Pub Date : 2022-09-02eCollection Date: 2022-09-01DOI: 10.33073/pjm-2022-029
Sara H Arafa, Wafa A Alshehri, Sameer R Organji, Khaled Elbanna, Najla A Obaid, Mohammad S Aldosari, Fatimah H Asiri, Iqbal Ahmad, Hussein H Abulreesh
To explore the prevalence of multidrug-resistant community-associated uropathogenic Escherichia coli (UPEC) and their virulence factors in Western Saudi Arabia. A total of 1,000 urine samples were examined for the presence of E. coli by selective plating on MacConkey, CLED, and sheep blood agar. Antimicrobial susceptibility patterns were determined using Vitek® 2 Compact (MIC) and the disc diffusion method with Mueller-Hinton agar. Genes encoding virulence factors (kpsMTII, traT, sat, csgA, vat, and iutA) were detected by PCR. The overall prevalence of UTI-associated E. coli was low, and a higher prevalence was detected in samples of female origin. Many of the isolates exhibited resistance to norfloxacin, and 60% of the isolates showed resistance to ampicillin. No resistance to imipenem, meropenem, or ertapenem was detected. In general, half of the isolates showed multiple resistance patterns. UPEC exhibited a weak ability to form biofilms, where no correlation was observed between multidrug resistance and biofilm-forming ability. All uropathogenic E. coli isolates carried the kpsMTII, iutA, traT, and csgA genes, whereas the low number of the isolates harbored the sat and vat genes. The diversity of virulence factors harbored by community-associated UPEC may render them more virulent and further explain the recurrence/relapse cases among community-associated UITs. To the best of our knowledge, this study constitutes the first exploration of virulence, biofilm-forming ability, and its association with multidrug resistance among UPEC isolates in Saudi Arabia. Further investigations are needed to elucidate the epidemiology of community-associated UPEC in Saudi Arabia.
{"title":"Antimicrobial Resistance, Virulence Factor-Encoding Genes, and Biofilm-Forming Ability of Community-Associated Uropathogenic <i>Escherichia coli</i> in Western Saudi Arabia.","authors":"Sara H Arafa, Wafa A Alshehri, Sameer R Organji, Khaled Elbanna, Najla A Obaid, Mohammad S Aldosari, Fatimah H Asiri, Iqbal Ahmad, Hussein H Abulreesh","doi":"10.33073/pjm-2022-029","DOIUrl":"https://doi.org/10.33073/pjm-2022-029","url":null,"abstract":"<p><p>To explore the prevalence of multidrug-resistant community-associated uropathogenic <i>Escherichia coli</i> (UPEC) and their virulence factors in Western Saudi Arabia. A total of 1,000 urine samples were examined for the presence of <i>E. coli</i> by selective plating on MacConkey, CLED, and sheep blood agar. Antimicrobial susceptibility patterns were determined using Vitek<sup>®</sup> 2 Compact (MIC) and the disc diffusion method with Mueller-Hinton agar. Genes encoding virulence factors (<i>kpsMTII</i>, <i>traT</i>, <i>sat</i>, <i>csgA</i>, <i>vat</i>, and <i>iutA</i>) were detected by PCR. The overall prevalence of UTI-associated <i>E. coli</i> was low, and a higher prevalence was detected in samples of female origin. Many of the isolates exhibited resistance to norfloxacin, and 60% of the isolates showed resistance to ampicillin. No resistance to imipenem, meropenem, or ertapenem was detected. In general, half of the isolates showed multiple resistance patterns. UPEC exhibited a weak ability to form biofilms, where no correlation was observed between multidrug resistance and biofilm-forming ability. All uropathogenic <i>E. coli</i> isolates carried the <i>kpsMTII</i>, <i>iutA</i>, <i>traT</i>, and <i>csgA</i> genes, whereas the low number of the isolates harbored the <i>sat</i> and <i>vat</i> genes. The diversity of virulence factors harbored by community-associated UPEC may render them more virulent and further explain the recurrence/relapse cases among community-associated UITs. To the best of our knowledge, this study constitutes the first exploration of virulence, biofilm-forming ability, and its association with multidrug resistance among UPEC isolates in Saudi Arabia. Further investigations are needed to elucidate the epidemiology of community-associated UPEC in Saudi Arabia.</p>","PeriodicalId":20272,"journal":{"name":"Polish Journal of Microbiology","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2022-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/88/b5/pjm-71-325.PMC9608162.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40337373","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Fengzhen Yang, Qi Zhao, Lipeng Wang, Jinying Wu, Lihua Jiang, Li Sheng, Leyan Zhang, Zhaoping Xue, Maoli Yi
Cefoperazone/sulbactam (CSL) and piperacillin/tazobactam (TZP) are commonly used in clinical practice in China because of their excellent antimicrobial activity. CSL and TZP-nonsusceptible Enterobacteriaceae are typically resistant to extended-spectrum cephalosporins such as ceftriaxone (CRO). However, 11 nonrepetitive Enterobacteriaceae strains, which were resistant to CSL and TZP yet susceptible to CRO, were collected from January to December 2020. Antibiotic susceptibility tests and whole-genome sequencing were conducted to elucidate the mechanism for this rare phenotype. Antibiotic susceptibility tests showed that all isolates were amoxicillin/clavulanic-acid resistant and sensitive to ceftazidime, cefepime, cefepime/tazobactam, cefepime/zidebactam, ceftazidime/avibactam, and ceftolozane/tazobactam. Whole-genome sequencing revealed three of seven Klebsiella pneumoniae strains harbored blaSHV-1 only, and four harbored blaSHV-1 and blaTEM-1B. Two Escherichia coli strains carried blaTEM-1B only, while two Klebsiella oxytoca isolates harbored blaOXY-1-3 and blaOXY-1-1, respectively. No mutation in the β-lactamase gene and promoter sequence was found. Outer membrane protein (Omp) gene detection revealed that numerous missense mutations of OmpK36 and OmpK37 were found in all strains of K. pneumoniae. Numerous missense mutations of OmpK36 and OmpK35 and OmpK37 deficiency were found in one K. oxytoca strain, and no OmpK gene was found in the other. No Omp mutations were found in E. coli isolates. These results indicated that narrow spectrum β-lactamases, TEM-1, SHV-1, and OXY-1, alone or in combination with Omp mutation, contributed to the resistance to CSL and TZP in CRO-susceptible Enterobacteriaceae. Antibiotic susceptibility tests Antibiotics Breakpoint, (μg/ml) Klebsiella pneumoniaeEscherichia cou Klebriehd axyoca E1 E3 E4 E7 E9 E10 E11 E6 E8 E2 E5 CRO≤1≥4≤0.5≤0.5≤0.5≤0.5 1≤0.51≤0.5≤0.511CAZ4 ≥161214444241 1FEP≤2 216 110.2512220.521 1AMC≤8 ≥32≥128≥128≥128≥128≥128≥128≥128≥128≥128≥128≥128CSL≤16 ≥6464646464≥128128≥12864128128≥128TZP≤16 ≥128≥256≥256≥256≥25622562256≥256≥256≥256≥256≥256FPT≤2 ≥1610.50.060.125212
{"title":"Diminished Susceptibility to Cefoperazone/Sulbactam and Piperacillin/Tazobactam in <i>Enterobacteriaceae</i> Due to Narrow-Spectrum β-Lactamases as Well as Omp Mutation.","authors":"Fengzhen Yang, Qi Zhao, Lipeng Wang, Jinying Wu, Lihua Jiang, Li Sheng, Leyan Zhang, Zhaoping Xue, Maoli Yi","doi":"10.33073/pjm-2022-023","DOIUrl":"https://doi.org/10.33073/pjm-2022-023","url":null,"abstract":"<p><p>Cefoperazone/sulbactam (CSL) and piperacillin/tazobactam (TZP) are commonly used in clinical practice in China because of their excellent antimicrobial activity. CSL and TZP-nonsusceptible <i>Enterobacteriaceae</i> are typically resistant to extended-spectrum cephalosporins such as ceftriaxone (CRO). However, 11 nonrepetitive <i>Enterobacteriaceae</i> strains, which were resistant to CSL and TZP yet susceptible to CRO, were collected from January to December 2020. Antibiotic susceptibility tests and whole-genome sequencing were conducted to elucidate the mechanism for this rare phenotype. Antibiotic susceptibility tests showed that all isolates were amoxicillin/clavulanic-acid resistant and sensitive to ceftazidime, cefepime, cefepime/tazobactam, cefepime/zidebactam, ceftazidime/avibactam, and ceftolozane/tazobactam. Whole-genome sequencing revealed three of seven <i>Klebsiella pneumoniae</i> strains harbored <i>bla</i> <sub>SHV-1</sub> only, and four harbored <i>bla</i> <sub>SHV-1</sub> and <i>bla</i> <sub>TEM-1B</sub>. Two <i>Escherichia coli</i> strains carried <i>bla</i> <sub>TEM-1B</sub> only, while two <i>Klebsiella oxytoca</i> isolates harbored <i>bla</i> <sub>OXY-1-3</sub> and <i>bla</i> <sub>OXY-1-1</sub>, respectively. No mutation in the β-lactamase gene and promoter sequence was found. Outer membrane protein (Omp) gene detection revealed that numerous missense mutations of OmpK36 and OmpK37 were found in all strains of <i>K. pneumoniae</i>. Numerous missense mutations of OmpK36 and OmpK35 and OmpK37 deficiency were found in one <i>K. oxytoca</i> strain, and no OmpK gene was found in the other. No Omp mutations were found in <i>E. coli</i> isolates. These results indicated that narrow spectrum β-lactamases, TEM-1, SHV-1, and OXY-1, alone or in combination with Omp mutation, contributed to the resistance to CSL and TZP in CRO-susceptible <i>Enterobacteriaceae</i>. Antibiotic susceptibility tests Antibiotics Breakpoint, (μg/ml) <i>Klebsiella pneumoniae</i> <i>Escherichia cou</i> Klebriehd axyoca E1 E3 E4 E7 E9 E10 E11 E6 E8 E2 E5 <b>CRO</b> <b>≤1≥4</b> <b>≤0.5</b> <b>≤0.5</b> <b>≤0.5</b> <b>≤0.5 1</b> <b>≤0.5</b> <b>1</b> <b>≤0.5</b> <b>≤0.5</b> <b>1</b> <b>1</b> <b>CAZ</b> <b>4 ≥16</b> <b>1</b> <b>2</b> <b>1</b> <b>4</b> <b>4</b> <b>4</b> <b>4</b> <b>2</b> <b>4</b> <b>1 1</b> <b>FEP</b> <b>≤2 216 1</b> <b>1</b> <b>0.25</b> <b>1</b> <b>2</b> <b>2</b> <b>2</b> <b>0.5</b> <b>2</b> <b>1 1</b> <b>AMC</b> <b>≤8 ≥32</b> <b>≥128</b> <b>≥128</b> <b>≥128</b> <b>≥128</b> <b>≥128</b> <b>≥128</b> <b>≥128</b> <b>≥128</b> <b>≥128</b> <b>≥128</b> <b>≥128</b> <b>CSL</b> <b>≤16 ≥64</b> <b>64</b> <b>64</b> <b>64</b> <b>64</b> <b>≥128</b> <b>128</b> <b>≥128</b> <b>64</b> <b>128</b> <b>128</b> <b>≥128</b> <b>TZP</b> <b>≤16 ≥128</b> <b>≥256</b> <b>≥256</b> <b>≥256</b> <b>≥256</b> <b>2256</b> <b>2256</b> <b>≥256</b> <b>≥256</b> <b>≥256</b> <b>≥256</b> <b>≥256</b> <b>FPT</b> <b>≤2 ≥16</b> <b>1</b> <b>0.5</b> <b>0.06</b> <b>0.125</b> <b>2</b> <b>1</b> <b>2","PeriodicalId":20272,"journal":{"name":"Polish Journal of Microbiology","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2022-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/1e/42/pjm-71-251.PMC9252146.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39985855","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
With the development of genome sequencing, many researchers have investigated the mechanism by which the intestinal microbiota influences sleep across the brain-gut axis. However, the relationship between gut microbiota and sleep disorder remains unclear. Thus, we studied the difference in gut microbiota composition between poor sleep quality- and normal populations, which helps set the ground for future research. The recruited college students provided baseline information and stool samples and completed the Pittsburgh Sleep Quality Index (PSQI). We compared the two groups' gut microbiota composition and functional differentiation by using the 16S rRNA gene sequencing analysis. The main bacterial difference and the most critical effect were mainly concentrated within Tenericutes and Elusimicrobia. Compared with the healthy control group, some functions of the gut microbiota were impaired in the poor sleep quality group, such as butanoate metabolism and propanoate metabolism. Bacterial taxa with significant differences raised the possibility for future diagnosis and treatment of sleep problems.
{"title":"The Component and Functional Pathways of Gut Microbiota Are Altered in Populations with Poor Sleep Quality - A Preliminary Report.","authors":"Jianghui Zhang, Xueqing Zhang, Kexin Zhang, Xiaoyan Lu, Guojing Yuan, Huayu Yang, Haiyun Guo, Zhihui Zhu, Tianli Wang, Jiahu Hao, Ying Sun, Puyu Su, Zhihua Zhang","doi":"10.33073/pjm-2022-021","DOIUrl":"https://doi.org/10.33073/pjm-2022-021","url":null,"abstract":"<p><p>With the development of genome sequencing, many researchers have investigated the mechanism by which the intestinal microbiota influences sleep across the brain-gut axis. However, the relationship between gut microbiota and sleep disorder remains unclear. Thus, we studied the difference in gut microbiota composition between poor sleep quality- and normal populations, which helps set the ground for future research. The recruited college students provided baseline information and stool samples and completed the Pittsburgh Sleep Quality Index (PSQI). We compared the two groups' gut microbiota composition and functional differentiation by using the 16S rRNA gene sequencing analysis. The main bacterial difference and the most critical effect were mainly concentrated within Tenericutes and Elusimicrobia. Compared with the healthy control group, some functions of the gut microbiota were impaired in the poor sleep quality group, such as butanoate metabolism and propanoate metabolism. Bacterial taxa with significant differences raised the possibility for future diagnosis and treatment of sleep problems.</p>","PeriodicalId":20272,"journal":{"name":"Polish Journal of Microbiology","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2022-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/b9/2a/pjm-71-241.PMC9252145.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39985856","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Aneta Guzek, Zbigniew Rybicki, Agnieszka Woźniak-Kosek, Dariusz Tomaszewski
Hospital-acquired bloodstream infections are a severe worldwide problem associated with significant morbidity and mortality. This retrospective, single-center study aimed to analyze bloodstream infections in patients hospitalized in the intensive care unit of the Military Institute of Medicine, Poland. Data from the years 2007-2019 were analyzed. When the infection was suspected, blood samples were drawn and analyzed microbiologically. When bacterial growth was observed, an antimicrobial susceptibility/resistance analysis was performed. Among 12,619 analyzed samples, 1,509 were positive, and 1,557 pathogens were isolated. In 278/1,509 of the positive cases, a central line catheter infection was confirmed. Gram-negative bacteria were the most frequently (770/1,557) isolated, including Acinetobacter baumannii (312/770), Klebsiella pneumoniae (165/770; 67/165 were the isolates that expressed extended spectrum beta-lactamases (ESBL), 5/165 isolates produced the New Delhi metallo-β-lactamases (NDM), 4/165 isolates expressed Klebsiella pneumoniae carbapenemase (KPC), and 1/165 isolate produced OXA48 carbapenemase), Pseudomonas aeruginosa (111/770; 2/111 isolates produced metallo-β-lactamase (MBL), and Escherichia coli (69/770; 11/69 - ESBL). Most Gram-positive pathogens were staphylococci (545/733), mainly coagulase-negative (368/545). Among 545 isolates of the staphylococci, 58 represented methicillin-resistant Staphylococcus aureus (MRSA). Fungi were isolated from 3.5% of samples. All isolated MRSA and methicillin-resistant coagulase-negative Staphylococcus (MRCNS) strains were susceptible to vancomycin, methicillin-sensitive Staphylococcus aureus (MSSA) isolates - to isoxazolyl penicillins, and vancomycin-resistant Enterococcus (VRE) - to linezolid and tigecycline. However, colistin was the only therapeutic option in some infections caused by A. baumannii and KPC-producing K. pneumoniae. P. aeruginosa was still susceptible to cefepime and ceftazidime. Echinocandins were effective therapeutics in the treatment of fungal infections.
{"title":"Bloodstream Infections in the Intensive Care Unit: a Single-Center Retrospective Bacteriological Analysis Between 2007 and 2019.","authors":"Aneta Guzek, Zbigniew Rybicki, Agnieszka Woźniak-Kosek, Dariusz Tomaszewski","doi":"10.33073/pjm-2022-025","DOIUrl":"https://doi.org/10.33073/pjm-2022-025","url":null,"abstract":"<p><p>Hospital-acquired bloodstream infections are a severe worldwide problem associated with significant morbidity and mortality. This retrospective, single-center study aimed to analyze bloodstream infections in patients hospitalized in the intensive care unit of the Military Institute of Medicine, Poland. Data from the years 2007-2019 were analyzed. When the infection was suspected, blood samples were drawn and analyzed microbiologically. When bacterial growth was observed, an antimicrobial susceptibility/resistance analysis was performed. Among 12,619 analyzed samples, 1,509 were positive, and 1,557 pathogens were isolated. In 278/1,509 of the positive cases, a central line catheter infection was confirmed. Gram-negative bacteria were the most frequently (770/1,557) isolated, including <i>Acinetobacter baumannii</i> (312/770), <i>Klebsiella pneumoniae</i> (165/770; 67/165 were the isolates that expressed extended spectrum beta-lactamases (ESBL), 5/165 isolates produced the New Delhi metallo-β-lactamases (NDM), 4/165 isolates expressed <i>Klebsiella pneumoniae</i> carbapenemase (KPC), and 1/165 isolate produced OXA48 carbapenemase), <i>Pseudomonas aeruginosa</i> (111/770; 2/111 isolates produced metallo-β-lactamase (MBL), and <i>Escherichia coli</i> (69/770; 11/69 - ESBL). Most Gram-positive pathogens were staphylococci (545/733), mainly coagulase-negative (368/545). Among 545 isolates of the staphylococci, 58 represented methicillin-resistant <i>Staphylococcus aureus</i> (MRSA). Fungi were isolated from 3.5% of samples. All isolated MRSA and methicillin-resistant coagulase-negative <i>Staphylococcus</i> (MRCNS) strains were susceptible to vancomycin, methicillin-sensitive <i>Staphylococcus aureus</i> (MSSA) isolates - to isoxazolyl penicillins, and vancomycin-resistant <i>Enterococcus</i> (VRE) - to linezolid and tigecycline. However, colistin was the only therapeutic option in some infections caused by <i>A. baumannii</i> and KPC-producing <i>K. pneumoniae</i>. <i>P. aeruginosa</i> was still susceptible to cefepime and ceftazidime. Echinocandins were effective therapeutics in the treatment of fungal infections.</p>","PeriodicalId":20272,"journal":{"name":"Polish Journal of Microbiology","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2022-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/2a/64/pjm-71-263.PMC9252137.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39986465","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Joanna Iwanicka, Tomasz Iwanicki, Marcin Kaczmarczyk, Włodzimierz Mazur
The rapidly spreading Coronavirus Disease 2019 (COVID-19) pandemic has led to a global health crisis and has left a deep mark on society, culture, and the global economy. Despite considerable efforts made to contain the disease, SARS-CoV-2 still poses a threat on a global scale. The current epidemiological situation caused an urgent need to understand the basic mechanisms of the virus transmission and COVID-19 severe course. This review summarizes current knowledge on clinical courses, diagnostics, treatment, and prevention of COVID-19. Moreover, we have included the latest research results on the genetic characterization of SARS-CoV-2 and genetic determinants of susceptibility and severity to infection.
{"title":"Clinical and Genetic Characteristics of Coronaviruses with Particular Emphasis on SARS-CoV-2 Virus.","authors":"Joanna Iwanicka, Tomasz Iwanicki, Marcin Kaczmarczyk, Włodzimierz Mazur","doi":"10.33073/pjm-2022-022","DOIUrl":"https://doi.org/10.33073/pjm-2022-022","url":null,"abstract":"<p><p>The rapidly spreading Coronavirus Disease 2019 (COVID-19) pandemic has led to a global health crisis and has left a deep mark on society, culture, and the global economy. Despite considerable efforts made to contain the disease, SARS-CoV-2 still poses a threat on a global scale. The current epidemiological situation caused an urgent need to understand the basic mechanisms of the virus transmission and COVID-19 severe course. This review summarizes current knowledge on clinical courses, diagnostics, treatment, and prevention of COVID-19. Moreover, we have included the latest research results on the genetic characterization of SARS-CoV-2 and genetic determinants of susceptibility and severity to infection.</p>","PeriodicalId":20272,"journal":{"name":"Polish Journal of Microbiology","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2022-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/ed/ba/pjm-71-141.PMC9252140.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9180833","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The identification and antibiotic susceptibility of two clinical isolates of Eggerthella lenta from bloodstream infections were determined. This microorganism is rarely pathogenic, and the findings are presented here to promote the detection and awareness of this infection. The bacteria were obtained from one patient with pressure sores and another with a malignant gastric tumor. Smears were prepared, stained, and examined by microscopy. Single colonies were analyzed by Gram staining, MALDI-TOF MS, and the 16S rRNA gene sequencing. Antibiotic sensitivity was assessed by the agar dilution method. The bacilli were found to be Gram-positive, and the MS results showed 99.8% homology with E. lenta. It was confirmed by gene sequencing. Antibiotic susceptibility tests demonstrated that E. lenta was sensitive to piperacillin-tazobactam, ampicillin-sulbactam, imipenem, meropenem, metronidazole, clindamycin, and vancomycin. This study could increase awareness of this rare infection.
{"title":"Identification and Antibiotic Susceptibility of <i>Eggerthella lenta</i> in Bloodstream Infections.","authors":"Xiangyun Li, Enjun Xu, Cuixiao Shi, Guanhua Qiao, Shuyi Chen, Yuanhong Xu, Yajing Liu, Xundi Bao","doi":"10.33073/pjm-2022-024","DOIUrl":"https://doi.org/10.33073/pjm-2022-024","url":null,"abstract":"<p><p>The identification and antibiotic susceptibility of two clinical isolates of <i>Eggerthella lenta</i> from bloodstream infections were determined. This microorganism is rarely pathogenic, and the findings are presented here to promote the detection and awareness of this infection. The bacteria were obtained from one patient with pressure sores and another with a malignant gastric tumor. Smears were prepared, stained, and examined by microscopy. Single colonies were analyzed by Gram staining, MALDI-TOF MS, and the 16S rRNA gene sequencing. Antibiotic sensitivity was assessed by the agar dilution method. The bacilli were found to be Gram-positive, and the MS results showed 99.8% homology with <i>E. lenta</i>. It was confirmed by gene sequencing. Antibiotic susceptibility tests demonstrated that <i>E. lenta</i> was sensitive to piperacillin-tazobactam, ampicillin-sulbactam, imipenem, meropenem, metronidazole, clindamycin, and vancomycin. This study could increase awareness of this rare infection.</p>","PeriodicalId":20272,"journal":{"name":"Polish Journal of Microbiology","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2022-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/f4/4d/pjm-71-257.PMC9252136.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39986463","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Oenococcus oeni is an important microorganism in wine-making-related engineering, and it improves wine quality and stability through malolactic fermentation. Although the genomes of more than 200 O. oeni strains have been sequenced, only a few include completed genome maps. Here, the genome sequence of O. oeni SD-2a, isolated from Shandong, China, has been determined. It is a fully assembled genome sequence of this strain. The complete genome is 1,989,703 bp with a G+C content of 37.8% without a plasmid. The genome includes almost all the essential genes involved in central metabolic pathways and the stress genes reported in other O. oeni strains. Some natural competence-related genes, like comEA, comEC, comFA, comG operon, and comFC, suggest that O. oeni SD-2a may have natural transformation potential. A comparative genomics analysis revealed 730 gene clusters in O. oeni SD-2a homologous to those in four other lactic acid bacteria species (O. oeni PSU-1, O. oeni CRBO-11381, Lactiplantibacillus plantarum UNQLp11, and Pediococcus pentosaceus KCCM40703). A collinearity analysis showed poor collinearity between O. oeni SD-2a and O. oeni PSU-1, indicating great differences in their evolutionary histories. The results provide general knowledge of O. oeni SD-2a and lay the foundation for specific gene function analyses.
{"title":"Genomic Analysis of an Excellent Wine-Making Strain <i>Oenococcus oeni</i> SD-2a.","authors":"Longxiang Liu, Shuai Peng, Weiyu Song, Hongyu Zhao, Hua Li, Hua Wang","doi":"10.33073/pjm-2022-026","DOIUrl":"https://doi.org/10.33073/pjm-2022-026","url":null,"abstract":"<p><p><i>Oenococcus oeni</i> is an important microorganism in wine-making-related engineering, and it improves wine quality and stability through malolactic fermentation. Although the genomes of more than 200 <i>O. oeni</i> strains have been sequenced, only a few include completed genome maps. Here, the genome sequence of <i>O. oeni</i> SD-2a, isolated from Shandong, China, has been determined. It is a fully assembled genome sequence of this strain. The complete genome is 1,989,703 bp with a G+C content of 37.8% without a plasmid. The genome includes almost all the essential genes involved in central metabolic pathways and the stress genes reported in other <i>O. oeni</i> strains. Some natural competence-related genes, like <i>com</i>EA, <i>com</i>EC, <i>com</i>FA, <i>com</i>G operon, and <i>com</i>FC, suggest that <i>O. oeni</i> SD-2a may have natural transformation potential. A comparative genomics analysis revealed 730 gene clusters in <i>O. oeni</i> SD-2a homologous to those in four other lactic acid bacteria species (<i>O. oeni</i> PSU-1, <i>O. oeni</i> CRBO-11381, <i>Lactiplantibacillus plantarum</i> UNQLp11, and <i>Pediococcus pentosaceus</i> KCCM40703). A collinearity analysis showed poor collinearity between <i>O. oeni</i> SD-2a and <i>O. oeni</i> PSU-1, indicating great differences in their evolutionary histories. The results provide general knowledge of <i>O. oeni</i> SD-2a and lay the foundation for specific gene function analyses.</p>","PeriodicalId":20272,"journal":{"name":"Polish Journal of Microbiology","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2022-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/b4/c8/pjm-71-279.PMC9252139.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39986464","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Hong Zhao, Lijie Yuan, Dongli Zhu, Banghao Sun, Juan Du, Jingyuan Wang
Abstract To explore the role of gut microbiota in Graves’ disease (GD) and Hashimoto’s thyroiditis (HT). Seventy fecal samples were collected, including 27 patients with GD, 27 with HT, and 16 samples from healthy volunteers. Chemiluminescence was used to detect thyroid function and autoantibodies (FT3, FT4, TSH, TRAb, TGAb, and TPOAb); thyroid ultrasound and 16S sequencing were used to analyze the bacteria in fecal samples; KEGG (Kyoto Encyclopedia of Genes and Genomes) and COG (Clusters of Orthologous Groups) were used to analyze the functional prediction and pathogenesis. The overall structure of gut microbiota in the GD and HT groups was significantly different from the healthy control group. Proteobacteria and Actinobacteria contents were the highest in the HT group. Compared to the control group, the GD and HT groups had a higher abundance of Erysipelotrichia, Cyanobacteria, and Ruminococcus_2 and lower levels of Bacillaceae and Megamonas. Further analysis of KEGG found that the “ABC transporter” metabolic pathway was highly correlated with the occurrence of GD and HT. COG analysis showed that the GD and HT groups were enriched in carbohydrate transport and metabolism compared to the healthy control group but not in amino acid transport and metabolism. Our data suggested that Bacillus, Blautia, and Ornithinimicrobium could be used as potential markers to distinguish GD and HT from the healthy population and that “ABC transporter” metabolic pathway may be involved in the pathogenesis of GD and HT.
探讨肠道菌群在Graves病(GD)和桥本甲状腺炎(HT)中的作用。收集了70份粪便样本，其中GD患者27例，HT患者27例，健康志愿者16例。化学发光法检测甲状腺功能及自身抗体(FT3、FT4、TSH、TRAb、TGAb、TPOAb);采用甲状腺超声和16S测序对粪便样品进行细菌分析;利用京都基因与基因组百科全书(KEGG)和COG (Clusters of Orthologous Groups)对其功能预测和发病机制进行分析。GD组和HT组的肠道菌群总体结构与健康对照组有显著差异。变形菌群和放线菌群含量以HT组最高。与对照组相比，GD和HT组丹毒毛菌、蓝藻菌和瘤胃球菌的丰度较高，杆菌科和巨单胞菌的丰度较低。进一步分析KEGG发现，“ABC转运体”代谢途径与GD和HT的发生高度相关。COG分析显示，与健康对照组相比，GD和HT组碳水化合物运输和代谢富集，但氨基酸运输和代谢不富集。我们的数据提示芽孢杆菌、Blautia和ornithinimicroum可以作为区分GD和HT与健康人群的潜在标志物，“ABC转运体”代谢途径可能参与了GD和HT的发病机制。
{"title":"Alterations and Mechanism of Gut Microbiota in Graves’ Disease and Hashimoto’s Thyroiditis","authors":"Hong Zhao, Lijie Yuan, Dongli Zhu, Banghao Sun, Juan Du, Jingyuan Wang","doi":"10.33073/pjm-2022-016","DOIUrl":"https://doi.org/10.33073/pjm-2022-016","url":null,"abstract":"Abstract To explore the role of gut microbiota in Graves’ disease (GD) and Hashimoto’s thyroiditis (HT). Seventy fecal samples were collected, including 27 patients with GD, 27 with HT, and 16 samples from healthy volunteers. Chemiluminescence was used to detect thyroid function and autoantibodies (FT3, FT4, TSH, TRAb, TGAb, and TPOAb); thyroid ultrasound and 16S sequencing were used to analyze the bacteria in fecal samples; KEGG (Kyoto Encyclopedia of Genes and Genomes) and COG (Clusters of Orthologous Groups) were used to analyze the functional prediction and pathogenesis. The overall structure of gut microbiota in the GD and HT groups was significantly different from the healthy control group. Proteobacteria and Actinobacteria contents were the highest in the HT group. Compared to the control group, the GD and HT groups had a higher abundance of Erysipelotrichia, Cyanobacteria, and Ruminococcus_2 and lower levels of Bacillaceae and Megamonas. Further analysis of KEGG found that the “ABC transporter” metabolic pathway was highly correlated with the occurrence of GD and HT. COG analysis showed that the GD and HT groups were enriched in carbohydrate transport and metabolism compared to the healthy control group but not in amino acid transport and metabolism. Our data suggested that Bacillus, Blautia, and Ornithinimicrobium could be used as potential markers to distinguish GD and HT from the healthy population and that “ABC transporter” metabolic pathway may be involved in the pathogenesis of GD and HT.","PeriodicalId":20272,"journal":{"name":"Polish Journal of Microbiology","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2022-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46814938","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Kishani N Naligama, Kavindi E. Weerasinghe, A. Halmillawewa
Abstract Exploring untapped microbial potentials in previously uncharted environments has become crucial in discovering novel secondary metabolites and enzymes for biotechnological applications. Among prokaryotes, actinomycetes are well recognized for producing a vast range of secondary metabolites and extracellular enzymes. In the present study, we have used surface sediments from ‘Kadolkele’ mangrove ecosystem located in the Negombo lagoon area, Sri Lanka, to isolate actinomycetes with bioactive potentials. A total of six actinomycetes were isolated on modified-starch casein agar and characterized. The isolates were evaluated for their antibacterial activity against four selected bacterial strains and to produce extracellular enzymes: cellulase, amylase, protease, and lipase. Three out of the six isolates exhibited antibacterial activity against Staphylococcus aureus, Escherichia coli, and Bacillus cereus, but not against Listeria monocytogenes. Five strains could produce extracellular cellulase, while all six isolates exhibited amylase activity. Only three of the six isolates were positive for protease and lipase assays separately. Ac-1, Ac-2, and Ac-9, identified as Streptomyces spp. with the 16S rRNA gene sequencing, were used for pigment extraction using four different solvents. Acetone-extracted crude pigments of Ac-1 and Ac-2 were further used in well-diffusion assays, and growth inhibition of test bacteria was observed only with the crude pigment extract of Ac-2. Further, six different commercially available fabrics were dyed with crude pigments of Ac-1. The dyed fabrics retained the yellow color after acid, alkaline, and cold-water treatments suggesting the potential of the Ac-1 pigment to be used in biotechnological applications.
{"title":"Characterization of Bioactive Actinomycetes Isolated from Kadolkele Mangrove Sediments, Sri Lanka","authors":"Kishani N Naligama, Kavindi E. Weerasinghe, A. Halmillawewa","doi":"10.33073/pjm-2022-017","DOIUrl":"https://doi.org/10.33073/pjm-2022-017","url":null,"abstract":"Abstract Exploring untapped microbial potentials in previously uncharted environments has become crucial in discovering novel secondary metabolites and enzymes for biotechnological applications. Among prokaryotes, actinomycetes are well recognized for producing a vast range of secondary metabolites and extracellular enzymes. In the present study, we have used surface sediments from ‘Kadolkele’ mangrove ecosystem located in the Negombo lagoon area, Sri Lanka, to isolate actinomycetes with bioactive potentials. A total of six actinomycetes were isolated on modified-starch casein agar and characterized. The isolates were evaluated for their antibacterial activity against four selected bacterial strains and to produce extracellular enzymes: cellulase, amylase, protease, and lipase. Three out of the six isolates exhibited antibacterial activity against Staphylococcus aureus, Escherichia coli, and Bacillus cereus, but not against Listeria monocytogenes. Five strains could produce extracellular cellulase, while all six isolates exhibited amylase activity. Only three of the six isolates were positive for protease and lipase assays separately. Ac-1, Ac-2, and Ac-9, identified as Streptomyces spp. with the 16S rRNA gene sequencing, were used for pigment extraction using four different solvents. Acetone-extracted crude pigments of Ac-1 and Ac-2 were further used in well-diffusion assays, and growth inhibition of test bacteria was observed only with the crude pigment extract of Ac-2. Further, six different commercially available fabrics were dyed with crude pigments of Ac-1. The dyed fabrics retained the yellow color after acid, alkaline, and cold-water treatments suggesting the potential of the Ac-1 pigment to be used in biotechnological applications.","PeriodicalId":20272,"journal":{"name":"Polish Journal of Microbiology","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2022-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43576260","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Huixia Chen, Huizhong Xie, Dong Shao, Lijun Chen, Siyu Chen, Lin Wang, Xiao Han
Abstract The oral cavity serves as another reservoir for gastric Helicobacter pylori and may contribute to the failure of gastric H. pylori eradication therapy. However, changes to the oral microbial composition after gastric H. pylori eradication therapy has not yet been identified. This study aims to dissect whether the oral microbiota is involved and which bacterium mediates the clinic failure in H. pylori eradication. In the present study, the oral microorganisms from patients who had received the gastric H. pylori eradication treatment were analyzed by a high-throughput 16S rRNA deep sequencing. We found that the β diversity and composition of oral microbiota were remarkably changed in the patients who had experienced successful gastric H. pylori eradication treatment (SE group) compared to the failure group (FE group). Significantly enriched families, including Prevotellaceae, Streptococcaceae, Caulobacteraceae, and Lactobacillaceae, were detected in the SE group. In contrast, the bacterial families, such as Weeksellaceae, Neisseriaceae, Peptostreptococcaceae, Spirochaetaceae, and Veillonellaceae, were abundantly expressed in the FE group. Five operational taxonomic units (OTUs) were positively correlated with DOB values, while two OTUs exhibited negative trends. These different enriched OTUs were extensively involved in the 20 metabolic pathways. These results suggest that a balanced environment in the oral microbiota contributes to H. pylori eradication and metabolic homeostasis in humans. Our data demonstrated that the changes in oral microbiota might contribute to the therapeutic effects of antibiotic therapy. Therefore, a different therapy on the detrimental oral microbiota will increase the therapeutic efficacy of antibiotics on H. pylori infection.
{"title":"Oral Microbiota, a Potential Determinant for the Treatment Efficacy of Gastric Helicobacter Pylori Eradication in Humans","authors":"Huixia Chen, Huizhong Xie, Dong Shao, Lijun Chen, Siyu Chen, Lin Wang, Xiao Han","doi":"10.33073/pjm-2022-020","DOIUrl":"https://doi.org/10.33073/pjm-2022-020","url":null,"abstract":"Abstract The oral cavity serves as another reservoir for gastric Helicobacter pylori and may contribute to the failure of gastric H. pylori eradication therapy. However, changes to the oral microbial composition after gastric H. pylori eradication therapy has not yet been identified. This study aims to dissect whether the oral microbiota is involved and which bacterium mediates the clinic failure in H. pylori eradication. In the present study, the oral microorganisms from patients who had received the gastric H. pylori eradication treatment were analyzed by a high-throughput 16S rRNA deep sequencing. We found that the β diversity and composition of oral microbiota were remarkably changed in the patients who had experienced successful gastric H. pylori eradication treatment (SE group) compared to the failure group (FE group). Significantly enriched families, including Prevotellaceae, Streptococcaceae, Caulobacteraceae, and Lactobacillaceae, were detected in the SE group. In contrast, the bacterial families, such as Weeksellaceae, Neisseriaceae, Peptostreptococcaceae, Spirochaetaceae, and Veillonellaceae, were abundantly expressed in the FE group. Five operational taxonomic units (OTUs) were positively correlated with DOB values, while two OTUs exhibited negative trends. These different enriched OTUs were extensively involved in the 20 metabolic pathways. These results suggest that a balanced environment in the oral microbiota contributes to H. pylori eradication and metabolic homeostasis in humans. Our data demonstrated that the changes in oral microbiota might contribute to the therapeutic effects of antibiotic therapy. Therefore, a different therapy on the detrimental oral microbiota will increase the therapeutic efficacy of antibiotics on H. pylori infection.","PeriodicalId":20272,"journal":{"name":"Polish Journal of Microbiology","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2022-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47730543","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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