Pub Date : 2024-03-04eCollection Date: 2024-03-01DOI: 10.33073/pjm-2024-003
Agnė Kirkliauskienė, Jonas Kriščiūnas, Jolanta Miciulevičienė, Daiva Radzišauskienė, Tomas Kačergius, Maksim Bratchikov, Lina Kaplerienė
This study aimed to determine resistance to antimicrobials of Staphylococcus aureus strains isolated from clinical specimens in Lithuanian hospitals and to identify the genes conferring resistance and virulence. The study was carried out from June 2019 to September 2021. S. aureus strains were isolated from skin, soft tissues, blood, lower respiratory tract, urine and other specimens. Antibiotic susceptibility testing was performed using the disc diffusion method according to EUCAST guidelines. All isolates were analyzed for detection of the ermA, ermC, mecA, mecC, tetK, tetM, and lukF-PV genes by multiplex real-time PCR. The 16S rRNA coding sequence was applied as an internal PCR control. Altogether, 745 S. aureus strains were analyzed. Antimicrobial susceptibility testing revealed that all isolates were susceptible to rifampin and vancomycin. Of the 745 strains, 94.8% were susceptible to tetracycline, 94.5% to clindamycin, and 88.3% to erythromycin. The lowest susceptibility rate was found for penicillin (25.8%). Six percent of the tested strains were methicillin-resistant S. aureus (MRSA). The majority of methicillin-resistant strains were isolated from skin and soft tissues (73.3%), with a smaller portion isolated from blood (17.8%) and respiratory tract (8.9%). The ermC gene was detected in 41.1% of erythromycin-resistant S. aureus strains, whereas ermA was detected in 32.2% of erythromycin-resistant S. aureus strains. 69.2% of tetracycline-resistant S. aureus strains had tetK gene, and 28.2% had tetM gene. 7.3% of S. aureus isolates harbored lukF-PV gene. The frequency of the pvl gene detection was significantly higher in MRSA isolates than in methicillin-susceptible S. aureus isolates (p < 0.0001).
{"title":"Antimicrobial Resistance and the Prevalence of the Panton-Valentine Leukocidin Gene among Clinical Isolates of <i>Staphylococcus aureus</i> in Lithuania.","authors":"Agnė Kirkliauskienė, Jonas Kriščiūnas, Jolanta Miciulevičienė, Daiva Radzišauskienė, Tomas Kačergius, Maksim Bratchikov, Lina Kaplerienė","doi":"10.33073/pjm-2024-003","DOIUrl":"10.33073/pjm-2024-003","url":null,"abstract":"<p><p>This study aimed to determine resistance to antimicrobials of <i>Staphylococcus aureus</i> strains isolated from clinical specimens in Lithuanian hospitals and to identify the genes conferring resistance and virulence. The study was carried out from June 2019 to September 2021. <i>S. aureus</i> strains were isolated from skin, soft tissues, blood, lower respiratory tract, urine and other specimens. Antibiotic susceptibility testing was performed using the disc diffusion method according to EUCAST guidelines. All isolates were analyzed for detection of the <i>ermA</i>, <i>ermC</i>, <i>mecA</i>, <i>mecC</i>, <i>tetK</i>, <i>tetM</i>, and <i>lukF-PV</i> genes by multiplex real-time PCR. The 16S rRNA coding sequence was applied as an internal PCR control. Altogether, 745 <i>S. aureus</i> strains were analyzed. Antimicrobial susceptibility testing revealed that all isolates were susceptible to rifampin and vancomycin. Of the 745 strains, 94.8% were susceptible to tetracycline, 94.5% to clindamycin, and 88.3% to erythromycin. The lowest susceptibility rate was found for penicillin (25.8%). Six percent of the tested strains were methicillin-resistant <i>S. aureus</i> (MRSA). The majority of methicillin-resistant strains were isolated from skin and soft tissues (73.3%), with a smaller portion isolated from blood (17.8%) and respiratory tract (8.9%). The <i>ermC</i> gene was detected in 41.1% of erythromycin-resistant <i>S. aureus</i> strains, whereas <i>ermA</i> was detected in 32.2% of erythromycin-resistant <i>S. aureus</i> strains. 69.2% of tetracycline-resistant <i>S. aureus</i> strains had <i>tetK</i> gene, and 28.2% had <i>tetM</i> gene. 7.3% of <i>S. aureus</i> isolates harbored <i>lukF-PV</i> gene. The frequency of the <i>pvl</i> gene detection was significantly higher in MRSA isolates than in methicillin-susceptible <i>S. aureus</i> isolates (<i>p</i> < 0.0001).</p>","PeriodicalId":94173,"journal":{"name":"Polish journal of microbiology","volume":"73 1","pages":"21-28"},"PeriodicalIF":0.0,"publicationDate":"2024-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10911699/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140029917","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Salmonella enterica is a common pathogen in humans and animals that causes food poisoning and infection, threatening public health safety. We aimed to investigate the genome structure, drug resistance, virulence characteristics, and genetic relationship of a Salmonella strain isolated from patients with food poisoning. The pathogen strain 21A was collected from the feces of patients with food poisoning, and its minimum inhibitory concentration against commonly used antibiotics was determined using the strip test and Kirby-Bauer disk methods. Subsequently, WGS analysis was used to reveal the genome structural characteristics and the carrying status of resistance genes and virulence genes of strain 21A. In addition, an MLST-based minimum spanning tree and an SNP-based systematic spanning tree were constructed to investigate its genetic evolutionary characteristics. The strain 21A was identified by mass spectrometry as S. enterica, which was found to show resistance to ampicillin, piperacillin, sulbactam, levofloxacin, and ciprofloxacin. The WGS and bioinformatics analyses revealed this strain as Salmonella Enteritidis belonging to ST11, which is common in China, containing various resistance genes and significant virulence characteristics. Strain 21A was closely related to the SJTUF strains, a series strains from animal, food and clinical sources, as well as from Shanghai, China, which were located in the same evolutionary clade. According to the genetic makeup of strain 21A, the change G > A was found to be the most common variation. We have comprehensively analyzed the genomic characteristics, drug resistance phenotype, virulence phenotype, and genetic evolution relationship of S. Enteritidis strain 21A, which will contribute towards an in-depth understanding of the pathogenic mechanism of S. Enteritidis and the effective prevention and control of foodborne diseases.
肠炎沙门氏菌是人类和动物中常见的病原体,可引起食物中毒和感染,威胁公共卫生安全。我们旨在研究从食物中毒患者体内分离出的一株沙门氏菌的基因组结构、耐药性、毒力特征和遗传关系。我们从食物中毒患者的粪便中采集了病原菌 21A 株,并采用条带试验法和柯比鲍尔盘法测定了其对常用抗生素的最小抑菌浓度。随后,利用 WGS 分析揭示了菌株 21A 的基因组结构特征以及耐药基因和毒力基因的携带状况。此外,还构建了基于 MLST 的最小生成树和基于 SNP 的系统生成树,以研究其遗传进化特征。经质谱鉴定,菌株 21A 为肠道病毒,对氨苄西林、哌拉西林、舒巴坦、左氧氟沙星和环丙沙星具有耐药性。WGS和生物信息学分析表明,该菌株属于中国常见的ST11肠炎沙门氏菌,含有多种耐药基因,毒力特征明显。21A 株与来自动物、食品和临床以及中国上海的一系列 SJTUF 株密切相关,位于同一进化支系。根据 21A 株的基因组成,发现 G > A 是最常见的变异。我们全面分析了肠炎双球菌 21A 株的基因组特征、耐药表型、毒力表型和遗传进化关系,这将有助于深入了解肠炎双球菌的致病机制,有效预防和控制食源性疾病。
{"title":"Isolation, Identification, Antimicrobial Resistance, Genotyping, and Whole-Genome Sequencing Analysis of <i>Salmonella</i> Enteritidis Isolated from a Food-Poisoning Incident.","authors":"Zhuru Hou, Benjin Xu, Ling Liu, Rongrong Yan, Jinjing Zhang","doi":"10.33073/pjm-2024-008","DOIUrl":"10.33073/pjm-2024-008","url":null,"abstract":"<p><p><i>Salmonella enterica</i> is a common pathogen in humans and animals that causes food poisoning and infection, threatening public health safety. We aimed to investigate the genome structure, drug resistance, virulence characteristics, and genetic relationship of a <i>Salmonella</i> strain isolated from patients with food poisoning. The pathogen strain 21A was collected from the feces of patients with food poisoning, and its minimum inhibitory concentration against commonly used antibiotics was determined using the strip test and Kirby-Bauer disk methods. Subsequently, WGS analysis was used to reveal the genome structural characteristics and the carrying status of resistance genes and virulence genes of strain 21A. In addition, an MLST-based minimum spanning tree and an SNP-based systematic spanning tree were constructed to investigate its genetic evolutionary characteristics. The strain 21A was identified by mass spectrometry as <i>S. enterica</i>, which was found to show resistance to ampicillin, piperacillin, sulbactam, levofloxacin, and ciprofloxacin. The WGS and bioinformatics analyses revealed this strain as <i>Salmonella</i> Enteritidis belonging to ST11, which is common in China, containing various resistance genes and significant virulence characteristics. Strain 21A was closely related to the SJTUF strains, a series strains from animal, food and clinical sources, as well as from Shanghai, China, which were located in the same evolutionary clade. According to the genetic makeup of strain 21A, the change G > A was found to be the most common variation. We have comprehensively analyzed the genomic characteristics, drug resistance phenotype, virulence phenotype, and genetic evolution relationship of <i>S</i>. Enteritidis strain 21A, which will contribute towards an in-depth understanding of the pathogenic mechanism of <i>S</i>. Enteritidis and the effective prevention and control of foodborne diseases.</p>","PeriodicalId":94173,"journal":{"name":"Polish journal of microbiology","volume":"73 1","pages":"69-89"},"PeriodicalIF":0.0,"publicationDate":"2024-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10911658/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140029923","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Hydrocarbon constituents of petroleum are persistent, bioaccumulated, and bio-magnified in living tissues, transported to longer distances, and exert hazardous effects on human health and the ecosystem. Bioaugmentation with microorganisms like bacteria is an emerging approach that can mitigate the toxins from environmental sources. The present study was initiated to target the petroleum-contaminated soil of gasoline stations situated in Lahore. Petroleum degrading bacteria were isolated by serial dilution method followed by growth analysis, biochemical and molecular characterization, removal efficiency estimation, metabolites extraction, and GC-MS of the metabolites. Molecular analysis identified the bacterium as Bacillus cereus, which exhibited maximum growth at 72 hours and removed 75% petroleum. Biochemical characterization via the Remel RapID™ ONE panel system showed positive results for arginine dehydrolase (ADH), ornithine decarboxylase (ODC), lysine decarboxylase (LDC), o-nitrophenyl-β-D-galactosidase (ONPG), p-nitrophenyl-β-D-glucosidase (βGLU), p-nitrophenyl-N-acetyl-β-D-glucosaminidase (NAG), malonate (MAL), adonitol fermentation (ADON), and tryptophane utilization (IND). GC-MS-based metabolic profiling identified alcohols (methyl alcohol, o-, p- and m-cresols, catechol, and 3-methyl catechol), aldehydes (methanone, acetaldehyde, and m-tolualdehyde), carboxylic acid (methanoic acid, cis,cis-muconic acid, cyclohexane carboxylic acid and benzoic acid), conjugate bases of carboxylic acids (benzoate, cis,cis-muconate, 4-hydroxybenzoate, and pyruvate) and cycloalkane (cyclohexene). It suggested the presence of methane, methylcyclohexane, toluene, xylene, and benzene degradation pathways in B. cereus.
{"title":"Molecular and metabolic characterization of petroleum hydrocarbons degrading <i>Bacillus cereus</i>.","authors":"Nadia Hussain, Fatima Muccee, Muhammad Hammad, Farhan Mohiuddin, Saboor Muarij Bunny, Aansa Shahab","doi":"10.33073/pjm-2024-012","DOIUrl":"10.33073/pjm-2024-012","url":null,"abstract":"<p><p>Hydrocarbon constituents of petroleum are persistent, bioaccumulated, and bio-magnified in living tissues, transported to longer distances, and exert hazardous effects on human health and the ecosystem. Bioaugmentation with microorganisms like bacteria is an emerging approach that can mitigate the toxins from environmental sources. The present study was initiated to target the petroleum-contaminated soil of gasoline stations situated in Lahore. Petroleum degrading bacteria were isolated by serial dilution method followed by growth analysis, biochemical and molecular characterization, removal efficiency estimation, metabolites extraction, and GC-MS of the metabolites. Molecular analysis identified the bacterium as Bacillus cereus, which exhibited maximum growth at 72 hours and removed 75% petroleum. Biochemical characterization via the Remel RapID<sup>™</sup> ONE panel system showed positive results for arginine dehydrolase (ADH), ornithine decarboxylase (ODC), lysine decarboxylase (LDC), <i>o</i>-nitrophenyl-β-D-galactosidase (ONPG), <i>p</i>-nitrophenyl-β-D-glucosidase (βGLU), <i>p</i>-nitrophenyl-N-acetyl-β-D-glucosaminidase (NAG), malonate (MAL), adonitol fermentation (ADON), and tryptophane utilization (IND). GC-MS-based metabolic profiling identified alcohols (methyl alcohol, <i>o</i>-, <i>p</i>- and <i>m</i>-cresols, catechol, and 3-methyl catechol), aldehydes (methanone, acetaldehyde, and <i>m</i>-tolualdehyde), carboxylic acid (methanoic acid, <i>cis,cis</i>-muconic acid, cyclohexane carboxylic acid and benzoic acid), conjugate bases of carboxylic acids (benzoate, <i>cis,cis</i>-muconate, 4-hydroxybenzoate, and pyruvate) and cycloalkane (cyclohexene). It suggested the presence of methane, methylcyclohexane, toluene, xylene, and benzene degradation pathways in <i>B. cereus</i>.</p>","PeriodicalId":94173,"journal":{"name":"Polish journal of microbiology","volume":"73 1","pages":"107-120"},"PeriodicalIF":0.0,"publicationDate":"2024-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10911661/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140029924","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-03-04eCollection Date: 2024-03-01DOI: 10.33073/pjm-2024-010
Sham Jamil Abdullah, Shahnaz Abdulkader Ali
Entamoeba histolytica infects the large intestine of humans, causing a spectrum of clinical appearances ranging from asymptomatic colonization to severe intestinal and extra-intestinal disease. The parasite is identical microscopically to commensal nonpathogenic amoeba. To detect the pathogenic Entamoeba and estimate the precise prevalence of the parasite among the symptomatic pediatric population using molecular techniques. 323 fecal samples were collected from symptomatic children admitted to Sulaimani Pediatric Teaching Hospital, Sulaimaniyah Province, Iraq, from June to October 2021. A structured, validated questionnaire was prepared and used to report participants' gender, residency, and drinking water source. Then, stool samples were microscopically examined, and the positive samples were submitted to molecular analysis by amplifying the 18s rRNA gene using nested PCR to differentiate E. histolytica from other nonpathogenic Entamoeba. Finally, gene sequences were done to confirm the species. Microscopically, 58 positive samples represented Entamoeba species infection rate of 18% among symptomatic patients. However, only 18 samples were positive for E. histolytica based on molecular methods, which accounts for 31% of the positive by microscopy and 5.6% among the 323 symptomatic populations. NCBI, available in their database, gives the gene sequence and accession number. Patients' sociodemographic data and water sources were directly related to the infection rate. Classical microscopic examination provides a misleading profile about the prevalence of E. histolytica in an endemic region that might lead to unnecessary treatments and a lack of appropriate management for patients.
{"title":"Molecular Detection of a Pathogenic <i>Entamoeba</i> among Symptomatic Children in Eastern Kurdistan of Iraq.","authors":"Sham Jamil Abdullah, Shahnaz Abdulkader Ali","doi":"10.33073/pjm-2024-010","DOIUrl":"10.33073/pjm-2024-010","url":null,"abstract":"<p><p><i>Entamoeba histolytica</i> infects the large intestine of humans, causing a spectrum of clinical appearances ranging from asymptomatic colonization to severe intestinal and extra-intestinal disease. The parasite is identical microscopically to commensal nonpathogenic amoeba. To detect the pathogenic <i>Entamoeba</i> and estimate the precise prevalence of the parasite among the symptomatic pediatric population using molecular techniques. 323 fecal samples were collected from symptomatic children admitted to Sulaimani Pediatric Teaching Hospital, Sulaimaniyah Province, Iraq, from June to October 2021. A structured, validated questionnaire was prepared and used to report participants' gender, residency, and drinking water source. Then, stool samples were microscopically examined, and the positive samples were submitted to molecular analysis by amplifying the 18s rRNA gene using nested PCR to differentiate <i>E. histolytica</i> from other nonpathogenic <i>Entamoeba</i>. Finally, gene sequences were done to confirm the species. Microscopically, 58 positive samples represented <i>Entamoeba</i> species infection rate of 18% among symptomatic patients. However, only 18 samples were positive for <i>E. histolytica</i> based on molecular methods, which accounts for 31% of the positive by microscopy and 5.6% among the 323 symptomatic populations. NCBI, available in their database, gives the gene sequence and accession number. Patients' sociodemographic data and water sources were directly related to the infection rate. Classical microscopic examination provides a misleading profile about the prevalence of <i>E. histolytica</i> in an endemic region that might lead to unnecessary treatments and a lack of appropriate management for patients.</p>","PeriodicalId":94173,"journal":{"name":"Polish journal of microbiology","volume":"73 1","pages":"99-105"},"PeriodicalIF":0.0,"publicationDate":"2024-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10911696/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140029925","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-03-04eCollection Date: 2024-03-01DOI: 10.33073/pjm-2024-004
Ning Huang, Xin Jin, Jin-Tao Wen, Yi-Fei Zhang, Xu Yang, Guang-Yu Wei, Yi-Kun Wang, Min Qin
Fungal diseases form perforated disease spots in tobacco plants, resulting in a decline in tobacco yield and quality. The present study investigated the antagonistic effect of Bacillus subtilis CTXW 7-6-2 against Rhizoctonia solani, its ability to promote the growth of tobacco seedlings, and the expression of disease resistance-related genes for efficient and eco-friendly plant disease control. Our results showed that CTXW 7-6-2 had the most vigorous growth after being cultured for 96 h, and its rate of inhibition of R. solani growth in vitro was 94.02%. The volatile compounds produced by CTXW 7-6-2 inhibited the growth of R. solani significantly (by 96.62%). The fungal growthinhibition rate of the B. subtilis CTXW 7-6-2 broth obtained after high-temperature and no-high-temperature sterile fermentation was low, at 50.88% and 54.63%, respectively. The lipopeptides extracted from the B. subtilis CTXW 7-6-2 fermentation broth showed a 74.88% fungal growth inhibition rate at a concentration of 100 mg/l. Scanning and transmission electron microscopy showed some organelle structural abnormalities, collapse, shrinkage, blurring, and dissolution in the R. solani mycelia. In addition, CTXW 7-6-2 increased tobacco seedling growth and improved leaf and root weight compared to the control. After CTXW 7-6-2 inoculation, tobacco leaves showed the upregulation of the PDF1.2, PPO, and PAL genes, which are closely related to target spot disease resistance. In conclusion, B. subtilis CTXW 7-6-2 may be an efficient biological control agent in tobacco agriculture and enhance plant growth potential.
{"title":"Biocontrol and Growth Promotion Potential of <i>Bacillus subtilis</i> CTXW 7-6-2 against <i>Rhizoctonia solani</i> that Causes Tobacco Target Spot Disease.","authors":"Ning Huang, Xin Jin, Jin-Tao Wen, Yi-Fei Zhang, Xu Yang, Guang-Yu Wei, Yi-Kun Wang, Min Qin","doi":"10.33073/pjm-2024-004","DOIUrl":"10.33073/pjm-2024-004","url":null,"abstract":"<p><p>Fungal diseases form perforated disease spots in tobacco plants, resulting in a decline in tobacco yield and quality. The present study investigated the antagonistic effect of <i>Bacillus subtilis</i> CTXW 7-6-2 against <i>Rhizoctonia solani</i>, its ability to promote the growth of tobacco seedlings, and the expression of disease resistance-related genes for efficient and eco-friendly plant disease control. Our results showed that CTXW 7-6-2 had the most vigorous growth after being cultured for 96 h, and its rate of inhibition of <i>R. solani</i> growth <i>in vitro</i> was 94.02%. The volatile compounds produced by CTXW 7-6-2 inhibited the growth of <i>R. solani</i> significantly (by 96.62%). The fungal growthinhibition rate of the <i>B. subtilis</i> CTXW 7-6-2 broth obtained after high-temperature and no-high-temperature sterile fermentation was low, at 50.88% and 54.63%, respectively. The lipopeptides extracted from the <i>B. subtilis</i> CTXW 7-6-2 fermentation broth showed a 74.88% fungal growth inhibition rate at a concentration of 100 mg/l. Scanning and transmission electron microscopy showed some organelle structural abnormalities, collapse, shrinkage, blurring, and dissolution in the <i>R. solani</i> mycelia. In addition, CTXW 7-6-2 increased tobacco seedling growth and improved leaf and root weight compared to the control. After CTXW 7-6-2 inoculation, tobacco leaves showed the upregulation of the <i>PDF1.2</i>, <i>PPO</i>, and <i>PAL</i> genes, which are closely related to target spot disease resistance. In conclusion, <i>B. subtilis</i> CTXW 7-6-2 may be an efficient biological control agent in tobacco agriculture and enhance plant growth potential.</p>","PeriodicalId":94173,"journal":{"name":"Polish journal of microbiology","volume":"73 1","pages":"29-38"},"PeriodicalIF":0.0,"publicationDate":"2024-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10911660/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140029919","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-12-16eCollection Date: 2023-12-01DOI: 10.33073/pjm-2023-035
Maria Teresa Szymankiewicz, Anna Szczepanska, Elzbieta Stefaniuk
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 plus 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 Staphylococcus aureus, followed by Escherichia coli, Pseudomonas aeruginosa, and Haemophilus influenzae. 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.
{"title":"Evaluation of the BioFire® FilmArray® Pneumonia <i>plus</i> Panel for Detecting Bacterial Etiological Agents of Lower Respiratory Tract Infections in an Oncologic Hospital. Comparison with Conventional Culture Method.","authors":"Maria Teresa Szymankiewicz, Anna Szczepanska, Elzbieta Stefaniuk","doi":"10.33073/pjm-2023-035","DOIUrl":"10.33073/pjm-2023-035","url":null,"abstract":"<p><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 <i>plus</i> 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 <i>Staphylococcus aureus</i>, followed by <i>Escherichia coli, Pseudomonas aeruginosa</i>, and <i>Haemophilus influenzae</i>. 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>","PeriodicalId":94173,"journal":{"name":"Polish journal of microbiology","volume":" ","pages":"391-398"},"PeriodicalIF":0.0,"publicationDate":"2023-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10725156/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41184590","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-12-16eCollection Date: 2023-12-01DOI: 10.33073/pjm-2023-046
Xiaoxiao Pang, Long Chen, Guoxin Xu
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.
{"title":"New Awareness of the Interplay Between the Gut Microbiota and Circadian Rhythms.","authors":"Xiaoxiao Pang, Long Chen, Guoxin Xu","doi":"10.33073/pjm-2023-046","DOIUrl":"10.33073/pjm-2023-046","url":null,"abstract":"<p><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.</p>","PeriodicalId":94173,"journal":{"name":"Polish journal of microbiology","volume":"72 4","pages":"355-363"},"PeriodicalIF":0.0,"publicationDate":"2023-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10725168/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138816109","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-12-16eCollection Date: 2023-12-01DOI: 10.33073/pjm-2023-039
Renata Matuszewska, Łukasz Mąka
The Clostridium perfringens bacteria are used to assess water quality as an indicator parameter. If detected, it can confirm the occurrence of past fecal contamination. Tests determining C. perfringens 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 C. perfringens (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.
{"title":"Comparison of mCP and TSC Media to Enumerate <i>Clostridium perfringens</i> in Surface Water Samples.","authors":"Renata Matuszewska, Łukasz Mąka","doi":"10.33073/pjm-2023-039","DOIUrl":"10.33073/pjm-2023-039","url":null,"abstract":"<p><p>The <i>Clostridium perfringens</i> bacteria are used to assess water quality as an indicator parameter. If detected, it can confirm the occurrence of past fecal contamination. Tests determining <i>C. perfringens</i> 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 <i>C. perfringens</i> (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.</p>","PeriodicalId":94173,"journal":{"name":"Polish journal of microbiology","volume":" ","pages":"413-419"},"PeriodicalIF":0.0,"publicationDate":"2023-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10725159/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138435602","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-12-16eCollection Date: 2023-12-01DOI: 10.33073/pjm-2023-045
Bilal Yahiaoui, Hadjira Bounabi, Amine M Boukerb, Meriem Gasmi
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 Bacillus halotolerans had the most interesting activity profile. Interestingly, HGR5 was substantially active against Fusarium graminearum, Phytophthora infestans, and Alternaria alternata. 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.
{"title":"Insights into Genomic Features and Potential Biotechnological Applications of <i>Bacillus halotolerans</i> Strain HGR5.","authors":"Bilal Yahiaoui, Hadjira Bounabi, Amine M Boukerb, Meriem Gasmi","doi":"10.33073/pjm-2023-045","DOIUrl":"10.33073/pjm-2023-045","url":null,"abstract":"<p><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 <i>Bacillus halotolerans</i> had the most interesting activity profile. Interestingly, HGR5 was substantially active against <i>Fusarium graminearum, Phytophthora infestans</i>, and <i>Alternaria alternata</i>. 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.</p>","PeriodicalId":94173,"journal":{"name":"Polish journal of microbiology","volume":"72 4","pages":"477-490"},"PeriodicalIF":0.0,"publicationDate":"2023-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10725166/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138816106","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-12-16eCollection Date: 2023-12-01DOI: 10.33073/pjm-2023-038
Hanna Kruszewska, Anna Zawistowska-Rojek, Stefan Tyski
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 Lactobacillaceae strains (including probiotic strains) in vitro. 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.
{"title":"Do NSAIDs and Other Pain Relief Drugs Can Inhibit the Growth of <i>Lactobacillaceae</i>?","authors":"Hanna Kruszewska, Anna Zawistowska-Rojek, Stefan Tyski","doi":"10.33073/pjm-2023-038","DOIUrl":"10.33073/pjm-2023-038","url":null,"abstract":"<p><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 <i>Lactobacillaceae</i> strains (including probiotic strains) <i>in vitro</i>. 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.</p>","PeriodicalId":94173,"journal":{"name":"Polish journal of microbiology","volume":" ","pages":"507-513"},"PeriodicalIF":0.0,"publicationDate":"2023-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10725164/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41224319","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}