scholarly journals A human respiratory tract-associated bacterium with an extremely small genome

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Kazumasa Fukuda ◽  
Kei Yamasaki ◽  
Yoshitoshi Ogura ◽  
Toshinori Kawanami ◽  
Hiroaki Ikegami ◽  
...  
Keyword(s):  
Respiratory Tract ◽  
Bacterial Infections ◽  
Pathogenic Bacteria ◽  
Gc Content ◽  
Clinical Samples ◽  
Human Respiratory Tract ◽  
Uncultured Bacterium ◽  
Intracellular Parasites ◽  
Culture Independent ◽  
Parasitic Lifestyle

AbstractRecent advances in culture-independent microbiological analyses have greatly expanded our understanding of the diversity of unculturable microbes. However, human pathogenic bacteria differing significantly from known taxa have rarely been discovered. Here, we present the complete genome sequence of an uncultured bacterium detected in human respiratory tract named IOLA, which was determined by developing a protocol to selectively amplify extremely AT-rich genomes. The IOLA genome is 303,838 bp in size with a 20.7% GC content, making it the smallest and most AT-rich genome among known human-associated bacterial genomes to our best knowledge and comparable to those of insect endosymbionts. While IOLA belongs to order Rickettsiales (mostly intracellular parasites), the gene content suggests an epicellular parasitic lifestyle. Surveillance of clinical samples provides evidence that IOLA can be predominantly detected in patients with respiratory bacterial infections and can persist for at least 15 months in the respiratory tract, suggesting that IOLA is a human respiratory tract-associated bacterium.

scholarly journals Identification of a Third Human Polyomavirus

2007 ◽  
Vol 81 (8) ◽  
pp. 4130-4136 ◽  
Author(s):  
Tobias Allander ◽  
Kalle Andreasson ◽  
Shawon Gupta ◽  
Annelie Bjerkner ◽  
Gordana Bogdanovic ◽  
...  
Keyword(s):  
Respiratory Tract ◽  
Large Scale ◽  
Severe Disease ◽  
Amino Acid Identity ◽  
Human Polyomavirus ◽  
Clinical Samples ◽  
Human Pathogens ◽  
Human Respiratory Tract ◽  
Ki Polyomavirus ◽  
Virus Screening

ABSTRACT We have previously reported on a system for large-scale molecular virus screening of clinical samples. As part of an effort to systematically search for unrecognized human pathogens, the technology was applied for virus screening of human respiratory tract samples. This resulted in the identification of a previously unknown polyomavirus provisionally named KI polyomavirus. The virus is phylogenetically related to other primate polyomaviruses in the early region of the genome but has very little homology (<30% amino acid identity) to known polyomaviruses in the late region. The virus was found by PCR in 6 (1%) of 637 nasopharyngeal aspirates and in 1 (0.5%) of 192 fecal samples but was not detected in sets of urine and blood samples. Since polyomaviruses have oncogenic potential and may produce severe disease in immunosuppressed individuals, continued searching for the virus in different medical contexts is important. This finding further illustrates how unbiased screening of respiratory tract samples can be used for the discovery of diverse virus types.

scholarly journals Pseudomonas aeruginosa and Staphylococcus aureus virulence factors as biomarkers of infection

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Artur J. Sabat ◽  
Daniele Pantano ◽  
Viktoria Akkerboom ◽  
Erik Bathoorn ◽  
Alexander W. Friedrich
Keyword(s):  
Staphylococcus Aureus ◽  
Pseudomonas Aeruginosa ◽  
Bacterial Infections ◽  
Clinical Status ◽  
Clinical Samples ◽  
Pathogenic Microorganisms ◽  
Bacterial Identification ◽  
Accurate Identification ◽  
Culture Independent ◽  
And Staphylococcus Aureus

Abstract The gold standard for the diagnosis of bacterial infections in clinical samples is based on culture tests that are time-consuming and labor-intense. For these reasons, an extraordinary effort has been made to identify biomarkers as the tools for sensitive, rapid and accurate identification of pathogenic microorganisms. Moreover, biomarkers have been tested to distinguish colonization from infection, monitor disease progression, determine the clinical status of patients or predict clinical outcomes. This mini-review describes Pseudomonas aeruginosa and Staphylococcus aureus biomarkers, which contribute to pathogenesis and have been used in culture-independent bacterial identification directly from patient samples.

scholarly journals Community-Acquired Pneumonia in Children: Myths and Facts

2019 ◽  
Vol 36 (S 02) ◽  
pp. S54-S57 ◽  
Author(s):  
Ki Wook Yun ◽  
Rebecca Wallihan ◽  
Alexis Juergensen ◽  
Asuncion Mejias ◽  
Octavio Ramilo
Keyword(s):  
Respiratory Tract ◽  
Bacterial Infections ◽  
Pathogenic Bacteria ◽  
Bacterial Pathogen ◽  
Transcriptome Profiling ◽  
Antibiotic Use ◽  
Respiratory Viruses ◽  
Community Acquired Pneumonia ◽  
Prognostic Indicators ◽  
Upper Respiratory Tract

AbstractCommunity-acquired pneumonia (CAP) is the leading cause of death in children < 5 years of age worldwide. It is also one of the most frequent infectious diseases in children, leading to large antibiotic use and hospitalization even in the industrialized countries. However, the optimal management of CAP in children is still not well defined. Currently, respiratory viruses are considered the most frequent etiologic agents, but detection of viruses in the upper respiratory tract does not guarantee causation of pneumonia, nor precludes the presence of a bacterial pathogen. In both the upper and lower respiratory tract, respiratory viruses and pathogenic bacteria interact. Emerging evidence indicates that dual viral–bacterial infections function synergistically in many cases and together likely enhance the severity of CAP. Therefore, new and advanced technologies capable of sensitively and specifically discriminating viral, bacterial, and viral–bacterial coinfections are needed. Instead of focusing on the pathogen, analysis of host immune transcriptome profiles from children with CAP can potentially offer diagnostic signatures, help to assess disease severity, and eventually, prognostic indicators. An optimized management strategy by using molecular pathogen testing and transcriptome profiling will facilitate prompt, more appropriate, and targeted therapies, which in turn will lead to improved clinical outcomes in children with CAP.

scholarly journals Distribution of Virulence Genes in Moraxella catarrhalis Isolated from Clinical Samples in the North of Iran

2019 ◽  
Vol 21 (1) ◽  
Author(s):  
Mina Eghbali ◽  
Majid Baserisalehi ◽  
Masood Ghane
Keyword(s):  
Respiratory Failure ◽  
Respiratory Tract ◽  
Otitis Media ◽  
Moraxella Catarrhalis ◽  
Virulence Genes ◽  
Clinical Samples ◽  
Control Group ◽  
P Value ◽  
Human Respiratory Tract ◽  
Cross Sectional

Background: Moraxella catarrhalis is an opportunistic bacterium that has pathogenicity in the human respiratory tract. The rates of colonization and infection of this bacterium are high in the respiratory tract of children and the elderly. Methods: In this descriptive cross-sectional study conducted from April 2016 to March 2018, 400 samples were collected from patients with pharyngitis (n = 92), sinusitis (n = 85), otitis media (n = 43), respiratory failure (n = 60), and healthy individuals as the control group (n = 120) in the Northern part of Iran. The isolates were identified by phenotyping methods. Finally, the virulence genes in the isolates were detected by polymerase chain reaction (PCR) technique. Results: Out of a total number of 400 samples, 32 samples (8%) were positive for M. catarrhalis. The frequency of this bacterium was found to be different in patients with pharyngitis as 5.44%, sinusitis as 8.24%, otitis media as 13.95%, respiratory failure as 15%, and in the control group as 4.16%. Since the P value from the Chi-square test was higher than 0.05, there was no relationship between the prevalence of M. catarrhalis and the type of the disease and control group. The PCR results showed that 100% of the isolates had mcaP, ompJ, and ompCD genes. However, the distribution of other virulence genes was varied. Conclusions: Overall, our findings verified the existence of M. catarrhalis in patients with respiratory diseases. Therefore, the rapid identification and successful treatment can play an important role in preventing their spread. In addition, the results verified the high prevalence of virulence genes in M. catarrhalis isolates from patients compared to controls. Regarding the results of this study and by comparing with similar studies, it can be concluded that the frequency of pathogenic isolates may be different even in regions that are not geographically different.

scholarly journals Probiotics for prevention of acute respiratory infections in children: therapeutic potential.

2021 ◽  
pp. 254-260
Author(s):  
Irina N. Zakharova ◽  
Narine G. Sugyan
Keyword(s):  
Respiratory Tract ◽  
Bacterial Infections ◽  
Viral Infections ◽  
Therapeutic Potential ◽  
Respiratory Infections ◽  
Short Chain Fatty Acids ◽  
Acute Respiratory Infections ◽  
Human Respiratory Tract ◽  
Local Immunity ◽  
Respiratory Viral Infections

Acute respiratory viral infections represent a group of clinically, pathomorphologically similar acute inflammatory respiratory diseases that manifest by fever, a runny nose, sneezing, cough, sore throat, a general feeling of ill health of varying severity. Activation of latent, persistent infections of viral and/or bacterial origin may occur in recurrent respiratory infections. Decreased production of local immunity contributes greatly to the development of viral and bacterial infections, persistence of pathogenic micro-organisms. Intestinal microflora can directly or indirectly affect the human respiratory tract through increased production of cytokines, short-chain fatty acids. In recent years, there has been a scientific interest in the therapeutic potential of probiotics for the prevention of acute respiratory viral infections. Earlier studies have shown a positive effect of probiotics on the respiratory tract with a view to prevent and reduce the incidence and severity of respiratory infectious diseases by expending the number of IgA secreting cells in the bronchial mucosa. Studies showed that the use of probiotics can reduce the incidence of acute respiratory infections, duration of fever, cough, and the need for antibacterial agents in children. Peptidoglycans and muramyl peptides that are constituents of the bacterial cell wall have antiviral activity. Probiotics can also inhibit virus attachment through a process of competing for the specific receptors. The regeneration of the mucous membrane is enhanced by the ability of mucin to prevent the virus from attaching to epithelial cells and suppress virus replication. The antiviral effect of probiotics may be caused by the ability to produce antimicrobial peptides, dehydrogenases and NOs. Probiotics can modulate the functions of epithelial and dendritic cells, CD4 +, CD8 + T lymphocytes, NK cells, stimulate the synthesis of secretory immunoglobulins, helping to neutralize the virus.

scholarly journals Studying bacterial infections through culture-independent approaches

2009 ◽  
Vol 58 (11) ◽  
pp. 1401-1418 ◽  
Author(s):  
Geraint B. Rogers ◽  
Mary P. Carroll ◽  
Kenneth D. Bruce
Keyword(s):  
Human Body ◽  
Bacterial Infections ◽  
Antimicrobial Agents ◽  
Bone Biopsy ◽  
Clinical Samples ◽  
Diagnostic Systems ◽  
Independent Manner ◽  
Culture Independent ◽  
The Impact ◽  
The Way

The ability to characterize accurately the cause of infection is fundamental to effective treatment. The impact of any antimicrobial agents used to treat infection will, however, always be constrained by both the appropriateness of their use and our ability to determine their effectiveness. Traditional culture-based diagnostic microbiology is, in many cases, unable to provide this information. Molecular microbiological approaches that assess the content of clinical samples in a culture-independent manner promise to change dramatically the types of data that are obtained routinely from clinical samples. We argue that, in addition to the technical advance that these methodologies offer, a conceptual advance in the way that we reflect on the information generated is also required. Through the development of both of these advances, our understanding of infection, as well as the ways in which infections can be treated, may be improved. In the analysis of the microbiological content of certain clinical samples, such as blood, cerebrospinal fluid, brain and bone biopsy, culture-independent approaches have been well documented. Herein, we discuss how extensions to such studies can shape our understanding of infection at the many sites of the human body where a mixed flora, or in more ecological terms, a community of microbes, is present. To do this, we consider the underlying principles that underpin diagnostic systems, describe the ways in which these systems can be applied to community characterization, and discuss the significance of the data generated. We propose that at all locations within the human body where infection is routinely initiated within the context of a community of microbes, the same principles will apply. To consider this further, we take insights from areas such as the gut, oral cavity and skin. The main focus here is understanding respiratory tract infection, and specifically the infections of the cystic fibrosis lung. The impact that the use of culture-independent, molecular analyses will have on the way we approach the treatment of infections is also considered.

scholarly journals Schizophyllum radiatum, an Emerging Fungus from Human Respiratory Tract

2016 ◽  
Vol 54 (10) ◽  
pp. 2491-2497 ◽  
Author(s):  
J. P. Z. Siqueira ◽  
D. Sutton ◽  
J. Gené ◽  
D. García ◽  
M. Guevara-Suarez ◽  
...  
Keyword(s):  
Respiratory Tract ◽  
Rna Polymerase Ii ◽  
Large Subunit ◽  
Schizophyllum Commune ◽  
The United States ◽  
Clinical Isolates ◽  
Clinical Samples ◽  
Human Respiratory Tract ◽  
Content Type

Schizophyllumis an important genus of basidiomycetes that, apart from being of genetic and biotechnological interest, is also reported to be a plant and animal pathogen.Schizophyllum communeis the best-known species and the only one reported from clinical specimens thus far, being recovered mainly from the respiratory tract. The aim of this study was to determine the species diversity of 23 clinical isolates ofSchizophyllumfrom the United States using multilocus phylogenetic analysis and theirin vitrosusceptibilities to six drugs. The markers used for sequencing were the internal transcribed spacer (ITS), a portion of the nuclear large subunit (LSU) of ribosomal DNA, the RNA polymerase II second-largest subunit (RPB2), and the translation elongation factor 1α (EF-1α) gene. The analyses revealed that 22 of the clinical isolates were in theSchizophyllum radiatumclade with high support values and 1 isolate was in theS. communeclade. This is the first report of this species in clinical samples. The two species mentioned above showed very similar morphological features in culture (i.e., white, cottony, unsporulated colonies composed of hyphae with clamp connections), making morphological discrimination between the two impossible. An epitype is designed forS. radiatum, and its sequences have been deposited in GenBank. The antifungal that showed the greatestin vitroactivity against the strains tested was shown to be amphotericin B. In general, the strains ofS. radiatumshowed higher MICs thanS. commune.

scholarly journals The Prevalence of Pathogenic Bacteria from Different Clinical Samples, Northern Part of Iraq.

2020 ◽  
Author(s):  
ALLAA MIYASAR
Keyword(s):  
Prevalence Rate ◽  
Bacterial Infections ◽  
Pathogenic Bacteria ◽  
Urine Samples ◽  
Clinical Samples ◽  
Coagulase Negative Staphylococci ◽  
Isolation And Identification ◽  
E Coli ◽  
Wide Range ◽  
Microbiological Techniques

Abstract Background Bacteria are prokaryotic which causes a wide range of diseases in human and animals as well, thus, early diagnosis of bacterial infection is an important step for their management. The vast majority of bacteria are harmless to human and some strains are even beneficial. However, some strains cause infections including pneumonia, meningitis and urinary tract infection…etc. The present study aimed to describe and determine the prevalence rate of pathogenic bacteria in different clinical samples from Duhok city, Kurdistan region of Iraq, as there are no available data of bacterial infections.Methods Totally, 200 adult patients enrolled in the present study during July 2017-July 2018. We collected different clinical specimens including (SFA, Bronchial Lavage, catheter, cerebrospinal fluid, body fluids, blood, semen, stool pus, urine, sputum and ear swabs). Standard microbiological techniques used for isolation and identification. All samples collected before antibiotic uses by specialized physician.Results The result reported that forty-six samples (23%) obtained from male and one hundred fifty-four samples (77%) obtained from females. A high diversity of pathogens was found but Staphylococcus aureus recorded the highest infection rate by (33.3%) which observed in 32 urine samples by and followed by E. coli (27.3%) and Coagulase-Negative Staphylococci (25.3%), which observed in 36 and 29 urine samples, respectively. Alternatively, Klebsiella, Streptococcus, Enterobacteriaceae and Pseudomonas aeruginosa were founded in few samples.Conclusion The highest diversity of potential pathogens observed in urine samples was E.coi. Over all, Staphlococcus aureus was predominant and recorded the highest prevalence rate by (33.3%) in 50 samples which followed by E. coli recorded in 41 samples (27.3%) and Coagulase-Negative Staphylococci observed in 38 samples (25.3%).

scholarly journals Antibiotic resistance pattern of bacteria isolated from outdoor patients in Dhaka city: a single center study

2020 ◽  
Vol 9 (1) ◽  
pp. 1-4
Author(s):  
Most Salma Khatun ◽  
Saimun Nahar ◽  
Md Shahidul Kabir
Keyword(s):  
Antibiotic Resistance ◽  
Bacterial Infections ◽  
Pathogenic Bacteria ◽  
Age Groups ◽  
Antibiotic Sensitivity ◽  
Clinical Samples ◽  
Resistance Pattern ◽  
Resistant Bacteria ◽  
Dhaka City ◽  
Female Patients

Bacterial infections are often found to cause morbidity and mortality around the globe. Indiscriminate use of antibiotic for treatment of such infections is reported to cause selective pressure and increase in drug resistance. Emergence of antibiotic resistance is a growing concern for people of all age having bacterial infections. It is important to determine the trend of antibiotic resistance patterns of pathogenic bacteria isolated from clinical samples for appropriate treatment of patients. A retrospective study was conducted on patient samples collected from 1 July 2018 to 15 March 2019. A total of 500 urine, 136 blood, 120 stool, 172 swab, 90 Sputum and 60 pus samples were randomly collected from both male and female patients of different age groups who reported to a diagnostic centre in Dhaka city. Pathogenic bacteria were isolated and identified from the collected samples following standard methods. Antibiotic sensitivity patterns of isolated bacteria were also determined by disc diffusion test. Proportion of UTI in female patients (71.67%) was found to be higher than the male (28.33%) patients and mostly caused by Escherichia coli (73.33%). Among Gram negative bacteria, E. coli (51%) was found to be predominant followed by Pseudomonas spp. (11.47%), Klebsiella (9.84%) and Salmonella Typhi (9.84%). Among Gram positive organism Staphylococcus aureus (9.0%), beta haemolytic streptococci (5.74%) and enterococci (3.28%) were found to be present. Among the tested antibiotics imipenem was found to be the most effective (93.02%) followed by gentamycin (76.03%) against all isolated bacteria. Amoxycillin was found to be least effective (21.29%) against all isolated bacteria. Increase in antibiotic resistance was possibly due to indiscriminate use of antibiotic for treatment of various infections. Prudent use of antimicrobial drugs will help reduce spread of resistant bacteria and complication of treatment of infected patients. Stamford Journal of Microbiology, Vol.9(1) 2019: 1-4

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