Wide Range Of Clinical Specimens Research Articles

Prevalence of Multidrug-Resistant Enterobacterales Isolated from 2019 to 2020 in a Tertiary Hospital in Dakar-Senegal

Background: Multi-resistant bacteria have emerged as a global threat to human health. In Africa, there are few data on AMR. The objective of this study was to determine antibiotic resistance profile of enterobacteria strains and prevalence of multidrug-resistant bacteria isolated in a university hospital in the suburbs of Dakar.
 Methods: Enterobacterales were isolated from a wide range of clinical specimens (urine, pus, blood, catheter tip and bronchoalveolar fluid) from inpatients and outpatients at Medical Biology Laboratory of National University Hospital Center of Pikine from November 2019 to October 2020. Enterobacterales were identified using API 20E. Antimicrobial susceptibility testing was performed with ATB G-EU (08) (bio Mérieuxs®) on all enterobacterales in accordance with CA-SFM/EUCAST 2020 guidelines.
 Results: Of the 3422 different clinical specimens tested, 623 (17.1%) were culture positive. Enterobacteriaceae accounted for 57.6% (n=359) of the strains; Escherichia coli and Klebsiella pneumoniae were predominant isolates with 53.5% and 20.6% respectively. Seventy-four(%) strains of enterobacterales were ESBL. Antibiotic resistance patterns showed a prevalence of multidrug resistant strains of 32.6%. The most active antibiotics on isolates were imipenem (25%), followed by amikacin (15%), fosfomycin (12%) and piperacillin-tazobactam (10%).
 Conclusion: High rates of ESBL and multidrug-resistant strains were found in both outpatients and inpatients. These results indicate need for an active surveillance system for antimicrobial resistance. Also, the application of good hospital hygiene practices and antibiotic therapy adapted to local data must be adopted.

Saliva specimen complements anal swab in assessing patients with COVID-19 for discharge from hospital

ABSTRACT Since December 2019, coronavirus disease 2019 (COVID-19) caused by SARS coronavirus 2 (SARS-CoV-2) has spread and threatens public health worldwide. The recurrence of SARS-CoV-2 RNA detection in patients after discharge from hospital signals a risk of transmission from such patients to the community and challenges the current discharge criteria of COVID-19 patients. A wide range of clinical specimens has been used to detect SARS-CoV-2. However, to date, a consensus has not been reached regarding the most appropriate specimens to use for viral RNA detection in assessing COVID-19 patients for discharge. An anal swab sample was proposed as the standard because of prolonged viral detection. In this retrospective longitudinal study of viral RNA detection in 60 confirmed COVID-19 patients, we used saliva, oropharyngeal/nasopharyngeal swab (O/N swab) and anal swab procedures from admission to discharge. The conversion times of saliva and anal swab were longer than that of O/N swab. The conversion time of hyper sensitive-CRP was the shortest and correlated with that of CT scanning and viral detection. Some patients were found to be RNA-positive in saliva while RNA-negative in anal swab while the reverse was true in some other patients, which indicated that false negatives were inevitable if only the anal swab is used for evaluating suitability for discharge. These results indicated that double-checking for viral RNA using multiple and diverse specimens was essential, and saliva could be a candidate to supplement anal swabs to reduce false-negative results and facilitate pandemic control.

Comparison of the efficacy of metagenomic next-generation sequencing and Xpert MTB/RIF in the diagnosis of tuberculous meningitis

Metagenomic next-generation sequencing (mNGS) is an emerging sequence-based method that detects genomic information of pathogenic microorganisms from a wide range of clinical specimens. The mNGS has moderate sensitivity and very high specificity for tuberculous meningitis, and the validity of mNGS was higher than that of Xpert MTB/RIF.

Prevalence of mycobacterium tuberculosis and its drug resistance pattern in different areas of Sindh, Pakistan

<h3>Introduction</h3> According to the World Health Organization (WHO) about 2 billion people worldwide have been infected by <i>Mycobacterium tuberculosis</i> complex of which nearly 2 million people are dying annually. Rifampicin and isoniazid are the drugs commonly used for treatment, but their excessive use has led to the emergence of mutations in the genome of MTB. <h3>Methods</h3> A total of 380 pulmonary and extra pulmonary clinical specimens of patients were collected from different regions of Sindh, Pakistan. Samples were decontaminated using NALC-NaOH protocol followed by DNA extraction, and amplification of extracted MTB DNA was done by real time PCR. To check the drug resistant strains, hybridization of amplified products of positive samples were carried out by line probe assay. <h3>Results</h3> Prevalence of MTB infection in this study population was 11% and among females and males it was 10.14% and 12.13%, respectively. The highest positive ratio among different specimens was determined in pus (52%) and the first age group (1–20 years) was found most susceptible (13.5%). Among positive samples 33.3% were resistant to rifampicin and 23.3% were resistant to isoniazid and 6.6% samples were resistant to both the drugs. <h3>Conclusions</h3> Real-time assay is a rapid diagnostic tool. It can be applied to a wide range of clinical specimens including pus which might show negative AFB smear. In Pakistan prevalence and drug resistance of TB is on rise due to many socio-economical and other issues. Determination of drug resistance is important for effective treatment, particularly in our region where MDR and XDR TB are not very uncommon.

Rapid and Sensitive Detection of KRAS Mutation After fast-COLD-PCR Enrichment and High-resolution Melting Analysis

KRAS mutations exhibit significant predictive and prognostic value in cancer. Efficient, sensitive, and accurate molecular approaches are required to evaluate KRAS mutation status, even when mutant alleles are restricted to a small portion of a clinical sample, which otherwise contains wild-type alleles. We describe a highly sensitive method to detect KRAS mutations by high-resolution melting (HRM) analysis after mutation enrichment by fast-COLDpolymerase chain reaction (PCR). Using 10 ng of starting DNA and after fast-COLD-PCR of a 76-bp region containing KRAS codons 12 and 13; the amplicons undergo a nested conventional PCR reaction followed by HRM analysis. Samples exhibiting aberrant melting profiles are sequenced to identify mutation type and position. Serial dilution experiments indicate a sensitivity of approximately 0.3% mutant-to-wild type for HRM-based mutation detection and the ability to directly sequence mutation-containing samples. A number of lung adenocarcinoma specimens earlier characterized were screened. Fast-COLD-PCR-HRM analysis correctly identified KRAS mutations and also showed a previously undetected, low-level missense GGT > TTT complex mutation. On account of the short target regions and low requirement of starting DNA, this rapid, cost-effective, and sensitive fast-COLD-PCR-HRM approach is expected to find broad application for detecting low-abundance KRAS mutations in a wide range of clinical specimens.

The role of electron microscopy in the rapid diagnosis of viral infections — review

Electron microscopy (EM) allows fast visualization of viruses in a wide range of clinical specimens. Viruses are grouped into families based on their morphology. Viruses from various families look distinctly and these morphological variances are the basis for identification of viruses by EM. The identification to the family level is often sufficient for the clinician or recognition of an unknown infectious agent. Diagnostic EM has two advantages over enzyme-linked immunosorbent assay and nucleic acid amplification tests. After a simple and fast negative staining, EM allows fast morphological identification and differential diagnosis of infectious agents contained in the specimen without the need for special considerations and/or reagents. Nevertheless, EM has the disadvantage of being unsuitable as a screening method.

Antimicrobial activity against gram negative bacilli from Yaounde Central Hospital, Cameroon.

Antimicrobial resistance among bacteria pathogens is a world-wide issue. The antimicrobial susceptibility patterns of common pathogenic bacteria are essential to guide empirical and pathogen-specific therapy; unfortunately, these data are scarse in Cameroon. To determine the antimicrobial susceptibility patterns of Gram-negative bacilli isolated in Yaounde Central Hospital Laboratory of Bacteriology. Gram-negative bacilli isolates (n = 505), obtained from a wide range of clinical specimens (urine, pus and blood) in Yaoundé Central Hospital Laboratory of Bacteriology between March 1995 and April 1998, were evaluated for resistance to antibiotics (amoxicillin, amoxicillin/clavulanate, piperacillin, cefazolin, cefoxitin, cefotaxime, ceftazidime, aztreonam, imipenem, gentamicin, tobramicin, ofloxacin and trimethoprim/sulfamethoxazole) by the Kirby-Bauer disk diffusion method. High rates of resistance were found in most of the bacteria studied. Resistance to all isolates was mostly observed for amoxicillin (87%), piperacillin (74%) and trimethoprim/sulfamethoxazole (73%). Susceptibilities to third generation cephalosporins (cefotaxime, ceftazidime) and monobactame (aztreonam) were = 91% for Escherichia coli, = 71% for Klebsiella spp., = 98% for Proteus mirabilis, = 50% for Enterobacter spp. and Citrobacter spp. Pseudomonas aeruginosa was less susceptible to cefotaxime (2%) and aztreonam (33%), and highly susceptible to ceftazidime (72%) whereas Acinetobacter baumannii was highly resistant to aztreonam (100%), to cefotaxime (96%) and cetazidime (62%). Imipenem (98%) was the most active antibiotic followed by the ofloxacine (88%). Susceptibility of all isolates to gentamicin was 67%. These results indicate that surveillance to antimicrobial resistance in Cameroon is necessary to monitor microbial trends, antimicrobial resistance pattern, and provide information for choosing empirical or direct therapy to physicians.

Antimicrobial resistance of Gram-negative bacilli isolates from inpatients and outpatients at Yaounde Central Hospital, Cameroon

Objective: To determine and compare antimicrobial susceptibility patterns of pathogenic bacteria from inpatients and outpatients at a university teaching hospital in Yaounde, Cameroon. Methods: Gram-negative bacilli isolates ( n=522), obtained from a wide range of clinical specimens (urine, pus and blood) from inpatients and outpatients at Yaounde Central Hospital between March 1995 and April 1998, were evaluated for resistance to antibiotics (amoxicillin, amoxicillin/clavulanate, piperacillin, cefazolin, cefoxitin, cefotaxime, ceftazidime, aztreonam, imipenem, gentamicin, tobramicin, ofloxacin and trimethoprim/sulfamethoxazole). Results: Of the 522 isolates recorded, 80.3% were Enterobacteriaceae. A high incidence of resistance to amoxicillin (85%), piperacillin (75%) and trimethoprim/sulfamethoxazole (71%) was observed. The proportion of antimicrobial-resistant isolates from inpatients was significantly higher than that from outpatients (P<0.05), except for piperacillin, tobramicin and trimethoprim/sulfamethoxazole. The combinations of antimicrobial and organism showed that the percentage of ceftazidime-resistant Pseudomonas aeruginosa and ceftazidime-resistant Enterobacter cloacae were 26.8% and 24% respectively. The rate of antimicrobial resistance in isolates from inpatients was not significantly higher than that in isolates from outpatients for all the antimicrobial/organism combinations, except for ceftazidime-resistant Escherichia coli, which was exclusively found in isolates from inpatients. Among Enterobacteriaceae, high and low level penicillinase (mostly in E. coli (13.6% and 11% respectively) and Klebsiella spp. (9% and 8% respectively) were the most important β-lactam resistance phenotypes (31.2% and 23.6%, respectively). Wild type (exclusively observed in E. coli, Proteus mirabilis and Salmonella spp.) and low level penicillinase were higher in outpatient than inpatient isolates (wild type—17.9% vs 10.8% and low level penicillinase—29.4% vs 20.5%, respectively; P<0.05). However, extended spectrum β-lactamase strains ( Klebsiella spp. (3.5%), E. coli (2.6%), Citrobacter spp. (0.7%), Enterobacter spp. (0.4%) and P. mirabilis (0.2%)) were exclusively recovered from inpatients. Penicillinase and high level cephalosporinase resistance phenotypes were frequently observed in non-fermenter Gram-negative bacilli (46.6% and 29.1% respectively). However, there were no significant differences in penicillinase and cephalosporinase resistance between inpatient and outpatient isolates. Conclusion: As the incidence of antimicrobial resistance is substantially higher in isolates from inpatient than outpatient pathogens, more resources should be allocated within the hospital to encourage good antibiotic practices and good hospital hygiene.

Molecular detection approaches for smoking associated tumors.

Smoking is directly responsible for approximately 90% of lung cancers and is also strongly associated with cancers of the head and neck, esophagus and urinary bladder. Our growing understanding of the molecular changes that underlie cancer progression has contributed to the development of novel molecular approaches for the detection of cancer. In this study, we review a number of recent studies that have used molecular techniques to detect neoplastic DNA from lung, head and neck, esophagus and bladder cancer. The majority of these approaches are based on polymerase chain reaction (PCR) based assays. These PCR-based techniques can detect a few clonal cancer cells containing a specific DNA mutation, microsatellite alteration, or CpG island methylation among an excess background of normal cells. The ability to accurately detect a small number of malignant cells in a wide range of clinical specimens including sputum, saliva, bronchoalveolar lavage fluid, urine, serum, plasma, or tissue has significant implications for screening high-risk individuals (such as cigarette smokers) for cancer.

Detection of Mycobacterium tuberculosis DNA using polymerase chain reaction in cutaneous tuberculosis and tuberculids

The objective of this study was to explore the role of the polymerase chain reaction (PCR) fo the detection of Mycobacterium tuberculosis DNA as a diagnostic aid in cutaneous tuberculosis using routinely processed skin biopsy specimens. A wide range of clinical specimens representing different forms of cutaneous tuberculosis and so-called tuberculids were studied. A sensitive and specific PCR assay targeting the sequence IS6110 of Mycobacterium tuberculosis complex was used. The specimens were categorized as follows. 1 Acid-fast bacilli (AFB) positive on biopsy (nine specimens from seven patients who were immunocompromised). PCR was positive in five specimens. Of these, one specimen was culture positive and three specimens were culture negative. 2 AFB negative on biopsy: (a) tuberculosis verrucosa cutis (23 specimens); (b) lupus vulgaris (three specimens); (c) cutaneous tuberculosis clinically suspected (six specimens). PCR was negative in all specimens. 3 Tuberculids.' (a) erythema induratum/nodular vasculitis (20 specimens); (b) papulonecrotic tuberculid (two specimens); (c) erythema nodosum (20 specimens). PCR was negative in all specimens. The role of PCR in clinical dermatologic practice, at this stage, may be in differentiating between cutaneous tuberculosis and atypical mycobacterial infections in the context of an immunocompromised patient where AFB can be demonstrated on biopsy and cultures may be negative. In this clinical situation, PCR allows the prompt diagnosis and early institution of appropriate therapy. We have not found PCR to be a useful complement to the clinical and histologic diagnosis of "paucibacillary" forms of cutaneous tuberculosis.

Nutritionally variant streptococci

Streptococci requiring either pyridoxal or L-cysteine for growth were first observed 30 years ago as organisms forming satellite colonies adjacent to colonies of "helper" bacteria. Although they were previously considered nutritional mutants of viridans streptococcal species, the nutritionally variant streptococci (NVS) are currently thought to belong to distinct species of the genus Streptococcus. NVS strains may display pleomorphic cellular morphologies, depending on their growth conditions, and are distinguished from most other streptococci by enzymatic and serological characteristics and the presence of a cell wall chromophore. NVS are found as normal inhabitants of the oral cavity, and in addition to their participation in endocarditis, they have been isolated from a wide range of clinical specimens. Endocarditis caused by NVS is often difficult to eradicate; combinations of penicillin and an aminoglycoside are recommended for treatment. The unique physiological features of the NVS contribute to the difficulties encountered in their recovery from clinical specimens and may play a role in the problems associated with successful treatment of NVS endocarditis.