Microbiologie médicale et diagnostic

Two subsets of Zika virus (ZIKV) polyprotein amino acid positions are identified. One subset (Exclusive) consists of mutating amino acid positions which were found only in polyproteins isolated from ZIKV of human origin. A second subset (Common) consists of mutating amino acid positions which were found both in ZIKV polyproteins of human origin and in ZIKV polyproteins of Aedes species mosquito origin. The dominance of the Exclusive subset in the polyprotein was found to range from the N-terminus structural proteins until non-structural protein NS3. Although no longer greater than the Common subset, elements of the Exclusive subset existed almost to the C-terminus of non-structural protein NS5. These results are considered in the context of reported epitopic and other biological characteristics of ZIKV.

Objectives: To identify the prevalent organisms associated with respiratory tract infections according to age groups. To identify the most common antibiotics prescribed among pediatric age groups. Methods: A retrospective cohort study conducted on patients aged 0-18 years, admitted to the inpatient department (IPD) diagnosed with respiratory tract infection between Jan 1 2009 to Jan 31 2015 in King Abdulaziz University Hospital (KAUH). Demographic information, diagnosis, date of admission, laboratory investigations, and treatment were collected from patients’ electronic and paper records then analyzed. Exclusion criteria were based on congenital defects, chronic diseases, and compromised immunity. Results: 122 patients with respiratory tract infections were selected for the study (73 males and 49 females). 45.9% of which were infants-toddlers (n=56). The most common diagnosis was pneumonia unspecific (n=32), followed by acute tonsillitis (n=24) and otitis media (n=22). 52 microorganisms were isolated from clinical samples, 14% being Pseudmonas aeruginosa and 13% Streptococcus pneumoniae. 171 antimicrobials were prescribed during the study period. Penicillins were the most frequent (n=78), followed by Cephalosporins (n=45) and Macrolides (n=22). 6.897% resistance was detected among 87 files with culture and sensitivity tests, 30% of which were positively cultured, ranking resistance with 20%. Conclusions: Despite the results showing minimal resistance, antibiotic resistant organisms remain a global concern that needs to be addressed to prevent the spread of antimicrobial resistant infections.

In this study, we evaluated the effect of three decontamination-homogenization-concentration (DHC) methods on COBAS Amplicor Mycobacterium tuberculosis (MTB) PCR system (Roche Diagnostics, Inc., Branchburg, USA) in three different periods. A total of 1210 clinical specimens (602 pulmonary, 608 extrapulmonary specimens) were investigated. Specimens were decontaminated periodically using three DHC methods (Method A: 3% NaOHtrisodium citrate-N-acetyl-L-cysteine (NALC), Method B: 4% NaOH-Bromothymol Blue (BTB) method-Direct, Method C: 4% NaOH-BTB method-irrigation before DNA extraction method). Definitive results were obtained from 1011 (83.6%) of 1210 samples. The inhibition rates according to DHC methods (Method A, B, C) were respectively 3.3% (10/302), 4.3% (7/162) and 17.3% (24/138) for pulmonary samples; 10.3% (30/291), 19.5% (33/169) and 35.1% (52/148) for extrapulmonary samples; 6.7% (40/593), 12.1% (40/331) and 26.5% (76/286) for all samples respectively When inhibition rates were compared in terms of samples types and numbers, high inhibitor rates were found in urine 24.4%, cerebrospinal fluid (CSF) 9.5% and gastric lavage fluid (GLF) 7.6%, respectively. Using culture results as standard, the sensitivity, specificity, positive (PPV) and negative (NPV) predictive values of COBAS Amplicor MTB PCR assay were, respectively, 68.2%, 99.1%, 75% and 98.8% for the method A, 66.7%, 98%, 75% and 96.9% for method B, 75.0%, 98.9%, 75% and 98.8% for method C. We conclude that laboratories planning to use nucleic acid amplification (NAA) methods as supplement to conventional methods, should be prefer 3% NaOH-trisodium citrate-NALC method.

Elimination of Clostridium difficile spores from the clinical setting requires stringent application of infection control procedures including the use of hard-surface disinfectants. A unique combination of sodium taurocholate together with amino acids has been reported as an alternative approach to potentially eliminating spores of C. difficile by increasing their sensitivity to common disinfectants. In this study, the efficacy of this spore germination solution was investigated to explore its effect on the sporulation process under aerobic conditions. Vegetative cells of C. difficile NCTC 11204 (Ribotype 001) and R20291 (Ribotype 027) were exposed to the germination solution comprising 6.9 mM sodium taurocholate and 50 mM of the following amino acids: histidine, glycine, arginine, aspartic acid, valine in TRIS buffer, and a control solution. Total viable counts, the rate and extent of sporulation, and percentage recovery of vegetative cells in both ribotypes were assessed by culture. At 24 hours, sporulation was protracted in ribotypes 001 and 027 and there were significantly more (p=<0.01) vegetative cells following exposure to the germination solution compared to those exposed to the control. No vegetative cells of either ribotype exposed to the control solution were detected at 24 hours. At 48 and 72 hours, vegetative cells of ribotype 027 were not detected however a significantly higher (p<0.001) percentage (43%) of viable vegetative cells of C. difficile 001 were recovered by culture. Exposing vegetative cells of C. difficile to a germination solution protracts the sporulation process in aerobic conditions. In previous studies, the application this solution to spores of C. difficile has been shown to initiate germination thus rendering them more sensitive to common disinfectants. In this investigation, the findings demonstrate that sodium taurocholate protracts the sporulation process and may provide an additional adjunct to future C. difficile infection control strategies.

Simple hepatic cysts occur in less than 5% of the population. As the technology we use for imaging advances, so does the frequency with which we identify them. Simple cysts, as presented here, do not generally require aspiration. The majority of these cysts do not require treatment, however, those larger than 4 cm are recommended for surveillance. We present two cases of simple cysts that were followed for 15 years and managed differently. The experience we acquired from these cases illustrates challenges in understanding and management and an implication that, perhaps, conservative surveillance might be best.

By means of the combined use of B cell epitope prediction (Bepipred) and measurement of information entropy (H) in envelope (E) protein of Zika virus (ZIKV) isolated from infected humans, five amino acid sequences were identified as containing probable epitopes. These five predicted epitopic sequences contained nine amino acid positions where H>0.0. It is proposed that some of the observed entropic positions may reflect mutational escape of the ZIKV from the immune response of the infected host and that such information, applied together with conventional epitope prediction, can guide and facilitate design of anti-ZIKV vaccines.

Bloodstream infections (BSIs) are important cause of morbidity and mortality in patients. Around 20 million cases of severe sepsis arise each year worldwide. Rapid and accurate identification of the etiologic pathogen is crucial to be able to initiate pathogen specific antibiotic therapy and decrease mortality rates, and for reducing length of hospitalization and hospital costs. These identification techniques are applied on various emerging blood culture techniques. This review summarized and presented the currently available technologies and different strategies of conventional laboratory diagnostic steps for blood stream infection. Based on their capability these techniques can be manual, semi-automated or fully automated. Considering the importance of blood cultures in diagnosis and management of bloodstream infections, it is prudent and relevant to understand the principles, technical requirements and limitations of these technologies. Nowadays, there are various emerging blood culture techniques for the diagnosis of blood stream infections and drug susceptibility testing. Among these are API, the BBL systems, the BACTEC systems, the VITEK systems, the BacT/Alert, the BacT/Alert 3D and the Versa TREK system can be mentioned. These systems depend on various detection principles and cultural environments to detect microorganisms. The selection of instrument for the identification and susceptibility testing of bacteria in diagnostic laboratory rely on speed, accuracy, ease of use and cost factors. All marketed identification systems are based on one of five different technologies or a combination of them. These include pH-based reactions, enzyme-based reactions, utilization of carbon sources, visual detection of bacterial growth, or detection of volatility fatty acids.

In leprosy, lepromatous form of the disease is more severe and results from suppression of T cell response. T regulatory cells which suppress T cell response has been found in higher frequency in blood and at the site of infection in leprosy. Therefore, present study was carried out to evaluate the role of Mycobacterium leprae antigens whole cell sonicate (WCS) and especially phenolic glycolipid-1 (PGL-1), which is known for its suppressive nature, in the induction of T regulatory cells expansion in peripheral blood of leprosy patients. For this purpose peripheral blood mononuclear cells (PBMCs) of different category of leprosy patients and healthy controls were stimulated with M. leprae antigens in vitro and percentage of T regulatory cells was determined by flow cytometry. We found higher frequency of T regulatory cells in PBMCs of untreated borderline lepromatous/lepromatous leprosy (BL/LL) patients. Further, PBMCs of untreated BL/LL patients also showed higher percentage of T regs after stimulation with PGL-1. Antigen mediated expansion of T regulatory cells was also supported by results of Carboxy fluorescein succinimidyl ester (CFSE) proliferation assay. None of the antigen induced T regs expansion in healthy controls, untreated tuberculoid/borderline tuberculoid (TT/BT) leprosy patients and treated leprosy patients. Therefore it is suggested that increased frequency of T regs in BL/LL patients may be due to the induction of T regs expansion mediated by PGL-1 of M. leprae and this high percentage of T regs resulted in T cell suppression in lepromatous disease.

Antihistaminic drugs are widely used for various indications during microbial infection. Hence, this paper has investigated the antibacterial activity of seven antihistaminic drugs belonging to both old and new generations against multiresistant K. pneumonia isolates. The bacteriostatic activity of these tested drugs was investigated by determining their MIC by agar dilution technique against thirty multiresistant K. pneumoniae isolates. Two drugs namely promethazine, cyproheptadine showed antibacterial activity against the tested K. pneumoniae isolates with MIC values rangining from 400-1000 μg/ml (far more than their biological levels). In contrast, other tested drugs showed no in-vitro antibacterial activity under the conditions of test. Investigation of the interaction between the tested drugs and different antibiotics against multiresistant K. pneumoniae isolates revealed that synergism was major in case of combination with macrolides, aminoglycosides and quinolones especially with promethazine, cyproheptadine, cetirizine and diphenhydramine. The effect of tested drugs on antibiotic efflux by the tested isolates was also investigated. It was observed that promethazine and cyproheptadine were the most effective efflux pump inhibitor at a concentration of 100 μg/ml. Upon studying the effect of tested drugs on biofilm formation by K. pneumoniae, it was found that promethazine was the most effective inhibitor of biofilm formation. It reduced biofilm formation by K. pneumoniae in a concentration-dependent manner and prevented biofilm formation at a concentration of 100 μg/ml. In the present study, it was found that the use of 100 μg/ml chlorpheniramine resulted in the conversion of separate rod shape of K. pneumoniae cells into long filaments. This was confirmed by transmission electron microscope where septum formation with no separation was recorded. In conclusion, the data obtained in this work showed that, among the tested drugs promethazine and cyproheptadine exerted high antibacterial activity against MDR K. pneumoniae isolates. So, it is possible to take the advantages of the obtained findings to introduce new ways to overcome different infectious diseases.

Capsular polysaccharides are important surface components of bacteria. These are virulence factors. Pasteurella multocida (DP1) was isolated from ducklings. The polysaccharide components were isolated from P. multocida (DP1) strain. The structural elucidations were done by Infra-Red (IR) and nuclear magnetic resonance (NMR) spectrum. The polysaccharides are potential candidates for development of vaccines.