective metal ions or selected antibiotics. Mutation analysis did not detect increased mutation accumulation nor mutations in <i>cop</i>, <i>cus</i>, <i>cue</i>, <i>sil</i>, <i>pco</i>, or general efflux genes known to actively maintain copper/silver homeostasis. Instead, during cyclic exposure, mutations in genes related to cellular barrier functions and sulfur metabolism were enriched, potentially suggesting that reducing bioavailability and passively restricting uptake of the toxic metals rather than active efflux is selected for on copper and silver surfaces. The changes detected in the evolved populations did not indicate an increased risk of antibiotic cross-resistance as a result of copper or silver surface exposure. However, rapid emergence of mutations in <i>silS</i> activated the cryptic <i>sil</i> efflux locus during silver ion challenge in liquid MBC assay with the evolved populations. The <i>silS</i> mutants showed no benefit on copper and silver surfaces but demonstrated decreased sensitivity to ampicillin and ciprofloxacin, as well as copper and silver ions in liquid tests, indicating that efflux might be specific to granting heavy metal tolerance in liquid but not surface exposure format. Our findings highlight the critical importance of appropriate exposure conditions not only in efficacy testing but also in risk assessment of antimicrobial surface applications.</p><p><strong>Importance: </strong>This study examines the evolutionary adaptations of <i>Escherichia coli</i> after semi-dry exposure to copper and silver surfaces, leading to an increase in surface tolerance but no increase in mutation accumulation or substantially enhanced metal ion tolerance in standard tests. Notably, enriched mutations indicate a shift toward more energy-passive mechanisms of metal tolerance. Additionally, while enhanced silver efflux was rapidly selected for in a single round of silver exposure in liquid tests and substantially increased copper and silver ion tolerance in conventional test formats, the causal mutations did not improve viability on silver and copper surfaces, underscoring the different fitness scenarios of tolerance mechanisms dependent on exposure conditions. These findings emphasize the need for appropriate exposure conditions in evaluating of both efficacy and the potential risks of using antimicrobial surfaces, as the results from conventional liquid-based tests may not apply in solid contexts.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0217324"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143414692","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":"Systemic inflammation is associated with worse outcomes from SARS-CoV-2 infection but not neutralizing antibody.","authors":"Christopher W Farnsworth, Brittany Roemmich, John Prostko, Gerard Davis, Gillian Murtagh, Laurel Jackson, Christopher Jacobson, Nicolette Jeanblanc, Timothy Griffiths, Edwin Frias, David J Daghfal","doi":"10.1128/spectrum.02459-24","DOIUrl":"10.1128/spectrum.02459-24","url":null,"abstract":"<p><p>Systemic inflammation is associated with COVID-19 mortality rates, but the impact of inflammation on neutralizing antibodies to severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) and on outcomes is poorly understood. This study aimed to determine the association between neutralizing antibody responses, inflammation, and clinical outcomes in hospitalized patients with COVID-19. Two hundred and eight patients presenting to the ED with symptomatic SARS-CoV-2 were included. Neutralization was assessed using the architect angiotensin-converting enzyme-2 (ACE2) binding inhibition assay, and inflammation was assessed using C reactive protein (CRP) and interleukin 6 (IL-6). Medical records were examined for 30-day mortality and 10-day intubation. Correlation between biomarkers was assessed and Kaplan-Meier curves and Cox proportional hazards models were constructed for outcomes. Thirty-seven (18%) patients died and 59 (28%) required intubation. There was a correlation between IL-6 and CRP (<i>r</i> = 0.34) but not ACE-2 (<i>r</i> < 0.06). Patients that died had higher CRP (14 mg/dl, 8-21) than those that survived (5 mg/dl, 2-11) and IL-6 (died = 344 pg/ml, 138-870 vs. survived = 65 pg/ml, 28-140). ACE-2 inhibition trended higher in those who survived (18%, 0%-65%) than those who died (3%, 0%-48%). Patients with elevated IL-6, elevated CRP, or low ACE2 inhibition had higher mortality. Only IL-6 (hazard ratio: 1.28, 95% CI 1.08-1.52) and age (1.04, 1.01-1.08) were associated with mortality in multivariate models. Elevated IL-6 was associated with 30-day mortality from SARS-CoV-2 infection. Lower ACE-2 inhibition was not independently associated with mortality or correlated with inflammatory markers, implying the importance of other aspects of the immune response for reducing SARS-CoV-2 mortality risk.IMPORTANCEWhile systemic inflammation associated with worse outcomes from SARS-CoV-2 infection, it is not associated with neutralizing antibody concentrations, implying the importance of other aspects of the immune response for reducing SARS-CoV-2 mortality risk.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0245924"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143449565","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":"Investigation of bedaquiline heteroresistance among <i>Mycobacterium tuberculosis</i> isolates from Pakistan.","authors":"Faiqa Rashid, Shaukat Iqbal, Sabira Tahseen, Yanlin Zhao","doi":"10.1128/spectrum.02181-24","DOIUrl":"10.1128/spectrum.02181-24","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Bedaquiline is a key drug recommended by the WHO for the treatment of multidrug-resistant tuberculosis (MDR-TB) and extensively drug-resistant (XDR) TB, and its use could potentially shorten treatment duration with improved outcomes. However, resistance against this drug has increased, resulting in serious concerns. Heteroresistance is among the important obstacles to complicate the detection and treatment of MTB drug resistance. We investigated the presence of bedaquiline heteroresistant MTB isolates from Pakistan to highlight their relevance to bedaquiline resistance. Whole genome sequencing of 50 phenotypically bedaquline-resistant and 50 bedaquiline-sensitive isolates revealed 29% bedaquiline heteroresistance in our study. No significant association of patient variables (age, gender, region and history of anti-tuberculosis treatment [ATT]) was found, while drug resistance pattern among MDR + bedaquiline and XDR patterns (OR, 0.53 [0.01-0.26]; &lt;i&gt;P&lt;/i&gt; ≤ 0.001 and OR, 0.09 [0.19-0.50]; &lt;i&gt;P&lt;/i&gt; = 0.006) were significantly different to bedaquiline heteroresistance. Higher proportion of bedaquiline heteroresistant cases with no history of bedaquiline containing treatment was found. Most bedaquiline heteroresistant strains (&lt;i&gt;n&lt;/i&gt; = 19) were from lineage 3, none of the strain bear mixed lineage, with &lt;i&gt;Rv0678&lt;/i&gt; mutations (95%) being the most prevalent genetic marker. We identified both new mutations (n = 17) and reported mutations (n = 21) that contribute to bedaquiline heteroresistance.The strains with missense variants had the highest percentage of heteroresistance (56%). Bedaquiline heteroresistance is an important indicator of emerging bedaquiline resistance, predominantly observed in previously treated cases without mixed infections, suggesting a higher likelihood of acquired resistance. Our findings accentuate the complexity of bedaquiline heteroresistance and the need for better diagnostic and appropriate therapeutic treatment approaches for drug-resistant TB with bedaquiline-containing regimens.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Importance: &lt;/strong&gt;This research is decisive as it investigates bedaquiline heteroresistance in &lt;i&gt;Mycobacterium tuberculosis&lt;/i&gt; (MTB) isolates from Pakistan, the sixth highest burden country for drug-resistant tuberculosis (DRTB). Bedaquiline is a key drug in the treatment of MDR/XDR-TB, and the emergence of resistance to this drug threatens global efforts to control tuberculosis. Heteroresistance, where drug-susceptible and drug-resistant strains coexist, complicates detection and treatment, potentially leading to treatment failure. By focusing on MTB isolates from Pakistan, this study addresses a critical gap in understanding the prevalence and genetic mechanisms of bedaquiline resistance in a high-burden region. The use of whole genome sequencing (WGS) adds a cutting-edge approach to identifying mutations associated with resistance, offering valuable insights that could inform more effective treatment strategies and","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0218124"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143483360","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":"Reevaluation of the gastrointestinal methanogenic archaeome in multiple sclerosis and its association with treatment.","authors":"Pei Yee Woh, Yehao Chen, Christina Kumpitsch, Rokhsareh Mohammadzadeh, Laura Schmidt, Christine Moissl-Eichinger","doi":"10.1128/spectrum.02183-24","DOIUrl":"10.1128/spectrum.02183-24","url":null,"abstract":"<p><p>The role of the gut archaeal microbiome (archaeome) in health and disease remains poorly understood. Methanogenic archaea have been linked to multiple sclerosis (MS), but prior studies were limited by small cohorts and inconsistent methodologies. To address this, we re-evaluated the association between methanogenic archaea and MS using metagenomic data from the International Multiple Sclerosis Microbiome Study. We analyzed gut microbiome profiles from 115 MS patients and 115 healthy household controls across Buenos Aires (27.8%), Edinburgh (33.9%), New York (10.4%), and San Francisco (27.8%). Metagenomic sequences were taxonomically classified using kraken2/bracken and a curated profiling database to detect archaea, specifically <i>Methanobrevibacter</i> species. Most MS patients were female (80/115), aged 25-72 years (median: 44.5), and 70% were undergoing treatment, including dimethyl fumarate (<i>n</i> = 21), fingolimod (<i>n</i> = 20), glatiramer acetate (<i>n</i> = 14), interferon (<i>n</i> = 18), natalizumab (<i>n</i> = 6), or ocrelizumab/rituximab (<i>n</i> = 1). We found no significant differences in overall archaeome profiles between MS patients and controls. However, treated MS patients exhibited higher abundances of <i>Methanobrevibacter smithii</i> and <i>M.</i> sp900766745 compared to untreated patients. Notably, <i>M.</i> sp900766745 abundance correlated with lower disease severity scores in treated patients. Our results suggest that gut methanogens are not directly associated with MS onset or progression but may reflect microbiome health during treatment. These findings highlight potential roles for <i>M. smithii</i> and <i>M.</i> sp900766745 in modulating treatment outcomes, warranting further investigation into their relevance to gut microbiome function and MS management.IMPORTANCEMultiple sclerosis (MS) is a chronic neuroinflammatory disease affecting the central nervous system, with approximately 2.8 million people diagnosed worldwide, mainly young adults aged 20-30 years. While recent studies have focused on bacterial changes in the MS microbiome, the role of gut archaea has been less explored. Previous research suggested a potential link between methanogenic archaea and MS disease status, but these findings remained inconclusive. Our study addresses this gap by investigating the gut archaeal composition in MS patients and examining how it changes in response to treatment. By focusing on methanogens, we aim to uncover novel insights into their role in MS, potentially revealing new biomarkers or therapeutic targets. This research is crucial for enhancing our understanding of the gut microbiome's impact on MS and improving patient management.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0218324"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143492962","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}