BMC Microbiology最新文献

{"title":"Comparative genomics of fatal ST308/O11 Pseudomonas aeruginosa from Egypt characterizes conserved resistance architecture, integron-associated multidrug resistance modules, and blaNDM-1 resistance islands.","authors":"Ahmed A Sanad, Ghada A El-Sherbeny, Adel A El-Morsi, Ahmed F Gad, Hossam I Gebeer, Mohamed G Seadawy","doi":"10.1186/s12866-026-05465-y","DOIUrl":"10.1186/s12866-026-05465-y","url":null,"abstract":"<p><p>Pseudomonas aeruginosa is a major cause of ventilator-associated pneumonia (VAP) and is increasingly associated with extensive antimicrobial resistance, limiting therapeutic options and contributing to poor clinical outcomes. The emergence of high-risk clones that combine multidrug resistance and virulence-associated traits represents a growing public health concern.In this study, 100 clinical P. aeruginosa isolates recovered from VAP patients were screened using culture-based identification and antimicrobial susceptibility testing. Two isolates exhibiting the most extensive resistance profiles, consistent with pandrug-resistant (PDR) phenotypes, and associated with fatal clinical outcomes were selected for whole-genome sequencing using Oxford Nanopore technology.Comprehensive genomic analyses were performed to characterize antimicrobial resistance determinants, chromosomal resistance mutations, virulence-associated genes, mobile genetic elements, genomic islands, and phylogenomic relationships. Both isolates were assigned to sequence type ST308 and serogroup O11, a globally disseminated high-risk lineage. Core-genome phylogenomic analysis of 52 genomes identified 144,617 informative SNPs across 5,085 shared core genes and showed that the two Egyptian isolates differed by only 74 core-genome SNPs while clustering within the international ST308 lineage.The isolates harbored an extensive resistome including blaNDM-1, blaOXA-10, blaOXA-488, qnrVC1, rmtF, sul1, sul2, floR, and msrE. High-confidence chromosomal resistance mutations were detected in gyrA (T83I), parC (S87L), oprD (Q402HfsTer99), nalC, nalD, and pmrB, supporting resistance to fluoroquinolones, carbapenems, and polymyxins. Two complete class 1 integrons and one In0 structure, all carrying the class 1 integrase IntI1, were identified, comprising integron-associated multidrug resistance modules containing qnrVC1, aadA11, aac(6')-II, dfrB5, sul1, qacEΔ1, rmtF, blaOXA-10, and blaPAC-1. In contrast, blaNDM-1 was located within a distinct ISVsa3-associated resistance island together with ble and msrE. Genomic island analysis further demonstrated the co-localization of key resistance determinants and the exoU virulence factor within predicted genomic islands.Both isolates carried a highly conserved virulome, including exoU, exoT, type VI secretion system components, iron-acquisition systems, and biofilm-associated genes. Collectively, these findings indicate the convergence of resistance islands, integron-associated multidrug resistance modules, chromosomal resistance mechanisms, and virulence-associated determinants within a globally disseminated ST308/O11 high-risk clone associated with fatal VAP cases in Egypt.To our knowledge, this study provides the first comprehensive genomic characterization of ST308/O11 P. aeruginosa exhibiting a pandrug-resistant phenotype based on the antimicrobial panel tested and associated with fatal ventilator-associated pneumonia in Egypt. Furthermore, by i","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"26 1","pages":""},"PeriodicalIF":5.4,"publicationDate":"2026-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13452102/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148688607","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":"Enhancing the degradation of cellulose and hemicellulose in chili pepper straw waste using Cellulomonas iranensis 7-12, which was isolated from naturally decayed chili pepper straw.","authors":"Mengting Chen, Zhiye Tian, Jiaya Chen, Xiaoping Li, Yongjun Wu, Xilong Shen, Shuoqiu Tong, Jin Jin, Cen Li, Meng Zhao, Liangcai Xiong, Sana Gul, Lintao Ren, Lincheng Zhang","doi":"10.1186/s12866-026-05520-8","DOIUrl":"https://doi.org/10.1186/s12866-026-05520-8","url":null,"abstract":"<p><p>The sustainable valorization of agricultural waste, such as chili pepper straw, is often challenged by the absence of effective microbes that can degrade cell wall components. In this study, metagenomic analysis found that Pseudomonadota was the dominant phylum in the carboxymethyl cellulose (CMC)-enriched microbial communities. In addition, a cellulolytic bacterial strain, designated as Cellulomonas iranensis 7-12, was isolated from naturally decayed chili pepper straw and identified by colony morphology, Gram staining, 16 S rRNA gene sequencing, and genome-based average nucleotide identity (ANI) analysis. Within 30 h, C. iranensis 7-12 displayed robust cellulolytic activity, causing nearly complete disintegration of filter paper, a cellulose model substrate. In contrast, chili pepper straw, a structurally more complex lignocellulosic substrate, was only partially degraded, with dry-weight loss increasing from 11.98% in the uninoculated control to 32.63% after 4 d of fermentation with C. iranensis 7-12. C. iranensis 7-12 exhibited a predominantly extracellular cellulase-xylanase activity profile, with extracellular xylanase activity reaching 3.41 U/mL and exceeding the measured cellulase activities. Whole-genome sequencing of C. iranensis 7-12 identified a complete 3.79-Mb circular chromosome and a diverse CAZyme repertoire, including glycoside hydrolase families related to cellulose and hemicellulose degradation, carbohydrate-binding modules, carbohydrate esterases, and secretion-associated proteins. Moreover, scanning electron microscopy (SEM) examination revealed that the surface and internal microstructure of chili pepper straw were disrupted. Similarly, Fourier-transform infrared (FTIR) spectroscopy analysis showed marked changes in the characteristic absorption bands associated with cellulose, hemicellulose, and lignin-containing structures, indicating partial degradation of polysaccharide components and lignin-associated structural alteration. Collectively, C. iranensis 7-12 shows great potential for the bioconversion of chili pepper straw and the high-performance microbes will be further developed for the effective use of biomass resources.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"26 1","pages":""},"PeriodicalIF":5.4,"publicationDate":"2026-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13491628/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148788272","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":"Urban green roofs host intrinsic resistomes shaped by management but not dominated by pathogenic resistance.","authors":"Rubén Martínez-Cuesta, Alexandra Craighero, Susanne Walch, Brigitte Helmreich, Michael Schloter, Stefanie Schulz","doi":"10.1186/s12866-026-05495-6","DOIUrl":"10.1186/s12866-026-05495-6","url":null,"abstract":"<p><strong>Background: </strong>Urban green roofs are increasingly introduced to enhance urban biodiversity and ecosystem services, yet their role in shaping antimicrobial resistance in cities remains unclear. Using long-read metagenomic sequencing, we characterized antimicrobial resistance genes (ARGs) across an experimental extensive green roof system with plots under four different management regimes specifically designed to test the influence of vegetation and organic amendments, as green waste, which although widely used to improve substrate quality, has been flagged as a potential ARG source.</p><p><strong>Results: </strong>We detected 62 ARGs across the four management regimes, which were dominated by target-modification and mixed mechanisms conferring resistance to naturally occurring antibiotics such as bacitracin (bacA) and rifamycin (arr, rox, rph), rather than efflux-based multidrug resistance, which is typically co-selected by anthropogenic pollutants. The ARGs were mainly chromosomally encoded, with only two ARGs located on plasmids, and associated with non-pathogenic environmental taxa. The management regime had a significant effect on ARG richness, ARG composition and plasmid abundance, but not on average genome size-normalized ARG abundance. We also detected aph3-II and tlmA as enriched in the unamended samples, which were carried by oligotrophic bacteria, pointing towards microbial competition in a nutrient-limited environment.</p><p><strong>Conclusions: </strong>Overall, our findings indicate that green roof management supports a substrate resistome driven by ecological constraints rather than clinical threats. However, further research is required to evaluate potential risks and support the safe integration of green roofs within a One Health framework.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"26 1","pages":""},"PeriodicalIF":5.4,"publicationDate":"2026-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13445745/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148677232","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":"Soil flooding suppresses Fusarium wilt in watermelon by modulating soil chemical properties and microbial community richness.","authors":"HuiFang Lv, Ying Zhang, LingLing Wang, Zulan Ou, CongSheng Yan, HuanXin Zhang","doi":"10.1186/s12866-026-05469-8","DOIUrl":"https://doi.org/10.1186/s12866-026-05469-8","url":null,"abstract":"<p><p>Soil flooding is a well-documented agricultural practice for disease control, but the underlying mechanisms are still poorly understood. The objective of this study was to investigate the effect of soil flooding on watermelon growth, soil chemical properties, enzyme activities, and the diversity and richness of microbial community structure, and to examine the relationships between these factors and wilt incidence. The results showed that soil flooding reduced the population of FON and Fusarium wilt incidence, promoted plant growth, increased soil AP and AK contents, increased UA and ALPA activities, but decreased soil SOM and AN contents (P < 0.05). Bacterial diversity and richness were significantly higher, whereas fungal diversity and richness were significantly lower under soil flooding (P < 0.05). The microbial community structure was significantly altered by soil flooding. The relative abundance of bacterial phyla such as Actinobacteriota, Chloroflexi, and Bacteroidota increased, whereas that of the dominant fungal phylum Ascomycota decreased. Compared with continuous cropping, soil flooding increased the relative abundance of potentially beneficial microbes like Geobacillus, Bacillus, Nocardioides, and Penicillium (P < 0.05). In addition, the relative abundance of potentially pathogenic fungi such as Fusarium was reduced on day 30 after soil flooding (P < 0.05). Soil AK and AN influenced both bacterial and fungal microbial communities. The SEM analysis revealed that the indirect pathways from bacterial and fungal community richness, AK, and AN to watermelon Fusarium wilt were the primary drivers of disease incidence. In conclusion, soil flooding improves soil chemical properties and rebuilds a healthy soil microbiota, thus effectively suppressing watermelon Fusarium wilt.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"26 1","pages":""},"PeriodicalIF":5.4,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13491702/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148788246","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":"Metagenomic and cultivation-based description of a syntrophic butyrate-oxidizing bacterium from a thermophilic and high-ammonia biogas process.","authors":"Malin Tiefensee, Nils Weng, Jonas A Ohlsson, Maria Westerholm","doi":"10.1186/s12866-026-05457-y","DOIUrl":"10.1186/s12866-026-05457-y","url":null,"abstract":"<p><strong>Background: </strong>Ammonia inhibition in anaerobic digestion can lead to butyrate accumulation and reduced methane yield. Despite the importance of syntrophic butyrate oxidation in mitigating this effect, the microorganisms and interactions involved under high-ammonia conditions remain poorly understood. Here, we combine metagenomics and cultivation studies to describe a novel ammonia-tolerant syntrophic butyrate-oxidizing bacterium and its interactions with acetate-oxidizing bacteria and hydrogenotrophic methanogens enriched from a high-ammonia, thermophilic biogas process.</p><p><strong>Results: </strong>The enrichment culture degraded butyrate at rates of 0.12-0.47 mmol/day. Amplicon sequencing and phylogenetic analyses of a retrieved metagenome-assembled genome (MAG) assigned the putative syntrophic butyrate-oxidizing bacterium (SBOB) to the genus Syntrophothermus, for which we propose the provisional species name 'Candidatus Syntrophothermus ammoniitolerans'. Metagenomic analyses revealed the genomic potential for β-oxidation and essential electron transfer pathways associated with syntrophic energy conservation. Furthermore, one additional MAG (MAG9) possessed a complete β-oxidation pathway but lacked key genes associated with reverse electron transfer, making its role as a SBOB uncertain. Acetate produced during butyrate oxidation was further oxidized by syntrophic acetate-oxidizing bacteria and ultimately converted to methane by hydrogenotrophic methanogens, illustrating a tightly coupled metabolic network that supports butyrate degradation under high-ammonia conditions. Three methanogenic MAGs, affiliated with the genera Methanoculleus and Methanothermobacter, were identified as potential hydrogen- or formate-consuming partners.</p><p><strong>Conclusions: </strong>Together, these results identify a novel syntrophic butyrate-oxidizing candidate that enables butyrate degradation under high-ammonia conditions via tightly coupled interactions with acetate-oxidizing bacteria and hydrogenotrophic methanogens, sustaining methane production under ammonia stress.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"26 1","pages":""},"PeriodicalIF":5.4,"publicationDate":"2026-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13422317/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148618655","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":"Targeting nontuberculous mycobacteria with phages: optimization of in vitro host range assays.","authors":"Tobias Weirauch, Eva Brügger, Kai Litzius, Maria J G T Vehreschild, Silvia M Würstle, Simone C Lieberknecht-Jouy","doi":"10.1186/s12866-026-05452-3","DOIUrl":"10.1186/s12866-026-05452-3","url":null,"abstract":"<p><p>The clinical implementation of mycobacteriophages is hampered by the lack of standardized in vitro methods and inconsistent host range results, limiting reliable assessment of their therapeutic potential. Nontuberculous mycobacterial (NTM) infections are frequently difficult to treat, emphasizing the urgent need for alternative or adjunctive strategies to antibiotics. To facilitate reproducible translational research, a detailed and systematic understanding of in vitro assay conditions is essential. Here, we comprehensively evaluated commonly used liquid and solid media for their suitability in supporting growth of multiple NTM strains and subsequent phage application. We compared bacterial growth kinetics, aggregation tendencies, and the efficiency of phage-induced lysis, including plaque formation, across three liquid media and corresponding solid agars. Our results demonstrate that Middlebrook-based media and agar consistently support robust NTM growth, reduce bacterial clumping, and enable reproducible detection of phage activity, outperforming TSB-based alternatives despite higher cost and labor requirements. These findings provide a standardized framework for in vitro NTM cultivation and phage testing, which is critical for reliable evaluation of host range, infection dynamics, and the development of mycobacteriophage-based therapies.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"26 1","pages":""},"PeriodicalIF":5.4,"publicationDate":"2026-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13422341/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148629435","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":"Astrovirus infection alters gut microbial communities in a widespread neotropical bat across human-modified landscapes.","authors":"Stefan D Brändel, Dominik W Melville, Kerstin Wilhelm, Victor M Corman, Rachel Page, Christian Drosten, Marco Tschapka, Simone Sommer, Wasimuddin","doi":"10.1186/s12866-026-05455-0","DOIUrl":"10.1186/s12866-026-05455-0","url":null,"abstract":"<p><p>Astroviruses are becoming a growing concern in public and veterinary health. In humans, astrovirus infections can cause severe diarrhea and may lead to neuropathological encephalitis, whereas in wildlife, these enteropathogenic viral infections often lack overt symptoms and thus remain unnoticed. Yet their close interaction with the host's gastrointestinal microbiome might drive cascading effects with disadvantages for host health. Bats harbor many zoonotic viruses without showing signs of disease, and many species move freely along the gradient from pristine to agricultural landscapes. To better understand the impact of astrovirus (AstV) infection under a One Health framework, we investigated the gut microbiome of naturally AstV-infected Seba's short-tailed bats (Carollia perspicillata, n = 234) inhabiting old-growth lowland forests or forest fragments embedded in an agricultural matrix in Panama. AstV prevalence was higher in forest fragments. We observed that AstV infection is associated with a shift in microbial beta but not alpha diversity, which points towards the replacement of common gut microbial taxa when infected. Indeed, potentially beneficial bacteria, such as Lactococcus, decreased in abundance, whereas potentially pathogenic bacteria from the Helicobacter genus increased in AstV-positive bats. Two Helicobacter haplotypes closely related to avian Helicobacter species were identified. We conclude that even though the impact of infection on the microbiome was not amplified in forest fragments, the higher infection likelihood in landscapes altered by humans implies more frequent or prolonged health repercussions for bats.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"26 1","pages":""},"PeriodicalIF":5.4,"publicationDate":"2026-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13421094/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148618619","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":"Contamination of dental simulation rooms with mycobacteria.","authors":"Anna M Oertel, Stefan Rupf, Matthias Hannig, Alexander Halfmann, Gudrun Wagenpfeil, Uwe Schlotthauer, Madline P Gund","doi":"10.1186/s12866-026-05428-3","DOIUrl":"10.1186/s12866-026-05428-3","url":null,"abstract":"<p><strong>Background: </strong>Dental unit waterlines (DUWLs) often provide optimal conditions for pathogens, including non-tuberculous mycobacteria, causing various infections in patients and practitioners. Preventive measures for non-tuberculous mycobacteria (NTM) remain unclear. Dental simulation units, which are used for student training, are very similar to classic dental units. While the water quality of dental units has been the subject of numerous studies, dental simulation units have received little attention to date. In particular, there are very few studies on the role of NTM in dental simulation units and on influencing factors such as water stagnation, structural conditions, and the effectiveness of a disinfection program.</p><p><strong>Methods: </strong>In this study, 24 dental simulation units from two rooms in two different buildings of the Department for Operative Dentistry, Periodontology and Preventive Dentistry were examined for NTM. Water samples were analyzed from all simulation units, and biofilm swabs were additionally examined from room 2. All samples were incubated on solid and liquid culture media for 8 weeks. The species of NTM were identified using GenoType line probe assays.</p><p><strong>Results: </strong>NTM were detected in 43 of 44 samples. Three different species were identified: M. gordonae was the most common, with 24 detections, followed by M. chelonae with 17 detections and M. chimaera with 3 detections.</p><p><strong>Conclusion: </strong>The high contamination rate of dental simulation units highlights the need for further research to ensure a safe environment. No significant differences in terms of structural conditions could be found, while the influence of water stagnation and disinfection protocols warrants further investigation.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"26 1","pages":""},"PeriodicalIF":5.4,"publicationDate":"2026-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13410582/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148599327","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":"Efficacy of phage vB_EcoP_ZCEC16 in controlling Escherichia coli contamination in fresh poultry meat.","authors":"Azza G Kamel, Zainab K Hammouda, Sohaila Tarek, Yousef Nassar, Eman E Elawsya, Ahmed Osama, Bishoy Maher Zaki, Mohammad Gharaibeh, Rashad Al-Hindi, Ihab Habib, Ayman El-Shibiny","doi":"10.1186/s12866-026-05119-z","DOIUrl":"10.1186/s12866-026-05119-z","url":null,"abstract":"<p><p>Avian pathogenic Escherichia coli (APEC) poses a substantial economic and health challenges for poultry and meat industries. One of the promising alternative approaches to overcome bacterial contamination in food products is bacteriophage, due to its high specificity, safety, and effectiveness. We aimed to isolate a bacteriophage against E. coli causing poultry diseases and investigate its potential as biocontrol/therapeutic agent. A novel E. coli phage vB_EcoP_ZCEC16 was isolated from poultry samples. vB_EcoP_ZCEC16 is a podophage as visualized by transmission electron microscope, and it exhibited a high thermal and pH stability, and high lytic activity at MOIs 0.1 and 1 demonstrated by rapid reduction in bacterial optical density. Whole-genome analysis clustered the phage within Kuravirus genus and confirmed its virulence and the absence of antimicrobial resistance genes. The phage was also safe at high concentration (10⁹ PFU/mL) on human fibroblast cells (HSF) and human colon carcinoma (Caco-2) cell lines as no cytotoxic effect was observed after 24 h. In addition, the lowest tested phage MOI (0.1) was the most protective to HSF cells against bacterial infection. Finally, phage vB_EcoP_ZCEC16 was evaluated for its biocontrol efficacy, where it significantly reduced the count of E. coli contaminating fresh poultry meat after 2 h of treatment. Our study introduced a novel virulent phage with the potential of biocontrol agent for enhancing food safety.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"26 1","pages":""},"PeriodicalIF":5.4,"publicationDate":"2026-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13417854/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148599367","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":"Molecular and phenotypic profiles of carbapenem- and third-generation cephalosporin-resistant Klebsiella pneumoniae isolates from the fecal microbiota of pediatric patients with COVID-19.","authors":"Mahmoud A F Khalil, Mahmoud R M El-Ansary, Sara I AboElnour, Shaimaa Madkour, Walid F Elkhatib, Eman E Mahmoud, Eman Fares, Fatma A Ahmed","doi":"10.1186/s12866-026-05426-5","DOIUrl":"10.1186/s12866-026-05426-5","url":null,"abstract":"<p><strong>Background: </strong>Gut colonization with multidrug-resistant (MDR) Klebsiella pneumoniae is commonly associated with an increased risk of extraintestinal infections among hospitalized patients. Extensive antibiotic exposure during the COVID-19 pandemic, is a critical contributing factor for the emergence of resistant strains. This investigation sought to elucidate the phenotypic and molecular resistance traits of carbapenem-resistant K. pneumoniae (CRKP) and extended-spectrum β-lactamase-producing K. pneumoniae (ESBL-KP) colonizing the gut of pediatric patients with confirmed COVID-19.</p><p><strong>Methods: </strong>A cross-sectional study was conducted from October 2020 to March 2022 at a tertiary pediatric hospital in Fayoum, Egypt. Fecal samples were collected from hospitalized pediatric COVID-19 patients. K. pneumoniae isolates were identified using standard microbiological methods. Antimicrobial susceptibility testing was carried out in accordance with the CLSI guidelines. ESBL and carbapenemase production were assessed phenotypically, while resistance genes were detected by multiplex and uniplex PCR. Microtiter plate method was used to assess biofilm formation.</p><p><strong>Results: </strong>K. pneumoniae was detected in 36 of 71 patients (50.7%) using antibiotic-supplemented selective culture. The isolated strains were exclusively resistant, including 22 CRKP and 14 ESBL-KP. Colistin susceptibility was maintained in all isolates. CRKP strains showed significantly increased rate of resistance to fluoroquinolones and amikacin compared with ESBL-KP. Bla_NDM gene (54.5%) and bla_KPC (45.5%) were detected among CRKP isolates. ESBL-associated genes bla_CTX-M, bla_TEM, and bla_SHV were prevalent in both groups. Biofilm formation was common and comparable between CRKP and ESBL-KP isolates.</p><p><strong>Conclusion: </strong>A high prevalence of fecal carriage of MDR K. pneumoniae, driven by carbapenemase-producing strains, was observed among hospitalized pediatric COVID-19 patients. These outcomes highlight the necessity for routine colonization surveillance, optimized antimicrobial stewardship, and strengthened infection control strategies in pediatric settings.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"26 1","pages":""},"PeriodicalIF":5.4,"publicationDate":"2026-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13393905/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148577224","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}