rss_2.0Polish Journal of Microbiology FeedSciendo RSS Feed for Polish Journal of Microbiologyhttps://sciendo.com/journal/PJMhttps://www.sciendo.comPolish Journal of Microbiology Feedhttps://sciendo-parsed.s3.eu-central-1.amazonaws.com/657db56879f7550bc9ea015e/cover-image.jpghttps://sciendo.com/journal/PJM140216Insights into Genomic Features and Potential Biotechnological Applications of Strain HGR5https://sciendo.com/article/10.33073/pjm-2023-045<abstract> <title style='display:none'>Abstract</title> <p>Algeria is one of the wealthiest countries in terms of hydrothermal sources, with more than two hundred hot springs. However, diverse and little-described microbial communities colonize these habitats, making them an intriguing research subject. This work reports the isolation of bacteria from two hot springs water samples in northeastern Algeria, evaluating their enzymatic activities and effect on plant pathogens. Out of the obtained 72 bacterial isolates and based on the 16S rRNA gene sequence analysis, the strain HGR5 belonging to <italic>Bacillus halotolerans</italic> had the most interesting activity profile. Interestingly, HGR5 was substantially active against <italic>Fusarium graminearum, Phytophthora infestans</italic>, and <italic>Alternaria alternata</italic>. Furthermore, this strain presented a high ability to degrade casein, Tween 80, starch, chitin, cellulose, and xylan. The genome sequence of HGR5 allowed taxonomic validation and screening of specific genetic traits, determining its antagonistic and enzymatic activities. Genome mining revealed that strain HGR5 encloses several secondary metabolite biosynthetic gene clusters (SM-BGCs) involved in metabolite production with antimicrobial properties. Thus, antimicrobial metabolites included bacillaene, fengycin, laterocidine, bacilysin, subtilosin, bacillibactin, surfactin, myxovirescin, dumulmycin, and elansolid A1. HGR5 strain genome was also mined for CAZymes associated with antifungal activity. Finally, the HGR5 strain exhibited the capacity to degrade polycaprolactone (PCL), a model substrate for polyester biodegradation. Overall, these results suggest that this strain may be a promising novel biocontrol agent with interesting plastic-degradation capability, opening the possibilities of its use in various biotechnological applications. <fig id="j_pjm-2023-045_fig_007" position="anchor" fig-type="figure"> <graphic xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="graphic/j_pjm-2023-045_fig_007.jpg"/> </fig></p> </abstract>ARTICLEtruehttps://sciendo.com/article/10.33073/pjm-2023-0452023-12-16T00:00:00.000+00:00The Effects of Antibiotics on the Development and Treatment of Non-Small Cell Lung Cancerhttps://sciendo.com/article/10.33073/pjm-2023-047<abstract> <title style='display:none'>Abstract</title> <p>There have been studies on antibiotic use concerning lung cancer and its potential impact on carcinogenesis and microbiome. However, subsequent research has failed to support these associations consistently. In terms of the potential carcinogenic of antibiotics on lung cancer, the available evidence has not been sufficient to draw any definitive conclusions. Maintaining immune homeostasis and preventing pathogen invasion is critically dependent on the microbiome. The subtle balance of the body microbiota, including the lungs, is susceptible to disruption by antibiotic use. There is an association between disruptions of the lung microbiome and respiratory diseases, including lung cancer, and decreased efficacy of treatments. Patients with lung cancer are often indicated for antibiotic treatment due to respiratory infections or other comorbidities. Pulmonary infections in the area of undetected lung tumors are not uncommon. They can be an early sign of malignancy, which may explain the association between antibiotic use and lung cancer diagnosis. Antibiotic use can also affect the effectiveness of immune checkpoint inhibitor therapy. Studies suggest that antibiotic use can impair the efficacy of immune checkpoint inhibitor therapy in lung cancer patients, particularly around the time when treatment is initiated. These findings require further study, understanding underlying mechanisms, and identifying microbiota signatures associated with treatment response.</p> </abstract>ARTICLEtruehttps://sciendo.com/article/10.33073/pjm-2023-0472023-12-16T00:00:00.000+00:00Molecular Identification of Strains within the Complex and Determination of Resistance to Macrolides and Aminoglycosideshttps://sciendo.com/article/10.33073/pjm-2023-048<abstract> <title style='display:none'>Abstract</title> <p>One of the most relevant and pathogenic groups among the rapidly growing mycobacteria (RGM) is <italic>Mycobacterium abscessus</italic> complex (MABC) that includes three subspecies: <italic>M. abscessus</italic> subsp. <italic>abscessus, M. abscessus</italic> subsp. <italic>bolletii</italic>, and <italic>M. abscessus</italic> subsp. <italic>massiliense</italic>. The aim of this study was the analysis of prevalence of MABC among other non-tuberculous mycobacteria isolated from patients in the Malopolska Region of Poland, between 2018 and 2021, as well as determination of their subspecies and molecular mechanisms of resistance to macrolides and aminoglycosides. The incidence of MABC was 5,4% (12/223). Eight strains were classified as <italic>M. abscessus</italic> subsp. <italic>abscessus</italic>, three as <italic>M. abscessus</italic> subsp. <italic>massiliense</italic> and one <italic>M. abscessus</italic> subsp. <italic>bolletii</italic>. Molecular analysis showed resistance to macrolides for eight strains of <italic>M. abscessus</italic> subsp. <italic>abscessus</italic> associated with <italic>erm</italic>(41)T28 gene mutations. One strain of <italic>M. abscessus</italic> subsp. <italic>abscessus</italic> showed resistance to macrolides (two mutations simultaneously: in <italic>erm</italic>(41)T28 and <italic>rrl</italic> genes) and aminoglycosides (point mutation in <italic>rrs</italic> gene). One strain of <italic>M. abscessus</italic> subs. <italic>bolletii</italic> was resistant to macrolides (<italic>erm</italic>(41)T28 mutation), whereas presented no mutations for aminoglycosides. <italic>M. abscessus</italic> subsp. <italic>massiliense</italic> reveal no mutations. High clarithromycin resistance of <italic>M. abscessus</italic>, determines the urgent need for susceptibility-based treatment. Molecular determination of resistance mechanisms to aminoglycosides and macrolides enables fast and accurate targeted treatment implementation.</p> </abstract>ARTICLEtruehttps://sciendo.com/article/10.33073/pjm-2023-0482023-12-16T00:00:00.000+00:00Microbiota Diversity in Non-Small Cell Lung Cancer Gut and Mouth Cavity Microbiota Diversity in Non-Small Cell Lung Cancer Patientshttps://sciendo.com/article/10.33073/pjm-2023-044<abstract> <title style='display:none'>Abstract</title> <p>Lung malignancies have a substantial impact on cancer incidence and mortality worldwide. Even though many factors involved in the development of the disease are known, many questions remain unanswered. Previous studies suggest that the intestinal microbiota may have a role in developing malignant diseases. According to some findings, the microbiota has proven to be a key modulator of carcinogenic processes and the immune response against cancer cells, potentially influencing the effectiveness of immunotherapy. In our study, we characterized culturable microorganisms associated with non-small cell lung cancer (NSCLC) that can be recovered from rectal swabs and mouthwash. In addition, we also explored differences in the culturable microbiota with two main types of NSCLC – adenocarcinoma (ADC) and squamous cell carcinoma (SCC). With 141 patients included in the study (86 ADC and 55 SCC cases), a significant difference was observed between the two types in seven bacterial species (<italic>Collinsella, Corynebacterium, Klebsiella, Lactobacillus, Neisseria, Rothia</italic>, and <italic>Streptococcus</italic>), including the site of origin. The relationship between microbial dysbiosis and lung cancer is poorly understood; future research could shed light on the links between gut microbiota and lung cancer development. <fig id="j_pjm-2023-044_fig_004" position="anchor" fig-type="figure"> <graphic xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="graphic/j_pjm-2023-044_fig_004.jpg"/> </fig></p> </abstract>ARTICLEtruehttps://sciendo.com/article/10.33073/pjm-2023-0442023-12-16T00:00:00.000+00:00New Awareness of the Interplay Between the Gut Microbiota and Circadian Rhythmshttps://sciendo.com/article/10.33073/pjm-2023-046<abstract> <title style='display:none'>Abstract</title> <p>Circadian rhythms influence various aspects of the biology and physiology of the host, such as food intake and sleep/wake cycles. In recent years, an increasing amount of genetic and epidemiological data has shown that the light/dark cycle is the main cue that regulates circadian rhythms. Other factors, including sleep/wake cycles and food intake, have necessary effects on the composition and rhythms of the gut microbiota. Interestingly, the gut microbiota can affect the circadian rhythm of hosts in turn through contact-dependent and contact-independent mechanisms. Furthermore, the gut microbiota has been shown to regulate the sleep/wake cycles through gut-brain-microbiota interaction. In addition to diabetes, the gut microbiota can also intervene in the progression of neuro- degenerative diseases through the gut-brain-microbiota interaction, and also in other diseases such as hypertension and rheumatoid arthritis, where it is thought to have a spare therapeutic potential. Even though fecal microbiota transplantation has good potential for treating many diseases, the risk of spreading intestinal pathogens should not be ignored. <fig id="j_pjm-2023-046_fig_002" position="float" fig-type="figure"> <graphic xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="graphic/j_pjm-2023-046_fig_002.jpg"/> </fig></p> </abstract>ARTICLEtruehttps://sciendo.com/article/10.33073/pjm-2023-0462023-12-16T00:00:00.000+00:00Diagnostic Efficacy of Photostimulated Chemiluminescence Assay for Detecting Anti-HIV Antibodies: A Retrospective Studyhttps://sciendo.com/article/10.33073/pjm-2023-043<abstract> <title style='display:none'>Abstract</title> <p>The transmission of human immunodeficiency virus (HIV) through blood poses a slightly increased risk. As a result, patients requiring blood transfusions should be screened for HIV antibodies. This study examined the diagnostic effectiveness of the photostimulated chemiluminescence assay in detecting anti-HIV antibodies and determined the cut-off value for this method. The performance of the fully automated photostimulated chemiluminescence assay system was validated according to CNAS-GL038:2019 (2020) and CNAS-GL037:2019 (2019) guidelines. A retrospective study was conducted at the Department of Medical Laboratory, Nanjing Tongren Hospital, affiliated with Southeast University, from January 2020 to December 2022. A total of 77,386 cases were tested for anti-HIV antibodies using the photostimulated chemiluminescence assay, with 79 cases initially testing positive. The method’s performance in detecting anti-HIV antibodies was evaluated using the Receiver Operating Characteristic (ROC) curve and the average Coefficient of Variation (CV) value of 3-year in-house quality control. The precision, detection limit, coincidence rate, and critical value of the performance verification results met the requirements. Using Western blotting (WB) as the reference method, positive cases were initially screened using the light-induced chemiluminescence method to determine the cut-off index (COI) value and draw the ROC curve. The maximum area under the ROC curve using the chemiluminescence method was 0.997, with a cutoff value of &lt; 28.56, sensitivity of 98%, specificity of 100%, Jordan index of 0.98, and an average CV value of 3.55%. In conclusion, the photostimulated chemiluminescence assay has good diagnostic efficacy in detecting anti-HIV antibodies and is suitable for rapid screening before blood transfusion and surgery.</p> </abstract>ARTICLEtruehttps://sciendo.com/article/10.33073/pjm-2023-0432023-12-16T00:00:00.000+00:00The Potential Role of Pyrroloquinoline Quinone to Regulate Thyroid Function and Gut Microbiota Composition of Graves’ Disease in Micehttps://sciendo.com/article/10.33073/pjm-2023-042<abstract> <title style='display:none'>Abstract</title> <p>Graves’ disease (GD) is an autoimmune disorder disease, and its prevalence continues to increase worldwide. Pyrroloquinoline quinone (PQQ) is a naturally antioxidant compound in milk, vegetables, and meat. We aim to identify the treatment efficacy of PQQ on GD and its regulatory effect on intestinal microbiota. The GD mice model was built by an adenovirus expressing autoantigen thyroid-stimulating hormone receptor (Ad-TSHR289). Fecal samples were collected for 16S rDNA sequencing after PQQ pretreatments (20, 40, or 60 mg/kg BW/day) for 4 weeks. Thyroid and intestine functions were measured. The levels of serum TSHR and T4 were significantly raised, and the thyroid gland size was typically enlarged in the GD group than in controls, reversed by PQQ therapy. After PQQ replenishment, <italic>IL6</italic> and <italic>TNFα</italic> levels in small intestine tissues were lower than those in the GD group, with <italic>Nrf2</italic> and <italic>HO1</italic> levels improved. Also, the PQQ supplement could maintain the mucosal epithelial barrier impaired by GD. In microbial analyses, PQQ treatment could prompt the diversity recovery of gut microbiota and reconstruct the microbiota composition injured by GD. <italic>Lactobacillus</italic> served as the most abundant genus in all groups, and the abundance of <italic>Lactobacillu</italic>s was increased in the GD group than in control and PQQ groups. Besides, <italic>Lactobacillus</italic> was highly correlative with all samples and the top 50 genera. PQQ supplementation regulates thyroid function and relieves intestine injury. PQQ changes the primary composition and abundance of GD’s intestine microbiota by moderating <italic>Lactobacillus</italic>, which may exert in the pathogenesis and progression of GD.</p> </abstract>ARTICLEtruehttps://sciendo.com/article/10.33073/pjm-2023-0422023-12-16T00:00:00.000+00:00Genomic Characterization of the Mycoparasite sp. Strain cr013 from https://sciendo.com/article/10.33073/pjm-2023-041<abstract> <title style='display:none'>Abstract</title> <p>The <italic>Pestalotiopsis</italic> sp. strain cr013 is a mycoparasite of <italic>Cronartium ribicola</italic>, a potential biocontrol fungus for Armand pine (<italic>Pinus armandii</italic>) blister rust. A previous study showed that the strain cr013 has great potential to produce new compounds. However, there has been no report of the whole-genome sequence of the mycoparasite <italic>Pestalotiopsis</italic> sp. In this study, the BGISEQ-500 and Oxford Nanopore GridION X5 sequencing platforms were used to sequence the strain cr013 isolates and assemble the reads to obtain the complete genome. We first report the whole-genome information of the mycoparasite <italic>Pestalotiopsis</italic> sp. strain cr013 (GenBank accession number: JACFXT010000000, BioProject ID: PRJNA647543, BioSample ID: SAMN15589943), and the genomic components and gene functions related to the mycoparasitism process were analyzed. This study provides a theoretical basis for understanding the lifestyle strategy of the mycoparasite <italic>Pestalotiopsis</italic> sp. and reveals the mechanisms underlying secondary metabolite diversity in the strain cr013.</p> </abstract>ARTICLEtruehttps://sciendo.com/article/10.33073/pjm-2023-0412023-12-16T00:00:00.000+00:00Comparative Transcriptome Analysis Reveals the Molecular Mechanisms of Acetic Acid Reduction by Adding NaHSO in GXAS137https://sciendo.com/article/10.33073/pjm-2023-036<abstract> <title style='display:none'>Abstract</title> <p>Acetic acid (AC) is a major by-product from fermentation processes for producing succinic acid (SA) using <italic>Actinobacillus succinogenes</italic>. Previous experiments have demonstrated that sodium bisulfate (NaHSO<sub>3</sub>) can significantly decrease AC production by <italic>A. succinogenes</italic> GXAS137 during SA fermentation. However, the mechanism of AC reduction is poorly understood. In this study, the transcriptional profiles of the strain were compared through Illumina RNA-seq to identify differentially expressed genes (DEGs). A total of 210 DEGs were identified by expression analysis: 83 and 127 genes up-regulated and down-regulated, respectively, in response to NaHSO<sub>3</sub> treatment. The functional annotation analysis of DEGs showed that the genes were mainly involved in carbohydrates, inorganic ions, amino acid transport, metabolism, and energy production and conversion. The mechanisms of AC reduction might be related to two aspects: (i) the lipoic acid synthesis pathway (LipA, LipB) was significantly down-regulated, which blocked the pathway catalyzed by pyruvate dehydrogenase complex to synthesize acetyl-coenzyme A (acetyl-CoA) from pyruvate; (ii) the expression level of the gene encoding bifunctional acetaldehyde-alcohol dehydrogenase was significantly up-regulated, and this effect facilitated the synthesis of ethanol from acetyl-CoA. However, the reaction of NaHSO<sub>3</sub> with the intermediate metabolite acetaldehyde blocked the production of ethanol and consumed acetyl-CoA, thereby decreasing AC production. Thus, our study provides new insights into the molecular mechanism of AC decreased underlying the treatment of NaHSO<sub>3</sub> and will deepen the understanding of the complex regulatory mechanisms of <italic>A. succinogenes</italic>. <fig id="j_pjm-2023-0036_fig_001" position="float" fig-type="figure"> <graphic xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="graphic/j_pjm-2023-0036_fig_001.jpg"/> </fig></p> </abstract>ARTICLEtruehttps://sciendo.com/article/10.33073/pjm-2023-0362023-12-16T00:00:00.000+00:00Comparison of mCP and TSC Media to Enumerate in Surface Water Sampleshttps://sciendo.com/article/10.33073/pjm-2023-039<abstract> <title style='display:none'>Abstract</title> <p>The <italic>Clostridium perfringens</italic> bacteria are used to assess water quality as an indicator parameter. If detected, it can confirm the occurrence of past fecal contamination. Tests determining <italic>C. perfringens</italic> in water samples are usually performed by membrane filtration where filters are incubated on selective media under anaerobic conditions. Available media include mCP and TSC. The aim of this study was to compare the relative recovery of <italic>C. perfringens</italic> (including spores) from surface water samples and to determine the performance characteristics of the membrane filtration method using both media. The results showed that, although the procedure using the mCP medium was more sensitive and specific, higher recoveries were obtained in the tests based on the TSC medium. <fig id="j_pjm-2023-039_fig_001" position="float" fig-type="figure"> <graphic xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="graphic/j_pjm-2023-039_fig_001.jpg"/> </fig></p> </abstract>ARTICLEtruehttps://sciendo.com/article/10.33073/pjm-2023-0392023-12-16T00:00:00.000+00:00Evaluating the Sensitivity of Different Molecular Techniques for Detecting Complex in Patients with Pulmonary Infectionhttps://sciendo.com/article/10.33073/pjm-2023-040<abstract> <title style='display:none'>Abstract</title> <p>This study aimed to evaluate the accuracy of detecting drug-resistant <italic>Mycobacterium tuberculosis</italic> complex (MTBC)-specific DNA in sputum specimens from 48 patients diagnosed with pulmonary tuberculosis. The presence of MTBC DNA in the specimens was validated using the GeneXpert MTB/RIF system and compared with a specific PCR assay targeting the IS<italic>6110</italic> and the <italic>mtp</italic>40 gene sequence fragments. Additionally, the results obtained by multiplex PCR assays to detect the most frequently encountered rifampin, isoniazid, and ethambutol resistance-conferring mutations were matched with those obtained by GeneXpert and phenotypic culture-based drug susceptibility tests. Of the 48 sputum samples, 25 were positive for MTBC using the GeneXpert MTB/RIF test. Nevertheless, the IS<italic>6110</italic> and <italic>mtp</italic>40 single-step PCR revealed the IS<italic>6110</italic> in 27 of the 48 sputum samples, while the <italic>mtp</italic>40 gene fragment was found in only 17 of them. Furthermore, multiplex PCR assays detected drug-resistant conferring mutations in 21 (77.8%) of the 27 samples with confirmed MTBC DNA, 10 of which contained single drug-resistant conferring mutations towards ethambutol and two towards rifampin, and the remaining nine contained double-resistant mutations for ethambutol and rifampin. In contrast, only five sputum specimens (18.5%) contained drug-resistant MTBC isolates, and two contained mono-drug-resistant MTBC species toward ethambutol and rifampin, respectively, and the remaining three were designated as multi-drug resistant toward both drugs using GeneXpert and phenotypic culture-based drug susceptibility tests. Such discrepancies in the results emphasize the need to develop novel molecular tests that associate with phenotypic non-DNA-based assays to improve the detection of drug-resistant isolates in clinical specimens in future studies.</p> </abstract>ARTICLEtruehttps://sciendo.com/article/10.33073/pjm-2023-0402023-12-16T00:00:00.000+00:00A Mini-Review of Enteroaggregative with a Specific Target on the Virulence Factors Controlled by the AggR Master Regulatorhttps://sciendo.com/article/10.33073/pjm-2023-037<abstract> <title style='display:none'>Abstract</title> <p>Enteroaggregative <italic>Escherichia coli</italic> (EAEC) strains have been linked to several outbreaks of severe diarrhea around the world, and this bacterium is now commonly resistant to antibiotics. As part of the pathophysiology of EAEC, the characteristic pattern of adherence looks like stacked bricks on the intestinal epithelium. This phenotype depends on an aggregative adhesion plasmid (pAA), which codes for a regulatory protein named AggR. The AggR protein is a master regulator that transcriptionally actives the main virulence genes in this <italic>E. coli</italic> pathotype, such as those that encode the aggregative adhesion fimbriae, dispersin and its secretion apparatus, Aar regulatory protein, and type VI secretion system. Several reports have shown that AggR positively affects most EAEC virulence genes, functioning as a classic transcriptional activator in the promoter region of these genes, interacting with the RNA polymerase. This minireview article integrates the information about virulence determinants of EAEC controlled by the AggR regulator. <fig id="j_pjm-2023-037_fig_003" position="float" fig-type="figure"> <graphic xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="graphic/j_pjm-2023-037_fig_003.jpg"/> </fig> </p> </abstract>ARTICLEtruehttps://sciendo.com/article/10.33073/pjm-2023-0372023-12-16T00:00:00.000+00:00Biological Characteristics of Strain MJ1015 and Optimization of Solid Medium Technology for Sporulationhttps://sciendo.com/article/10.33073/pjm-2023-033<abstract> <title style='display:none'>Abstract</title> <p>The entomopathogenic fungus <italic>Beauveria majiangensis</italic> strain MJ1015, recently isolated from white grubs on a blueberry farm in Guizhou, China, could be used as a biocontrol agent. As a first step toward determining the effect of different solid culture media, temperature, and pH on colony growth rate and sporulation, we evaluated the optimum solid medium for mycelial growth and conidia production on a commercial scale. Subsequently, we also used single-factor analysis and response surface optimization to optimize the composition of the solid culture medium. On potato dextrose agar (PDA) medium, MJ1015 grew fastest and produced the highest spore yield at 29°C and pH 5. The best solid medium for the growth and sporulation of strain MJ1015 comprised 64.70 g/l of rice, 13.00 g/l of wheat, 0.30 g/l of NaNO<sub>3</sub>, 0.36 g/l of K<sub>2</sub>HPO<sub>4</sub> · 3H<sub>2</sub>O, and 1.00 g/l of CaCO<sub>3</sub>. Rice, NaNO<sub>3</sub>, and K<sub>2</sub>HPO<sub>4</sub> · 3H<sub>2</sub>O were the main influencing factors. The predicted value of cultured spores using the optimal medium was 4.56 x 10<sup>10</sup> conidia/l. The validation test results showed that the average growth rate of strain MJ1015 on the optimal medium was 85% and 96% faster than that on Sabouraud dextrose agar with yeast extracts medium (SDAY) and PDA, respectively. Sporulation was 43.90 times and 9.65 times of that produced on SDAY and PDA, respectively. Our findings provide a theoretical basis for the commercial production of <italic>B. majiangensis</italic> to control white grubs.</p> </abstract>ARTICLEtruehttps://sciendo.com/article/10.33073/pjm-2023-0332023-12-16T00:00:00.000+00:00Do NSAIDs and Other Pain Relief Drugs Can Inhibit the Growth of ?https://sciendo.com/article/10.33073/pjm-2023-038<abstract> <title style='display:none'>Abstract</title> <p>Non-steroidal anti-inflammatory drugs (NSAIDs) commonly used in clinical practice may cause gastrointestinal injuries and influence the gut microbiota. This study investigated the effects of various NSAIDs and some analgesics on the viability of <italic>Lactobacillaceae</italic> strains (including probiotic strains) <italic>in vitro</italic>. It was found that diclofenac, ibuprofen, ketoprofen, dexketoprofen, flurbiprofen, and acetylsalicylic acid inhibited the growth of lactobacilli at a concentration of 0.05−3.2 mg/ml. These MICs of NSAIDs are well above therapeutic plasma concentrations achieved in humans, indicating that the tested drugs should not inhibit the growth of lactobacilli in the human digestive tract. <fig id="j_pjm-2023-038__fig_001" position="float" fig-type="figure"> <graphic xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="graphic/j_pjm-2023-038_fig_001.jpg"/> </fig></p> </abstract>ARTICLEtruehttps://sciendo.com/article/10.33073/pjm-2023-0382023-12-16T00:00:00.000+00:00Evaluation of the BioFire® FilmArray® Pneumonia Panel for Detecting Bacterial Etiological Agents of Lower Respiratory Tract Infections in an Oncologic Hospital. Comparison with Conventional Culture Methodhttps://sciendo.com/article/10.33073/pjm-2023-035<abstract> <title style='display:none'>Abstract</title> <p>Conventional methods used to determine pneumonia pathogens are characterized by low sensitivity and long turnaround times. Introducing new tests with better parameters in patients at higher risk of infections is highly anticipated. The results of the conventional quantitative culture method (CM) in determining the bacterial etiology of pneumonia were compared with the results of the Pneumonia <italic>plus</italic> Panel test (PNP; BioFire® Diagnostics, USA) in 79 samples of bronchoalveolar lavage (BAL). Materials were collected from 79 patients with suspected pneumonia treated in an oncologic hospital due to solid tumors. Only 16/79 BAL samples (20.3%) were true positive (TP) for bacterial etiology in CM vs. 27/79 samples (34.2%) true positive in the PNP test. The total agreement between methods of interpreting the result (positive or negative) was 84.8%. The most prevalent pathogens in both methods were <italic>Staphylococcus aureus</italic>, followed by <italic>Escherichia coli, Pseudomonas aeruginosa</italic>, and <italic>Haemophilus influenzae</italic>. The PNP test identified several respiratory pathogens that were not grown in culture. The semiquantitative value reported by the PNP test was higher than that reported by culture. The PNP test vs. combined test (PNP test and CM methods) demonstrated positive predictive value (PPV) and negative predictive value (NPV) values of 100.0% and 98.1%, and the sensitivity and specificity were 96.4% and 100.0%. The PNP test is a good tool for determining the etiology of bacterial pneumonia and may support the care of an oncologic patient. However, further large-sample studies are needed to research in strictly defined groups of oncologic patients.</p> </abstract>ARTICLEtruehttps://sciendo.com/article/10.33073/pjm-2023-0352023-12-16T00:00:00.000+00:00Kestose Increases the Relative Abundance of spp. and Nominally Increases Cow Milk Tolerant Dose in Children with Cow's Milk Allergy – Preliminary Resultshttps://sciendo.com/article/10.33073/pjm-2023-030<abstract> <title style='display:none'>Abstract</title> <p>A single-arm study was conducted with 10 children aged 2–12 years with severe cow's milk allergy (CMA) requiring complete allergen elimination. Subjects were administered kestose, a prebiotic, at 1 or 2 g/day for 12 weeks. Results of a subsequent oral food challenge (OFC) showed a statistically significant increase in the total dose of cow's milk ingestion (1.6 ml vs. 2.7 ml, <italic>p</italic> = 0.041). However, the overall evaluation of the OFC results, TS/Pro (total score of Anaphylaxis Scoring Aichi (ASCA)/cumulative dose of protein), showed no statistically significant improvement, although the values were nominally improved in seven out of 10 subjects. The 16S rDNA analysis of fecal samples collected from the subjects revealed a statistically significant increase in the proportion of <italic>Faecalibacterium</italic> spp. (3.8 % vs. 6.8%, <italic>p</italic> = 0.013), a type of intestinal bacterium that has been reported to be associated with food allergy. However, no statistically significant correlation was found between <italic>Faecalibacterium</italic> spp. abundance and the results of the OFC. <fig id="j_pjm-2023-030_fig_004" position="anchor" fig-type="figure"> <graphic xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="graphic/j_pjm-2023-030_fig_004.jpg"/> </fig></p> </abstract>ARTICLEtruehttps://sciendo.com/article/10.33073/pjm-2023-0302023-09-20T00:00:00.000+00:00Dissemination and characterization of isolates from Dairy Cows in Northeast Chinahttps://sciendo.com/article/10.33073/pjm-2023-032<abstract> <title style='display:none'>Abstract</title> <p>This work investigated the genetic relationship among <italic>Stenotrophomonas maltophilia</italic> strains in fecal samples from dairy cows in northeast China and identified the dominant β-lactamase genotype. One hundred and six samples were collected from two randomly selected cow farms in northeast China, and the isolates were identified with MALDI-TOF/MS. Whole-genome sequencing was conducted using Illumina HiSeq 4000-PE150 platform (Illumina, Inc., USA). The antimicrobial resistance genes were detected using CGE services. The phylogenetic analysis of <italic>S. maltophilia</italic> strains was performed by Roary and MEGA X. In total, 24 <italic>S. maltophilia</italic> isolates were isolated. The results of resistome analysis showed all <italic>S. maltophilia</italic> strains carrying <italic>bla</italic><sub>L1</sub> gene, which was the only β-lactamase genotype. In addition, the aminoglycoside resistance genes <italic>aac(6′)-Iz</italic> and <italic>aph(3′)-IIc</italic> were found. The phylogenetic tree indicated the clonal diversity of <italic>S. maltophilia</italic> in these two regions and the clonal relatedness of the strains from these regions. This study first investigated the dissemination and characterization of <italic>S. maltophilia</italic> isolates from dairy cows in northeast China and provided evidence of the potential transmission between two provinces. Furthermore, it indicated <italic>bla</italic><sub>L1</sub> was the most prevalent genotype of β-lactamase in these regions.</p> </abstract>ARTICLEtruehttps://sciendo.com/article/10.33073/pjm-2023-0322023-09-20T00:00:00.000+00:00The Impacts of Fecal Microbiota Transplantation from Same Sex on the Symptoms of Ulcerative Colitis Patientshttps://sciendo.com/article/10.33073/pjm-2023-025<abstract> <title style='display:none'>Abstract</title> <p>We aimed to compare the clinical efficacy of fecal microbiota transplantation (FMT) from the same sex on ulcerative colitis (UC) patients. A total of 272 UC patients were selected in the prospective clinical study, which incorporated four distinct groups, each comprising male and female patients, who were either receiving FMT or placebo, respectively. FMT was performed by sending the gut microbiota of healthy female or male adolescents to the same gender patients via gastroscope three times (one time/three weeks), and a placebo was used with an equal volume of saline. Abdominal pain, diarrhea, thick bloody stool, intestinal mucosal lesion, and Mayo scores were measured. Self-rating anxiety scale (SAS) and self-rating depression scale (SDS) were evaluated. The changes of intestinal flora were detected by the 16S rRNA sequencing. FMT reduced the scores of diarrhea, abdominal pain, mucosal lesion, and Mayo, SAS, and SDS in UC patients compared to the placebo group (<italic>p</italic> &lt; 0.05). Clostridiales and <italic>Desulfovibrionaceae</italic> were dominant in gut microbiota from male patients and were reduced after FMT. Meanwhile, the abundance of <italic>Prevotella</italic>, <italic>Lactobacillus</italic>, and <italic>Bifidobacterium</italic> was increased in the male group. Female patients had a higher abundance of <italic>Escherichia-Shigella</italic>, <italic>Desulfovibrionaceae</italic>, and <italic>Staphylococcaceae</italic> before FMT, and it was reduced after FMT. Meanwhile, the abundance of <italic>Porphyromonadaceae</italic>, <italic>Prevotella</italic>, <italic>Lactobacillus</italic>, and <italic>Bifidobacterium</italic> was increased in the female group. There were no significant changes for the species in the corresponding placebo groups. FMT improved the UC symptoms of male and female patients, which may be associated with different gut microbiota changes.</p> </abstract>ARTICLEtruehttps://sciendo.com/article/10.33073/pjm-2023-0252023-09-20T00:00:00.000+00:00A Recombinase-Aided Amplification Assay for the Detection of https://sciendo.com/article/10.33073/pjm-2023-029<abstract> <title style='display:none'>Abstract</title> <p><italic>Chlamydia felis</italic> is an important zoonotic agent for humans and various animals. A recombinase-aided amplification (RAA) assay was developed for detecting <italic>C. felis</italic>. RAA can be performed in a closed tube at 39°C within 30 min. The detection limit was 10.6 copies of the <italic>C. felis</italic> plasmid DNA per reaction. No positive signals for other pathogens were detected. The coincidence rate of RAA and conventional PCR was 95.24% (20/21) and 100% (96/96) for positive and negative samples, respectively. The established RAA assay is a simple, rapid, highly sensitive, and specific method for detecting <italic>C. felis</italic>.</p> </abstract>ARTICLEtruehttps://sciendo.com/article/10.33073/pjm-2023-0292023-09-20T00:00:00.000+00:00Control Effect and Mechanism of TM11 against Blueberry Root Rothttps://sciendo.com/article/10.33073/pjm-2023-034<abstract> <title style='display:none'>Abstract</title> <p><italic>Fusarium oxysporum</italic> is the primary pathogen of blueberry root rot; furthermore, we found that <italic>Fusarium commune</italic> can also cause root rot in blueberries. <italic>Trichoderma</italic> spp. is widely used to control plant diseases. We isolated <italic>Trichoderma asperellum</italic> (TM11) from blueberry rhizosphere soil to explore its control effect and mechanism on <italic>F. oxysporum</italic> and <italic>F. commune</italic>. We found that the inhibitory effects of TM11 volatiles and broth metabolites on <italic>F. oxysporum</italic> were significant, but only <italic>F. commune</italic> volatile metabolites had a significant inhibitory effect on its growth. Twelve known antimicrobial metabolites were detected from the methanol extract of TM11 fermentation broth by HPLC-MS. TM11 lysed and coiled around the hyphae of <italic>F. oxysporum</italic> and <italic>F. commune</italic>. The pot experiment showed that TM11 had significant control effects against <italic>F. oxysporum</italic> and <italic>F. commune</italic>, and inoculation of TM11 prior to that of <italic>F. oxysporum</italic> and <italic>F. commune</italic> was more effective. The TM11, TM11 and <italic>F. oxysporum</italic>, or <italic>F. commune</italic> and distilled water treatments had different effects on the activities of superoxide dismutase, peroxidase and catalase, and the enzyme activity levels exhibited the following order: TM11 &gt; TM11 and <italic>F. oxysporum</italic> or <italic>F. commune</italic> &gt; distilled water. The results showed that TM11 provided effective control of blueberry root rot.</p> </abstract>ARTICLEtruehttps://sciendo.com/article/10.33073/pjm-2023-0342023-09-20T00:00:00.000+00:00en-us-1