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Use of pre-reduced swabs in bacteriology of chronic suppurative otitis media

Indudharan R, Haq JA

J Laryngol Otol, 1996 Oct;110(10):950-1.
PMID: 8977860

A simple, safe and effective procedure for improving the bacterial isolation in chronic suppurative otitis media (CSOM) is described. It is most useful for the isolation of aerobes as well as anaerobes from the middle ear.

Matched MeSH terms: Specimen Handling
Fulltext Detection of metabolomic profile of saliva in healthy Malaysian adults

Lee, Han Hing, Lee, Chee Yen, Shoji, Yoshinobu, Chin, Hoe Teh

Compendium of Oral Science, 2015;2(1):40-46.
MyJurnal

Background: Saliva is a readily accessible biofluid that is important for the overall quality of life, func-tionally essential in the chewing, swallowing, tasting, regulation mouth flora and prevention of caries. The aim of this study is to assess the global metabolomic profile of saliva in healthy Malaysian adults. Methods: As a first step to determining and understanding the metabolomic profile of saliva in healthy Malaysian adults, we have collected saliva samples of 50 adults and measured the salivary metabolite to establish a profiling metabolite data, Human Metabolome Database (HMDB). Metabolites concentrations of saliva in healthy subjects were measured by using 1H NMR spectroscopy. Results: The results showed there was no significant inter-individual variations of the key metabolites observed among the healthy Malaysian adults and there was no significant variation of the metabolites between female and male subjects. Conclusion: The metabolomic profile of saliva in healthy Malaysian adults could be used to establish the metabolomic database and used as a comparison for future study of the saliva of specific diseases.

Matched MeSH terms: Specimen Handling
A review of recent advances in microsampling techniques of biological fluids for therapeutic drug monitoring

Tey HY, See HH

J Chromatogr A, 2021 Jan 04;1635:461731.
PMID: 33285415 DOI: 10.1016/j.chroma.2020.461731

Conventional sampling of biological fluids often involves a bulk quantity of samples that are tedious to collect, deliver and process. Miniaturized sampling approaches have emerged as promising tools for sample collection due to numerous advantages such as minute sample size, patient friendliness and ease of shipment. This article reviews the applications and advances of microsampling techniques in therapeutic drug monitoring (TDM), covering the period January 2015 - August 2020. As whole blood is the gold standard sampling matrix for TDM, this article comprehensively highlights the most historical microsampling technique, the dried blood spot (DBS), and its development. Advanced developments of DBS, ranging from various automation DBS, paper spray mass spectrometry (PS-MS), 3D dried blood spheroids and volumetric absorptive paper disc (VAPD) and mini-disc (VAPDmini) are discussed. The volumetric absorptive microsampling (VAMS) approach, which overcomes the hematocrit effect associated with the DBS sample, has been employed in recent TDM. The sample collection and sample preparation details in DBS and VAMS are outlined and summarized. This review also delineates the involvement of other biological fluids (plasma, urine, breast milk and saliva) and their miniaturized dried matrix forms in TDM. Specific features and challenges of each microsampling technique are identified and comparison studies are reviewed.

Matched MeSH terms: Specimen Handling
Fulltext Metagenomic data on bacterial diversity profiling of high-microbial-abundance tropical marine sponges Aaptos aaptos and Xestospongia muta from waters off terengganu, South China Sea

Amelia TSM, Lau NS, Amirul AA, Bhubalan K

Data Brief, 2020 Aug;31:105971.
PMID: 32685631 DOI: 10.1016/j.dib.2020.105971

Marine sponges are acknowledged as a bacterial hotspot and resource of novel natural products or genetic material with industrial or commercial potential. However, sponge-associated bacteria are difficult to be cultivated and the production of their desirable metabolites is inadequate in terms of rate and quantity, yet bioinformatics and metagenomics tools are steadily progressing. Bacterial diversity profiles of high-microbial-abundance wild tropical marine sponges Aaptos aaptos and Xestospongia muta were obtained by sample collection at Pulau Bidong and Pulau Redang islands, 16S rRNA amplicon sequencing on Illumina HiSeq2500 platform (250 bp paired-end) and metagenomics analysis using Ribosomal Database Project (RDP) classifier. Raw sequencing data in fastq format and relative abundance histograms of the dominant 10 species are available in the public repository Discover Mendeley Data (http://dx.doi.org/10.17632/zrcks5s8xp). Filtered sequencing data of operational taxonomic unit (OTU) with chimera removed is available in NCBI accession numbers from MT464469 to MT465036.

Matched MeSH terms: Specimen Handling
Fulltext Evaluation of blood sampling times and indications for therapeutic drug monitoring services

Aishah Hamzah, Ab Fatah Ab Rahman

Malaysian Journal of Pharmaceutical Science, 2008;6(1):1-11.
MyJurnal

The appropriateness of sampling times and indications for monitoring of serum drug concentrations for the purpose of therapeutic drug monitoring (TDM) were evaluated at three hospitals on the east coast of Malaysia. Appropriateness criteria for indication and sampling were adapted from previously published criteria and with input from local TDM pharmacists. Six drugs were chosen, namely gentamicin, digoxin, carbamazepine, phenobarbital, phenytoin, and valproic acid. A total of 265 TDM requests were evaluated. Appropriateness of the indication for TDM ranged from 77.4% to 82%, while that for sampling ranged from 34.2% to 62.1%. There were no significant differences between the three hospitals in both categories of appropriateness. Among different drug groups, the percentage of appropriate indication was found to be highest with antiepileptic drugs. Antiepileptic drugs, however, had the lowest rate of appropriate sampling. Overall, findings from the three hospitals showed very encouraging results with almost 80% of the requests considered as appropriately indicated. However, the percentage of appropriateness of sampling was lower, and thus may require further investigation.

Matched MeSH terms: Specimen Handling
Fulltext Evaluation of the salivary flow rate and ph in patients with recurrent oral ulcers

Mustafa Al-Ahmad, Basma Ezzat, Sukmasari S., Abdul Jabbar O.

International Medical Journal Malaysia, 2018;17(2):49-56.
MyJurnal

Introductions: Recurrent oral ulcers primarily effect mucosal surfaces and are among the most common chronic inflammatory diseases. Numerous studies to find the aetiopathogenesis have been conducted however the cause still remains unclear. Saliva is of utmostimportance for oral health maintenance. In current study, saliva was used as a diagnostic tool for comparison of salivary flow rate and pH in patients suffering from recurrent oral ulcers and control group. Materials and Methods: Saliva samples taken from 20 recurrent aphthous ulcer patients and 20 control (healthy) patients using a convient sampling method. Drooling method was used to collect unstimulated whole saliva sample. Pre-weighted specimen bottles were used and then weighed after sample collection on a graduated scale where as chair-side pH meter was used to determine the salivary pH. Independent t-test and Pearson’s correlation were performed. A p-value of less than 0.05 was considered statistically significance. Results: Positive correlation was found between the flow rate and pH in recurrent oral ulcer patients. Patients with recurrent oral ulcers had higher flow rate and pH compared to the control group. These effects were exaggerated in female patients with ulcers. Conclusions: Disturbances in salivary flow rate and pH were not significantly associated with recurrent oral ulcers.

Matched MeSH terms: Specimen Handling
Fulltext Isolation of Janthinobacterium lividum from early onset neonatal sepsis patients in Malaysia

Shinkafi SH, Umar S, Neela VK, Noordin SM, Noordin SA, Hudu SA, et al.

Afr Health Sci, 2019 Sep;19(3):2378-2389.
PMID: 32127808 DOI: 10.4314/ahs.v19i3.11

Background: The term early onset neonatal septicaemia (EONS) refers to invasive bacterial infections that primarily involve the blood stream of neonates during the first 3 days of life. Although early onset neonatal septicaemia is relatively uncommon, it may be associated with case fatality rates of 15-30% and substantial morbidity in surviving infants.
Objectives: This study describes an unusual septicaemia cases with Janthinobacterium lividum in neonatal Intensive Care Units.
Methods: Bacterial causes of early onset neonatal sepsis in Kuala Lumpur Hospital Malaysia were investigated using broad range 16S rDNA PCR and sequencing. The bacterial DNA was isolated directly from blood without pre-incubation. All samples collected were equally cultured and incubated in automated BACTEC system.
Results: Two hundred and fifty two neonates were recruited in this study with mean (SD) gestational age of 35.9. Neonates with J. lividum infection lacked microbiological evidence of septicaemia as their blood culture yielded no bacterial growth. However, the PCR analysis of these samples yielded 1100bp corresponding to bacteria species.
Conclusion: This study demonstrates the value of PCR in detecting bacteria where special growth requirement is involved.

Matched MeSH terms: Specimen Handling
Non-Invasive DNA Sampling for Molecular Analysis of Beta-Thalassemia: Amiable Alternative Sampling Methods with Accurate Results for Pediatric Patients

Abd Rahim MR, Kho SL, Kuppusamy UR, Tan JA

Clin. Lab., 2015;61(9):1325-30.
PMID: 26554253

BACKGROUND: Beta-thalassemia is the most common genetic disorder in Malaysia. Confirmation of the β-globin gene mutations involved in thalassemia is usually carried out by molecular analysis of DNA extracted from leukocytes in whole blood. Molecular analysis is generally carried out when affected children are around 1 - 2 years as clinical symptoms are expressed during this period. Blood taking at this age can be distressing for the child. High yield and pure DNA extracted from non-invasive sampling methods can serve as alternative samples in molecular studies for genetic diseases especially in pediatric cases.
METHODS: In this study, mouthwash, saliva, and buccal cytobrush samples were collected from β-thalassemia major patients who had previously been characterized using DNA extracted from peripheral blood. DNA was extracted from mouthwash, saliva, and buccal cytobrush samples using the conventional inexpensive phenol-chloroform method and was measured by spectrophotometry for yield and purity. Molecular characterization of β-globin gene mutations was carried out using the amplification refractory mutation system (ARMS).
RESULTS: DNA extracted from mouthwash, saliva, and buccal cytobrush samples produced high concentration and pure DNA. The purified DNA was successfully amplified using ARMS. Results of the β-globin gene mutations using DNA from the three non-invasive samples were in 100% concordance with results from DNA extracted from peripheral blood.
CONCLUSIONS: The conventional in-house developed methods for non-invasive sample collection and DNA extraction from these samples are effective and negate the use of more expensive commercial kits. In conclusion, DNA extracted from mouthwash, saliva, and buccal cytobrush samples provided sufficiently high amounts of pure DNA suitable for molecular analysis of β-thalassemia.

Matched MeSH terms: Specimen Handling/instrumentation; Specimen Handling/methods*
Fulltext Investigation of CPD and HMDS sample preparation techniques for cervical cells in developing computer-aided screening system based on FE-SEM/EDX

Jusman Y, Ng SC, Abu Osman NA

ScientificWorldJournal, 2014;2014:289817.
PMID: 25610902 DOI: 10.1155/2014/289817

This paper investigated the effects of critical-point drying (CPD) and hexamethyldisilazane (HMDS) sample preparation techniques for cervical cells on field emission scanning electron microscopy and energy dispersive X-ray (FE-SEM/EDX). We investigated the visualization of cervical cell image and elemental distribution on the cervical cell for two techniques of sample preparation. Using FE-SEM/EDX, the cervical cell images are captured and the cell element compositions are extracted for both sample preparation techniques. Cervical cell image quality, elemental composition, and processing time are considered for comparison of performances. Qualitatively, FE-SEM image based on HMDS preparation technique has better image quality than CPD technique in terms of degree of spread cell on the specimen and morphologic signs of cell deteriorations (i.e., existence of plate and pellet drying artifacts and membrane blebs). Quantitatively, with mapping and line scanning EDX analysis, carbon and oxygen element compositions in HMDS technique were higher than the CPD technique in terms of weight percentages. The HMDS technique has shorter processing time than the CPD technique. The results indicate that FE-SEM imaging, elemental composition, and processing time for sample preparation with the HMDS technique were better than CPD technique for cervical cell preparation technique for developing computer-aided screening system.

Matched MeSH terms: Specimen Handling/methods*
An improved stool concentration procedure for the detection of Cryptosporidium oocysts in Orang Asli stool samples

Salleh FM, Moktar N, Yasin AM, Al-Mekhlafi HM, Anuar TS

J Microbiol Methods, 2014 Nov;106:143-145.
PMID: 25193442 DOI: 10.1016/j.mimet.2014.08.019

To improve the stool concentration procedure, we modified different steps of the standard formalin-ether concentration technique and evaluated these modifications by examining stool samples collected in the field. Seven samples were found positive by the modified formalin-ether concentration technique (M-FECT). Therefore, the M-FECT procedure provides enhanced detection of Cryptosporidium oocysts.

Matched MeSH terms: Specimen Handling/methods*
Quantity and quality assessment of DNA extracted from saliva and blood

Looi ML, Zakaria H, Osman J, Jamal R

Clin. Lab., 2012;58(3-4):307-12.
PMID: 22582505

Saliva has been suggested as an attractive resource for evaluating physiological and pathological conditions in humans. This study aims to evaluate saliva sampling as an alternative to blood sampling for molecular testing.

Matched MeSH terms: Specimen Handling/methods*
Validation and application of capillary electrophoresis for the analysis of lidocaine in a skin tape stripping study

Chik Z, Johnston A, Tucker AT, Burn RT, Perrett D

Biomed Chromatogr, 2007 Aug;21(8):775-9.
PMID: 17497758

A fast and simple capillary zone electrophoresis method was developed and validated for the determination of lidocaine in skin using tape samples. Separation was performed in a 350 mm (265 mm to window) x 50 microm i.d. fused silica capillary using a background electrolyte of phosphoric acid-Tris pH 2.5. The extraction of lidocaine from tape samples was achieved using methanol, which was diluted to 50% with water before injection. Procaine was the internal standard. The migration times for procaine and lidocaine were 2.9 and 3.2 min, respectively. The limit of quantification for lidocaine was 50 microg, with signal to noise ratio greater than 10. The calibration curve was linear from 50 to 1000 microg with r(2) greater than 0.99. The CV for both within- and between-assay imprecision and the percentage of inaccuracy for the quality control samples including lower and upper limits of quantitation were 97%. The accuracy and selectivity of this method allowed the measurement of lidocaine in tape samples obtained from a skin tape stripping study of local anesthetics in healthy subjects.

Matched MeSH terms: Specimen Handling/methods*
Paper-based sample-to-answer molecular diagnostic platform for point-of-care diagnostics

Choi JR, Tang R, Wang S, Wan Abas WA, Pingguan-Murphy B, Xu F

Biosens Bioelectron, 2015 Dec 15;74:427-39.
PMID: 26164488 DOI: 10.1016/j.bios.2015.06.065

Nucleic acid testing (NAT), as a molecular diagnostic technique, including nucleic acid extraction, amplification and detection, plays a fundamental role in medical diagnosis for timely medical treatment. However, current NAT technologies require relatively high-end instrumentation, skilled personnel, and are time-consuming. These drawbacks mean conventional NAT becomes impractical in many resource-limited disease-endemic settings, leading to an urgent need to develop a fast and portable NAT diagnostic tool. Paper-based devices are typically robust, cost-effective and user-friendly, holding a great potential for NAT at the point of care. In view of the escalating demand for the low cost diagnostic devices, we highlight the beneficial use of paper as a platform for NAT, the current state of its development, and the existing challenges preventing its widespread use. We suggest a strategy involving integrating all three steps of NAT into one single paper-based sample-to-answer diagnostic device for rapid medical diagnostics in the near future.

Matched MeSH terms: Specimen Handling/instrumentation
A prospective study of mycobacterial viability in refrigerated, unpreserved sputum batched for up to 8 weeks

Rashid Ali MR, Parameswaran U, William T, Bird E, Wilkes CS, Lee WK, et al.

Int J Tuberc Lung Dis, 2015 May;19(5):620-1.
PMID: 25868033 DOI: 10.5588/ijtld.14.0938
Matched MeSH terms: Specimen Handling/methods
Free-living ciliates in CSF of a patient with meningoencephalitis: a contaminant?

Isa NH, Sulaiman S, Shahid MS, Rose IM, Eugene CB

Southeast Asian J. Trop. Med. Public Health, 1994 Mar;25(1):212-4.
PMID: 7825018
Matched MeSH terms: Specimen Handling*
Collection and storage of capillary blood in glass fibre filters for glycated haemoglobin measurement by a microcolorimetric method

Ng ML, Sazali BS, Khalid BA

Ann. Clin. Biochem., 1991 Nov;28 ( Pt 6):613-7.
PMID: 1776812

A filter method for collection and storage of capillary blood spots for glycated haemoglobin (gHb) has been developed. Glass fibre filters (GFB) impregnated with 0.8 M boric acid were used to collect and store capillary blood. Haemoglobin from the dried blood spots was eluted into water and determined by Drabkin's method, while gHb in the eluates was determined by the microcolorimetric method. The intraassay coefficients of variation (CVs) were 4.5, 4.5 and 3.1% at 882, 1101 and 1704 pmol HMF/mg Hb, respectively. The corresponding inter-assay CVs were 8.6, 8.6 and 6.3%, respectively. A total of 63 paired capillary and venous blood samples were measured by both the direct and GFB method. The GFB method showed excellent correlation with the direct method (r = 0.948 and r = 0.994) after 7 and 14 days' storage at room temperature. The GFB method will enable prior collection and postage of blood samples by patients.

Matched MeSH terms: Specimen Handling/methods*
Fulltext A novel strategy for community screening of SARS-CoV-2 (COVID-19): Sample pooling method

Lim KL, Johari NA, Wong ST, Khaw LT, Tan BK, Chan KK, et al.

PLoS One, 2020;15(8):e0238417.
PMID: 32857823 DOI: 10.1371/journal.pone.0238417

The rapid global spread of the coronavirus disease (COVID-19) has inflicted significant health and socioeconomic burden on affected countries. As positive cases continued to rise in Malaysia, public health laboratories experienced an overwhelming demand for COVID-19 screening. The confirmation of positive cases of COVID-19 has solely been based on the detection of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) using real-time reverse transcription polymerase chain reaction (qRT-PCR). In efforts to increase the cost-effectiveness and efficiency of COVID-19 screening, we evaluated the feasibility of pooling clinical Nasopharyngeal/Oropharyngeal (NP/OP) swab specimens during nucleic acid extraction without a reduction in sensitivity of qRT-PCR. Pools of 10 specimens were extracted and subsequently tested by qRT-PCR according to the WHO-Charité protocol. We demonstrated that the sample pooling method showed no loss of sensitivity. The effectiveness of the pooled testing strategy was evaluated on both retrospective and prospective samples, and the results showed a similar detection sensitivity compared to testing individual sample alone. This study demonstrates the feasibility of using a pooled testing strategy to increase testing capacity and conserve resources, especially when there is a high demand for disease testing.

Matched MeSH terms: Specimen Handling/methods*
Fulltext Intraspecific macroscopic digestive anatomy of ring-tailed lemurs (Lemur catta), including a comparison of frozen and formalin-stored specimens

Clauss M, Trümpler J, Ackermans NL, Kitchener AC, Hantke G, Stagegaard J, et al.

Primates, 2021 Mar;62(2):431-441.
PMID: 33180215 DOI: 10.1007/s10329-020-00873-8

Digestive tract measurements are often considered species specific, but little information exists on the degree to which they change during ontogeny within a species. Additionally, access to anatomical material from nondomestic species is often limited, with fixed tissues possibly representing the only available source, though the degree to which this material is representative in terms of dimensions and weight is debatable. In the present study, the macroscopic anatomy of the digestive tract (length of intestinal sections, and tissue weights of stomach and intestines) of 58 Lemur catta [ranging in age from 1 month (neonates) to 25 years], which had been stored frozen (n = 27) or fixed in formalin (n = 31), was quantified. Particular attention was paid to the caecum and the possible presence of an appendix. The intraspecific allometric scaling of body mass (BM)0.46[0.40;0.51] for total intestine length and BM0.48[0.41;0.54] for small intestine length was higher than the expected geometric scaling of BM0.33, and similar to that reported in the literature for interspecific scaling. This difference in scaling is usually explained by the hypothesis that, to maintain optimal absorption, the diameter of the intestinal tube cannot increase geometrically. Therefore, geometric volume gain of increasing body mass is accommodated for by more-than-geometric length scaling. According to the literature, not all L. catta have an appendix. No appendix was found in the specimens in the present study. The proportions of length measurements did not change markedly during ontogeny, indicating that the proportions of the foetus are representative of those of the adult animal. By contrast, width and tissue-mass scaling of the caecum indicated disproportionate growth of this organ during ontogeny that was not reflected in its length. Compared to overall intraspecific variation, the method of storage (frozen vs. formalin) had no relevant impact on length or weight measurements.

Matched MeSH terms: Specimen Handling/methods*
Fulltext Identification of Gingival Crevicular Fluid Sampling, Analytical Methods, and Oral Biomarkers for the Diagnosis and Monitoring of Periodontal Diseases: A Systematic Review

Nazar Majeed Z, Philip K, Alabsi AM, Pushparajan S, Swaminathan D

Dis Markers, 2016;2016:1804727.
PMID: 28074077 DOI: 10.1155/2016/1804727

Background. Several studies in the last decades have focused on finding a precise method for the diagnosis of periodontal disease in its early stages. Aim. To evaluate from current scientific literature the most common and precise method for gingival crevicular fluid (GCF) sample collection, biomarker analytical methods, and the variability of biomarker quantification, even when using the same analytical technique. Methodology. An electronic search was conducted on in vivo studies that presented clinical data on techniques used for GCF collection and biomarker analysis. Results. The results showed that 71.1%, 24.7%, and 4.1% of the studies used absorption, microcapillary, and washing techniques, respectively, in their gingival crevicular fluid collection. 73.1% of the researchers analyzed their samples by using enzyme-linked immunosorbent assay (ELISA). 22.6%, 19.5%, and 18.5% of the researchers included interleukin-1 beta (IL-1β), matrix metalloproteinase-8 (MMP-8), and tumor necrosis factor-alpha (TNF-α), respectively, in their studies as biomarkers for periodontal disease. Conclusion. IL-1β can be considered among the most common biomarkers that give precise results and can be used as an indicator of periodontal disease progression. Furthermore, paper strips are the most convenient and accurate method for gingival crevicular fluid collection, while enzyme-linked immunosorbent assay can be considered the most conventional method for the diagnosis of biofluids.

Matched MeSH terms: Specimen Handling/methods*
Fulltext Molecular identification of Malaysian Chrysomya megacephala (Fabricius) and Chrysomya rufifacies (Macquart) using life stage specific mitochondrial DNA

Kavitha R, Tan TC, Lee HL, Nazni WA, Sofian AM

Trop Biomed, 2013 Jun;30(2):211-9.
PMID: 23959486 MyJurnal

DNA identification of blow fly species can be a very useful tool in forensic entomology. One of the potential benefits that mitochondrial DNA (mtDNA) has offered in the field of forensic entomology is species determination. Conventional identification methods have limitations for sibling and closely related species of blow fly and stage and quality of the specimen used. This could be overcome by DNA-based identification methods using mitochondrial DNA which does not demand intact or undamaged specimens. Mitochondrial DNA is usually isolated from whole blow fly and legs. Alternate sources for mitochondrial DNA isolation namely, egg, larva, puparium and empty puparium were explored in this study. The sequence of DNA obtained for each sample for every life cycle stage was 100% identical for a particular species, indicating that the egg, 1st instar, 2nd instar, 3rd instar, pupa, empty puparium and adult from the same species and obtained from same generation will exhibit similar DNA sequences. The present study also highlighted the usefulness of collecting all life cycle stages of blow fly during crime scene investigation with proper preservation and subsequent molecular analysis. Molecular identification provides a strong basis for species identification and will prove an invaluable contribution to forensic entomology as an investigative tool in Malaysia.

Matched MeSH terms: Specimen Handling/methods

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