scholarly journals CAPSULAR GENOTYPING OF Klebsiella pneumoniae ISOLATED FROM CLINICAL SAMPLES AT SANGLAH GENERAL HOSPITAL IN 2013

2017 ◽  
Vol 1 (1) ◽  
pp. 21
Author(s):  
I Made Sutha Saskara ◽  
Ni Nengah Dwi Fatmawati ◽  
Ni Nyoman Sri Budayanti ◽  
Ni Nyoman Sri Budayanti ◽  
Wahyu Hidayati
Keyword(s):  
Klebsiella Pneumoniae ◽  
General Hospital ◽  
Clinical Microbiology ◽  
Defense Mechanism ◽  
Wide Spectrum ◽  
Host Cells ◽  
Clinical Isolates ◽  
Clinical Samples ◽  
Clinical Microbiology Laboratory ◽  
Hospital Associated Infections

Klebsiella pneumoniae, one of hospital associated infections agents, become more prevalence in worldwide. It is an opportunistic pathogen that can cause wide spectrum of diseases such as pneumonia and sepsis. Capability of this bacterium in causing diseases is influenced by its virulence factors. Capsule (K) is considered as the major virulence factor responsible in avoiding first defense mechanism of host cells. Almost no study about molecular characterization of capsule is reported in Bali; therefore, this study is aimed to determine the capsular genotype of  K. pneumoniae isolated from clinical specimens at Sanglah General Hospital. Samples were collected between January until Desember 2013 in Sanglah General Hospital at Clinical Microbiology Laboratory. Total of 56 samples were examined taken from blood, urine, pus, sputum, and other sources. All  K. pneumoniae DNA were then subjected to PCR using specific primer pairs against K1, K2 and K5. The results showed that from 56  K. pneumoniae clinical isolates only 12 (21.4%) were PCR positive, and all (100%) of them were positive for K2 capsule gene. Ten (83.3) of them were from blood, 1 (8.3%) from sputum, and 1 (8.3%) from other specimens. Finding of K2 capsule gene in most K. pneumoniae clinical isolates at Clinical Microbiology Laboratory in Sanglah General Hospital might figure out the relationship of capsular type with severity of diseases. However, further study of capsule in Bali with higher isolates number will help in understanding of pathogenicity of K2 capsule in order to treat the infections itself.

scholarly journals Applications of Flow Cytometry to Clinical Microbiology

2000 ◽  
Vol 13 (2) ◽  
pp. 167-195 ◽  
Author(s):  
Alberto Álvarez-Barrientos ◽  
Javier Arroyo ◽  
Rafael Cantón ◽  
César Nombela ◽  
Miguel Sánchez-Pérez
Keyword(s):  
Flow Cytometry ◽  
Clinical Microbiology ◽  
Ex Vivo ◽  
Analytical Techniques ◽  
Clinical Samples ◽  
Clinical Microbiology Laboratory ◽  
Commercial Kits ◽  
Antimicrobial Treatments ◽  
Near Future

SUMMARY Classical microbiology techniques are relatively slow in comparison to other analytical techniques, in many cases due to the need to culture the microorganisms. Furthermore, classical approaches are difficult with unculturable microorganisms. More recently, the emergence of molecular biology techniques, particularly those on antibodies and nucleic acid probes combined with amplification techniques, has provided speediness and specificity to microbiological diagnosis. Flow cytometry (FCM) allows single- or multiple-microbe detection in clinical samples in an easy, reliable, and fast way. Microbes can be identified on the basis of their peculiar cytometric parameters or by means of certain fluorochromes that can be used either independently or bound to specific antibodies or oligonucleotides. FCM has permitted the development of quantitative procedures to assess antimicrobial susceptibility and drug cytotoxicity in a rapid, accurate, and highly reproducible way. Furthermore, this technique allows the monitoring of in vitro antimicrobial activity and of antimicrobial treatments ex vivo. The most outstanding contribution of FCM is the possibility of detecting the presence of heterogeneous populations with different responses to antimicrobial treatments. Despite these advantages, the application of FCM in clinical microbiology is not yet widespread, probably due to the lack of access to flow cytometers or the lack of knowledge about the potential of this technique. One of the goals of this review is to attempt to mitigate this latter circumstance. We are convinced that in the near future, the availability of commercial kits should increase the use of this technique in the clinical microbiology laboratory.

scholarly journals Serotype Is Associated With High Rate of Colistin Resistance Among Clinical Isolates of Salmonella

2020 ◽  
Vol 11 ◽  
Author(s):  
Qixia Luo ◽  
Yuan Wang ◽  
Hao Fu ◽  
Xiao Yu ◽  
Beiwen Zheng ◽  
...  
Keyword(s):  
Clinical Microbiology ◽  
Core Genome ◽  
Clinical Isolates ◽  
High Rate ◽  
Clinical Microbiology Laboratory ◽  
Nucleotide Polymorphisms ◽  
Microbiology Laboratory ◽  
Colistin Resistance ◽  
Single Nucleotide ◽  
Blood Samples

To investigate the prevalence, probable mechanisms and serotype correlation of colistin resistance in clinical isolates of Salmonella from patients in China, Salmonella isolates were collected from fecal and blood samples of patients. In this study, 42.8% (136/318) clinical isolated Salmonella were resistant to colistin. MIC distribution for colistin at serotype level among the two most prevalent serotypes originating from humans in China indicated that Salmonella Enteritidis (83.9% resistance, 125/149) were significantly less susceptible than Salmonella Typhimurium (15.3% resistance, 9/59, P < 0.01). mcr genes and mutations in PmrAB confer little for rate of colistin resistant Salmonella isolated from human patients. Phylogenetic tree based on core-genome single nucleotide polymorphisms (SNPs) was separately by the serotypes and implied a diffused distribution of MICs in the same serotype isolates. Relatvie expression levels of colistin resistant related pmr genes were significantly higher in non-mcr colistin resistant S. Typhimurium than in colistin sensitive S. Typhimurium, but no discernable differences between colistin resistant and sensitive S. Enteritidis, indicating a different mechanism between colistin resistant S. Typhimurium and S. Enteritidis. In conclusion, colistin susceptibility and colistin resistant mechanism of clinical isolated Salmonella were closely associated with specific serotypes, at least in the two most prevalent serotype Enteritidis and Typhimurium. We suggest clinical microbiology laboratory interpreting Salmonella colistin MIC results in the serotype level.

scholarly journals Carbapenem-Resistant Klebsiella pneumonia Isolated from Patients Admitted in Tertiary Care Hospital in Saudi Arabia

2020 ◽  
pp. 76-85
Author(s):  
Enas Sh. Khater ◽  
AbdAlazim A. AlFaki ◽  
Shehata Said Abd Elmoaty
Keyword(s):  
Risk Factors ◽  
Klebsiella Pneumoniae ◽  
Positive Predictive Value ◽  
General Hospital ◽  
Negative Predictive Value ◽  
Predictive Value ◽  
Screening Test ◽  
Clinical Isolates ◽  
Invasive Procedures ◽  
Carbapenem Resistant

Background: Carbapenem-resistant klebsiella pneumoniae is an emerging threat worldwide causing high rates of morbidity and mortality Aim: To evaluate the prevalence of carbapenem-resistant K. pneumonia (CRKP), associated risk factors, type of infections caused by CRKP and their antimicrobial susceptibility. To evaluate Carbapenemase Detection Set (D70C) as screening test for CRKP Place and Duration of the Study: A cross sectional study and prospective cohort study was performed from June 2019 to February 2020 in intensive care unit and medical units of Al Quwayiyah General hospital. Methodology: 541 samples were collected from different patient sources. Klebsiella pneumoniae strain was only selected identified to the species level and AST was done using the Vitek-2. Minimum inhibitory concentration (MIC) of meropenem and imipenem was carried out. A Carbapenemase Detection Set (D70C) was used as screening test for CRKP while Modified Hodge test and multiplex PCR as confirmatory tests. Results: A total of 132 isolates were diagnosed as Enterobacteriaceae out of 541 patient samples.78 clinical isolates were klebsiella pneumoniae which were collected. Out of the 78 clinical isolates CRKP were 36 (46.2%) and CSKP were 42 (53.8%).) CRKP cases aged from (18-84 years) with the median patient age 59 year. Seventeen of 36 patients (47.2%) were males. the majority of the nosocomial CRKP infections were pneumonia 12 (33.3%) followed by urinary tract infection 9 (25%). The most common associated disease was diabetes (30%) followed by renal disease (27.8%). For invasive procedures, Urinary catheter was 27(75%) and 29(69%) followed by Mechanical ventilation 25(69.4%) and 22(52.4%) in CRKP and CSKP patients respectively. Reports of PCR for the 41 isolates which sent to regional laboratory for confirmation revealed that 36 isolates had carbapenemase genes; twenty eight (77.8%) K. pneumonia isolates positive for bla OXA-48 and 5 (13.9%) isolates were positive for blaNDM. in 2 (5.6%) bla KPC were detected, one isolate contained blaIMP. 5 isolates contain both blaOXA-48 and blaNDM. The sensitivity of MHT was analysed to be 91.7%. (95%Cl ratio 77.53% - 98.25%) and the specificity was 100% (95%Cl ratio 54.07% to 100%). The positive predictive value was 100% and the Negative predictive value was 66.7% ( 95%Cl ratio 40.36% to 85.53%). The sensitivity of Carbapenemase Detection Set (D70C) was 94.4% (81.34% to 99.32%) and the specificity was 80% (95%Cl ratio 28.36% to 99.49%). The positive predictive value was 97.1% (95%Cl ratio 85.46% to 99.49%).and the Negative predictive value was 66.7% (95%Cl ratio 32.67% to 89.18%). Conclusion: CRKP prevalence was 46.2% among K. pneumoniae isolates in Al Quwayiya General Hospital. Using invasive procedures such as urinary catheters or mechanical ventilator and misuse of antibiotics were risk factors associated with CRKP indicating that infection control guidelines and effective preventive measures should be strictly applied. It is very important to monitor and report changes in antimicrobial-resistant isolates but Carbapenemase Detection Set (D70C) has low specificity makes it less reliable and need PCR confirmation.

scholarly journals Automated Broad-Range Molecular Detection of Bacteria in Clinical Samples

2016 ◽  
Vol 54 (4) ◽  
pp. 934-943 ◽  
Author(s):  
Andries E. Budding ◽  
Martine Hoogewerf ◽  
Christina M. J. E. Vandenbroucke-Grauls ◽  
Paul H. M. Savelkoul
Keyword(s):  
Clinical Microbiology ◽  
Molecular Detection ◽  
Bacterial Species ◽  
Added Value ◽  
Detection Methods ◽  
23S Rrna ◽  
Clinical Samples ◽  
Clinical Microbiology Laboratory ◽  
Rrna Gene ◽  
Culture Negative

Molecular detection methods, such as quantitative PCR (qPCR), have found their way into clinical microbiology laboratories for the detection of an array of pathogens. Most routinely used methods, however, are directed at specific species. Thus, anything that is not explicitly searched for will be missed. This greatly limits the flexibility and universal application of these techniques. We investigated the application of a rapid universal bacterial molecular identification method, IS-pro, to routine patient samples received in a clinical microbiology laboratory. IS-pro is a eubacterial technique based on the detection and categorization of 16S-23S rRNA gene interspace regions with lengths that are specific for each microbial species. As this is an open technique, clinicians do not need to decide in advance what to look for. We compared routine culture to IS-pro using 66 samples sent in for routine bacterial diagnostic testing. The samples were obtained from patients with infections in normally sterile sites (without a resident microbiota). The results were identical in 20 (30%) samples, IS-pro detected more bacterial species than culture in 31 (47%) samples, and five of the 10 culture-negative samples were positive with IS-pro. The case histories of the five patients from whom these culture-negative/IS-pro-positive samples were obtained suggest that the IS-pro findings are highly clinically relevant. Our findings indicate that an open molecular approach, such as IS-pro, may have a high added value for clinical practice.

scholarly journals Prevalence of Quinolones Resistance Proteins Encoding Genes (qnr genes) and Co-Resistance with β-lactams among Klebsiella pneumoniae Isolates from Iraqi Patients

2020 ◽  
Vol 17 (2) ◽  
pp. 0406
Author(s):  
Mustafa Mustafa et al.
Keyword(s):  
Klebsiella Pneumoniae ◽  
Biochemical Properties ◽  
The Other ◽  
Clinical Isolates ◽  
Clinical Samples ◽  
Missense Mutations ◽  
High Association ◽  
Resistance Proteins ◽  
Major Threat ◽  
Encoding Genes

This study investigated the prevalence of quinolones resistance proteins encoding genes (qnr genes) and co-resistance for fluoroquinolones and β-lactams among clinical isolates of Klebsiella pneumoniae.  Out of 150 clinical samples, 50 isolates of K. pneumoniae were identified according to morphological and biochemical properties. These isolates were collected from different clinical samples, including 15 (30%) urine, 12 (24%) blood, 9 (18%) sputum, 9 (18%) wound, and 5 (10%) burn. The minimum inhibitory concentrations (MICs) assay revealed that 15 (30%) of isolates were resistant to ciprofloxacin (≥4µg/ml), 11 (22%) of isolates were resistant to levofloxacin (≥8 µg/ml), 21 (42%) of isolates were resistant to ertapenem (≥8 µg/ml), 18 (36%) of isolates were resistant to imipenem (4- ≥16µg/ml), 43 (86%) of isolates were resistant to ceftriaxone (4- ≥64 µg/ml), 42 (84%) of isolates were resistant to ceftazidime (16-64 µg/ml), and 40 (80%) of isolates were resistant to cefepime (4- ≥16µg/ml). The results revealed that all fluoroquinolone resistant K. pneumoniae isolates were resistant for β-lactams that used in this study. Genotypic detection of qnr genes revealed that qnrS and qnrB were found in 38 (76%) and 18 (36%) of K. pneumoniae isolates, respectively. On the other hand, qnrA, qnrC, and qnrD were not found among K. pneumoniae isolates. DNA sequencing of qnrB gene revealed that the presence of silent and missense mutations that may have led to increase the resistance values of MICs for ciprofloxacin and levofloxacin. These variants were registered in NCBI at the accession numbers LC373260 and LC381730. The phylogenetic tree of qnrB variants showed a significant deviation of these variants from K. pneumoniae species. The spread of qnr genes among clinical isolates of  K. pneumoniae and high association observed between resistance to fluoroquinolones and β-lactams have led to a major threat to public health through development of MDR K. pneumoniae.  

Overview of Molecular Diagnosis in Medical Microbiology

2018 ◽  
Vol 1 (1) ◽  
pp. 25-32
Author(s):  
Samuel S. Taiwo
Keyword(s):  
Molecular Diagnosis ◽  
Clinical Microbiology ◽  
Host Cells ◽  
Clinical Microbiology Laboratory ◽  
Test Results ◽  
Microbiological Test ◽  
Alternative Technologies ◽  
Human Interactions ◽  
Health And Disease ◽  
Fit For Purpose

Clinical microbiology diagnosis became objectively possible at the end of 19th century with the seminar contributions of researchers such as Louis Pasteur, Robert Koch and other colleagues. The concept of diagnosis then was the ‘culture and isolate’ paradigm, which accelerated to a large extent the growth of bacteriology, as a number of bacteria were able to fulfill the Koch’s postulates, but delayed the growth of other fields of microbiology most especially virology because viruses were not culturable outside of host cells. This paradigm, together with the application of micros-copy, serology and the use of animal models in research in the early 20th century, constituted the ‘first revolution’ in the field of microbiology that is referred to as the conventional microbiological diagnosis. Although this conventional diagnosis has remained valuable, assessments have shown that many of the conventional techniques are not demonstrably ‘fit for purpose’ in the 21st century. This has necessitated the consideration of complementary or alternative technologies, the molecular diagnosis, which has ushered in a ‘second revolution’ in microbiology that is as profound as the first in its impact on our understanding of the microbe-human interactions in health and disease. In this mini-review, an overview of the technologies underlying molecular diagnosis in microbiology is presented. The application of these molecular methods in clinical microbiology laboratory to ensure accurate, reliable and timely release of microbiological test results for better patients’ management and outcome is highlighted.

scholarly journals From Clinical Microbiology to Infection Pathogenesis: How Daring To Be Different Works for Staphylococcus lugdunensis

2008 ◽  
Vol 21 (1) ◽  
pp. 111-133 ◽  
Author(s):  
Kristi L. Frank ◽  
José Luis del Pozo ◽  
Robin Patel
Keyword(s):  
Clinical Microbiology ◽  
Antimicrobial Agents ◽  
Host Cells ◽  
Clinical Microbiology Laboratory ◽  
Coagulase Negative Staphylococci ◽  
Staphylococcus Lugdunensis ◽  
Native Valve ◽  
Implanted Medical Devices ◽  
Membrane Bound ◽  
Intravascular Catheters

SUMMARY Staphylococcus lugdunensis has gained recognition as an atypically virulent pathogen with a unique microbiological and clinical profile. S. lugdunensis is coagulase negative due to the lack of production of secreted coagulase, but a membrane-bound form of the enzyme present in some isolates can result in misidentification of the organism as Staphylococcus aureus in the clinical microbiology laboratory. S. lugdunensis is a skin commensal and an infrequent pathogen compared to S. aureus and S. epidermidis, but clinically, infections caused by this organism resemble those caused by S. aureus rather than those caused by other coagulase-negative staphylococci. S. lugdunensis can cause acute and highly destructive cases of native valve endocarditis that often require surgical treatment in addition to antimicrobial therapy. Other types of S. lugdunensis infections include abscess and wound infection, urinary tract infection, and infection of intravascular catheters and other implanted medical devices. S. lugdunensis is generally susceptible to antimicrobial agents and shares CLSI antimicrobial susceptibility breakpoints with S. aureus. Virulence factors contributing to this organism's heightened pathogenicity remain largely unknown. Those characterized to date suggest that the organism has the ability to bind to and interact with host cells and to form biofilms on host tissues or prosthetic surfaces.

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