Issues

Journal & Issues

Volume 71 (2022): Issue 3 (September 2022)

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 71 (2022): Issue 2 (June 2022)

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

Search

12 Articles

Original Paper

Open Access

Growth Behavior and Transcriptome Profile Analysis of Proteus mirabilis Strain Under Long- versus Short-Term Simulated Microgravity Environment

Published Online: 23 May 2022
Page range: 161 - 171

Abstract

Abstract

Spaceflight missions affect the behavior of microbes that are inevitably introduced into space environments and may impact astronauts’ health. Current studies have mainly focused on the biological characteristics and molecular mechanisms of microbes after short-term or long-term spaceflight, but few have compared the impact of various lengths of spaceflight missions on the characteristics of microbes. Researchers generally agree that microgravity (MG) is the most critical factor influencing microbial physiology in space capsules during flight missions. This study compared the growth behavior and transcriptome profile of Proteus mirabilis cells exposed to long-term simulated microgravity (SMG) with those exposed to short-term SMG. The results showed that long-term SMG decreased the growth rate, depressed biofilm formation ability, and affected several transcriptomic profiles, including stress response, membrane transportation, metal ion transportation, biological adhesion, carbohydrate metabolism, and lipid metabolism in contrast to short-term SMG. This study improved the understanding of long-term versus short-term SMG effects on P. mirabilis behavior and provided relevant references for analyzing the influence of P. mirabilis on astronaut health during spaceflights.

Keywords

  • simulated microgravity
  • length of time
  • phenotype
  • transcriptomics
Open Access

Alterations and Mechanism of Gut Microbiota in Graves’ Disease and Hashimoto’s Thyroiditis

Published Online: 09 Jun 2022
Page range: 173 - 189

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.

Keywords

  • gut microbiota
  • autoimmune thyroid disease
  • Graves’ disease
  • Hashimoto’s thyroiditis
Open Access

Characterization of Bioactive Actinomycetes Isolated from Kadolkele Mangrove Sediments, Sri Lanka

Published Online: 11 Jun 2022
Page range: 191 - 204

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.

Keywords

  • mangrove sediment bacteria
  • bioactive actinomycetes
  • extracellular enzymes
  • bacterial pigments
Open Access

Prevalence and Drug Resistance Pattern of Mycobacterium tuberculosis Isolated from Tuberculosis Patients in Basra, Iraq

Published Online: 31 May 2022
Page range: 205 - 215

Abstract

Abstract

Drug-resistant Mycobacterium tuberculosis (DR-MTB) is a major health threat to human beings. This study aimed to evaluate the prevalence and drug resistance profile of MTB. Data were collected from 2,296 newly diagnosed, and 246 retreated tuberculosis (TB) patients who attended the Advisory Clinic for Chest Diseases and Respiratory in Basra province from January 2016 to December 2020. Both new diagnostic and retreated TB cases showed that DR-MTB cases were significantly higher at age 15–34 years, pulmonary TB, and urban residents but with no significant difference regarding gender. The drugs resistance was significantly higher among the retreated cases compared with the new diagnostic patients (20.3% vs. 2.4%, p < 0.0001), with the percentage of the resistance to first-line drugs in primary and secondary cases including isoniazid (1% and 17.1%), rifampicin (0.78% and 15.8%), ethambutol (0.56% and 8.5%), streptomycin (1.3% and 9.75%). Notice that the most common drug resistance was against streptomycin with 1.3% in new patients and against isoniazid (17.1%) in retreated patients. The rate of total drug-resistant TB, multi-drug resistant TB, mono-drug resistant TB, and rifampicin-resistant TB among new tuberculosis cases increased in this period from 2.2 to 6.7%, 0.17 to 1.6%, 0.85 to 4%, and 0.17 to 4%, with a percentage change of 204.54, 841.17, 370.58, 22.5%, respectively. The rates of poly drug-resistant TB and ethambutol-resistant-TB dropped in this period by 15.96%, and 0.7%, with a decrease from 1.19 to 1% and from 1 to 0.3%, respectively. Similarly, the increase of drug-resistant TB among secondary cases has also occurred. In conclusion, the temporal trend showed an increase in the rate of drug resistance of M. tuberculosis since 2016, with a predominant multi-drug-resistant TB and isoniazid-resistant TB.

Keywords

  • drug resistance
  • MDR-TB
  • retreated TB
  • Basra
Open Access

Analysis of Gut Microbiota in Patients with Breast Cancer and Benign Breast Lesions

Published Online: 31 May 2022
Page range: 217 - 226

Abstract

Abstract

Breast cancer (BC) and benign breast lesions (BBLs) are common diseases in women worldwide. The gut microbiota plays a vital role in regulating breast diseases’ formation, progression, and therapy response. Hence, we explored the structure and function of gut microflora in patients with BC and BBLs. A cohort of 66 subjects was enrolled in the study. Twenty-six subjects had BC, 20 subjects had BBLs, and 20 matched healthy controls. High throughput 16S ribosomal RNA (16S rRNA) gene sequencing technology was used to determine the microbial community structure. Compared with healthy individuals, BC patients had significantly lower alpha diversity indices (Sobs index, p = 0.019; Chao1 index, p = 0.033). Sobs and Chao1 indices were also lower in patients with BBLs than healthy individuals, without statistical significance (p = 0.279, p = 0.314, respectively). Both unweighted and weighted UniFrac analysis showed that beta diversity differed significantly among the three groups (p = 3.376e–14, p < 0.001, respectively). Compared with healthy individuals, the levels of Porphyromonas and Peptoniphilus were higher in BC patients (p = 0.004, p = 0.007, respectively), whereas Escherichia and Lactobacillus were more enriched in the benign breast lesion group (p < 0.001, p = 0.011, respectively). Our study indicates that patients with BC and BBLs may undergo significant changes in intestinal microbiota. These findings can help elucidate the role of intestinal flora in BC and BBLs patients.

Keywords

  • gut microbiota
  • 16S rRNA gene sequencing
  • breast cancer
  • benign breast lesions
Open Access

Oral Microbiota, a Potential Determinant for the Treatment Efficacy of Gastric Helicobacter pylori Eradication in Humans

Published Online: 31 May 2022
Page range: 227 - 239

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.

Keywords

  • eradication
  • therapeutic effects
  • oral microbiota
  • sequencing
Open Access

The Component and Functional Pathways of Gut Microbiota Are Altered in Populations with Poor Sleep Quality – A Preliminary Report

Published Online: 19 Jun 2022
Page range: 241 - 250

Abstract

Abstract

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.

Keywords

  • sleep disorder
  • poor sleep quality
  • gut microbiota
  • 16S rRNA
  • college students
Open Access

Clinical and Genetic Characteristics of Coronaviruses with Particular Emphasis on SARS-CoV-2 Virus

Published Online: 19 Jun 2022
Page range: 141 - 159

Abstract

Abstract

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.

Keywords

  • COVID-19
  • SARS-CoV-2
  • genetic determinants
  • diagnostics
  • vaccine
Open Access

Diminished Susceptibility to Cefoperazone/Sulbactam and Piperacillin/Tazobactam in Enterobacteriaceae Due to Narrow-Spectrum β-Lactamases as Well as Omp Mutation

Published Online: 19 Jun 2022
Page range: 251 - 256

Abstract

Abstract

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 pneumoniae
Escherichia 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 ≤0.5 1 ≤0.5 ≤0.5 1 1
CAZ 4 ≥16 1 2 1 4 4 4 4 2 4 1 1
FEP ≤2 216 1 1 0.25 1 2 2 2 0.5 2 1 1
AMC ≤8 ≥32 ≥128 ≥128 ≥128 ≥128 ≥128 ≥128 ≥128 ≥128 ≥128 ≥128 ≥128
CSL ≤16 ≥64 64 64 64 64 ≥128 128 ≥128 64 128 128 ≥128
TZP ≤16 ≥128 ≥256 ≥256 ≥256 ≥256 2256 2256 ≥256 ≥256 ≥256 ≥256 ≥256
FPT ≤2 ≥16 1 0.5 0.06 0.125 2 1 2 0.25 1 0.125 0.25
FPZ ≤2 216 0.25 0.25 0.06 0.125 0.25 0.25 1 0.125 0.25 0.125 0.125
CZA ≤8 216 1 0.5 0.25 0.25 1 0.25 1 0.5 0.5 0.5 0.25
CZT ≤2 28 2 1 0.5 1 2 2 2 1 1 2 2

CROceftriaxone, CAZceftazidime, FEPcefepime, AMC:amoxicillin clavulanic-acid, CSLcefoperazone/sulbactam, TZP:piperadllin/tazobactam, FPT:cefepime tazobactam, FPZ:cefepime/zidebactam, CZA:ceftazidime/avibactam, CZTceftolozane/tazobactam

Gene sequencing results

Number Strain ST p-Lactamase gene Promoter sequence mutation Omp mutation
El Kpn 45 blaSHV-1, blaTEM-lB none OmpK36, OmpK3 7
E3 Kpn 45 blaSHV-1, blaTEM-lB none OmpK36. OmpK3 7
E4 Kpn 2854 blaSHV-1 none OmpK36, OmpK3 7
E7 Kpn 2358 blaSHV-1 - blaTEM-lB none OmpK36, OmpK3 7
E9 Kpn 2358 blaSHV-1. blaTEM-lB none OmpK36. OmpK3 7
E10 Kpn 18 9 blaSHV-1 none OmpK36. OmpK3 7
Ell Kpn 45 blaSHV-1 none OmpK36, OmpK3 7
E6 Eco 88 blaTEM-lB none none
ES Eco 409 blaTEM-1B none none
E2 Kox 194 blaOXY-1-3 none OmpK36 mutations. OmpK35 and OmpK 37 deficiency
E5 Kox 11 blaOXY-1-1 none no OmpK (OmpK3 5, OmpK36 and OmpK37) gene found

Keywords

  • cefoperazone/sulbactam
  • piperacillin/tazobactam
  • TEM
  • SHV
  • OXY
Open Access

Identification and Antibiotic Susceptibility of Eggerthella lenta in Bloodstream Infections

Published Online: 19 Jun 2022
Page range: 257 - 261

Abstract

Abstract

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.

Keywords

  • bacteremia
  • identification
  • antibiotic sensitivity
Open Access

Bloodstream Infections in the Intensive Care Unit: a Single-Center Retrospective Bacteriological Analysis Between 2007 and 2019

Published Online: 19 Jun 2022
Page range: 263 - 277

Abstract

Abstract

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.

Keywords

  • central line-associated bloodstream infections
  • Gram-positive pathogens
  • Gram-negative pathogens
  • antimicrobial susceptibility
  • antimicrobial resistance
  • intensive care unit
Open Access

Genomic Analysis of an Excellent Wine-Making Strain Oenococcus oeni SD-2a

Published Online: 19 Jun 2022
Page range: 279 - 292

Abstract

Abstract

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.

Keywords

  • SD-2a
  • genome
  • homologous genes
  • collinearity
12 Articles

Original Paper

Open Access

Growth Behavior and Transcriptome Profile Analysis of Proteus mirabilis Strain Under Long- versus Short-Term Simulated Microgravity Environment

Published Online: 23 May 2022
Page range: 161 - 171

Abstract

Abstract

Spaceflight missions affect the behavior of microbes that are inevitably introduced into space environments and may impact astronauts’ health. Current studies have mainly focused on the biological characteristics and molecular mechanisms of microbes after short-term or long-term spaceflight, but few have compared the impact of various lengths of spaceflight missions on the characteristics of microbes. Researchers generally agree that microgravity (MG) is the most critical factor influencing microbial physiology in space capsules during flight missions. This study compared the growth behavior and transcriptome profile of Proteus mirabilis cells exposed to long-term simulated microgravity (SMG) with those exposed to short-term SMG. The results showed that long-term SMG decreased the growth rate, depressed biofilm formation ability, and affected several transcriptomic profiles, including stress response, membrane transportation, metal ion transportation, biological adhesion, carbohydrate metabolism, and lipid metabolism in contrast to short-term SMG. This study improved the understanding of long-term versus short-term SMG effects on P. mirabilis behavior and provided relevant references for analyzing the influence of P. mirabilis on astronaut health during spaceflights.

Keywords

  • simulated microgravity
  • length of time
  • phenotype
  • transcriptomics
Open Access

Alterations and Mechanism of Gut Microbiota in Graves’ Disease and Hashimoto’s Thyroiditis

Published Online: 09 Jun 2022
Page range: 173 - 189

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.

Keywords

  • gut microbiota
  • autoimmune thyroid disease
  • Graves’ disease
  • Hashimoto’s thyroiditis
Open Access

Characterization of Bioactive Actinomycetes Isolated from Kadolkele Mangrove Sediments, Sri Lanka

Published Online: 11 Jun 2022
Page range: 191 - 204

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.

Keywords

  • mangrove sediment bacteria
  • bioactive actinomycetes
  • extracellular enzymes
  • bacterial pigments
Open Access

Prevalence and Drug Resistance Pattern of Mycobacterium tuberculosis Isolated from Tuberculosis Patients in Basra, Iraq

Published Online: 31 May 2022
Page range: 205 - 215

Abstract

Abstract

Drug-resistant Mycobacterium tuberculosis (DR-MTB) is a major health threat to human beings. This study aimed to evaluate the prevalence and drug resistance profile of MTB. Data were collected from 2,296 newly diagnosed, and 246 retreated tuberculosis (TB) patients who attended the Advisory Clinic for Chest Diseases and Respiratory in Basra province from January 2016 to December 2020. Both new diagnostic and retreated TB cases showed that DR-MTB cases were significantly higher at age 15–34 years, pulmonary TB, and urban residents but with no significant difference regarding gender. The drugs resistance was significantly higher among the retreated cases compared with the new diagnostic patients (20.3% vs. 2.4%, p < 0.0001), with the percentage of the resistance to first-line drugs in primary and secondary cases including isoniazid (1% and 17.1%), rifampicin (0.78% and 15.8%), ethambutol (0.56% and 8.5%), streptomycin (1.3% and 9.75%). Notice that the most common drug resistance was against streptomycin with 1.3% in new patients and against isoniazid (17.1%) in retreated patients. The rate of total drug-resistant TB, multi-drug resistant TB, mono-drug resistant TB, and rifampicin-resistant TB among new tuberculosis cases increased in this period from 2.2 to 6.7%, 0.17 to 1.6%, 0.85 to 4%, and 0.17 to 4%, with a percentage change of 204.54, 841.17, 370.58, 22.5%, respectively. The rates of poly drug-resistant TB and ethambutol-resistant-TB dropped in this period by 15.96%, and 0.7%, with a decrease from 1.19 to 1% and from 1 to 0.3%, respectively. Similarly, the increase of drug-resistant TB among secondary cases has also occurred. In conclusion, the temporal trend showed an increase in the rate of drug resistance of M. tuberculosis since 2016, with a predominant multi-drug-resistant TB and isoniazid-resistant TB.

Keywords

  • drug resistance
  • MDR-TB
  • retreated TB
  • Basra
Open Access

Analysis of Gut Microbiota in Patients with Breast Cancer and Benign Breast Lesions

Published Online: 31 May 2022
Page range: 217 - 226

Abstract

Abstract

Breast cancer (BC) and benign breast lesions (BBLs) are common diseases in women worldwide. The gut microbiota plays a vital role in regulating breast diseases’ formation, progression, and therapy response. Hence, we explored the structure and function of gut microflora in patients with BC and BBLs. A cohort of 66 subjects was enrolled in the study. Twenty-six subjects had BC, 20 subjects had BBLs, and 20 matched healthy controls. High throughput 16S ribosomal RNA (16S rRNA) gene sequencing technology was used to determine the microbial community structure. Compared with healthy individuals, BC patients had significantly lower alpha diversity indices (Sobs index, p = 0.019; Chao1 index, p = 0.033). Sobs and Chao1 indices were also lower in patients with BBLs than healthy individuals, without statistical significance (p = 0.279, p = 0.314, respectively). Both unweighted and weighted UniFrac analysis showed that beta diversity differed significantly among the three groups (p = 3.376e–14, p < 0.001, respectively). Compared with healthy individuals, the levels of Porphyromonas and Peptoniphilus were higher in BC patients (p = 0.004, p = 0.007, respectively), whereas Escherichia and Lactobacillus were more enriched in the benign breast lesion group (p < 0.001, p = 0.011, respectively). Our study indicates that patients with BC and BBLs may undergo significant changes in intestinal microbiota. These findings can help elucidate the role of intestinal flora in BC and BBLs patients.

Keywords

  • gut microbiota
  • 16S rRNA gene sequencing
  • breast cancer
  • benign breast lesions
Open Access

Oral Microbiota, a Potential Determinant for the Treatment Efficacy of Gastric Helicobacter pylori Eradication in Humans

Published Online: 31 May 2022
Page range: 227 - 239

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.

Keywords

  • eradication
  • therapeutic effects
  • oral microbiota
  • sequencing
Open Access

The Component and Functional Pathways of Gut Microbiota Are Altered in Populations with Poor Sleep Quality – A Preliminary Report

Published Online: 19 Jun 2022
Page range: 241 - 250

Abstract

Abstract

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.

Keywords

  • sleep disorder
  • poor sleep quality
  • gut microbiota
  • 16S rRNA
  • college students
Open Access

Clinical and Genetic Characteristics of Coronaviruses with Particular Emphasis on SARS-CoV-2 Virus

Published Online: 19 Jun 2022
Page range: 141 - 159

Abstract

Abstract

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.

Keywords

  • COVID-19
  • SARS-CoV-2
  • genetic determinants
  • diagnostics
  • vaccine
Open Access

Diminished Susceptibility to Cefoperazone/Sulbactam and Piperacillin/Tazobactam in Enterobacteriaceae Due to Narrow-Spectrum β-Lactamases as Well as Omp Mutation

Published Online: 19 Jun 2022
Page range: 251 - 256

Abstract

Abstract

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 pneumoniae
Escherichia 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 ≤0.5 1 ≤0.5 ≤0.5 1 1
CAZ 4 ≥16 1 2 1 4 4 4 4 2 4 1 1
FEP ≤2 216 1 1 0.25 1 2 2 2 0.5 2 1 1
AMC ≤8 ≥32 ≥128 ≥128 ≥128 ≥128 ≥128 ≥128 ≥128 ≥128 ≥128 ≥128 ≥128
CSL ≤16 ≥64 64 64 64 64 ≥128 128 ≥128 64 128 128 ≥128
TZP ≤16 ≥128 ≥256 ≥256 ≥256 ≥256 2256 2256 ≥256 ≥256 ≥256 ≥256 ≥256
FPT ≤2 ≥16 1 0.5 0.06 0.125 2 1 2 0.25 1 0.125 0.25
FPZ ≤2 216 0.25 0.25 0.06 0.125 0.25 0.25 1 0.125 0.25 0.125 0.125
CZA ≤8 216 1 0.5 0.25 0.25 1 0.25 1 0.5 0.5 0.5 0.25
CZT ≤2 28 2 1 0.5 1 2 2 2 1 1 2 2

CROceftriaxone, CAZceftazidime, FEPcefepime, AMC:amoxicillin clavulanic-acid, CSLcefoperazone/sulbactam, TZP:piperadllin/tazobactam, FPT:cefepime tazobactam, FPZ:cefepime/zidebactam, CZA:ceftazidime/avibactam, CZTceftolozane/tazobactam

Gene sequencing results

Number Strain ST p-Lactamase gene Promoter sequence mutation Omp mutation
El Kpn 45 blaSHV-1, blaTEM-lB none OmpK36, OmpK3 7
E3 Kpn 45 blaSHV-1, blaTEM-lB none OmpK36. OmpK3 7
E4 Kpn 2854 blaSHV-1 none OmpK36, OmpK3 7
E7 Kpn 2358 blaSHV-1 - blaTEM-lB none OmpK36, OmpK3 7
E9 Kpn 2358 blaSHV-1. blaTEM-lB none OmpK36. OmpK3 7
E10 Kpn 18 9 blaSHV-1 none OmpK36. OmpK3 7
Ell Kpn 45 blaSHV-1 none OmpK36, OmpK3 7
E6 Eco 88 blaTEM-lB none none
ES Eco 409 blaTEM-1B none none
E2 Kox 194 blaOXY-1-3 none OmpK36 mutations. OmpK35 and OmpK 37 deficiency
E5 Kox 11 blaOXY-1-1 none no OmpK (OmpK3 5, OmpK36 and OmpK37) gene found

Keywords

  • cefoperazone/sulbactam
  • piperacillin/tazobactam
  • TEM
  • SHV
  • OXY
Open Access

Identification and Antibiotic Susceptibility of Eggerthella lenta in Bloodstream Infections

Published Online: 19 Jun 2022
Page range: 257 - 261

Abstract

Abstract

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.

Keywords

  • bacteremia
  • identification
  • antibiotic sensitivity
Open Access

Bloodstream Infections in the Intensive Care Unit: a Single-Center Retrospective Bacteriological Analysis Between 2007 and 2019

Published Online: 19 Jun 2022
Page range: 263 - 277

Abstract

Abstract

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.

Keywords

  • central line-associated bloodstream infections
  • Gram-positive pathogens
  • Gram-negative pathogens
  • antimicrobial susceptibility
  • antimicrobial resistance
  • intensive care unit
Open Access

Genomic Analysis of an Excellent Wine-Making Strain Oenococcus oeni SD-2a

Published Online: 19 Jun 2022
Page range: 279 - 292

Abstract

Abstract

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.

Keywords

  • SD-2a
  • genome
  • homologous genes
  • collinearity

Plan your remote conference with Sciendo