Microbiology spectrum最新文献

{"title":"Association of infection-induced antibody levels with risk of subsequent SARS-COV-2 reinfection among healthcare professionals, Rhode Island, 1 March 2020-17 February 2021.","authors":"Jianrong Shi, M Gayle Gabriel, Monica Epperson, Phil A Chan, Jefferson M Jones, Lyle R Petersen, Melissa Briggs Hagen, Natalie J Thornburg, Sharon Saydah, Claire M Midgley","doi":"10.1128/spectrum.02086-24","DOIUrl":"https://doi.org/10.1128/spectrum.02086-24","url":null,"abstract":"<p><p>Numerous studies have investigated vaccine-induced correlates of protection (CoP) against severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) infection, but data on infection-induced CoP are limited. Given differences between vaccine- and infection-induced immune responses, in conjunction with low vaccination in many US populations, a better understanding of infection-induced CoP is needed. We used residual sera from a mid-2020 Rhode Island serosurvey of healthcare professionals (HCP) and corresponding state-collected SARS-CoV-2 testing data through February 2021 to generate an analytic cohort of HCP with a first SARS-CoV-2 infection prior to serosurvey blood collection and multiple viral tests after blood collection to assess for reinfection (defined as a positive viral test ≥90 days after their first positive). We tested sera for levels of IgG and IgA targeting ancestral spike (S), receptor-binding domain (RBD), or nucleocapsid (N). We used adjusted Cox proportional hazard ratios to assess the association between categorical antibody level and the risk of subsequent reinfection. Among 170 HCP included in this analysis (median age = 47 years; interquartile range: 35-55 years), 30 were reinfected during the analytic period. Adjusted Cox proportional hazard ratios indicated that higher levels of anti-S or anti-RBD IgG were significantly associated with a lower risk of reinfection. These findings support the use of anti-S or anti-RBD IgG levels as markers of immunologic protection, such as in population serosurveys, or immune-bridging studies in settings of high prevalence of prior infection.  IMPORTANCEThe measurement of antibodies in blood is a relatively simple process and commonly used to estimate overall levels of past infection in populations. But, if someone has antibodies, does this mean that they are protected from being infected again? And are people with higher levels of antibody better protected? There are good data in the literature exploring how antibodies from the coronavirus disease 2019 (COVID-19) vaccination are associated with protection. But, there is still a lot to learn about protection conferred by antibodies that develop after a severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) infection. In our study, we measure the levels of six different antibody types developed after infection and compare levels to the risk of subsequent infection to better understand which antibody types are best associated with protection. Our data are important for improving studies that use antibodies as proxies for protection, such as population immunity estimates, or those assessing new prevention products.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0208624"},"PeriodicalIF":3.7,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143492887","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":"Simplifying SARS-CoV-2 wastewater-based surveillance using an automated FDA EUA assay.","authors":"Shivaprasad H Sathyanarayana, Ashlee A Robins, Diana M Toledo, Torrey L Gallagher, Gregory J Tsongalis, Jacqueline A Hubbard, Joel A Lefferts, Isabella W Martin","doi":"10.1128/spectrum.02490-24","DOIUrl":"https://doi.org/10.1128/spectrum.02490-24","url":null,"abstract":"<p><p>Wastewater-based surveillance (WBS) can track the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in communities. Laboratory methods for this testing involve labor-intensive, multi-step processes. This study assessed the feasibility of performing WBS with an off-label use of an automated commercial SARS-CoV-2 assay that had received Emergency Use Authorization for human diagnostic testing from the United States Food and Drug Administration (FDA EUA). Twenty-four-hour composite samples of primary influent wastewater from seven municipalities in New Hampshire and Vermont were collected between September 2020 and February 2021, and were centrifuged upon receipt. An aliquot of fresh supernatant was immediately tested with the Abbott <i>m</i>2000 RealTi<i>m</i>e SARS-CoV-2 assay (Abbott Molecular, Des Plaines, IL, USA). Corresponding aliquots were then stored at -80°C until they were thawed, polyethylene glycol (PEG) concentrated, and tested by two PCR-based laboratory-developed tests (LDTs). Wastewater samples (103) were tested with successful detection of SARS-CoV-2 viral RNA by all three methods. Bland-Altman analysis showed overall concordant results with a bias of -0.13 and -0.42 log copies/mL detected by the FDA EUA assay compared to the LDTs. Specimen stability assessment demonstrated a decrease of 33.9% measurable viral RNA after three freeze-thaw cycles. SARS-CoV-2 detection in wastewater using an FDA EUA assay on an automated commercial testing platform performed comparably but with more efficient workflow when compared to two LDTs. This sample-to-answer automated method could save time and labor for surveillance testing, but further validation of its ability to quantitate SARS-CoV-2 viral RNA is necessary.IMPORTANCEThis proof-of-principle study evaluates an off-label use of an automated United States Food and Drug Administration (FDA) Emergency Use Authorization (EUA) severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) human diagnostic assay for wastewater surveillance. Compared to standard, labor-intensive, multi-step methods currently in use for wastewater surveillance testing, an off-label use of an FDA EUA assay on an automated platform offers a sample-to-answer testing requiring less labor and a faster turnaround time.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0249024"},"PeriodicalIF":3.7,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143492912","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":"Fur-regulated urease contributes to the environmental adaptation of <i>Yersinia pseudotuberculosis</i>.","authors":"Junyang Wang, Peishuai Fu, Xinquan He, Yuqi Liu, Yuxin Zuo, Zhiyan Wei, Yao Wang, Yantao Yang, Changfu Li, Xihui Shen, Lingfang Zhu","doi":"10.1128/spectrum.02756-24","DOIUrl":"https://doi.org/10.1128/spectrum.02756-24","url":null,"abstract":"<p><p>Urease converts urea into ammonia and carbon dioxide, providing a nitrogen and carbon source for microbial growth and serving as an important mechanism for human bacterial pathogens to survive in acidic conditions, which can be regulated by many factors. As a global regulator, the ferric uptake regulator (Fur) regulates a series of genes and pathways involved in many different cellular processes and the virulence of the enteric bacterium <i>Yersinia pseudotuberculosis</i> (<i>Yptb</i>). However, whether Fur regulates the urease activity in <i>Yptb</i> was still unknown. In this study, we found that urease is positively regulated by Fur in response to manganese ions (Mn²⁺), and this regulation by Fur is mediated by specific recognition of the promoter region of urease in <i>Yptb</i>. Furthermore, urease is induced by Mn²⁺ via Fur under low nutrient conditions. Moreover, we provided evidence that urease plays an important role in acid and osmotic stress resistance, biofilm formation, and virulence of <i>Yptb</i>. Our findings provide insights into understanding the regulatory mechanism and multiple functions of urease in <i>Yptb</i>.IMPORTANCEUrease catalyzes the breakdown of urea into ammonia and carbamate, which are widely distributed among bacterial species and play an important role as an important acid resistance system and virulence factor. In most bacterial species, urease expression is tightly regulated in response to environmental cues such as nitrogen status, pH, growth phase, substrate availability, or transcriptional regulators. In this study, we found that urease from <i>Yptb</i> is positively regulated by Fur in response to Mn²⁺ under low nutrient conditions, which functions to combat acid and osmotic stress and enhance biofilm formation, and plays a crucial role in virulence. Importantly, this is the first demonstration of a direct role for Fur and Mn²⁺ in regulating urease expression in <i>Yptb</i>. This study provides a comprehensive understanding of the regulatory mechanisms and functions of urease from <i>Yptb</i>.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0275624"},"PeriodicalIF":3.7,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143492951","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":"Human bocavirus-1 infection in hospitalized pediatric patients with acute respiratory tract infections.","authors":"Jie Tan, Ziyin Huang, Wenting Tang, Guangbing Liu, Peiqun Li, Jiaqi Wen, Lishai Mo, Chenglan Yan, Zhao Dang, Huiping Huang, Qifei Li, Chunyun Fu","doi":"10.1128/spectrum.02985-24","DOIUrl":"https://doi.org/10.1128/spectrum.02985-24","url":null,"abstract":"<p><p>Human bocavirus-1 (HBoV1) is an emerging viral pathogen associated with acute respiratory tract infections (ARTIs) in pediatric populations. This study aimed to evaluate the infection status and clinical characteristics of HBoV1 among hospitalized children suffering from ARTIs. A cohort of 5,021 pediatric patients with respiratory infections was analyzed using targeted next-generation sequencing to identify HBoV1 and other co-existing respiratory pathogens. Results indicated a detection rate of HBoV1 of 8.48%, predominantly among infants under 24 months, with a higher prevalence observed in males. Among the 426 children with HBoV1 detected, there were 17 cases (4%) of single HBoV1 infection, and 409 cases (96%) were co-infected with HBoV1 and other pathogens. The predominant infection pattern was HBoV1-bacteria-virus co-infection (155 cases). A total of 48 other pathogens were detected in children with HBoV1 co-infections, with rhinovirus and human herpesvirus being the most common. The median hospitalization duration for the children with HBoV1 was 8 days, and 16.26% required ICU admission for monitoring. The study offers a comprehensive analysis of the distribution of co-infecting pathogens, clinical features, and outcomes in hospitalized children with HBoV one infection.</p><p><strong>Importance: </strong>There is currently a poor understanding of the characteristics and clinical manifestations of human bocavirus-1 (HBoV1) infection. In the past decade, few studies have thoroughly analyzed co-infecting pathogens, such as viruses, bacteria, and fungi and their patterns in relation to HBoV1. This study utilizes targeted next-generation sequencing (tNGS) technology to identify HBoV1 and other common respiratory pathogens in 5,021 hospitalized children suffering from respiratory infections in the Guangxi region. It offers a detailed analysis of the distribution of co-infecting pathogens, infection patterns, laboratory findings, clinical manifestations, imaging features, complications, and prognoses related to HBoV1 infection in this population. The study highlights the high co-infection rates associated with HBoV1 and offers important insights for diagnosing, treating, and managing children with HBoV1 infection.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0298524"},"PeriodicalIF":3.7,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143492955","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":"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":"https://doi.org/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":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Wild raccoons (<i>Procyon lotor</i>) as a potential reservoir of cytolethal distending toxin-producing <i>Providencia</i> strains in Japan.","authors":"Okechukwu John Obi, Atsushi Hinenoya, Sharda Prasad Awasthi, Noritoshi Hatanaka, Shah M Faruque, Shinji Yamasaki","doi":"10.1128/spectrum.02616-24","DOIUrl":"https://doi.org/10.1128/spectrum.02616-24","url":null,"abstract":"&lt;p&gt;&lt;p&gt;In view of increasing reports of infections due to virulent &lt;i&gt;Providencia&lt;/i&gt; species including cytolethal distending toxin (&lt;i&gt;cdt&lt;/i&gt;) gene-positive strains, it is important to identify the reservoirs and transmission routes of such pathogenic strains. Raccoons considered to be a source of zoonotic pathogens were monitored for the presence of &lt;i&gt;Providencia&lt;/i&gt; species in Japan and analyzed for &lt;i&gt;cdt&lt;/i&gt; genes. Of 384 wild raccoon rectal swabs analyzed, 60% were positive for &lt;i&gt;Providencia&lt;/i&gt; species, of which 20% carried &lt;i&gt;cdt&lt;/i&gt;-genes. Among seven &lt;i&gt;Providencia&lt;/i&gt; species isolated (&lt;i&gt;P. alcalifaciens, P. rustigianii, P. rettgeri, P. stuartii, P. heimbachae, P. vermicola,&lt;/i&gt; and &lt;i&gt;P. huaxiensis&lt;/i&gt;), &lt;i&gt;cdt&lt;/i&gt; genes were distributed in &lt;i&gt;P. alcalifcaiens&lt;/i&gt; (63%), &lt;i&gt;P. rustigianii&lt;/i&gt; (16%), and novel in &lt;i&gt;P. rettgeri&lt;/i&gt; (21%). Complete &lt;i&gt;cdt&lt;/i&gt; gene clusters were identified in &lt;i&gt;P. alcalifaciens&lt;/i&gt; and &lt;i&gt;P. rustigianii&lt;/i&gt; strains, whereas &lt;i&gt;P. rettgeri&lt;/i&gt; had intact &lt;i&gt;cdtB&lt;/i&gt; but truncated &lt;i&gt;cdtA&lt;/i&gt; and &lt;i&gt;cdtC&lt;/i&gt; genes. Phylogenetic analyses showed divergent pulsotypes among the &lt;i&gt;cdt&lt;/i&gt; gene-positive &lt;i&gt;Providencia&lt;/i&gt; strains. Cytotoxicity assay revealed that &lt;i&gt;P. alcalifaciens&lt;/i&gt; and &lt;i&gt;P. rustigianii&lt;/i&gt; produced CDT more toxic to eukaryotic cells compared to human clinical strains, which were neutralized by anti-PaCdtB serum. As expected, the &lt;i&gt;P. rettgeri&lt;/i&gt; strains with truncated &lt;i&gt;cdt&lt;/i&gt; genes had no biological activity. Molecular analysis revealed that all the &lt;i&gt;cdt&lt;/i&gt; genes were located on plasmids as determined by S1-nuclease pulsed-field gel electrophoresis (S1-PFGE) and Southern hybridization assay. Intriguingly, the &lt;i&gt;cdtB&lt;/i&gt; gene in &lt;i&gt;P. rustigianii&lt;/i&gt; strains was detected on dual plasmids. Notably, all the &lt;i&gt;cdt&lt;/i&gt; gene-positive &lt;i&gt;Providencia&lt;/i&gt; strains were found to carry plasmid-mediated T3SS-related genes. These results suggest that wild raccoons are possible reservoir of virulent &lt;i&gt;Providencia&lt;/i&gt; strains in Japan.IMPORTANCE&lt;i&gt;Providencia&lt;/i&gt; species considered normal flora are occasionally associated with gastroenteritis in healthy humans. Cytolethal distending toxin (CDT), a bacterial virulence factor found in various Gram-negative bacteria and associated with gastroenteritis and extra-intestinal infection has also been reported in at least two &lt;i&gt;Providencia&lt;/i&gt; species (&lt;i&gt;P. alcalifaciens&lt;/i&gt; and &lt;i&gt;P. rustigianii&lt;/i&gt;). Determination of the transmission routes of such virulent &lt;i&gt;Providencia&lt;/i&gt; is crucial for the implementation of evidence-based control programs. In this study, we identified raccoons as the probable reservoir of the &lt;i&gt;cdt&lt;/i&gt; gene-positive &lt;i&gt;Providencia&lt;/i&gt; strains in Japan. Interestingly, CDTs produced by raccoon-derived &lt;i&gt;Providencia&lt;/i&gt; strains exerted more toxic effects on the eukaryotic cells compared to the clinical &lt;i&gt;Providencia&lt;/i&gt; strains. In addition, the identification of a novel &lt;i&gt;cdt&lt;/i&gt; gene cluster in another species &lt;i&gt;P. ret","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0261624"},"PeriodicalIF":3.7,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143492569","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 establishment and optimization of a <i>Mycoplasma pneumoniae</i> detection system based on ERA-CRISPR/Cas12a.","authors":"Fo Yang, Qianlin Wu, Xiaotong Zeng, Qiuyang Jiang, Shanshan Zhang, Jin Wang, Qi Zhang, Feng Li, Dayong Xu","doi":"10.1128/spectrum.03235-24","DOIUrl":"https://doi.org/10.1128/spectrum.03235-24","url":null,"abstract":"<p><p><i>Mycoplasma pneumoniae</i> (MP) is a significant pathogen associated with community-acquired pneumonia, with considerable infectious risks posed, particularly to children and immunocompromised individuals. The current methods for detecting MP in research and clinical settings are recognized as time-consuming, instrument-dependent, and prone to non-specific cross-reactivity. Therefore, the creation of a rapid and sensitive detection method is urgently required. In this study, the MP-ERA-Cas12a system, integrating enzyme restriction amplification (ERA) with clustered regularly interspaced short palindromic repeats (CRISPR)/Cas12a technology, was introduced. Three detection methods were evaluated: the two-pot system, a modified one-pot system, and a lateral flow assay (LFA) strip-based system. In the one-pot system, the amplification and detection steps were consolidated within a single reaction vessel, effectively minimizing the risk of contamination and false positives that may arise from the handling of multiple tubes. It was observed that the one-pot system generated a fluorescent signal within 1 h and produced 1.6 times higher fluorescence signal intensity compared to the two-pot system, achieving a detection limit of 1 copy/μL. In contrast, the LFA system facilitated rapid on-site screening, with visible band results appearing on the strip within 5 min of the reaction, and a detection limit of 10² copies/μL was achieved. High specificity for MP was demonstrated by all methods. Significant advantages, including rapid processing, the absence of complex instrumentation, and ease of use are offered by this detection system, making it particularly suitable for resource-limited clinical settings. The system is seen as an efficient tool for the early diagnosis of MP, with substantial public health and clinical relevance.</p><p><strong>Importance: </strong>This study successfully combined enzyme restriction amplification (ERA) with the specific detection capabilities of clustered regularly interspaced short palindromic repeats (CRISPR)/Cas12a. Based on the two-pot system established before, the one-pot system and lateral flow assay (LFA) system were developed for <i>Mycoplasma pneumoniae</i> (MP) detection. The MP-ERA-Cas12a system eliminates the need to open the lid during the reaction, reducing aerosol contamination, and minimizing the risk of false positives. The method does not require the use of advanced instruments or equipment and shows strong specificity while not being affected by other pathogens. As a new method of MP detection, the MP-ERA-Cas12a system has an important practical application prospect.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0323524"},"PeriodicalIF":3.7,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143492469","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":"Characterization of vaginal microbiomes in clinician-collected bacterial vaginosis diagnosed samples.","authors":"Hayden N Brochu, Qimin Zhang, Kuncheng Song, Ling Wang, Emily A Deare, Jonathan D Williams, Crystal R Icenhour, Lakshmanan K Iyer","doi":"10.1128/spectrum.02582-24","DOIUrl":"https://doi.org/10.1128/spectrum.02582-24","url":null,"abstract":"<p><p>Bacterial vaginosis (BV) is a type of vaginal inflammation caused by bacterial overgrowth, upsetting the healthy microbiome of the vagina. Existing clinical testing for BV is primarily based upon physical and microscopic examination of vaginal secretions. Modern PCR-based clinical tests target panels of BV-associated microbes, such as the Labcorp NuSwab test that targets <i>Atopobium</i> (<i>Fannyhessea</i>) <i>vaginae</i>, <i>Megasphaera-1</i>, and <i>Bacterial Vaginosis Associated Bacterium (BVAB)-2</i>. Remnant clinician-collected NuSwab vaginal swabs underwent DNA extraction and 16S V3-V4 rRNA gene sequencing to profile microbes in addition to those included in the Labcorp NuSwab test. Community state types (CSTs) were determined using the most abundant taxon detected in each sample. PCR results for NuSwab panel microbial targets were compared against the corresponding microbiome profiles. Metabolic pathway abundances were characterized via metagenomic prediction from amplicon sequence variants (ASVs). 16S V3-V4 rRNA gene sequencing of 75 remnant vaginal swabs yielded 492 unique 16S V3-V4 ASVs, identifying 83 unique genera. NuSwab microbe quantification was strongly concordant with quantification by sequencing (<i>P</i> < 0.01). Samples in CST-I (18 of 18, 100%), CST-II (three of three, 100%), CST-III (15 of 17, 88%), and CST-V (one of one, 100%) were largely categorized as BV-negative via the NuSwab panel, while most CST-IV samples (28 of 36, 78%) were BV-positive or BV-indeterminate. BV-associated microbial and predicted metabolic signatures were shared across multiple CSTs. These findings highlight robust sequencing-based quantification of Labcorp NuSwab BV microbes, accurate discrimination of vaginal microbiome CSTs dominated by distinct <i>Lactobacilli</i>, and expanded the identification of BV-associated bacterial and metabolic biomarkers.IMPORTANCEBacterial vaginosis (BV) poses a significant health burden for women during reproductive years and onward. Current BV diagnostics rely on either panels of select microbes or on physical and microscopic evaluations by technicians. Here, we sequenced the microbiome profiles of samples previously diagnosed by the Labcorp NuSwab test to better understand disruptions to the vaginal microbiome during BV. We show that microbial sequencing can faithfully reproduce targeted PCR diagnostic results and can improve our knowledge of healthy and BV-associated microbial and metabolic biomarkers. This work highlights a robust, agnostic BV classification scheme with potential for future development of sequencing-based BV diagnostic tools.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0258224"},"PeriodicalIF":3.7,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143492889","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":"Coexistence of <i>tmexCD-toprJ</i>, <i>bla</i>_NDM-1, and <i>bla</i>_PME-1 in multi-drug-resistant <i>Pseudomonas juntendi</i> isolates recovered from stool samples.","authors":"Wugao Liu, Yi Liu, Jing Jin, Ningjun Wu, Weiping Wu, Chunsheng Qu","doi":"10.1128/spectrum.01136-24","DOIUrl":"https://doi.org/10.1128/spectrum.01136-24","url":null,"abstract":"<p><p><i>Pseudomonas juntendi</i> has received limited research attention, yet strains carrying multi-drug resistance genes pose a threat to global public health. We aimed to characterize the genome of two fecal-derived strains of <i>Pseudomonas juntendi</i>, both harboring <i>tmexCD-toprJ</i>, <i>bla</i>_NDM-1, and <i>bla</i>_PME-1 on the chromosome, recovered from two patients. Average nucleotide identity (ANI) analysis showed that L4008hy and L4046hy were remarkably similar. They showed high levels of resistance to aztreonam, imipenem, ciprofloxacin, amikacin, piperacillin-tazobactam, ceftazidime-avibactam, and polymyxin B in antimicrobial susceptibility testing using agar dilution method and broth microdilution methods. Additionally, an integrative and conjugative element (ICE) similar to ICE<i>6660</i> was detected on the chromosome, which contains all resistance genes and has a relatively complete transfer module, and potential transfer mechanisms were identified. Phylogenetic analysis of <i>P. juntendi</i> reveals the genomic diversity of the species and sheds light on environmental-human transmission.IMPORTANCEUp to now, research on <i>Pseudomonas juntendi</i> is still very limited. Our findings suggest that <i>P. juntendi</i> commonly carries diversity resistance genes on chromosomes and is stably inherited, highlighting the need for further studies on the antimicrobial properties of this bacterium. The coexistence of <i>tmexCD-toprJ</i>, <i>bla</i>_NDM-1, and <i>bla</i>_PME-1 on the chromosome in <i>P. juntendi</i> was reported for the first time. The identified integrative and conjugative element (ICE) contains all the identified resistance genes and serves as a vector for resistance gene transfer between bacteria. <i>P. juntendi</i>, which harbors multi-drug resistance genes, particularly those encoding carbapenemases, acts as a reservoir of resistance genes. Its spread in clinical settings poses additional challenges to treatment.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0113624"},"PeriodicalIF":3.7,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143492890","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":"Co-existence of plasmid-mediated <i>bla</i>_NDM-1 and <i>bla</i>_NDM-5 in <i>Escherichia coli</i> sequence type 167 and ST101 and their discrimination through restriction digestion.","authors":"Amrita Bhattacharjee, Priyanka Basak, Shravani Mitra, Jagannath Sarkar, Shanta Dutta, Sulagna Basu","doi":"10.1128/spectrum.00987-24","DOIUrl":"https://doi.org/10.1128/spectrum.00987-24","url":null,"abstract":"&lt;p&gt;&lt;p&gt;The concurrent presence of multiple New Delhi metallo-β-lactamase (&lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDM&lt;/sub&gt;) variants within an isolate often goes undetected without next-generation sequencing. This study detects and characterizes dual &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDM&lt;/sub&gt; variants in &lt;i&gt;Escherichia coli&lt;/i&gt; through Sanger and whole-genome sequencing. Additionally, a rapid identification method utilizing restriction digestion was designed for detecting &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDM&lt;/sub&gt; variants carrying M154L mutation. Antibiotic susceptibility, minimal inhibitory concentration for meropenem and ertapenem, PCR, and Sanger sequencing of &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDM&lt;/sub&gt; along with genome sequencing using Illumina and Nanopore technology were conducted. Transmissibility and replicon types of &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDM&lt;/sub&gt;-harboring plasmids were evaluated. Restriction digestion using restriction enzyme, BtsCI was developed to distinguish between &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDM-1&lt;/sub&gt; and &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDM&lt;/sub&gt; variants possessing M154L mutation, such as &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDM-5&lt;/sub&gt;, &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDM-7&lt;/sub&gt; etc. Two isolates belonging to phylogroups A; ST167 and B1; ST101 and resistant to meropenem and ertapenem (≥16 mg/L) were recovered from the blood of a neonate and the rectal swab of a pregnant woman, respectively. &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDM&lt;/sub&gt; was detected by PCR, and Sanger sequences of &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDM&lt;/sub&gt; showed two peaks at 262 (G and T) and 460 (A and C) nucleotide positions indicative of more than one &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDM&lt;/sub&gt; variant. Hybrid assembly confirmed co-existence of &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDM-1&lt;/sub&gt; and &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDM-5&lt;/sub&gt; in each isolate. &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDM-1&lt;/sub&gt; was located on IncY (ST167) and IncHI1A/HI1B (ST101), while &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDM-5&lt;/sub&gt; was on IncFIA/FII (ST167) and IncC (ST101) plasmids in the two isolates. Digestion with BtsC1 could discriminate between &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDM-1&lt;/sub&gt; and &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDM-5&lt;/sub&gt;. The co-existence of multiple &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDMs&lt;/sub&gt;, &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDM-1&lt;/sub&gt;, and &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDM-5&lt;/sub&gt; in epidemic clones of &lt;i&gt;E. coli&lt;/i&gt; is concerning. Restriction digestion method and Sanger sequencing can facilitate quick identification of dual &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDM&lt;/sub&gt; variants in a single isolate.IMPORTANCEThe global dissemination of antimicrobial resistance genes is a serious concern. One such gene, &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDM&lt;/sub&gt;, has spread globally via plasmids. &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDM&lt;/sub&gt; confers resistance against all β-lactam antibiotics, except monobactams. Most of the earlier literature reported the presence of single &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDM&lt;/sub&gt; variant. However, this study reports the prevalence of dual &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDM&lt;/sub&gt; variants (&lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDM-1&lt;/sub&gt; and &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDM-5&lt;/sub&gt;) located on two separate plasmids identified in two distinct &lt;i&gt;Escherichia coli&lt;/i&gt; epidemic clones ST167 and ST101 isolated from a septicemic neonate and a pregnant mother, respectively. &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDM-5&lt;/sub&gt; differs from &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDM-1&lt;/sub&gt; ","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0098724"},"PeriodicalIF":3.7,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143492892","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}