Microbiology spectrum最新文献

{"title":"Validation of rectal swabbing for total and aerobic gut microbiota study.","authors":"Julie Marin, Paul Albin Bertoye, Andre Birgy, Samira Dziri, Mathilde Lescat","doi":"10.1128/spectrum.01823-24","DOIUrl":"10.1128/spectrum.01823-24","url":null,"abstract":"<p><p>In microbiota research, whole stool sampling is the conventional approach but can be problematic or infeasible for certain patients. This study aims to validate the use of rectal swabbing as an alternative method for microbiota analysis and determine optimal storage conditions suitable for various clinical settings, including intensive care units. We evaluated different sampling techniques and storage temperatures. Our findings indicated that rectal swabs yield microbiota diversity comparable to whole stool samples. Notably, storage conditions significantly impacted microbiota profiles, with increased <i>E. coli</i> and <i>Enterococcus sp</i>. quantifications observed at room temperature (RT). Consequently, we recommend immediate refrigeration of rectal swabs to reliably assess aerobic and total microbiota, particularly for patients requiring urgent care, such as antibiotic treatment.</p><p><strong>Importance: </strong>We developed a pragmatic approach to study total and aerobic gut microbiota, applicable in numerous clinical units, such as intensive care or emergency units, where whole stool sampling is often impractical. This approach employs ESwab devices, which are already commonly used in hospitals.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0182324"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143449498","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":"Persistence and decay of neutralizing antibody responses elicited by SARS-CoV-2 infection and hybrid immunity in a Canadian cohort.","authors":"Amy Nouanesengsy, Anthony Semesi, Kim Quach, Danton Ivanochko, Walter Byrne, Matthew Hwang, Maria-Rosa La Neve, Matilde Leon-Ponte, Alice Litosh, Nicole Wisener, Khosrow Adeli, Aaron Campigotto, Eyal Grunebaum, Allison McGeer, Theo J Moraes, Lusia Sepiashvili, Julia Upton, Jean-Philippe Julien, Upton Allen","doi":"10.1128/spectrum.01333-24","DOIUrl":"10.1128/spectrum.01333-24","url":null,"abstract":"<p><p>A major challenge with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), has been assessing the intensity, dynamics, and determinants of the antibody responses after infection and/or vaccination. Therefore, we aimed to characterize the longitudinal dynamics of the antibody responses among naturally infected individuals and individuals who achieved hybrid immunity in a large Canadian cohort. We demonstrate that anti-Spike IgGs and neutralizing antibody dynamics vary greatly among individuals with COVID-19, in peak antibody levels, rate of waning, and longevity of the antibody response. Additionally, we found an association between robust antibody responses and individuals with severe COVID-19 clinical symptoms during the first-month post-symptom onset. For individuals who achieved hybrid immunity, a robust increase in anti-S1 IgGs and neutralizing antibodies followed the first vaccination dose; however, there was a minimal increase in the anti-S1 IgGs and neutralizing antibody titers after administration of the second dose of the vaccine. Furthermore, neutralizing antibodies elicited by the wild-type virus alone were largely ineffective against emerging variants of concern in our natural infection-only cohort, in contrast to a much broader and more robust neutralization profile observed in individuals who achieved hybrid immunity. Our findings emphasize the need for global SARS-CoV-2 vaccination efforts to further sustain protective immune responses required to minimize viral spread and disease severity in the population. As SARS-CoV-2 variants continue to emerge, understanding the interplay between previous infections, vaccine durability, and virus evolution will be critical for guiding ongoing vaccination strategies.</p><p><strong>Importance: </strong>A major challenge with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), has been assessing the intensity, dynamics, and determinants of the antibody response after infection and/or vaccination. Our paper addresses this in a large Canadian cohort with antibody responses that were generated by natural infection as well as vaccine in some persons studied.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0133324"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143449563","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":"Peste des petits ruminants virus virulence is associated with an early inflammatory profile in the tonsils and cell cycle arrest in lymphoid tissue.","authors":"Roger-Junior Eloiflin, Llorenç Grau-Roma, Vincent Lasserre, Sylvie Python, Stephanie Talker, Philippe Totte, Obdulio García-Nicolás, Artur Summerfield, Arnaud Bataille","doi":"10.1128/spectrum.03124-24","DOIUrl":"10.1128/spectrum.03124-24","url":null,"abstract":"<p><p>Using a systems immunology approach, this study comprehensively explored the immunopathogenesis of peste des petits ruminants (PPR) focussing on strain-dependent differences in virulence. Saanen goats were infected either with the highly virulent (Morocco 2008 [MA08]) or the low-virulent (Ivory Coast 1989 [IC89]) strain of the PPR virus (PPRV). As expected, MA08-infected goats exhibited higher clinical scores, pronounced lymphocyte depletion, and lesions affecting mucosal and lymphoid tissues. CD4 T cells were more affected in terms of depletion and infection in peripheral blood. Transcriptional analyses of the blood and lymphoid tissue demonstrated activation of interferon type I (IFN-I) responses at 3 days post-infection (dpi) only with MA08, but comparable IFN-I expression levels with MA08 and IC89 at 6 dpi. MA08 strain induced strong inflammatory and myeloid cell-related transcriptional responses observed in tonsils but not in mesenteric lymph node. This inflammatory response in the tonsils was associated with an extensive damage and infection of the tonsillar epithelium in the crypts, pointing to a barrier defect as a possible cause of inflammation. An early and prominent downregulation of cell cycle gene networks was observed in all compartments analyzed in MA08-infected animals. This effect can be interpreted as suppressed lymphocyte proliferation that may cause immunosuppression during the first week following MA08 infection. A proteome analysis confirmed synthesis of IFN-I response proteins during infection with both strains, but only MA08 strain additionally upregulated ribosomal and inflammation-related proteins. In conclusion, the present comprehensive investigation delineates strain-dependent differences in early immunopathological processes associated with severe inflammation disease and a blunted lymphocyte proliferation.</p><p><strong>Importance: </strong>Field observations show that the severity of PPR is highly dependent on the viral (PPRV) strains and the host infected, but the mechanisms behind these variations are not well understood. Here we compare immune response in Saanen goats infected with high (MA08) and low (IC89) virulent PPRV strains. Analyses revealed a differential immune response: early activation of IFN-I responses only with MA08 but comparable IFN-I expression levels with MA08 and IC89 at later stages. Additionally, MA08 strain triggered inflammatory and myeloid cell-related responses in the tonsils and marked suppression of lymphocyte proliferation evidenced by cell cycle arrest. CD4 T cells were found to be most affected in terms of depletion in the peripheral blood. Massive infection of the tonsils seems to induce epithelial lesions that promote the inflammatory responses. These results underscore the need to understand strain-specific differences for PPR surveillance and control.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0312424"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143483365","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":"(p)ppGpp and DksA play a crucial role in reducing the efficacy of β-lactam antibiotics by modulating bacterial membrane permeability.","authors":"Meenal Chawla, Jyoti Verma, Shashi Kumari, Tushar Matta, Tarosi Senapati, Prabhakar Babele, Yashwant Kumar, Rupak K Bhadra, Bhabatosh Das","doi":"10.1128/spectrum.01169-24","DOIUrl":"10.1128/spectrum.01169-24","url":null,"abstract":"<p><p>The key signaling molecules in the bacterial stress-sensing pathway, the alarmone (p)ppGpp and the transcription factor DksA, play a crucial role in bacterial survival during nutritional deprivation and exposure to xenobiotics by modulating cellular metabolic pathways. In <i>Vibrio cholerae</i>, (p)ppGpp metabolism is solely linked with the functions of three proteins: RelA, SpoT, and RelV. The effects of threshold or elevated concentrations of (p)ppGpp on cellular metabolites and proteins, both in the presence and absence of DksA, have not yet been comprehensively studied in <i>V. cholerae</i> or other bacteria. We engineered the genome of <i>V. cholerae</i> to develop DksA null mutants in the presence and absence of (p)ppGpp biosynthetic enzymes. We observed that the N16:Δ<i>relA</i>Δ<i>relV</i>Δ<i>spoT</i>Δ<i>dksA V. cholerae</i> mutant, which lacks both (p)ppGpp and DksA, exhibits higher sensitivity to different ꞵ-lactam antibiotics compared with the wild-type (WT) strain. Our whole-cell metabolomic and proteome analysis revealed that the cell membrane and peptidoglycan biosynthesis pathways are significantly altered in the N16:Δ<i>relA</i>Δ<i>relV</i>Δ<i>spoT</i>, N16:Δ<i>dksA</i>, and N16:Δ<i>relA</i>Δ<i>relV</i>Δ<i>spoT</i>Δ<i>dksA V. cholerae</i> strains. Furthermore, the mutant strains displayed enhanced inner and outer membrane permeabilities in comparison to the WT strains. These results correlate with <i>V. cholerae's</i> tolerance and survival against β-lactam antibiotics and may inform the development of adjuvants that inhibit stringent response modulators.IMPORTANCEThe (p)ppGpp biosynthetic pathway is widely conserved in bacteria. Intracellular levels of (p)ppGpp and the transcription factor DksA play crucial roles in bacterial multiplication and viability in the presence of antibiotics and/or other xenobiotics. The present findings have shown that (p)ppGpp and DksA significantly reduce the efficacy of ꞵ-lactam and other antibiotics by modulating the availability of peptidoglycan and cell membrane-associated metabolites by reducing membrane permeability. Nevertheless, the whole-cell proteome analysis of N16:Δ<i>relA</i>Δ<i>relV</i>Δ<i>spoT</i>, N16:Δ<i>dksA</i>, and N16:Δ<i>relA</i>Δ<i>relV</i>Δ<i>spoT</i>Δ<i>dksA</i> strains identified the biosynthetic pathways and associated enzymes that are directly modulated by the stringent response effector molecules. Thus, the (p)ppGpp metabolic pathways and DksA could be a potential target for increasing the efficacy of antibiotics and developing antibiotic adjuvants.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0116924"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143483704","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":"CD86 immunohistochemical staining for the detection of <i>Talaromyces marneffei</i> in lesions.","authors":"Jinling Fang, Huiyuan Chen, Krishna Hamal, Donghua Liu","doi":"10.1128/spectrum.02063-24","DOIUrl":"10.1128/spectrum.02063-24","url":null,"abstract":"<p><p>Talaromycosis is an invasive fungal disease caused by the pathogenic thermodimorphic fungus <i>Talaromyces marneffei</i> (TM), which is often overlooked in tropical and subtropical regions of Asia. In view of the diversity of clinical manifestations in patients with TM infection, early diagnosis remains challenging. We assessed the sensitivity and specificity of a novel immunohistochemical staining by performing CD86 immunohistochemical staining on 56 tissue sections from patients with talaromycosis who had fungal culture or metagenomic next-generation sequencing confirmed to exist in clinical specimens, as well as 26 patients with other fungi that had been culture-proven. Hematoxylin and eosin and periodic acid Schiff (PAS) stains were also applied to each specimen. We found that anti-CD86 antibody can label TM pathogens in 38 HIV-negative specimens (38/42) and 14 HIV-positive specimens (14/14); conversely, PAS staining yielded positive results in seven cases of HIV-negative specimens (7/42) and 13 cases of HIV-positive specimens (13/14). Additionally, CD86 immunohistochemical staining was negative in other fungi. Importantly, CD86 immunohistochemical staining significantly outperformed PAS staining in terms of localizing and highlighting TM yeasts, as well as demonstrating the specificity of 100% and a significantly higher sensitivity compared to PAS staining at 92.9% versus 35.7% (<i>P</i> < 0.05, McNemar test). Our findings suggest that CD86 immunohistochemical staining has the potential for the rapid diagnosis of talaromycosis.IMPORTANCETalaromycosis is an opportunistic endemic disease without typical clinical manifestations that has emerged as a fungal disease impacting the survival and mortality of immunocompromised individuals and HIV-positive individuals in endemic regions. Nonetheless, talaromycosis is completely curable if it is accurately diagnosed and treated effectively at an early stage. Rapid pathological diagnosis relies on the unique morphological features of <i>Talaromyces marneffei</i> observed under the microscope. This study introduces a novel pathological diagnostic approach, CD86 immunohistochemical staining, to enhance the early detection of TM-infected lesions.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0206324"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143483705","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":"Virus-neutralizing monoclonal antibodies against bovine viral diarrhea virus and classical swine fever virus target conformational and linear epitopes on E2 glycoprotein subdomains.","authors":"Gleyder Roman-Sosa, Denise Meyer, Mariano Dellarole, Doris À Wengen, Susanne Lerch, Alexander Postel, Paul Becher","doi":"10.1128/spectrum.02041-24","DOIUrl":"10.1128/spectrum.02041-24","url":null,"abstract":"<p><p>The envelope glycoprotein E2 of pestiviruses plays a crucial role in viral entry and elicits a virus-neutralizing humoral immune response. Consequently, the epitopes recognized by monoclonal antibodies (mAbs) on E2 are a significant focus in pestivirus research and diagnostics. In this study, we characterized a panel of murine mAbs against the E2 protein of classical swine fever virus (CSFV) and bovine viral diarrhea virus (BVDV), two major pathogens for swine and cattle, respectively. The majority of mAbs neutralized the virus <i>in vitro</i> and recognized conformational epitopes, which were also detected by sera from infected animals. Notably, binding to these epitopes was retained after low-pH treatment, although conformational epitopes were disrupted upon disulfide bond reduction. The epitopes of the anti-CSFV mAbs were located in various domains of E2, including the interdomain linker sequences. Conversely, all but one of the anti-BVDV mAb epitopes were located in domain A. Moreover, the reactivity of one mAb suggests a conformational interdependence among the linker sequences of pestivirus E2. The panel of mAbs characterized in this study holds potential to support basic research on the mechanism of early pestivirus invasion and to assist in the design of E2-based diagnostic tools and vaccines.</p><p><strong>Importance: </strong>Classical swine fever virus (CSFV) and bovine viral diarrhea virus (BVDV), which belong to the family Flaviviridae, cause economically significant diseases in pigs and cattle. The pestivirus glycoprotein E2 is located on the viral surface and is targeted by antibodies that neutralize virus infection. Due to its variability, E2 is a useful antigen for the development of diagnostic tests to differentiate between infections caused by different pestiviruses. In the present study, two panels of monoclonal antibodies (mAbs) specifically reactive with either CSFV or BVDV E2 were characterized. Interestingly, the majority of mAbs neutralized the respective virus <i>in vitro</i>. Epitope mapping revealed that the mAbs recognized low-pH-resistant epitopes of conformational nature located in different domains of CSFV E2 (anti-CSFV mAbs) or in domain A of BVDV E2 (anti-BVDV mAbs). The recombinant proteins along with the characterized mAbs have the potential to develop improved pestivirus-specific diagnostic tests and vaccines.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0204124"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143492549","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":"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":"2025-04-01","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":"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":"2025-04-01","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":"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":"2025-04-01","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}

{"title":"Comparative phenotypic and genotypic antimicrobial susceptibility surveillance in <i>Achromobacter</i> spp. through whole genome sequencing.","authors":"Sreejana Ray, Laurie K Flemming, Chelsea J Scudder, Melissa A Ly, Harry S Porterfield, Richard D Smith, Andrew E Clark, J Kristie Johnson, Sanchita Das","doi":"10.1128/spectrum.02527-24","DOIUrl":"10.1128/spectrum.02527-24","url":null,"abstract":"<p><p>Treatment of <i>Achromobacter</i> infections remains challenging due to intrinsic and acquired resistance to commonly used antimicrobial agents and no established clinical breakpoints. We attempted accurate species-level identification and compared the presence of genotypic resistance markers to phenotypic susceptibility patterns in retrospectively collected clinical isolates of <i>Achromobacter</i> spp. Our study concludes that <i>Achromobacter xylosoxidans</i> is the most prevalent species. Commercial matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) systems cannot accurately identify all <i>Achromobacter</i> species due to the limited inclusion of spectra in the databases. Phenotypic antimicrobial susceptibility testing (AST) confirms resistance to the majority of antibiotics tested. Newer agents like delafloxacin, plazomicin, and omadacycline showed little or no activity, while minimum inhibitory concentrations were low for eravacycline. In general, the species other than <i>A. xylosoxidans</i> showed lower MIC₅₀ and MIC₉₀, especially to carbapenems and β-lactamase inhibitor combinations like piperacillin-tazobactam, meropenem-vaborbactam, and imipenem-relebactam. Genotypic analysis confirmed that <i>A. xylosoxidans</i> carries a high number of resistance genes, including multidrug efflux pump AxyXY-OprZ, several class D (OXA-type), and the Class A ß-lactamase <i>bla_AXC</i>, while <i>Achromobacter mucicolens</i> has the lowest number of resistance genes and no efflux pumps. This study concludes that there is significant genotypic and phenotypic diversity within the different species of <i>Achromobacter,</i> which are important for the identification of the species and for appropriate antimicrobial therapy.IMPORTANCEIdentification and susceptibility testing of Gram-negative non-fermenting bacteria belonging to the genus <i>Achromobacter</i> is difficult due to the lack of robust databases in commercial identification systems such as matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) and clinical breakpoints for antimicrobial agents. Most clinical laboratories interpret minimum inhibitory concentration data using the \"non-<i>Enterobacterales</i>\" breakpoints included in the Clinical and Laboratory Standards Institute (CLSI) M100. These are breakpoints used for a group of organisms for which data is insufficient to provide species-specific interpretation. Our study provides phenotypic data regarding identification and susceptibility testing and correlates this with the genotypic characterization of 109 clinical isolates belonging to <i>Achromobacter</i> spp. This comprehensive study sheds light on the phenotypic and genotypic character of this bacteria, that is of increasing clinical relevance in hospital-acquired infections.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0252724"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143516079","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}