Frontiers in Microbiology最新文献

Tigecycline (TGC) is currently used to treat carbapenem-resistant Acinetobacter baumannii (CRAB) infections, while eravacycline (ERV), a new-generation tetracycline, holds promise as a novel therapeutic option for these infections. However, differences in resistance mechanism between ERV and TGC against A. baumannii remain unclear. This study sought to compare the characteristics and mechanisms of ERV and TGC resistance among clinical A. baumannii isolates. A total of 492 isolates, including 253 CRAB and 239 carbapenem-sensitive A. baumannii (CSAB) isolates, were collected from hospitalized patients in China. The MICs of ERV and TGC against A. baumannii were determined by broth microdilution. Genetic mutations and expressions of adeB, adeG, adeJ, adeS, adeL, and adeN in resistant strains were examined by PCR and qPCR, respectively. The in vitro recombination experiments were used to verify the resistance mechanism of ERV and TGC in A. baumannii. The MIC₉₀ of ERV in CRAB and CSAB isolates were lower than those of TGC. A total of 24 strains resistant to ERV and/or TGC were categorized into three groups: only ERV-resistant (n = 2), both ERV- and TGC-resistant (n = 7), and only TGC-resistant (n = 15). ST208 (75%, n = 18) was a major clone that has disseminated in all three groups. The ISAba1 insertion in adeS was identified in 66.7% (6/9) of strains in the only ERV-resistant and both ERV- and TGC-resistant groups, while the ISAba1 insertion in adeN was found in 53.3% (8/15) of strains in the only TGC-resistant group. The adeABC and adeRS expressions were significantly increased in the only ERV-resistant and both ERV- and TGC-resistant groups, while the adeABC and adeIJK expressions were significantly increased and adeN was significantly decreased in the only TGC-resistant group. Expression of adeS with the ISAba1 insertion in ERV- and TGC-sensitive strains significantly increased the ERV and TGC MICs and upregulated adeABC and adeRS expressions. Complementation of the wildtype adeN in TGC-resistant strains with the ISAba1 insertion in adeN restored TGC sensitivity and significantly downregulated adeIJK expression. In conclusion, our data illustrates that ERV is more effective against A. baumannii clinical isolates than TGC. ERV resistance is correlated with the ISAba1 insertion in adeS, while TGC resistance is associated with the ISAba1 insertion in adeN or adeS in A. baumannii.

Introduction: This study aimed to evaluate the prevalence of Klebsiella pneumoniae contamination in raw lettuce from Risalpur, Pakistan, and to analyze the antibiotic susceptibility profiles of the isolated strains. The presence of foodborne pathogens such as K. pneumoniae poses significant public health risks, particularly in regions with suboptimal hygiene practices and improper food handling.

Methods: Lettuce samples were collected from various sources in Risalpur and screened for K. pneumoniae. Antimicrobial susceptibility testing was performed to evaluate the effectiveness of various antibiotics against the isolated strains. Statistical analyses, including ANOVA and linear regression, were conducted to assess differences in inhibition zones and to predict antibiotic effectiveness based on concentration.

Results: The results revealed a significant prevalence of K. pneumoniae in the lettuce samples, highlighting the risks associated with poor hygiene, transportation, storage, and contaminated irrigation water. The isolated strains exhibited high susceptibility to gentamicin but demonstrated notable resistance to doxycycline, vancomycin, and ticarcillin. Multidrug-resistant (MDR) strains were identified. ANOVA showed significant differences in inhibition zones, and the linear regression model predicted a Zone of Inhibition based on antibiotic concentration (β₀ = 10.6667, β₁ = 0.4556).

Discussion: The identification of MDR strains of K. pneumoniae underscores the urgent need for enhanced antibiotic stewardship and food safety protocols to manage foodborne pathogens. Improved hygiene practices throughout the food production and supply chain are critical to mitigate health risks and address the challenge of growing antibiotic resistance.

Streptococcus pneumoniae is an important cause of community-acquired pneumonia (CAP) in Japan. Here, we report the serotype distribution and antimicrobial susceptibility of cultured pneumococcal isolates from Japanese adults aged ≥18 years with CAP. This was a prospective, population-based, active surveillance study conducted in Goto City, Japan from December 2015 to November 2020. Pneumococcal isolates from sterile sites (blood and pleural fluid) and non-sterile sites (sputum and bronchoalveolar lavage) were cultured as part of the standard of care. S. pneumoniae were serotyped using the Quellung reaction. Antimicrobial susceptibility was tested using microdilution and interpreted according to the Clinical and Laboratory Standards Institute criteria. Isolates resistant to erythromycin were phenotyped using the triple-risk test and genotyped by polymerase chain reaction. A total of 156 pneumococcal isolates were collected (138 from sputum, 15 from blood, and 3 from bronchoalveolar lavage) from 1992 patients. Of these, 142 were non-duplicate isolates from unique patients and were included in the analyses. Serotypes contained within the 13-valent pneumococcal conjugate vaccine (PCV13) (including 6C), PCV15 (including 6C), and PCV20 (including 6C and 15C) were detected in 39 (27%), 45 (32%), and 80 (56%) of 142 isolates, respectively. The most common serotypes were 35B (12%), 11A (11%), and 3 (11%). Multidrug resistance (MDR) was detected in 96/142 (68%) isolates. Of the 96 MDR isolates, 31, 32, and 59% were PCV13, PCV15, and PCV20 serotypes, respectively; the most common MDR serotypes were 35B (16%), 6C, 10A, and 15A (9% each), and 3 and 11A (8% each). A total of 119 isolates were resistant to macrolides; 41 (35%) had an M phenotype, 53 (45%) had an iMcLS phenotype, and 25 (21%) had a cMLS phenotype. In conclusion, pneumococcal serotypes 35B, 11A and 3 were most frequently associated with pneumonia and antimicrobial resistance was common among pneumococcal isolates from adults with CAP in Goto City, Japan. Implementing higher-valency PCVs May help reduce vaccine-type CAP among Japanese adults.

Introduction: The rising prevalence of Extended-Spectrum Beta-Lactamase (ESBL)-producing Klebsiella species (spp.) poses a significant threat to human and animal health and environmental safety. To address this pressing issue, a comprehensive study was undertaken to elucidate the burden and dissemination mechanisms of ESBL-Klebsiella spp. in dairy cattle farms.

Methods: Fifty-seven Klebsiella species were isolated on CHROMagar™ ESBL plates and confirmed with MADLI-TOF MS and whole genome sequenced from 14 dairy farms.

Results and discussion: Six families of beta-lactamase (bla) (bla _CTX-M, bla _SHV, bla _TEM, bla _OXY, bla _OXA, and bla _SED) were detected in ESBL-Klebsiella spp. genomes. Most (73%) of isolates had the first three types of beta-lactamase genes, with bla _SHV being the most frequent, followed by bla _CTX-M. Most (93%) isolates harbored two or more bla genes. The isolates were genotypically MDR, with 26 distinct types of antibiotic resistance genes (ARGs) and point mutations in gyrA, gyrB, and parC genes. The genomes also harbored 22 different plasmid replicon types, including three novel IncFII. The IncFII and Col440I plasmids were the most frequent and were associated with bla _CTXM-27 and qnrB19 genes, respectively. Eighteen distinct sequence types (STs), including eight isolates with novel STs of K. pneumoniae, were detected. The most frequently occurring STs were ST353 (n = 8), ST469 (n = 6), and the novel ST7501 (n = 6). Clusters of ESBL-Klebsiella strains with identical STs, plasmids, and ARGs were detected in multiple farms, suggesting possible clonal expansion. The same ESBL variant was linked to identical plasmids in different Klebsiella STs in some farms, suggesting horizontal spread of the resistance gene. The high burden and dual spread mechanism of ESBL genes in Klebsiella species, combined with the emergence of novel sequence types, could swiftly increase the prevalence of ESBL-Klebsiella spp., posing significant risks to human, animal, and environmental health. Immediate action is needed to implement rigorous surveillance and control measures to mitigate this risk.

Old Wallow is an underexplored, hyper-arid coastal desert in Antarctica's Vestfold Hills. Situated near an elephant seal wallow, we examined how stochastic nutrient inputs from the seal wallow affect soil communities amid environmental changes along a spatially explicit sampling transect. We hypothesized that nutrient levels would be elevated due to proximity to the seal wallow, influencing community distributions. While the soil bacterial and eukaryotic communities at the phylum level were similar to other terrestrial environments, analysis at class and family levels revealed a dominance of unclassified taxa that are often linked to marine environments. Elevated nutrient concentrations (NO₃ ^-, SO₄ ^2-, SO₃) were found at Old Wallow, with conductivity and Cl^- levels up to 10-fold higher at the lowest elevation soils, correlating with significantly (p < 0.05) higher abundances of halophilic (Halomonadaceace) and uncultivated lineages (Ca Actinomarinales, unclassified Bacillariophyta and unclassified Opisthonkonta). An improved Gradient Forest model was used to quantify microbial responses to 26 soil gradients at OW, revealing variable responses to environmental predictors and identifying critical environmental thresholds or drivers of community turnover. Major tipping points were projected for eukaryotes with SO₄ ^2-, pH, and SO₃, and for bacteria with moisture, Na₂O, and Cl^-. Thus, the Old Wallow ecosystem is primarily shaped by salt, sulphate, and moisture and is dominated by uncultivated taxa, which may be sensitive to environmental changes once critical tipping points are reached. This study provides critical baseline data for future regional monitoring under threats of environmental change.

Global climate warming has led to changes in the suitable habitats for fungi. Colletotrichum acutatum, a common fungus causing anthracnose disease, is widely distributed in southern China. Currently, research on the relationship between C. acutatum and environmental warming was limited. In this study, MaxEnt and ArcGIS software were used to predict the suitable habitats of C. acutatum under current and future climate conditions based on its occurrence records and environmental factors. The optimal MaxEnt model parameters were set as feature combination (FC) = lp and regularization multiplier (RM) = 2.6. Bio15, Bio12, Bio09, and Bio19 were identified as the main environmental factors influencing the distribution of C. acutatum. Under current climate conditions, C. acutatum was distributed across all continents globally, except Antarctica. In China, C. acutatum was primarily distributed south of the Qinling-Huaihe Line, with a total suitable area of 259.52 × 10⁴ km². Under future climate conditions, the potential suitable habitat area for C. acutatum was expected to increase and spread towards inland China. The results of this study provided timely risk assessment for the distribution and spread of C. acutatum in China and offer scientific guidance for monitoring and timely controlled of its distribution areas.

The mulch film (MF) management model of the agricultural field affects the physical and chemical properties of soil (PCPS) and the structure of the microorganism community; however, studies on the relationship between the rhizosphere microorganism community structure and the thickness of MF are still limited. To understand the interactions among the MF thickness, PCPS, and rhizosphere microorganism, a study was conducted by using an integrated metagenomic strategy, where tobacco rhizosphere soil was treated with four commonly representative and used thicknesses of MFs (0.004, 0.006, 0.008, and 0.010 mm) in Yunnan laterite. The results showed that agronomic traits such as the tobacco plant height (TPH), leaf number (LN), fresh leaf weight (FLW), and dry leaf weight (DLW) were significantly (p < 0.01) improved in the field mulched with the thickest film (0.010 mm) compared with the exposed field (CK), and there was a 6.81 and 5.54% increase in the FLW and TPH, separately. The correlation analyses revealed a significant positive correlation of the MF thickness with the soil water content (SWC), soil organic matter (SOM), total nitrogen (TN), available nitrogen (AN), total phosphorus (TP), and available phosphorus (AP; all p < 0.01), while the MF thickness was negatively correlated with the soil temperature (ST; p < 0.01). In addition, the community structure of the rhizosphere soil bacteria was significantly changed overall by the MF thickness, which also interfered with the function of the rhizosphere soil bacteria. The correlation analyses also showed that the abundance of Bradyrhizobium and Nitrospira was positively correlated with the MF thickness, while the abundance of Sphinsinomonas and Massilia was negatively correlated with it. This indicated that with the increase of the MF thickness, the ability of the rhizosphere soil to utilize N and remove harmful molecules was strengthened, while the capacity of the rhizosphere soil to degrade pollutants was greatly reduced. These findings provide additional insights into the potential risks of the application of different thicknesses of MFs, particularly concerning the PCPS and soil microbial communities.

The class Limnochordia harbors a single cultivated member, the mesophilic Limnochorda pilosa, which was isolated from a meromictic lake. Despite numerous molecular signatures reported in various ecosystems, the ecophysiological versatility of this deeply branched lineage of Firmicutes (Bacillota) remains poorly understood. The objective of this study was to use targeted cultivation, based on metagenome-assembled genomes from a deep terrestrial aquifer in Western Siberia, to isolate two new thermophilic members of the class. These isolates, described as Geochorda subterranea gen. nov. sp. nov. and Carboxydochorda subterranea gen. nov. sp. nov. within the Geochordaceae fam. nov., were capable of both anaerobic and aerobic respiration using fumarate and O₂, respectively, with simple sugars as electron donors. The cultivated Geochordaceae have demonstrated fermentative growth and degradation of various polymers, including starch, maltose, maltodextrin, xylan, and chitin. The carboxydotrophic C. subterranea sp. nov. exhibited autotrophic growth via the Calvin-Benson-Bassham cycle, using CO, H₂, and formate as electron donors and O₂ as an electron acceptor, adding metabolic flexibility to the bacterium in the nutrient-depleted "deep biosphere" and supporting the possibility of aerobic metabolism in the deep subsurface. The broad physiological potential deciphered from physiological experiments and comparative genomic data explains the widespread distribution of uncultivated members of the class Limnochordia in various ecosystems, where they can oxidize complex organic substrates through both aerobic and anaerobic respiration, as well as pursue a chemolithotrophic lifestyle through the oxidation of H₂ or CO.

Archaea continues to be one of the least investigated domains of life, and in recent years, the advent of metagenomics has led to the discovery of many new lineages at the phylum level. For the majority, only automatic genomic annotations can provide information regarding their metabolic potential and role in the environment. Here, genomic data from 2,978 archaeal genomes was used to perform automatic annotations using bioinformatics tools, alongside synteny analysis. These automatic classifications were done to assess how good these different tools perform in relation to archaeal data. Our study revealed that even with lowered cutoffs, several functional models do not capture the recently discovered archaeal diversity. Moreover, our investigation revealed that a significant portion of archaeal genomes, approximately 42%, remain uncharacterized. In comparison, within 3,235 bacterial genomes, a diverse range of unclassified proteins is obtained, with well-studied organisms like Escherichia coli having a substantially lower proportion of uncharacterized regions, ranging from <5 to 25%, and less studied lineages being comparable to archaea with the range of 35-40% of unclassified regions. Leveraging this analysis, we were able to identify metabolic protein markers, thereby providing insights into the metabolism of the archaea in our dataset. Our findings underscore a substantial gap between automatic classification tools and the comprehensive mapping of archaeal metabolism. Despite advances in computational approaches, a significant portion of archaeal genomes remains unexplored, highlighting the need for extensive experimental validation in this domain, as well as more refined annotation methods. This study contributes to a better understanding of archaeal metabolism and underscores the importance of further research in elucidating the functional potential of archaeal genomes.