Journal of Applied Microbiology最新文献

This review provides a comprehensive overview of the current landscape in Bacillus spp. fermentation processes for high-value bioproducts such as proteases, amylases, and surfactin in lab-scale bioreactors, highlighting critical process features. An analysis of key findings over the past five years shows that an efficient fermentation requires customized bioreactor conditions dependent on the substrate, strain type, and the target product. Major challenges include overcoming foaming, ensuring oxygen mass transfer, and precisely balancing the growth and production phases. A combined approach using statistical modeling, such as response surface methodology, along with experimental validation in different bioreactor designs is recommended for the process optimization. This integrated strategy can significantly improve the efficiency, predictability, and overall success of Bacillus-based bioprocesses.

Gram-negative bacterial infections are increasingly becoming resistant to available antibiotic treatment options. The World Health Organization attributed over 1 million deaths to bacterial antimicrobial resistance (AMR) in 2021. While there is a crisis in terms of the available effective antibiotic repertoire, there is also a simultaneous decline in novel drug discovery. In this scenario, the search for alternative or complementary therapeutic options is not only relevant, but also urgently needed. Bacterial virulence factors have been proposed as alternative therapeutic targets since there is lesser propensity for emergence of resistance to these effector molecules. Type 1 fimbriae or FimH of Enterobacteriaceae constitute such a potential target as these structures are crucial for the initial adhesion and colonization by binding mannose-rich host cell-surface receptors. Additionally, FimH has been associated with multiple diseases, including urinary tract infections (UTIs) and Crohn's disease (CD). The elucidation of Escherichia coli FimH crystal structure has opened the possibility for structure-based drug design to combat these diseases. Many mannose-based compounds are being tried as alternative therapeutics against UTIs and CD with a few molecules showing promise. In this review, we discuss the role of FimH in different diseases, its potential and scope for structure-based development of different mannose-based compounds and other advanced FimH blocking therapeutics in preventing these infections.

Aims: Biofilms formed by Salmonella are a significant concern in the poultry industry due to their role in pathogen persistence. However, there is a lack of data observing the expression of biofilm related genes in different Salmonella serovars. The aim of this study was to investigate the expression patterns of key biofilm-associated genes across three Salmonella serovars, namely S. Typhimurium, Kentucky, and Reading, throughout their biofilm growth cycles.

Methods and results: The expressions of csgD, bapA, bcsA, adrA, and luxS were analyzed in cultures representing different biofilm growth phases: 12 h and 24 h planktonic cells, 4-day old biofilms, and 5-day old biofilms under nutrient deprivation. The findings from this study revealed that only S. Reading exhibited upregulation of these genes at the 24 h planktonic stage at a maximum of 9.58-fold. In contrast, a downregulation of all five genes was noted in the 4-day old biofilms for all serovars. Most notably, bapA was downregulated by 3,765-fold in S. Typhimurium. Upon subjecting the biofilms to nutrient deprivation, there was a notable recovery in the activity of these genes across all serovars with the exception of csgD in S. Typhimurium.

Conclusion: These results suggest that expression of biofilm-associated genes is stimulated by nutrient availability even at biofilm maturity and may vary among different serovars.

Aims: 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 C. albicans ATCC 10231, C. tropicalis PNT31, and azole-tolerant C. 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 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: 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 Pseudomonas 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: This study aimed to investigate the diversity and determinants of biofilm formation among clinical Acinetobacter baumannii Indian isolates and assess their relationship with antimicrobial resistance profiles, biofilm-associated genes, and genetic lineages revealed through whole-genome analysis.

Methods and results: 230 A. baumannii clinical isolates across India (2015-2022) were tested for antibiotic susceptibility using the VITEK 2 system. Biofilm formation was quantified via the Tissue Culture Plate method. Whole genome sequencing (Illumina MiSeq) and bioinformatic analysis were performed to identify biofilm-associated genes, antimicrobial resistance genes and sequence types. Statistical associations were assessed using Kruskal-Wallis, Spearman's, and Fisher's tests. 85.22% of isolates were multidrug-resistant (MDR), and 100% exhibited biofilm formation, with 52.17% strong, 39.57% moderate, and 8.26% weak biofilm producers. Genes including ompA, bfmR, pgaA, pgaB, and pgaD were universally present. No significant association was observed between biofilm formation and antibiotic resistance (P = 0.55), specimen type (P = 0.54), or the presence of specific biofilm-related genes (P > 0.05). 21 sequence types (STs) were identified, with ST2 being the most prevalent (51.73%). Strong biofilm formation was more common in ST164, ST1, and ST575.

Conclusions: This study demonstrates a high prevalence of MDR and strong biofilm-forming A. baumannii isolates in India. Biofilm formation appeared independent of resistance or gene carriage but showed lineage-linked variation across sequence types.

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, non-typeable) and associated with transposons (Tn4401, Tn125, 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: Malassezia restricta is a lipid-dependent opportunistic pathogen that is associated with various skin disorders including seborrheic dermatitis, dandruff, and tinea versicolor. This study aimed to investigate the antifungal activity and mechanism of piroctone olamine (OCT) and sorbitan caprylate (SC) in combination against M. restricta.

Methods and results: The combination of 3.125 μg mL-1 OCT and 0.39 μg mL-1 SC effectively inhibited the growth of M. restricta. Microscopic observation of the fungal morphology, propidium iodide staining assay, and content leakage test indicate that the combinations OCT-SC complex 5 (OCT: SC = 4:1, OS-5) and OCT-SC complex 9 (OCT: SC = 8: 1, OS-9) effectively disrupt the cell membrane of M. restricta. Crystal violet staining experiments show that these combinations inhibit biofilm formation of M. restricta, which helps reduce its survival on the surface of mammalian skin. Reverse transcription quantitative PCR and HPLC assays reveal that after treatment with the combinations, genes involved in ergosterol synthesis and cell membrane formation in M. restricta are upregulated, whereas the fungal ergosterol content is markedly reduced, suggesting a compensatory transcriptional response to inhibited ergosterol synthesis.

Conclusion: OCT-SC combinations exert strong antifungal activity against M. restricta by disrupting the cell membrane and inhibiting biofilm formation and reducing ergosterol content despite upregulation of related genes. The results highlight their potential as promising candidates for antifungal drug development. They may also serve as active ingredients in personal care products targeting skin diseases caused by M. restricta.

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 S. 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: This study investigated colistin resistance in Gram-negative bacteria isolated from wastewater. The research focuses on understanding the genetic mechanisms of mcr-mediated resistance and the role of wastewater as a reservoir for colistin-resistant bacterial pathogens.

Methods and results: The study utilized 16 sewage effluent samples collected from four discharge points (three hospitals and one municipal wastewater treatment plant), during May 2024. Bacterial isolates were obtained using the membrane filtration method, resulting in the recovery of 50 Gram-negative isolates, including Enterobacteriaceae and Aeromonas species. Identification was conducted using MALDI-TOF mass spectrometry. Whole-genome sequencing (WGS) and comprehensive bioinformatics analysis were performed to characterize resistance genes and phylogenetic relationships. Colistin resistance was found in Escherichia coli (mcr-1), Aeromonas veronii (mcr-3), and Enterobacter kobei (mcr-9). Escherichia coli was the predominant species, accounting for 50% of the isolates. WGS revealed predominant resistance profiles across isolates, with E. coli harboring 95 resistance genes, E. kobei 21, and A. veronii. 14. Genomic analysis identified mobile genetic elements (MGEs) like ISCR1 and tnpA, suggesting the potential for horizontal gene transfer. Comparative genomic analysis identified the genetic context of mcr genes, with the mcr-1 gene found on a plasmid in E. coli, mcr-3 on a conjugative plasmid in A. veronii, and mcr-9 on a plasmid in E. kobei.

Conclusions: These findings highlight the role of wastewater in the spread of colistin-resistant bacteria. The presence of mcr genes on mobile elements underscores the need for robust surveillance strategies to monitor the dissemination of these resistance traits in the environment.