Journal of Applied Microbiology最新文献

Background: Streptococcus pneumoniae remains a major global health threat, causing diseases ranging from mild respiratory infections to severe conditions like pneumonia, sepsis, and meningitis. Although pneumococcal conjugate vaccines (PCVs) including PCV7, PCV10, and PCV13 have significantly reduced disease burden, especially in children, S. pneumoniae continues to exhibit high serotype and genetic diversity. Whole genome sequencing (WGS) analysis offers high-resolution insights into clonal lineages and multidrug-resistant strains. However, genomic data on Malaysian isolates remain limited.

Methods: This study characterised the whole genome features and comparative profiles of seven invasive S. pneumoniae isolates from two tertiary hospitals in Malaysia. WGS analyses described serotype, sequence type (ST), antimicrobial resistance determinant genes, pan-genome structure, and recombination events.

Results: The average genome size was ∼2.12 Mbp, with 1 988-2 205 coding sequences. WGS-based MLST identified five sequence types (ST236, ST320, ST386, ST671, ST695), with ST236 linked to serotypes 19A and 19F related to PMEN clones Taiwan19F-14 and CC271. Core genome analysis with 35 global reference strains revealed three major clades. Notably, isolates TSP95, SSP45, and SSP46 clustered closely with strains from South Korea, suggesting a long-term persistence of ST320 over a decade. Recombination analysis identified both shared and isolate-specific events, forming distinct phylogenetic clusters. Extensive shared recombination was observed in several isolates, while others displayed isolate-specific events, indicating ongoing genetic diversification.

Conclusion: These findings underscore the critical role of recombination in shaping pneumococcal population structure, evolution, and adaptation.

Background: Intestinal colonization by multidrug-resistant (MDR) Enterobacteriaceae represents a major public health concern as it can lead to difficult-to-treat infections, environmental contamination, and transmission. This study evaluated the efficacy of a prophylactic treatment using Escherichia coli strains isolated from murine feces (comEc) to reduce intestinal colonization by extended-spectrum beta-lactamase-producing E. coli (ESBL-E. coli) in a murine model of antibiotic-induced dysbiosis.

Methods and results: The comEc treatment was administered intragastrically one day prior to ESBL-E. coli challenge. Colonization levels were monitored daily using culture-based quantification. Fecal microbiota composition was analyzed before the ESBL-E. coli challenge to identify predictors of treatment efficacy. The comEc treatment significantly reduced mean ESBL-producing E. coli levels during the first 4 days. Notably, 14% of treated mice exhibited marked and sustained decolonization, whereas others had only a limited and transient effect.

Conclusion: In this proof-of-concept study, prophylactic treatment with murine-derived E. coli strains transiently reduced fecal ESBL-E. coli titers, although pronounced efficacy was observed in a small subset of animals.

Aims: Species invasion is one of the key issues in global ecosystems. This study investigated the changes in the rhizosphere community structure of complete ammonia-oxidizing bacteria (Comammox) after the invasion of the long-rooted submerged macrophyte Vallisneria spiralis L. into the community of the short-rooted submerged macrophyte Myriophyllum spicatum L.

Methods and results: Different planting ratios simulated varying invasion intensities. Increasing invasion intensity significantly altered rhizosphere factors, increasing invasion intensity significantly reduced dissolved organic carbon (DOC) and lowered pH, thereby causing distinct alterations in the rhizosphere environment. Comammox Clade A remained dominant with stable abundance, indicating strong adaptability. In contrast, Clade B abundance increased under low-moderate invasion but declined sharply under high intensity, suggesting a preference for mixed roots or low-intensity invasion. Higher pH and dissolved organic carbon provided a stable niche for Clade A. High invasion intensities elevated NH₄⁺-N and NO₃⁻-N concentrations, which coupled with stronger oxidative conditions promoted ammonia-oxidizing bacteria (AOB) and certain Clade A subgroups, thereby suppressing the low-nitrogen-adapted Clade B.

Conclusions: This study demonstrates that submerged macrophyte invasion reshapes the rhizosphere environment and drives Comammox community differentiation, offering new insights into plant invasion's ecological effects and nitrogen cycling regulation.

Aims: This study aimed to isolate virulent bacteriophages (phages) with the capacity to lyse clinical strains belonging to the genus Serratia. Furthermore, we aimed to characterize these phages both genomically and in terms of their potential to treat experimental Serratia infections.

Methods and results: Virulent phages were isolated from water samples collected close to sewage outlets around Nottinghamshire, UK, using the clinical bloodstream isolate Serratia marcescens UMH9 as the host. Two phages, vB_SmaP_10b_1 (Sm10b_1) and vB_SmaS_12 (Sm12) were selected for whole genome sequencing and further characterization. Comparative genomics and proteome-based analyses identified Sm10b_1 represents a novel genus within the order Autographivirales whereas Sm12 represents a novel species belonging to a novel genus within the subfamily Queuovirinae. Host range analysis against a collection of clinical and environmental Serratia spp. (n = 19) confirmed both phages produced plaques on at least 40% of the strains tested. In vivo efficacy of Sm10b_1 was determined by infecting Galleria mellonella larvae with S. marcescens UMH9 or Serratia odorifera Me113 (catheter-associated urinary tract infection isolate) followed by injection of phage Sm10b_1 (1 × 107 pfu). Phage treatment significantly improved survival of larvae infected with S. marcescens (0% survival untreated vs 67% survival treated, P < 0.0001) or S. odorifera (7% survival untreated vs 70% survival treated, P < 0.0001).

Conclusions: Sm10b_1 and Sm12 represent novel lytic phages with broad host ranges against clinical isolates of the genus Serratia. Sm10b_1 was found to be highly effective at treating experimental infections caused by S. marcescens and S. odorifera.

Aims: Avian pathogenic Escherichia coli (APEC) causes colibacillosis, incurring significant economic losses. Toxin-antitoxin (TA) systems regulate bacterial virulence, biofilm formation, and antibiotic resistance. This study focuses on RatA, a toxin characterized as a ribosomal large subunit from our Tn5 transposon mutant library biofilm screen. In the clinical isolate APEC81, ratA is co-transcribed with its putative antitoxin gene, ratB, in the ratAB operon. This study aims to characterize the function of ratA in APEC and determine if ratB affects its regulation.

Methods and results: We found that deletion of ratA (ΔratA and ΔratAB) significantly impaired bacterial growth, biofilm formation, and motility, while deletion of the antitoxin gene ratB had no observable effect, indicating that RatA acts independently of RatB in modulating these traits. Further analysis identified four key active sites (V34, W103, F117, F147) essential for RatA binding to coenzyme Q. Mutating these sites recapitulated the ΔratA phenotype, confirming their functional importance.In host-pathogen interactions assays, the ΔratA mutant exhibited markedly reduced adhesion and invasion in HD-11 macrophages, diminished colonization in murine tissues, and a weakened capacity to provoke host inflammatory responses.

Conclusion: Studies demonstrate RatA as a central virulence factor in APEC, governing multiple pathogenic traits-from bacterial fitness to host interaction. These results underscore the potential of ratA as a target for anti-virulence strategies against APEC infections.

Aims: A heterotrophic nitrification-aerobic denitrification bacterial strain that could effectively remove nitrogen from wastewater was identified, and its nitrogen removal characteristics and possible mechanism underlying were investigated.

Methods and results: A nitrogen-removing strain was isolated from produced water of Changqing oilfield in the Ordos Basin and identified as Pseudomonas stutzeri 4-3 by physiological and biochemical characteristics as well as the phylogenetic analysis. Nitrification and denitrification capabilities were tested under different nitrogen sources, showing that strain 4-3 possessed heterotrophic nitrification and aerobic denitrification capabilities, with a maximum total nitrogen removal rate of 91.345%. Comparative studies under aerobic and anoxic conditions revealed that this strain effectively removed nitrogen sources, and the total nitrogen removal rates were slightly higher under aerobic conditions than those in anoxic conditions, achieving an ammonia nitrogen removal rate of 10.603 mg·L-1·h-1. The extracellular polymeric substances secreted by strain 4-3 could enhance nitrogen removal capacity, and the removal efficiency was increased by 23.5% with the increase of exogenous EPS concentration.

Conclusions: The newly isolated P. stutzeri strain 4-3 was a facultative anaerobic bacterium that carried functional genes of denitrification and exhibited efficient heterotrophic nitrification and aerobic denitrification capabilities. Moreover, EPS secreted by this strain played an auxiliary role in the denitrification process.

Aims: The purpose of this paper was to develop a dual-active topical gel combining clotrimazole (0.5%) and methyl eugenol (0.15%) and to evaluate its planktonic and antibiofilm efficacy against Candida spp., cytocompatibility, pharmaceutical performance, and benchmarking versus commercial antifungals.

Methods and results: Antimicrobial activity was measured by CLSI-adapted agar diffusion and broth microdilution against Candida albicans ATCC 10231, Candida tropicalis PNT31, and azole-tolerant Candida glabrata (ND31, ND32, 961), together with four representative bacteria (Escherichia coli ATCC 25922, Pseudomonas aeruginosa ATCC 27853, Staphylococcus aureus ATCC 29213, and Enterococcus faecalis ATCC 29212). Biofilm inhibition was quantified in a 96-well static model using the minimum biofilm inhibitory concentration (MBIC50​-MBIC100). The gel achieved minimum inhibitory concentrations (MICs) of 125-250 µg·mL-1 and MBIC50 values 2-4 × the MICs. Compared with Canesten® and Daktarin®, MIC and MBIC50 values were consistently lower (≈30-35% lower for azole-tolerant C. glabrata isolates). Cell viability remained > 85% at MIC/MBIC50​, rheology was shear-thinning/thixotropic, and active contents were ≥ 96% retained during stability testing.

Conclusions: In vitro, the clotrimazole-methyl eugenol gel showed low MIC/MBIC50​ values (including against azole-tolerant C. glabrata), maintained cytocompatibility (>85% viability at MIC/MBIC50), and demonstrated robust pharmaceutical attributes, supporting further in vivo validation for biofilm-associated candidiasis.

Aims: To evaluate the diversity, prevalence, and phenotypic and genotypic characteristics of carbapenem-resistant Gram-negative bacteria (CR-GNB) causing bloodstream infections, and assess the mechanisms driving their dissemination through a multi-center study in nine hospitals of Ecuador.

Methods and results: Between November 2021 and May 2022, 297 Gram-negative bacteria (GNB) were isolated from 273 patients across nine hospitals in Ecuador. Genotypic characterization of carbapenem-resistant GNB from blood cultures was performed by whole genome sequencing (WGS). CR-GNB accounted for 18.8% (56/297), predominantly Klebsiella pneumoniae (41.1%), followed by Enterobacter cloacae complex (16.1%), Acinetobacter baumannii (12.5%), and Pseudomonas aeruginosa (7.1%). CR-GNB showed high resistance to cephalosporins (80%-95%), piperacillin-tazobactam (85.7%), ampicillin-sulbactam (91.1%), and ciprofloxacin (78.6%). Genomic analysis revealed carbapenemase genes blaKPC-2 (most frequent), blaNDM-1, and blaOXA-181 across high-risk clones (e.g. K. pneumoniae ST307, ST258, ST147; A. baumannii ST1187). Carbapenemase genes were plasmid-borne (IncA/C, IncM, IncN, IncF, IncHI2, IncX3, and non-typeable) and associated with transposons (Tn4401, Tn125, and Tn3). Also, blaVIM-2 in Pseudomonas spp. was plasmid- and chromosomally encoded.

Conclusions: Our findings demonstrate a high burden of CR-GNB, primarily due to K. pneumoniae and E. cloacae complex. Furthermore, the widespread distribution of blaKPC-2, blaNDM-1, and blaOXA-181 in high-risk clones, coupled with the frequent plasmid- and transposon-mediated mobilization of these genes, highlights the crucial role of horizontal gene transfer in the dissemination of resistance.

Aims: Vaginal health is crucial to a woman's overall well-being. Bacterial vaginosis, a common gynecological condition resulting from dysbiosis, remains a significant clinical challenge. This study aims to investigate whether postbiotics derived from vaginal Lactobacillus strains exhibit therapeutic effects against bacterial vaginitis.

Methods and results: Postbiotics, consisting of inanimate microorganisms and/or their components, were analyzed and found to contain lactic acid and acetic acid as the primary acidic constituents. In a model of Gardnerella vaginalis-induced bacterial vaginosis, postbiotics demonstrated enhanced antibacterial and antioxidant activities. They significantly alleviated clinical symptoms, modulated the composition of the vaginal microbiota, and increased microbial diversity. Specifically, postbiotics reduced the abundance of endotoxin-producing Escherichia-Shigella and Enterobacteriaceae, while promoting beneficial bacteria such as Muribaculaceae, Lachnospiraceae, and Streptococcus. Additionally, postbiotic treatment restored the balance between Th17 and Treg cells and regulated associated inflammatory factors.

Conclusions: These findings indicate that postbiotics improve bacterial vaginitis through multiple mechanisms, including antibacterial and antioxidant effects, immune regulation, and restoration of vaginal flora structure and metabolic balance. This study highlights the potential clinical value of postbiotics in the treatment of bacterial vaginosis.

Aims: Most chemically defined media for Bacillus are developed with a focus on an individual species. To broaden the applicability, this study aimed to formulate a chemically defined medium that supports the growth of multiple food-relevant Bacillus species. Specifically, it was the aim to support growth of both food fermentation strains from the Bacillus subtilis clade as well as pathogenic strains from the Bacillus cereus clade.

Methods and results: We developed a new chemically defined medium, named Pafoba, using thirteen Bacillus strains: two from the Bacillus cereus clade and eleven strains from the Bacillus subtilis clade, representing seven species. Medium optimisation involved substituting ammonium chloride and sodium chloride with ammonium sulphate and trisodium citrate, enriching glucose, iron, and phosphate concentrations, and applying nutrientomission assays to identify growth requirements. All strains exhibited growth on Pafoba. Ten strains reached a comparable or higher maximum optical density (OD600) on Pafoba medium compared to Brain Heart Infusion broth. Strain-specific nutrient requirements were identified, including a biotin dependency for Bacillus subtilis strain PRO64, and essential amino acid requirements in Bacillus mycoides and Bacillus cereus strains.

Conclusions: The Pafoba medium supports consistent growth across diverse Bacillus species, making it suitable for both fundamental studies and practical applications such as detection and isolation of Bacillus spp. in food-related contexts.