Microbiology spectrum最新文献

{"title":"Intra-serotype variation of <i>Streptococcus pneumoniae</i> capsule and its quantification.","authors":"Hannes Eichner, Cindy Wu, Michael Cammer, Elizabeth N H Tran, Timothy R Hirst, James C Paton, Jeffrey N Weiser","doi":"10.1128/spectrum.03087-24","DOIUrl":"10.1128/spectrum.03087-24","url":null,"abstract":"<p><p><i>Streptococcus pneumoniae</i> (<i>Spn</i>) is a leading respiratory pathogen that depends on a thick layer of capsular polysaccharide (CPS) to evade immune clearance. Disease prevention by CPS-based vaccines is limited because of the species' high genome plasticity and ability to express over 100 different capsule types (serotypes). Generally, intra-serotype variations in capsulation are overlooked, despite the genetic variability of the bacterium. This oversight may result from a lack of standardized, reliable, and easily available methodology to quantify capsulation. Here, we have modified two methods to analyze the <i>Spn</i> capsule: immunoblot quantification of CPS in bacterial lysates and light microscopy to assess capsule thickness. Two assays were used because each measures distinct aspects of capsulation that could be differentially affected by the density of CPS. Quantification of either CPS amount or capsule thickness predicted the effectiveness of immune serum in opsonophagocytic killing assays for isogenic strains. Our standardized approaches both revealed significant differences in both CPS amount and capsule thickness among clinical isolates of the same serotype, challenging the assumption that intra-serotype capsulation is a conserved feature. As expected, these two methods show limited intra-strain correlation between amounts of CPS production and capsule thickness.</p><p><strong>Importance: </strong>Despite the availability of vaccines, <i>Streptococcus pneumoniae</i> remains a leading cause of respiratory and invasive diseases. These vaccines target a polysaccharide capsule the bacterium uses to evade the immune system. Variation of the capsule composition subdivides the organism into serotypes and influences its protective potency. Another critical factor affecting this protection is capsule size. It is commonly assumed that <i>S. pneumoniae</i> strains of the same serotype produce capsules of consistent size, despite the organism's heterogeneity. In this study, we challenge this assumption by analyzing clinical isolates of the same serotype. Existing methods were modified to achieve high reproducibility and increase accessibility. Our data reveal significant fluctuations in capsule production within a given serotype. Our findings suggest that <i>S. pneumoniae</i> research should consider capsule size, not just its presence and type. The results imply that standardized vaccine efficacy tests may yield variable results depending on the capsule production of target strains.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0308724"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11960111/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143414695","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 double-antibody sandwich ELISA based on monoclonal antibodies against the viral spike protein detects porcine deltacoronavirus infection.","authors":"Yingjie Bai, Ruiming Yu, Guangqing Zhou, Liping Zhang, TianTian Wang, Ya Liu, Dongsheng Wang, Zhongwang Zhang, Yonglu Wang, Huichen Guo, Li Pan, Xinsheng Liu","doi":"10.1128/spectrum.02854-24","DOIUrl":"10.1128/spectrum.02854-24","url":null,"abstract":"<p><p>Porcine deltacoronavirus (PDCoV) is a significant emerging pathogen that causes severe enteric disease in swine, and therefore significant economic losses in the pig farming industry. Here, we developed a novel double-antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA) based on two monoclonal antibodies directed against the PDCoV spike protein. These two monoclonal antibodies were obtained through hybridoma fusion and screening, and they can specifically react with the PDCoV spike protein. The detection limits of the DAS-ELISA for the recombinant spike protein and viral titer were approximately 0.12 ng/mL and 1.96 × 10³ copies/μL, respectively. The DAS-ELISA did not cross-react with other swine enteric coronaviruses, including porcine epidemic diarrhea virus, transmissible gastroenteritis virus, or porcine rotavirus. A total of 145 rectal swab samples were collected and tested for the presence of PDCoV with the DAS-ELISA and reverse transcription-quantitative PCR (RT-qPCR). The coincidence rate between the DAS-ELISA and RT-qPCR was 91.03%, with a kappa value of 0.814, indicating that the DAS-ELISA is a reliable method for viral antigen detection in clinical samples. DAS-ELISA had a sensitivity of 92.85% and a specificity of 89.89%. The positive predictive value and negative predictive value of this method are 85.25% and 95.24%, respectively. Furthermore, the DAS-ELISA can also be used to detect the spike protein in PDCoV vaccines, making it a valuable tool for assessing the efficacy of PDCoV vaccines.</p><p><strong>Importance: </strong>Since 2014, porcine deltacoronavirus (PDCoV) has spread widely across multiple countries and regions, causing significant economic losses to the global livestock industry. Currently, no commercially available vaccine exists for the prevention of PDCoV infection; therefore, accurate and effective diagnostic methods are crucial for its control and prevention. In this study, the PDCoV S protein expressed in Chinese Hamster Ovary (CHO) cells was used to immunize mice, and a novel double-antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA) was established based on two monoclonal antibodies. The DAS-ELISA had high sensitivity, good repeatability, strong specificity, and high consistency for detecting clinical samples and spike protein in PDCoV vaccines. Therefore, the DAS-ELISA established in this study may be a reliable and effective tool for detecting PDCoV infection and the efficacy of PDCoV vaccines.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0285424"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11960065/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143516126","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":"Pathological characterization of female reproductive organs prior to miscarriage induced by Zika virus infection in the pregnant common marmoset.","authors":"Toshifumi Imagawa, Kazuo Tanaka, Masahiko Ito, Mami Matsuda, Tadaki Suzuki, Tsuyoshi Ando, Chizuko Yaguchi, Kazuyoshi Miyamoto, Shuji Takabayashi, Ryosuke Suzuki, Tomohiko Takasaki, Hiroaki Itoh, Isao Kosugi, Tetsuro Suzuki","doi":"10.1128/spectrum.02282-24","DOIUrl":"10.1128/spectrum.02282-24","url":null,"abstract":"<p><p>While Zika virus (ZIKV) infection in pregnant women is known to increase the risk of miscarriage and stillbirth, the mechanism by which ZIKV infection leads to the inability to continue a pregnancy is not clear. In our common marmoset models of ZIKV infection in pregnant individuals, miscarriage was observed in dams infected in the first or second trimester, and preterm delivery was observed in a dam infected in the third trimester. Serum progesterone levels were significantly lower prior to miscarriage or preterm delivery in the infected marmosets. To elucidate the pathology of the placental region just before the onset of ZIKV-induced miscarriage, we newly prepared an infected marmoset in the first trimester of pregnancy and euthanized it when the serum progesterone concentration was markedly reduced. Pathological analysis revealed significant degeneration in cells at the maternal-fetal interface, presumably trophoblasts. Cleaved-caspase was widely observed in the endometrial to placental region, and TNFα at 200 pg/mL was detected in the amniotic fluid, suggesting that apoptosis may progress in the endometrium and placenta, leading to decreased trophoblast function and miscarriage. ZIKV NS1 protein was found sporadically in the cellular degeneration area and widely in the basal layer of the endometrium. Furthermore, the viral protein was frequently detected in the follicles and corpus luteum of the ovary. The developed ZIKV infection model in pregnant marmosets would be useful not only to better understand the mechanism of ZIKV-induced miscarriage but also to analyze the effects of the viral infection on female reproductive tissues.</p><p><strong>Importance: </strong>Although several viruses, including Zika virus (ZIKV), are known to increase the risk of miscarriage upon viral infection, the mechanism by which miscarriage is induced by viral infection is largely unknown. This is partly due to the difficulty of pathological analysis of maternal tissues in the period following viral infection and prior to miscarriage. In this study, we predicted the occurrence of miscarriage by monitoring serum progesterone levels and performed pathological analysis of peri-placental tissues at a time point assumed to be just before miscarriage. This is the first report of trophoblast degeneration prior to miscarriage, suggesting that the experimental method used here is useful for analyzing the pathogenesis of virus infection-related miscarriage. Further immunostaining revealed that ZIKV NS1 was distributed not only in the uterus but also in the ovaries, with particularly pronounced staining of oocytes. Whether ZIKV infection affects female reproductive function should be clarified in the future.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0228224"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11960083/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143492958","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":"Revealing the clinical relevance of <i>Staphylococcus borealis</i>.","authors":"Jorunn Pauline Cavanagh, Claus Klingenberg, Hermoine Jean Venter, Jan Egil Afset, Olaf Stromme, Paul Christoffer Lindemann, Therese Johansen, Kyriakos Zaragkoulias, Hege Vangstein Aamot, Ståle Tofteland, Pia Littauer","doi":"10.1128/spectrum.01988-24","DOIUrl":"10.1128/spectrum.01988-24","url":null,"abstract":"<p><p><i>Staphylococcus borealis</i>, previously misidentified as <i>Staphylococcus haemolyticus</i>, was first described as a new species in 2020. In this study, we aimed to describe the clinical relevance of <i>S. borealis</i> by combining clinical data, antibiotic susceptibility profiles, and biofilm formation in isolates obtained from hospitalized and non-hospitalized patients. We established a collection of 129 <i>S</i>. <i>borealis</i> isolates from 129 adult patients from seven Norwegian hospitals. We describe clinical data at the time of microbiological specimen collection. Antibiotic susceptibility and biofilm formation were tested using established methods. Of 129 isolates (37%), 48 were from patients admitted to a hospital, the remaining from outpatients. The median (IQR) age was 62 (51-78) years, and 85/129 (66%) of the isolates were from male patients. The majority (81/129, 63%) of the <i>S. borealis</i> isolates were isolated from urine cultures, followed by isolation from skin and soft tissue cultures (35/129, 27%), blood cultures (8/129, 6%), and two implant-associated infections (2/129, 2%). Resistance to ≥3 antibiotic classes was observed in 43/129 (33%) of the isolates. All isolates formed a biofilm under the conditions tested; 59/129 (46%) weak, 40/129 (31%) medium, and 29/129 (23%) were strong biofilm producers. <i>S. borealis</i> clinical samples were predominately obtained from elderly male patients, and the majority of samples were from patients with suspected urinary tract or skin and soft tissue infections. The level of multidrug resistance was comparable to other coagulase-negative staphylococcal species, but resistance toward methicillin and penicillin was lower than in clinical <i>S. haemolyticus</i> isolates.</p><p><strong>Importance: </strong>This study contributes novel knowledge on the clinical relevance of <i>Staphylococcus borealis</i>; this is of importance when clinical microbiologists encounter <i>S. borealis</i> identified in patient samples. <i>S. borealis</i> was mainly identified in microbiological specimens from middle-aged to elderly patients, predominantly males. Hospitalized patients were also frequently immunocompromised and had other underlying conditions accompanying a suspected S. borealis infection.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0198824"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11960051/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143605684","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":"Clinical presentation, treatment, and antimicrobial susceptibility of 155 sequential <i>Staphylococcus lugdunensis</i> infections.","authors":"Kurt D Palumbo, Natasia F Jacko, Michael Z David","doi":"10.1128/spectrum.02749-24","DOIUrl":"10.1128/spectrum.02749-24","url":null,"abstract":"<p><p><i>Staphylococcus lugdunensis</i> is known to be virulent, but there are few large-scale epidemiologic studies of this species to define types of infection, susceptibility patterns, and severity. <i>S. lugdunensis</i> isolates from any culture at four U.S. tertiary care hospitals between 1 April 2021 and 1 April 2022 were identified. For the first isolate from each subject, clinical, demographic, and outcome data were recorded. Of 291 isolates, 223 were obtained from a clinically significant infection. Of these 223 isolates, 86 (38.6%) were from monomicrobial cultures; additionally, <i>S. lugdunensis</i> was considered a true pathogen in 69/137 polymicrobial infections. Among 155 subjects with <i>S. lugdunensis</i> infections, 49.7% were female, 46.5% were black, and 41.9% were white; 51.6% of infections were community associated. The most common infection sites were skin and soft tissue (SSTI) (<i>n</i> = 98, 63.2%), urinary tract (<i>n</i> = 16, 10.3%), and sinusitis (<i>n</i> = 14, 9%). Of nine monomicrobial bloodstream infections (BSIs), two were fatal, three involved foreign bodies, and two had infective endocarditis. Greater than half of SSTIs required an invasive procedure for cure. Among 138/291 isolates from colonization or infection, tetracycline, trimethoprim-sulfamethoxazole, oxacillin, and vancomycin susceptibility rates were 94.8% (128/135), 95.9% (94/98), 84.1% (116/138), and 100% (138/138), respectively. There were similarities in types of infection comparing <i>S. lugdunensis</i> in this study and prior reports on <i>Staphylococcus aureus</i>. SSTI was the predominant <i>S. lugdunensis</i> infection type; more than 50% of SSTIs required procedural intervention. Of nine BSIs, three involved a foreign body, and there were two cases of infective endocarditis. Oxacillin resistance was identified in 16% of isolates.</p><p><strong>Importance: </strong>In recent years, <i>Staphylococcus lugdunensis</i> has been identified with increasing frequency as a human pathogen causing a wide variety of clinical syndromes, from soft tissue infections to fatal cases of bloodstream infection. Despite this, there are few large-scale epidemiologic studies examining this highly virulent organism. Our study adds to the growing literature on this emerging pathogen by analyzing a large case series of sequential <i>S. lugdunensis</i> infections at four U.S. hospitals to define its contemporary epidemiology, including the types of infections it causes, their outcomes, treatment approaches, and antimicrobial susceptibilities. These data provide valuable insights for clinicians in diagnosing and treating patients with these often debilitating infections. The findings also improve upon our understanding of the incidence of each infection syndrome and variability in antimicrobial susceptibilities of isolates to guide the design of future studies on the genomic epidemiology of this important pathogen.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0274924"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11960052/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143586264","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":"Performance characteristics of an automated, high-throughput RT-PCR assay for the detection of <i>Candida auris</i> on 3-point and nasal swabs.","authors":"Nhi T Nhan, Tianxi Liu, Abdulaala A Almushajrah, Ashish Mozumder, Momka Narlieva, Wendy A Szymczak, Phyu M Thwe, Erika P Orner, Doctor Y Goldstein","doi":"10.1128/spectrum.02114-24","DOIUrl":"10.1128/spectrum.02114-24","url":null,"abstract":"<p><p><i>Candida auris</i> is a multidrug-resistant yeast responsible for invasive infections with high mortality rates, primarily spread through prolonged colonization on biotic and abiotic surfaces and traveling. Effective control necessitates comprehensive screening protocols, as recommended by the Centers for Disease Control and Prevention, which endorses a real-time polymerase chain reaction-based assay for <i>C. auris</i> screening. This study evaluates the performance of this assay on the Hologic Panther Fusion System using nasal and 3-point swab specimens (nares/axilla/groin) compared with culture. The assay was assessed for accuracy, sensitivity, specificity, and reproducibility, alongside an evaluation of probe primer reagent (PPR) onboard stability over 30 working days. Analytical sensitivity studies determined limits of detection of 1.95 Log CFU/mL for nasal swabs and 2.18 Log CFU/mL for 3-point swabs, both with >95.0% confidence intervals. The assay demonstrated 100% specificity (<i>n</i> = 25), with no false positives from genetically similar or clinically relevant species, and no significant interference from co-infecting microbes on cycle threshold (CT) values. Both swab types exhibited high intra- and inter-reproducibility, with low coefficients of variation (1.79% and 1.06%, respectively). The assay detected <i>C. auris</i> in 100% of 108 spiked-positive samples across both swab types. Clinical analysis showed 100% concordance with culture for 3-point swabs. Additionally, the nasal swab method showed 96.0% overall agreement, with 86.2% sensitivity and 100.0% specificity. The PPR mixes remained stable over 30 working days, with no significant CT value changes. This study confirms the assay's robust sensitivity, specificity, reproducibility, and accuracy for both nasal and 3-point screening swabs.</p><p><strong>Importance: </strong><i>Candida auris</i> is a multidrug-resistant yeast responsible for severe infections with high mortality rates. Rapid and accurate detection is critical for preventing the spread of this pathogen in healthcare settings. This study assesses the performance of an automated real-time PCR screening assay for detecting <i>C. auri</i>s using nasal and 3-point swabs. The findings demonstrate the assay's high sensitivity, specificity, and reproducibility, making it a valuable tool for infection control. By providing a reliable and efficient screening method, this assay can significantly enhance efforts to control <i>C. auris</i> outbreaks, ultimately improving patient outcomes and reducing the spread of this dangerous pathogen.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0211424"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11960114/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143414697","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":"Identification of <i>Escherichia coli</i> 166 isolate as an effective inhibitor of African swine fever virus replication.","authors":"Jinya Zhang, Hongyu Cui, Zhenjiang Zhang, Wenqing Wang, Fengwei Jiang, Encheng Sun, Yuanmao Zhu, Fang Li, Zhigao Bu, Dongming Zhao","doi":"10.1128/spectrum.03009-24","DOIUrl":"10.1128/spectrum.03009-24","url":null,"abstract":"<p><p>African swine fever is a lethal disease with mortality rates approaching 100% in both domestic pigs and wild boars. With no effective vaccines or treatments available, there is an urgent need for new biologics to combat the African swine fever virus (ASFV). In this study, we isolated bacteria from the intestinal contents of wild boar using culture-based methods and identified them through 16S ribosomal DNA (rDNA) sequencing. These isolates underwent high-throughput screening to evaluate their immunomodulatory effects on J774-Dual cells and their ability to inhibit ASFV replication <i>in vitro</i>. Among them, an <i>Escherichia coli</i> strain, designated as <i>E. coli</i> 166, exhibited strong inhibitory effects on various ASFV strains' replication, including three genotype II strains: virulent strain HLJ/18, moderately virulent strain HLJ/HRB1/20, genetically modified low-virulent strain HLJ/18-6GD, and one genotype I low-virulent strain SD/DY-I/21. Notably, this inhibition did not require direct interaction between the bacteria and porcine alveolar macrophages (PAMs). Both live and heat-inactivated <i>E. coli</i> 166 demonstrated a strong inhibitory effect on ASFV replication. Genetic modification of <i>E. coli</i> 166 did not alter its inhibitory phenotype. Further analysis revealed that PAMs pretreated with <i>E. coli</i> 166 showed upregulation of NF-κB and downregulation of CD163 at different time points post-infection, whereas PAMs only infected with ASFV exhibited the opposite trend. These findings suggest that <i>E. coli</i> 166 holds promise as a biological agent for controlling ASFV infection, through indirect mechanisms involving bacterial metabolites or lysis products. Future studies should focus on identifying the specific components responsible for its antiviral effects.IMPORTANCEThe emergence of the African swine fever virus (ASFV) as a devastating pathogen in swine populations necessitates the development of novel strategies for its control. In this study, <i>Escherichia coli</i> strain 166 (<i>E. coli</i> 166) demonstrated a remarkable ability to inhibit the replication of multiple ASFV strains in porcine alveolar macrophages (PAMs), even without direct bacterial contact. Both live and heat-inactivated <i>E. coli</i> 166 retained this inhibitory effect, suggesting that secreted metabolites or lysis products may play a key role. Furthermore, pretreatment of PAMs with <i>E. coli</i> 166 resulted in upregulated NF-κB activity and downregulated expression of the ASFV entry receptor CD163, presenting an immune-modulatory mechanism distinct from PAMs solely infected with ASFV. These findings highlight the potential of <i>E. coli</i> 166 as a biological agent to combat ASFV, offering a promising alternative or complementary approach to traditional antiviral strategies.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0300924"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11960076/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143502483","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":"Impact of first-void urine volume on chlamydia and gonorrhea positivity rates in men who have sex with men and transgender women.","authors":"Clayton W Hall, Adam Pyke, Mikhail Davydov, Katelin Urbanoski, Tim H Guimond, Kevin Woodward","doi":"10.1128/spectrum.03072-24","DOIUrl":"10.1128/spectrum.03072-24","url":null,"abstract":"","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0307224"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11960044/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143483423","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":"Broad-range polymerase chain reaction and sequencing for the diagnosis of infectious diseases.","authors":"Nicole E Putnam, Drew W Charles, James B Doub, J Kristie Johnson","doi":"10.1128/spectrum.02505-24","DOIUrl":"10.1128/spectrum.02505-24","url":null,"abstract":"<p><p>Broad-range polymerase chain reaction (BR-PCR) identifies molecular signatures of microorganisms directly from clinical specimens without requiring microbial growth in culture. BR-PCR may be a powerful tool to reveal microbial causes of infectious diseases, but the impact on diagnosis and clinical management has yet to be fully defined. Consequently, the aims here were to investigate how bacterial, fungal, and mycobacterial (AFB) BR-PCR perform compared to microbiology culture methods in detecting microorganisms and to assess clinical utility, defined as the ability of the results to change antimicrobial therapy or treatment duration. Between 2018 and 2021, 348 unique specimens were sent from 327 patients seen within the University of Maryland Medical System (UMMS). Patient charts were reviewed retrospectively. Organisms identified by BR-PCR were compared to bacterial (<i>n</i> = 302), fungal (<i>n</i> = 137), and AFB (<i>n</i> = 111) cultures to determine concordance and were evaluated to determine if they led to a change in clinical management. Agreement in organism(s) reported by BR-PCR and culture was considered concordant for calculating performance data. Sensitivity of BR-PCR compared to concordant culture results was 30.9% for bacteria (25/81; 95% CI: 21.8-41.6%), 18.8% for fungi (3/16; 95% CI: 5.8-43.8%), and 33.3% for AFB (1/3; 95% CI: 5.6-79.8%) detection. The bacterial negative percent agreement of 80.1% (165/206) may reflect antibiotic pretreatment or detection of fastidious organisms. Despite longer turnaround times, BR-PCR results changed clinical care in 6% of cases. Based on these findings herein, the clinical use of BR-PCR would be best utilized when fastidious organisms are suspected, or specimens remain culture negative, but should not replace routine culture methods at this time.IMPORTANCEDetermining infectious etiology can be challenging in patients with chronic presentation and in those receiving empiric therapy. In addition to the standard of care (microbiology cultures), providers can order a broad-range polymerase chain reaction and sequencing (BR-PCR) test to identify microorganisms directly from clinical specimens and independently from culture. While studies have been done from individual hospitals or systems, there is a lack of broadly applicable clinical evidence detailing clinical scenarios in which BR-PCR should be utilized. This study adds to the growing body of literature surrounding BR-PCR clinical usage, examining assay performance and clinical utility of BR-PCR test results. Although BR-PCR and culture had low concordance among organisms identified, it was shown to complement the standard of care for uncommonly isolated and fastidious organisms. Overall, BR-PCR results changed clinical management in 6% of cases, which is similar to other studies that include a broad representation of specimen types.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0250524"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11960090/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143557425","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 influence of trace metal supplementation on the presence of ceftriaxone resistance in <i>Enterobacteriaceae</i> in the gastrointestinal tract of dairy cattle.","authors":"Charles-Antoine Martineau, Mélissa Duplessis, Jennifer Ronholm, Renée M Petri","doi":"10.1128/spectrum.01090-24","DOIUrl":"10.1128/spectrum.01090-24","url":null,"abstract":"<p><p>The addition of trace minerals into the diet of lactating cows frequently exceeds national recommendations for industry practices. However, the presence of certain heavy metals, such as zinc and copper, has been shown to exert selection pressure on the gut microbiota, favoring metal resistance and potential co-selection for antimicrobial resistance. To determine whether oversupplementation of dietary zinc alters the gut microbiota of dairy cattle, a cross-over design was used to feed either recommended or surplus levels of dietary zinc (0.89×; high mineral diet) compared to the recommended levels (control diet). Rumen, duodenum, and fecal samples were collected to analyze the 16S rRNA microbial community for diversity and relative abundance, with a greater focus on the <i>Enterobacteriaceae</i> family, while mixed enriched gut content samples were cultured to determine the presence of zinc, copper, and ceftriaxone resistances in gram-negative bacteria. Alpha-diversity analysis showed a decrease in richness and evenness (Simpson index) when cows were in the HIGH treatment (<i>P =</i> 0.0464) and a tendency to decrease (<i>P =</i> 0.0592) diversity according to the Shannon index. Despite alpha-diversity differences, <i>Enterobacteriaceae</i> abundance showed no difference between treatments. For culturing, a tendency (<i>P =</i> 0.0956) for decreased fecal resistance to zinc on MacConkey mixed enriched isolates was observed for the HIGH group. This study showed that there were differences between niches but no significant increase in resistance in response to zinc, copper, and ceftriaxone in the enriched <i>Enterobacteriaceae</i> populations from the rumen, duodenum, and fecal niches and that zinc oversupplementation had minimal impact on gut microbiota communities.</p><p><strong>Importance: </strong>The addition of trace minerals into the diet of lactating cows, at levels exceeding national recommendations, is a common industry practice. However, there are new concerns as the presence of certain heavy metals, such as zinc, has been shown to exert selection pressure on the gut microbiota, favoring metal resistance and potential co-selection for antimicrobial resistance. We evaluated how the addition of zinc in the diet of lactating cows affects the bacterial community's relative abundance and diversity, with a focus on the <i>Enterobacteriaceae</i> family throughout the gastrointestinal tract, due to their importance for human health. Using samples from the rumen, duodenum, and feces, we cultivated gram-negative bacteria from enriched samples in the presence of zinc, copper, and ceftriaxone resistances to confirm phenotype resistances. This study contributes to our understanding of how dairy diets oversupplemented with minerals may alter the microbial community of the animal and could contribute to the dissemination of antibiotic resistance.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0109024"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11960429/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143449495","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}