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Volume 71 (2022): Issue 2 (June 2022)

Volume 71 (2022): Issue 1 (March 2022)

Volume 70 (2021): Issue 4 (December 2021)

Volume 70 (2021): Issue 3 (September 2021)

Volume 70 (2021): Issue 2 (June 2021)

Volume 70 (2021): Issue 1 (March 2021)

Volume 69 (2020): Issue 4 (December 2020)

Volume 69 (2020): Issue 3 (September 2020)

Volume 69 (2020): Issue 2 (June 2020)

Volume 69 (2020): Issue 1 (March 2020)

Volume 68 (2019): Issue 4 (January 2019)

Volume 68 (2019): Issue 3 (September 2019)

Volume 68 (2019): Issue 2 (June 2019)

Volume 68 (2019): Issue 1 (March 2019)

Volume 67 (2018): Issue 4 (December 2018)

Volume 67 (2018): Issue 3 (September 2018)

Volume 67 (2018): Issue 2 (June 2018)

Volume 67 (2018): Issue 1 (January 2018)

Volume 66 (2017): Issue 4 (December 2017)

Volume 66 (2017): Issue 3 (September 2017)

Volume 66 (2017): Issue 2 (June 2017)

Volume 66 (2017): Issue 1 (March 2017)

Volume 65 (2016): Issue 4 (December 2016)

Volume 65 (2016): Issue 3 (August 2016)

Volume 65 (2016): Issue 2 (June 2016)

Volume 65 (2016): Issue 1 (March 2016)

Journal Details
Format
Journal
eISSN
2544-4646
First Published
04 Mar 1952
Publication timeframe
4 times per year
Languages
English

Search

Volume 70 (2021): Issue 3 (September 2021)

Journal Details
Format
Journal
eISSN
2544-4646
First Published
04 Mar 1952
Publication timeframe
4 times per year
Languages
English

Search

14 Articles

original-paper

Open Access

Hydrolytic Enzymes Producing Bacterial Endophytes of Some Poaceae Plants

Published Online: 17 Sep 2021
Page range: 297 - 304

Abstract

Abstract

Endophytic bacteria represent microorganisms that live during the whole life cycle within the tissues of healthy plants without causing any obvious signs of disease. In this study, the ability of 128 endophyte bacterial isolates from some cultivated and wild grain plants (Poaceae family) in Van, Turkey, were investigated in terms of producing several extracellular hydrolytic enzymes. It was demonstrated that lipases, proteases, amylases, cellulases, pectinases, and xylanases were produced by the bacteria with relative frequencies of 74.2%, 65.6%, 55.4%, 32%, 21.8%, and 7.8%, respectively. In addition, molecular identification of a certain number of isolates selected according to their enzyme-producing capabilities was performed by 16S rRNA gene sequencing using a next-generation sequencing platform. As a result of the analysis, the isolates yielded certain strains belonging to Pseudomonas, Micrococcus, Paenibacillus, Streptococcus, Curtobacterium, Chryseobacterium, and Bacillus genera. Also, the strain G117Y1T was evaluated as a member of potential novel species based on 16S rRNA sequencing results.

Keywords

  • endophytic bacteria
  • extracellular enzymes
  • 16S rRNA gene
  • Poaceae family
  • Illumina MiSeq
Open Access

Transcriptome Analysis of Komagataeibacter europaeus CGMCC 20445 Responses to Different Acidity Levels During Acetic Acid Fermentation

Published Online: 17 Sep 2021
Page range: 305 - 313

Abstract

Abstract

In the industrial production of high-acidity vinegar, the initial ethanol and acetic acid concentrations are limiting factors that will affect acetic acid fermentation. In this study, Komagataeibacter europaeus CGMCC 20445 was used for acetic acid shake flask fermentation at an initial ethanol concentration of 4.3% (v/v). We conducted transcriptome analysis of K. europaeus CGMCC 20445 samples under different acidity conditions to elucidate the changes in differentially expressed genes throughout the fermentation process. We also analyzed the expression of genes associated with acid-resistance mechanisms. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis showed that the differentially expressed genes were enriched in ribosomes, citrate cycle, butanoate metabolism, oxidative phosphorylation, pentose phosphate, and the fatty acid biosynthetic pathways. In addition, this study found that K. europaeus CGMCC 20445 regulates the gene expression levels of cell envelope proteins and stress-responsive proteins to adapt to the gradual increase in acidity during acetic acid fermentation. This study improved the understanding of the acid resistance mechanism of K. europaeus and provided relevant reference information for the further genetic engineering of this bacterium.

Keywords

  • acetic acid bacteria
  • acid resistance
  • transcriptomics
Open Access

Mycobacterium chimaera as an Underestimated Cause of NTM Lung Diseases in Patients Hospitalized in Pulmonary Wards

Published Online: 17 Sep 2021
Page range: 315 - 320

Abstract

Abstract

Mycobacterium chimaera is the newly described species belonging to Mycobacterium avium complex (MAC), with morphology and growth characteristics closely related to Mycobacterium intracellulare. The aim of this retrospective study was to analyze the frequency and clinical significance of M. chimaera identification in the population of patients with previous positive respiratory cultures for M. intracellulare or MAC. 200 strains of M. intracellulare or MAC, isolated from respiratory specimens of patients hospitalized in pulmonary wards, between 2011 and 2020, were retrospectively analyzed with GenoType NTM-DR test. 88 (44%) of strains were re-classified to M. chimaera species. Analysis of clinical data in 30 patients with positive M. chimaera isolates revealed that they were diagnosed with chronic obstructive pulmonary disease (COPD) – 27%, past tuberculosis – 20%, or interstitial lung diseases – 17%, respectively. Non-tuberculous mycobacterial lung disease (NTMLD) caused by M. chimaera has been recognized in 53% of patients, most often in those presenting with post-tuberculous lung lesions. M. chimaera was almost exclusively isolated from respiratory specimens of patients with underlying lung diseases, especially those with COPD and/or past tuberculosis. NTMLD due to M. chimaera was diagnosed predominantly in patients with past tuberculosis.

Keywords

  • chronic obstructive lung disease
  • cystic fibrosis
  • mycobacteriosis
  • tuberculosis
Open Access

Clinical Characteristics of Patients with Micrococcus luteus Bloodstream Infection in a Chinese Tertiary-Care Hospital

Published Online: 17 Sep 2021
Page range: 321 - 326

Abstract

Abstract

Few pieces of research have focused on Micrococcus luteus bloodstream infection (BSI) because of its low incidence; hence data is needed to illustrate this uncommon infection. This study aimed to explore the clinical characteristics of patients with M. luteus BSI. From January 2010 to December 2019, inpatients that met the criteria for M. luteus BSI were included in this study. Data was collected by reviewing electronic records. Ninety-seven patients were enrolled in this study. Sixty-three percent of the patients have a higher neutrophil percentage (NEUT%). The average blood C-reactive protein (CRP) concentration was 5.5 ± 6.4 mg/dl. 48.5% of the patients had malignancy, and 40.2% underwent invasive surgeries. Linezolid was found to have the largest average diameter of the inhibition zone (36 mm), while erythromycin was found to have the smallest average zone diameter (15 mm). However, some M. luteus strains had a potentially broad antimicrobial resistance spectrum. Cephalosporins (59.2%) and quinolones (21.4%) were the most commonly used antibiotics for empirical therapies. In conclusion, M. luteus BSI mainly happens in immunocompromised patients or those with former invasive surgeries or indwelling catheters. M. luteus strains are less responsive to erythromycin. Cephalosporins and quinolones are effective empirical antibiotics for M. luteus BSI; however, vancomycin and teicoplanin should be considered for potentially broadly drug-resistant M. luteus strains.

Keywords

  • antimicrobial resistance
  • bloodstream infection
  • clinical characteristics
Open Access

The Effect of Long-Term Storage on Mycobacterium bovis

Published Online: 17 Sep 2021
Page range: 327 - 337

Abstract

Abstract

It was established that when stored for many years (10–13 years) in low-temperature conditions (3°C), without sub-culture on a nutrient medium, Mycobacterium bovis grew as visible colonies along the line of inoculation. However, due to long-term storage in conditions of low temperature (3°C) morphology of mycobacteria differed significantly from initial cultures formed by rod-shaped bacteria. Some of them became pigment-forming and smooth on the surface. Unlike the initial strain of mycobacteria, a perennial bacteria stored under hard conditions did not cause the death of guinea pigs or their sensitization to a purified protein derivative for mammals. Morphological forms of the perennial mycobacteria had the following changes: pigment forming, L-forms of the vesicular type, non-acid-fast thread-like (filamentous) bacillary forms, and elementary bodies when compared to the initial strain. There were also some genetic changes in the target DNA due to the long-term storage of M. bovis. It may indicate a mutation in the pathogen’s DNA. These mycobacteria had altered biochemical activity during storage. The number of passages on the solid nutrient medium did not affect their fermentative activity. However, the low cultivation temperature increases mycobacterial catalase activity and the ability to hydrolyze Tween-80.

Keywords

  • tuberculosis
  • survival
  • morphology
  • acid-fast
  • variability
Open Access

Use of Ultrasounds to Reduce the Count of Campylobacter coli in Water

Published Online: 17 Sep 2021
Page range: 339 - 343

Abstract

Abstract

The present study aimed to evaluate the effectiveness of low-frequency ultrasounds applied to eliminate Campylobacter spp. from water. The strains used in this research were isolated from water contaminated with sewage. Campylobacter coli alone was detected in the samples and used for further research. The reference strain C. coli ATCC 33559 was simultaneously tested. The isolate was exposed to ultrasounds at frequencies of 37 kHz and 80 kHz in a continuous operation device with ultrapure deionized water. After 5 min of sonication, the count of C. coli decreased by 5.78% (37 kHz) and 6.27% (80 kHz), whereas the temperature increased by 3°C (37 kHz), and 6°C (80 kHz). After 30 min of sonication, the death rates of bacterial cells were 40.15% (37 kHz) and 55.10% (80 kHz), whereas the temperature reached the maximum values of 36°C (37 kHz), and 39°C (80 kHz). Sonication at the frequency of 80 kHz reduced the bacterial count from 6.86 log CFU/ml to 3.08 log CFU/ml, whereas the frequency of 37 kHz reduced the bacterial count from 6.75 log CFU/ml to 4.04 log CFU/ml. Despite significant differences (p < 0.05) in the number of C. coli cells, the cell death rate remained at the same level.

Keywords

  • sonication
  • sewage
Open Access

Characteristics of Vaginal Microbiome in Women with Pelvic Inflammatory Disease in Korea

Published Online: 17 Sep 2021
Page range: 345 - 357

Abstract

Abstract

Human vaginal microorganisms play an important role in maintaining good health throughout the human life cycle. An imbalance in the vaginal microbiota is associated with an increased risk of pelvic inflammatory disease (PID). This study aimed to characterize and compare vaginal microbial profiles of premenopausal Korean women with and without PID. 74 Korean premenopausal female vaginal samples were obtained; 33 were from healthy women (a control group) and 41 from PID patients. Vaginal fluid samples were collected from the vaginal wall and posterior cervix and then analyzed by 16S ribosomal ribonucleic acid (rRNA) gene-based amplicon sequencing. Results showed a significant difference between the vaginal microbial communities of the two groups (Jensen-Shannon, p = 0.014; Bray-Curtis, p = 0.009; Generalized UniFrac, p = 0.007; UniFrac, p = 0.008). Lactobacillus accounted for the highest percentage (61.0%) of the control group but was significantly decreased (34.9%) in PID patients; this was the most significant difference among all bacterial communities (p = 0.028, LDA effect size = 5.129). In addition, in the PID patient group, species diversity significantly increased (Simpson, p = 0.07) as the proportion of various pathogens increased evenly, resulting in a polymicrobial infection. Similarly, lactate, which constituted the highest percentage of the organic acids in the control group, was significantly decreased in the PID patient group (p = 0.04). The present study’s findings will help understand PID from the microbiome perspective and are expected to contribute to the development of more efficient PID diagnosis and treatment modalities.

Keywords

  • vaginal microflora
  • pelvic inflammatory disease
  • 16S rRNA amplicon sequencing
  • premenopausal
  • Korean
Open Access

Latent Pathogenic Fungi in the Medicinal Plant Houttuynia cordata Thunb. Are Modulated by Secondary Metabolites and Colonizing Microbiota Originating from Soil

Published Online: 17 Sep 2021
Page range: 359 - 372

Abstract

Abstract

Latent pathogenic fungi (LPFs) affect plant growth, but some of them may stably colonize plants. LPFs were isolated from healthy Houttuynia cordata rhizomes to reveal this mechanism and identified as Ilyonectria liriodendri, an unidentified fungal sp., and Penicillium citrinum. Sterile H. cordata seedlings were cultivated in sterile or non-sterile soils and inoculated with the LPFs, followed by the plants’ analysis. The in vitro antifungal activity of H. cordata rhizome crude extracts on LPF were determined. The effect of inoculation of sterile seedlings by LPFs on the concentrations of rhizome phenolics was evaluated. The rates of in vitro growth inhibition amongst LPFs were determined. The LPFs had a strong negative effect on H. cordata in sterile soil; microbiota in non-sterile soil eliminated such influence. There was an interactive inhibition among LPFs; the secondary metabolites also regulated their colonization in H. cordata rhizomes. LPFs changed the accumulation of phenolics in H. cordata. The results provide that colonization of LPFs in rhizomes was regulated by the colonizing microbiota of H. cordata, the secondary metabolites in the H. cordata rhizomes, and the mutual inhibition and competition between the different latent pathogens.

Keywords

  • antifungal activities
  • latent pathogens
  • maintaining stable colonization
  • medicinal plant
  • phenolic accumulation
  • rhizome extracts
Open Access

Bacterial Community Analysis and Potential Functions of Core Taxa in Different Parts of the Fungus Cantharellus cibarius

Published Online: 17 Sep 2021
Page range: 373 - 385

Abstract

Abstract

Cantharellus cibarius is a widely distributed, popular, edible fungus with high nutritional and economic value. However, significant challenges persist in the microbial ecology and artificial cultivation of C. cibarius. Based on the 16S rRNA sequencing data, this study analyzed bacterial community structures and diversity of fruit bodies and rhizomorph parts of C. cibarius and mycosphere samples (collected in the Wudang District, Guiyang, Guizhou Province, China). It explored the composition and function of the core bacterial taxa. The analyzed results showed that the rhizomorph bacterial community structure was similar to mycosphere, but differed from the fruit bodies. Members of the Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium complex had the highest abundance in the fruit bodies. However, they were either absent or low in abundance in the rhizomorphs and mycosphere. At the same time, members of the Burkholderia-Caballeronia-Paraburkholderia complex were abundant in the fruit bodies and rhizomorphs parts of C. cibarius, as well as mycosphere. Through functional annotation of core bacterial taxa, we found that there was an apparent trend of potential functional differentiation of related bacterial communities in the fruit body and rhizomorph: potential functional groups of core bacterial taxa in the fruit bodies centered on nitrogen fixation, nitrogen metabolism, and degradation of aromatic compounds, while those in rhizomorphs focused on aerobic chemoheterotrophy, chemoheterotrophy, defense against soil pathogens, decomposition of complex organic compounds, and uptake of insoluble inorganic compounds. The analysis of functional groups of bacteria with different structures is of great significance to understand that bacteria promote the growth and development of C. cibarius.

Keywords

  • bacteria
  • core bacterial taxa
  • potential function
Open Access

Rapid Detection and Differentiation of KPC and MBL Carbapenemases among Enterobacterales Isolates by a Modified Combined-Disk Test

Published Online: 17 Sep 2021
Page range: 387 - 394

Abstract

Abstract

This study was conducted to develop a cheap, rapid, and accurate modified combined-disk test (mCDT) approach to detect and differentiate KPC and MBL carbapenemases among clinical carbapenem-resistant Enterobacterales (CRE) isolates and simultaneously distinguish them from carbapenem-susceptible Enterobacterales (CSE) isolates. A total of 163 CRE and 90 third-generation cephalosporin-resistant Enterobacterales isolates were tested using imipenem and meropenem disks and different concentrations of carbapenemase inhibitors. The optimal sensitivity and specificity for detecting KPC carbapenemase were 97.2% and 100%, respectively. The sensitivity and specificity for detecting MBL carbapenemase were 100% and 100% with imipenem or meropenem and carbapenemase inhibitors within six hours. The inhibitory zone diameter of 18 mm for imipenem or meropenem disks without inhibitor could distinguish CRE from CSE isolates. Therefore, this mCDT approach may be a useful tool in clinical laboratories to detect CRE isolates and differentiate KPC and MBL producers, which is beneficial for patient management and hospital infection prevention and control.

Keywords

  • carbapenem-resistant Enterobacterales
  • carbapenemase
  • rapid detection and differentiation
  • modified combined-disk test
Open Access

Fungal Infections in COVID-19 Intensive Care Patients

Published Online: 17 Sep 2021
Page range: 395 - 400

Abstract

Abstract

Opportunistic fungal infections increase morbidity and mortality in COVID-19 patients monitored in intensive care units (ICU). As patients’ hospitalization days in the ICU and intubation period increase, opportunistic infections also increase, which prolongs hospital stay days and elevates costs. The study aimed to describe the profile of fungal infections and identify the risk factors associated with mortality in COVID-19 intensive care patients. The records of 627 patients hospitalized in ICU with the diagnosis of COVID-19 were investigated from electronic health records and hospitalization files. The demographic characteristics (age, gender), the number of ICU hospitalization days and mortality rates, APACHE II scores, accompanying diseases, antibiotic-steroid treatments taken during hospitalization, and microbiological results (blood, urine, tracheal aspirate samples) of the patients were recorded. Opportunistic fungal infection was detected in 32 patients (5.10%) of 627 patients monitored in ICU with a COVID-19 diagnosis. The average APACHE II score of the patients was 28 ± 6. While 25 of the patients (78.12%) died, seven (21.87%) were discharged from the ICU. Candida parapsilosis (43.7%) was the opportunistic fungal agent isolated from most blood samples taken from COVID-19 positive patients. The mortality rate of COVID-19 positive patients with candidemia was 80%. While two out of the three patients (66.6%) for whom fungi were grown from their tracheal aspirate died, one patient (33.3%) was transferred to the ward. Opportunistic fungal infections increase the mortality rate of COVID-19-positive patients. In addition to the risk factors that we cannot change, invasive procedures should be avoided, constant blood sugar regulation should be applied, and unnecessary antibiotics use should be avoided.

Keywords

  • COVID-19
  • fungal infections
  • intensive care

short-communication

Open Access

Discovery and Full Genome Characterization of SARS-CoV-2 in Stool Specimen from a Recovered Patient, China

Published Online: 17 Sep 2021
Page range: 401 - 404

Abstract

Abstract

SARS-CoV-2 was found in a recovered patient’s stool specimen by combining quantitative reverse transcription PCR (qRT-PCR) and genome sequencing. The patient was virus positive in stool specimens for at least an additional 15 days after he was recovered, whereas respiratory tract specimens were negative. The discovery of the complete genome of SARS-CoV-2 in the stool sample of the recovered patient demonstrates a cautionary warning that the potential mode of the virus transmission cannot be excluded through the fecal-oral route after viral clearance in the respiratory tract.

Keywords

  • COVID-19
  • SARS-CoV-2
  • genome sequencing
  • recovered patient
Open Access

First Isolation of Exiguobacterium aurantiacum in Serbia

Published Online: 17 Sep 2021
Page range: 405 - 407

Abstract

Abstract

Exiguobacterium aurantiacum is isolated from a variety of environmental samples but rarely from patients. The aim of the study was to represent isolation of unusual bacterial strains that could cause infection in patients. Final identification was performed using matrix-assisted description/ionization time-of-flight mass spectrometry (MALDI-TOF). Two isolates strains of E. aurantiacum were isolated, one isolate from distilled water used during surgical treatment and the second one from a patient with bacteremia after radical prostatectomy, both sensitive to all tested antimicrobials. Environmental strains could cause infection, especially in immunocompromised patients; therefore, rare bacteria testing is required, in which identification special assistance is provided by an automated system MALDI-TOF.

Keywords

  • identification
  • MALDI-TOF
Open Access

Comparative Genomic Analysis and Phenotypic Characterization of Bronchoscope-Associated Klebsiella aerogenes

Published Online: 17 Sep 2021
Page range: 409 - 412

Abstract

Abstract

Bronchoscopes have been linked to outbreaks of nosocomial infections. The phenotypic and genomic profiles of bronchoscope-associated Klebsiella aerogenes isolates are largely unknown. In this work, a total of 358 isolates and 13 isolates were recovered from samples after clinical procedures and samples after decontamination procedures, respectively, over the five months. Antimicrobial susceptibility testing found seven K. aerogenes isolates exhibiting a low-level resistance to antimicrobial agents. Among seven K. aerogenes isolates, we found five sequence types (STs) clustered into three main clades. Collectively, this study described for the first time the phenotypic and genomic characteristics of bronchoscope-associated K. aerogenes.

Keywords

  • bronchoscope-associated
  • phenotypic
  • genomics characteristics
14 Articles

original-paper

Open Access

Hydrolytic Enzymes Producing Bacterial Endophytes of Some Poaceae Plants

Published Online: 17 Sep 2021
Page range: 297 - 304

Abstract

Abstract

Endophytic bacteria represent microorganisms that live during the whole life cycle within the tissues of healthy plants without causing any obvious signs of disease. In this study, the ability of 128 endophyte bacterial isolates from some cultivated and wild grain plants (Poaceae family) in Van, Turkey, were investigated in terms of producing several extracellular hydrolytic enzymes. It was demonstrated that lipases, proteases, amylases, cellulases, pectinases, and xylanases were produced by the bacteria with relative frequencies of 74.2%, 65.6%, 55.4%, 32%, 21.8%, and 7.8%, respectively. In addition, molecular identification of a certain number of isolates selected according to their enzyme-producing capabilities was performed by 16S rRNA gene sequencing using a next-generation sequencing platform. As a result of the analysis, the isolates yielded certain strains belonging to Pseudomonas, Micrococcus, Paenibacillus, Streptococcus, Curtobacterium, Chryseobacterium, and Bacillus genera. Also, the strain G117Y1T was evaluated as a member of potential novel species based on 16S rRNA sequencing results.

Keywords

  • endophytic bacteria
  • extracellular enzymes
  • 16S rRNA gene
  • Poaceae family
  • Illumina MiSeq
Open Access

Transcriptome Analysis of Komagataeibacter europaeus CGMCC 20445 Responses to Different Acidity Levels During Acetic Acid Fermentation

Published Online: 17 Sep 2021
Page range: 305 - 313

Abstract

Abstract

In the industrial production of high-acidity vinegar, the initial ethanol and acetic acid concentrations are limiting factors that will affect acetic acid fermentation. In this study, Komagataeibacter europaeus CGMCC 20445 was used for acetic acid shake flask fermentation at an initial ethanol concentration of 4.3% (v/v). We conducted transcriptome analysis of K. europaeus CGMCC 20445 samples under different acidity conditions to elucidate the changes in differentially expressed genes throughout the fermentation process. We also analyzed the expression of genes associated with acid-resistance mechanisms. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis showed that the differentially expressed genes were enriched in ribosomes, citrate cycle, butanoate metabolism, oxidative phosphorylation, pentose phosphate, and the fatty acid biosynthetic pathways. In addition, this study found that K. europaeus CGMCC 20445 regulates the gene expression levels of cell envelope proteins and stress-responsive proteins to adapt to the gradual increase in acidity during acetic acid fermentation. This study improved the understanding of the acid resistance mechanism of K. europaeus and provided relevant reference information for the further genetic engineering of this bacterium.

Keywords

  • acetic acid bacteria
  • acid resistance
  • transcriptomics
Open Access

Mycobacterium chimaera as an Underestimated Cause of NTM Lung Diseases in Patients Hospitalized in Pulmonary Wards

Published Online: 17 Sep 2021
Page range: 315 - 320

Abstract

Abstract

Mycobacterium chimaera is the newly described species belonging to Mycobacterium avium complex (MAC), with morphology and growth characteristics closely related to Mycobacterium intracellulare. The aim of this retrospective study was to analyze the frequency and clinical significance of M. chimaera identification in the population of patients with previous positive respiratory cultures for M. intracellulare or MAC. 200 strains of M. intracellulare or MAC, isolated from respiratory specimens of patients hospitalized in pulmonary wards, between 2011 and 2020, were retrospectively analyzed with GenoType NTM-DR test. 88 (44%) of strains were re-classified to M. chimaera species. Analysis of clinical data in 30 patients with positive M. chimaera isolates revealed that they were diagnosed with chronic obstructive pulmonary disease (COPD) – 27%, past tuberculosis – 20%, or interstitial lung diseases – 17%, respectively. Non-tuberculous mycobacterial lung disease (NTMLD) caused by M. chimaera has been recognized in 53% of patients, most often in those presenting with post-tuberculous lung lesions. M. chimaera was almost exclusively isolated from respiratory specimens of patients with underlying lung diseases, especially those with COPD and/or past tuberculosis. NTMLD due to M. chimaera was diagnosed predominantly in patients with past tuberculosis.

Keywords

  • chronic obstructive lung disease
  • cystic fibrosis
  • mycobacteriosis
  • tuberculosis
Open Access

Clinical Characteristics of Patients with Micrococcus luteus Bloodstream Infection in a Chinese Tertiary-Care Hospital

Published Online: 17 Sep 2021
Page range: 321 - 326

Abstract

Abstract

Few pieces of research have focused on Micrococcus luteus bloodstream infection (BSI) because of its low incidence; hence data is needed to illustrate this uncommon infection. This study aimed to explore the clinical characteristics of patients with M. luteus BSI. From January 2010 to December 2019, inpatients that met the criteria for M. luteus BSI were included in this study. Data was collected by reviewing electronic records. Ninety-seven patients were enrolled in this study. Sixty-three percent of the patients have a higher neutrophil percentage (NEUT%). The average blood C-reactive protein (CRP) concentration was 5.5 ± 6.4 mg/dl. 48.5% of the patients had malignancy, and 40.2% underwent invasive surgeries. Linezolid was found to have the largest average diameter of the inhibition zone (36 mm), while erythromycin was found to have the smallest average zone diameter (15 mm). However, some M. luteus strains had a potentially broad antimicrobial resistance spectrum. Cephalosporins (59.2%) and quinolones (21.4%) were the most commonly used antibiotics for empirical therapies. In conclusion, M. luteus BSI mainly happens in immunocompromised patients or those with former invasive surgeries or indwelling catheters. M. luteus strains are less responsive to erythromycin. Cephalosporins and quinolones are effective empirical antibiotics for M. luteus BSI; however, vancomycin and teicoplanin should be considered for potentially broadly drug-resistant M. luteus strains.

Keywords

  • antimicrobial resistance
  • bloodstream infection
  • clinical characteristics
Open Access

The Effect of Long-Term Storage on Mycobacterium bovis

Published Online: 17 Sep 2021
Page range: 327 - 337

Abstract

Abstract

It was established that when stored for many years (10–13 years) in low-temperature conditions (3°C), without sub-culture on a nutrient medium, Mycobacterium bovis grew as visible colonies along the line of inoculation. However, due to long-term storage in conditions of low temperature (3°C) morphology of mycobacteria differed significantly from initial cultures formed by rod-shaped bacteria. Some of them became pigment-forming and smooth on the surface. Unlike the initial strain of mycobacteria, a perennial bacteria stored under hard conditions did not cause the death of guinea pigs or their sensitization to a purified protein derivative for mammals. Morphological forms of the perennial mycobacteria had the following changes: pigment forming, L-forms of the vesicular type, non-acid-fast thread-like (filamentous) bacillary forms, and elementary bodies when compared to the initial strain. There were also some genetic changes in the target DNA due to the long-term storage of M. bovis. It may indicate a mutation in the pathogen’s DNA. These mycobacteria had altered biochemical activity during storage. The number of passages on the solid nutrient medium did not affect their fermentative activity. However, the low cultivation temperature increases mycobacterial catalase activity and the ability to hydrolyze Tween-80.

Keywords

  • tuberculosis
  • survival
  • morphology
  • acid-fast
  • variability
Open Access

Use of Ultrasounds to Reduce the Count of Campylobacter coli in Water

Published Online: 17 Sep 2021
Page range: 339 - 343

Abstract

Abstract

The present study aimed to evaluate the effectiveness of low-frequency ultrasounds applied to eliminate Campylobacter spp. from water. The strains used in this research were isolated from water contaminated with sewage. Campylobacter coli alone was detected in the samples and used for further research. The reference strain C. coli ATCC 33559 was simultaneously tested. The isolate was exposed to ultrasounds at frequencies of 37 kHz and 80 kHz in a continuous operation device with ultrapure deionized water. After 5 min of sonication, the count of C. coli decreased by 5.78% (37 kHz) and 6.27% (80 kHz), whereas the temperature increased by 3°C (37 kHz), and 6°C (80 kHz). After 30 min of sonication, the death rates of bacterial cells were 40.15% (37 kHz) and 55.10% (80 kHz), whereas the temperature reached the maximum values of 36°C (37 kHz), and 39°C (80 kHz). Sonication at the frequency of 80 kHz reduced the bacterial count from 6.86 log CFU/ml to 3.08 log CFU/ml, whereas the frequency of 37 kHz reduced the bacterial count from 6.75 log CFU/ml to 4.04 log CFU/ml. Despite significant differences (p < 0.05) in the number of C. coli cells, the cell death rate remained at the same level.

Keywords

  • sonication
  • sewage
Open Access

Characteristics of Vaginal Microbiome in Women with Pelvic Inflammatory Disease in Korea

Published Online: 17 Sep 2021
Page range: 345 - 357

Abstract

Abstract

Human vaginal microorganisms play an important role in maintaining good health throughout the human life cycle. An imbalance in the vaginal microbiota is associated with an increased risk of pelvic inflammatory disease (PID). This study aimed to characterize and compare vaginal microbial profiles of premenopausal Korean women with and without PID. 74 Korean premenopausal female vaginal samples were obtained; 33 were from healthy women (a control group) and 41 from PID patients. Vaginal fluid samples were collected from the vaginal wall and posterior cervix and then analyzed by 16S ribosomal ribonucleic acid (rRNA) gene-based amplicon sequencing. Results showed a significant difference between the vaginal microbial communities of the two groups (Jensen-Shannon, p = 0.014; Bray-Curtis, p = 0.009; Generalized UniFrac, p = 0.007; UniFrac, p = 0.008). Lactobacillus accounted for the highest percentage (61.0%) of the control group but was significantly decreased (34.9%) in PID patients; this was the most significant difference among all bacterial communities (p = 0.028, LDA effect size = 5.129). In addition, in the PID patient group, species diversity significantly increased (Simpson, p = 0.07) as the proportion of various pathogens increased evenly, resulting in a polymicrobial infection. Similarly, lactate, which constituted the highest percentage of the organic acids in the control group, was significantly decreased in the PID patient group (p = 0.04). The present study’s findings will help understand PID from the microbiome perspective and are expected to contribute to the development of more efficient PID diagnosis and treatment modalities.

Keywords

  • vaginal microflora
  • pelvic inflammatory disease
  • 16S rRNA amplicon sequencing
  • premenopausal
  • Korean
Open Access

Latent Pathogenic Fungi in the Medicinal Plant Houttuynia cordata Thunb. Are Modulated by Secondary Metabolites and Colonizing Microbiota Originating from Soil

Published Online: 17 Sep 2021
Page range: 359 - 372

Abstract

Abstract

Latent pathogenic fungi (LPFs) affect plant growth, but some of them may stably colonize plants. LPFs were isolated from healthy Houttuynia cordata rhizomes to reveal this mechanism and identified as Ilyonectria liriodendri, an unidentified fungal sp., and Penicillium citrinum. Sterile H. cordata seedlings were cultivated in sterile or non-sterile soils and inoculated with the LPFs, followed by the plants’ analysis. The in vitro antifungal activity of H. cordata rhizome crude extracts on LPF were determined. The effect of inoculation of sterile seedlings by LPFs on the concentrations of rhizome phenolics was evaluated. The rates of in vitro growth inhibition amongst LPFs were determined. The LPFs had a strong negative effect on H. cordata in sterile soil; microbiota in non-sterile soil eliminated such influence. There was an interactive inhibition among LPFs; the secondary metabolites also regulated their colonization in H. cordata rhizomes. LPFs changed the accumulation of phenolics in H. cordata. The results provide that colonization of LPFs in rhizomes was regulated by the colonizing microbiota of H. cordata, the secondary metabolites in the H. cordata rhizomes, and the mutual inhibition and competition between the different latent pathogens.

Keywords

  • antifungal activities
  • latent pathogens
  • maintaining stable colonization
  • medicinal plant
  • phenolic accumulation
  • rhizome extracts
Open Access

Bacterial Community Analysis and Potential Functions of Core Taxa in Different Parts of the Fungus Cantharellus cibarius

Published Online: 17 Sep 2021
Page range: 373 - 385

Abstract

Abstract

Cantharellus cibarius is a widely distributed, popular, edible fungus with high nutritional and economic value. However, significant challenges persist in the microbial ecology and artificial cultivation of C. cibarius. Based on the 16S rRNA sequencing data, this study analyzed bacterial community structures and diversity of fruit bodies and rhizomorph parts of C. cibarius and mycosphere samples (collected in the Wudang District, Guiyang, Guizhou Province, China). It explored the composition and function of the core bacterial taxa. The analyzed results showed that the rhizomorph bacterial community structure was similar to mycosphere, but differed from the fruit bodies. Members of the Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium complex had the highest abundance in the fruit bodies. However, they were either absent or low in abundance in the rhizomorphs and mycosphere. At the same time, members of the Burkholderia-Caballeronia-Paraburkholderia complex were abundant in the fruit bodies and rhizomorphs parts of C. cibarius, as well as mycosphere. Through functional annotation of core bacterial taxa, we found that there was an apparent trend of potential functional differentiation of related bacterial communities in the fruit body and rhizomorph: potential functional groups of core bacterial taxa in the fruit bodies centered on nitrogen fixation, nitrogen metabolism, and degradation of aromatic compounds, while those in rhizomorphs focused on aerobic chemoheterotrophy, chemoheterotrophy, defense against soil pathogens, decomposition of complex organic compounds, and uptake of insoluble inorganic compounds. The analysis of functional groups of bacteria with different structures is of great significance to understand that bacteria promote the growth and development of C. cibarius.

Keywords

  • bacteria
  • core bacterial taxa
  • potential function
Open Access

Rapid Detection and Differentiation of KPC and MBL Carbapenemases among Enterobacterales Isolates by a Modified Combined-Disk Test

Published Online: 17 Sep 2021
Page range: 387 - 394

Abstract

Abstract

This study was conducted to develop a cheap, rapid, and accurate modified combined-disk test (mCDT) approach to detect and differentiate KPC and MBL carbapenemases among clinical carbapenem-resistant Enterobacterales (CRE) isolates and simultaneously distinguish them from carbapenem-susceptible Enterobacterales (CSE) isolates. A total of 163 CRE and 90 third-generation cephalosporin-resistant Enterobacterales isolates were tested using imipenem and meropenem disks and different concentrations of carbapenemase inhibitors. The optimal sensitivity and specificity for detecting KPC carbapenemase were 97.2% and 100%, respectively. The sensitivity and specificity for detecting MBL carbapenemase were 100% and 100% with imipenem or meropenem and carbapenemase inhibitors within six hours. The inhibitory zone diameter of 18 mm for imipenem or meropenem disks without inhibitor could distinguish CRE from CSE isolates. Therefore, this mCDT approach may be a useful tool in clinical laboratories to detect CRE isolates and differentiate KPC and MBL producers, which is beneficial for patient management and hospital infection prevention and control.

Keywords

  • carbapenem-resistant Enterobacterales
  • carbapenemase
  • rapid detection and differentiation
  • modified combined-disk test
Open Access

Fungal Infections in COVID-19 Intensive Care Patients

Published Online: 17 Sep 2021
Page range: 395 - 400

Abstract

Abstract

Opportunistic fungal infections increase morbidity and mortality in COVID-19 patients monitored in intensive care units (ICU). As patients’ hospitalization days in the ICU and intubation period increase, opportunistic infections also increase, which prolongs hospital stay days and elevates costs. The study aimed to describe the profile of fungal infections and identify the risk factors associated with mortality in COVID-19 intensive care patients. The records of 627 patients hospitalized in ICU with the diagnosis of COVID-19 were investigated from electronic health records and hospitalization files. The demographic characteristics (age, gender), the number of ICU hospitalization days and mortality rates, APACHE II scores, accompanying diseases, antibiotic-steroid treatments taken during hospitalization, and microbiological results (blood, urine, tracheal aspirate samples) of the patients were recorded. Opportunistic fungal infection was detected in 32 patients (5.10%) of 627 patients monitored in ICU with a COVID-19 diagnosis. The average APACHE II score of the patients was 28 ± 6. While 25 of the patients (78.12%) died, seven (21.87%) were discharged from the ICU. Candida parapsilosis (43.7%) was the opportunistic fungal agent isolated from most blood samples taken from COVID-19 positive patients. The mortality rate of COVID-19 positive patients with candidemia was 80%. While two out of the three patients (66.6%) for whom fungi were grown from their tracheal aspirate died, one patient (33.3%) was transferred to the ward. Opportunistic fungal infections increase the mortality rate of COVID-19-positive patients. In addition to the risk factors that we cannot change, invasive procedures should be avoided, constant blood sugar regulation should be applied, and unnecessary antibiotics use should be avoided.

Keywords

  • COVID-19
  • fungal infections
  • intensive care

short-communication

Open Access

Discovery and Full Genome Characterization of SARS-CoV-2 in Stool Specimen from a Recovered Patient, China

Published Online: 17 Sep 2021
Page range: 401 - 404

Abstract

Abstract

SARS-CoV-2 was found in a recovered patient’s stool specimen by combining quantitative reverse transcription PCR (qRT-PCR) and genome sequencing. The patient was virus positive in stool specimens for at least an additional 15 days after he was recovered, whereas respiratory tract specimens were negative. The discovery of the complete genome of SARS-CoV-2 in the stool sample of the recovered patient demonstrates a cautionary warning that the potential mode of the virus transmission cannot be excluded through the fecal-oral route after viral clearance in the respiratory tract.

Keywords

  • COVID-19
  • SARS-CoV-2
  • genome sequencing
  • recovered patient
Open Access

First Isolation of Exiguobacterium aurantiacum in Serbia

Published Online: 17 Sep 2021
Page range: 405 - 407

Abstract

Abstract

Exiguobacterium aurantiacum is isolated from a variety of environmental samples but rarely from patients. The aim of the study was to represent isolation of unusual bacterial strains that could cause infection in patients. Final identification was performed using matrix-assisted description/ionization time-of-flight mass spectrometry (MALDI-TOF). Two isolates strains of E. aurantiacum were isolated, one isolate from distilled water used during surgical treatment and the second one from a patient with bacteremia after radical prostatectomy, both sensitive to all tested antimicrobials. Environmental strains could cause infection, especially in immunocompromised patients; therefore, rare bacteria testing is required, in which identification special assistance is provided by an automated system MALDI-TOF.

Keywords

  • identification
  • MALDI-TOF
Open Access

Comparative Genomic Analysis and Phenotypic Characterization of Bronchoscope-Associated Klebsiella aerogenes

Published Online: 17 Sep 2021
Page range: 409 - 412

Abstract

Abstract

Bronchoscopes have been linked to outbreaks of nosocomial infections. The phenotypic and genomic profiles of bronchoscope-associated Klebsiella aerogenes isolates are largely unknown. In this work, a total of 358 isolates and 13 isolates were recovered from samples after clinical procedures and samples after decontamination procedures, respectively, over the five months. Antimicrobial susceptibility testing found seven K. aerogenes isolates exhibiting a low-level resistance to antimicrobial agents. Among seven K. aerogenes isolates, we found five sequence types (STs) clustered into three main clades. Collectively, this study described for the first time the phenotypic and genomic characteristics of bronchoscope-associated K. aerogenes.

Keywords

  • bronchoscope-associated
  • phenotypic
  • genomics characteristics

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