Journal of Applied Microbiology最新文献

Aims: We propose coffee cartridge filtration as an alternative method for the concentration of nucleic acids from microorganisms in wastewater.

Methods and results: In this study, coffee cartridge filtration was directly compared with PEG precipitation through mass balance analysis. The utility of coffee cartridge filtration was further demonstrated through a 10-month longitudinal analysis of Giardia, human norovirus genogroup I and II, and hepatitis A virus in 45 wastewater samples from Guelph, Ontario, Canada. Fourteen of these wastewater samples were enriched with the Illumina Viral Surveillance Panel v2 and sequenced with the Illumina NextSeq 1000. PEG precipitation was more efficient at concentrating nucleic acids from all microorganisms and viruses, but all endogenous targets were detected following coffee cartridge filtration. Hepatitis A was detected in four wastewater samples and best correlated with four clinical cases when a one-week wastewater lead time was applied. HuNoV-GI and HuNoV-GII were detected within the RT-qPCR linear dynamic range in 44/45 samples. Nucleic acids from the Polyomaviridae, Astroviridae, and Calciviridae families were most identified in coffee cartridge-filtered wastewater samples.

Conclusions: Coffee cartridge filtration is an effective method to concentrate nucleic acids from microorganisms in wastewater in resource-limited settings.

Aims: ood-grade titanium dioxide (E171) is widely used as a food additive, yet concerns persist regarding potential gastrointestinal effects, possibly mediated by interactions with the gut microbiome. This study aimed to investigate the physicochemical behavior of E171 under different digestive contexts and to assess its effects on gut microbial composition and metabolic activity.

Methods and results: The dynamic in vitro colon model TIM-2 was used to expose human fecal microbiota to E171 under fasted (aqueous suspension; E171-aq) and fed (yogurt matrix; E171-yog) conditions. Particle size distribution, reactive oxygen species formation, microbiome composition (16S rRNA gene sequencing), and short-chain fatty acid production were analyzed. Larger aggregates were observed under fasted conditions (mean diameter ~210 nm), whereas digestion in yogurt produced smaller aggregates (mean diameter ~167 nm) and a higher nanoparticle fraction, reaching up to 20%. No ROS production was detected following fermentation. Both E171-aq and E171-yog significantly increased butyrate levels, indicating altered microbial metabolic activity. Microbiome profiling revealed compositional shifts, including a decreased relative abundance of Blautia and an increased relative abundance of Lachnospiraceae, taxa associated with inflammatory and metabolic responses.

Conclusions: E171 undergoes distinct physicochemical transformations depending on the digestive context, with enhanced nanoparticle formation under fed conditions. E171 exposure also modulates gut microbiome composition and function, notably by stimulating butyrate production.

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: Biofilm is a continuing issue of food microbial safety. This study combined microbubble (MB) with 50 mg/L sodium hypochlorite (NaClO) or chlorine dioxide (ClO2) to inactivate the biofilms of Salmonella Typhimurium and Staphylococcus aureus on stainless steel (SS) and polyvinyl chloride (PVC).

Methods and results: The biofilms were treated with the combinations of MB and NaClO (NMB) or ClO2 (CMB). After 10-min treatment, populations of S. Typhimurium on SS were below the detection limit (1.1 log CFU piece-1) for NMB and 2.6 log CFU piece-1 for CMB; the populations on PVC were 1.6 and 3.3 log CFU piece-1 for NMB and CMB, respectively. For S. aureus, 7.5-min NMB and CMB treatments reduced the populations on SS to below the detection limit and 1.6 log CFU piece-1, respectively, and to 1.3 log CFU piece-1 on PVC. Compared with water washing and sanitizers alone, NMB and CMB obtained an additional 5 to 6 log reductions. Higher residual populations of both bacteria were obtained on PVC, and S. Typhimurium had higher residual populations on both surfaces. Observation under a scanning electron microscope revealed that no biofilm remained on the NMB-treated SS and PVC pieces, but biofilm remained on the NaClO- and water-treated pieces. Furthermore, calcofluor white staining confirmed that NMB treatment achieved the greatest removal of extracellular substances.

Conclusion: This is the first study showing that the combinations of MB and sanitizers inactivate the biofilm of these two bacteria on SS and PVC and demonstrate the potential for application in the food industry.

Aims: Ready-to-eat dry-cured meats are characterized by combined hurdles such as reduced water activity, elevated salt content, and variable temperatures. Listeria monocytogenes may survive or adapt under these conditions. This study aimed to evaluate the behavior of L. monocytogenes under combined water activity (aw), sodium chloride (NaCl), and temperature stresses using a dry-cured meat-based agar designed to simulate physicochemical conditions encountered on cured meat surfaces and during dry-curing and storage processing conditions. Socol, a traditional Brazilian dry-cured pork loin, was used as the reference product for the development of this model system.

Methods and results: The influence of aw (0.806-0.974), NaCl concentration (1.97%-9.53% w/w), and temperature (0.9°C-31.1°C) on the growth and/or survival of L. monocytogenes was investigated over 12, 24, 48, and 72 h using a Central Composite Rotatable Design (CCRD). Survival after 72 h of incubation was also evaluated in simulated gastric fluid (SGF). The predictive models accurately described the effects of aw, NaCl, and temperature on bacterial behavior, showing excellent validation performance (R² ≥ 0.96; Af ≥ 1.14; Bf ≥ 1.14). Water activity was the dominant factor influencing pathogen behavior, with increased growth observed at aw > 0.92. Temperature had no significant inhibitory effect, indicating that L. monocytogenes can survive under refrigeration conditions. The bacterium was fully inactivated in SGF under all tested conditions.

Conclusions: The results emphasize the importance of water activity control to limit L. monocytogenes survival and growth in ready-to-eat dry-cured meats.

Aims: This study reports the first documented cases of Castellaniella spp. infection in dogs, describing associated clinical and pathological findings and characterizing a novel species within this genus.

Methods and results: Pleural effusions from two dogs presenting with acute respiratory distress and systemic illness were evaluated via cytology, bacterial culture, and next-generation sequencing. Both cases exhibited neutrophilic-macrophagic inflammation with intracellular Gram-negative rods, primarily within macrophages. Bacterial culture failed to identify the organisms. Metagenomic analysis identified organisms belonging to the genus Castellaniella in both cases. In case 2, an unclassified Castellaniella species was detected, suggesting the presence of a previously undescribed species within the genus. Both dogs died shortly after presentation, and necropsy and histopathology findings were described.

Conclusions: Castellaniella spp. warrant consideration as potential emerging pathogens in domestic animals, challenging their previous classification as non-pathogenic environmental bacteria. The identification of a novel species also underscores the genus's genetic diversity and adaptive potential.

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.