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Fulltext Loop-mediated isothermal amplification (LAMP): a versatile technique for detection of micro-organisms

Wong YP, Othman S, Lau YL, Radu S, Chee HY

J Appl Microbiol, 2018 Mar;124(3):626-643.
PMID: 29165905 DOI: 10.1111/jam.13647

Loop-mediated isothermal amplification (LAMP) amplifies DNA with high specificity, efficiency and rapidity under isothermal conditions by using a DNA polymerase with high displacement strand activity and a set of specifically designed primers to amplify targeted DNA strands. Following its first discovery by Notomi et al. ( Nucleic Acids Res 28: E63), LAMP was further developed over the years which involved the combination of this technique with other molecular approaches, such as reverse transcription and multiplex amplification for the detection of infectious diseases caused by micro-organisms in humans, livestock and plants. In this review, available types of LAMP techniques will be discussed together with their applications in detection of various micro-organisms. Up to date, there are varieties of LAMP detection methods available including colorimetric and fluorescent detection, real-time monitoring using turbidity metre and detection using lateral flow device which will also be highlighted in this review. Apart from that, commercialization of LAMP technique had also been reported such as lyophilized form of LAMP reagents kit and LAMP primer sets for detection of pathogenic micro-organisms. On top of that, advantages and limitations of this molecular detection method are also described together with its future potential as a diagnostic method for infectious disease.

Matched MeSH terms: Communicable Diseases/microbiology
Fulltext Paratyphoid fever: splicing the global analyses

Teh CS, Chua KH, Thong KL

Int J Med Sci, 2014;11(7):732-41.
PMID: 24904229 DOI: 10.7150/ijms.7768

The incidence of enteric fever caused by Salmonella enterica serovar Paratyphi A (S. Paratyphi A) is increasing in many parts of the world. Although there is no major outbreak of paratyphoid fever in recent years, S. Paratyphi A infection still remains a public health problem in many tropical countries. Therefore, surveillance studies play an important role in monitoring infections and the emergence of multidrug resistance, especially in endemic countries such as India, Nepal, Pakistan and China. In China, enteric fever was caused predominantly by S. Paratyphi A rather than by Salmonella enterica serovar Typhi (S. Typhi). Sometimes, S. Paratyphi A infection can evolve into a carrier state which increases the risk of transmission for travellers. Hence, paratyphoid fever is usually classified as a "travel-associated" disease. To date, diagnosis of paratyphoid fever based on the clinical presentation is not satisfactory as it resembles other febrile illnesses, and could not be distinguished from S. Typhi infection. With the availability of Whole Genome Sequencing technology, the genomes of S. Paratyphi A could be studied in-depth and more specific targets for detection will be revealed. Hence, detection of S. Paratyphi A with Polymerase Chain Reaction (PCR) method appears to be a more reliable approach compared to the Widal test. On the other hand, due to increasing incidence of S. Paratyphi A infections worldwide, the need to produce a paratyphoid vaccine is essential and urgent. Hence various vaccine projects that involve clinical trials have been carried out. Overall, this review provides the insights of S. Paratyphi A, including the bacteriology, epidemiology, management and antibiotic susceptibility, diagnoses and vaccine development.

Matched MeSH terms: Communicable Diseases/microbiology
Fulltext Preserve a Voucher Specimen! The Critical Need for Integrating Natural History Collections in Infectious Disease Studies

Thompson CW, Phelps KL, Allard MW, Cook JA, Dunnum JL, Ferguson AW, et al.

mBio, 2021 Jan 12;12(1).
PMID: 33436435 DOI: 10.1128/mBio.02698-20

Despite being nearly 10 months into the COVID-19 (coronavirus disease 2019) pandemic, the definitive animal host for SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), the causal agent of COVID-19, remains unknown. Unfortunately, similar problems exist for other betacoronaviruses, and no vouchered specimens exist to corroborate host species identification for most of these pathogens. This most basic information is critical to the full understanding and mitigation of emerging zoonotic diseases. To overcome this hurdle, we recommend that host-pathogen researchers adopt vouchering practices and collaborate with natural history collections to permanently archive microbiological samples and host specimens. Vouchered specimens and associated samples provide both repeatability and extension to host-pathogen studies, and using them mobilizes a large workforce (i.e., biodiversity scientists) to assist in pandemic preparedness. We review several well-known examples that successfully integrate host-pathogen research with natural history collections (e.g., yellow fever, hantaviruses, helminths). However, vouchering remains an underutilized practice in such studies. Using an online survey, we assessed vouchering practices used by microbiologists (e.g., bacteriologists, parasitologists, virologists) in host-pathogen research. A much greater number of respondents permanently archive microbiological samples than archive host specimens, and less than half of respondents voucher host specimens from which microbiological samples were lethally collected. To foster collaborations between microbiologists and natural history collections, we provide recommendations for integrating vouchering techniques and archiving of microbiological samples into host-pathogen studies. This integrative approach exemplifies the premise underlying One Health initiatives, providing critical infrastructure for addressing related issues ranging from public health to global climate change and the biodiversity crisis.

Matched MeSH terms: Communicable Diseases/microbiology
Fulltext An Overview of the Potential Therapeutic Applications of Essential Oils

Aljaafari MN, AlAli AO, Baqais L, Alqubaisy M, AlAli M, Molouki A, et al.

Molecules, 2021 Jan 26;26(3).
PMID: 33530290 DOI: 10.3390/molecules26030628

The emergence of antimicrobial resistance (AMR) has urged researchers to explore therapeutic alternatives, one of which includes the use of natural plant products such as essential oils (EO). In fact, EO obtained from clove, oregano, thymus, cinnamon bark, rosemary, eucalyptus, and lavender have been shown to present significant inhibitory effects on bacteria, fungi, and viruses; many studies have been done to measure EO efficacy against microorganisms. The strategy of combinatory effects via conventional and non-conventional methods revealed that the combined effects of EO-EO or EO-antibiotic exhibit enhanced efficacy. This paper aims to review the antimicrobial effects of EO, modes of EO action (membrane disruption, efflux inhibition, increase membrane permeability, and decrease in intracellular ATP), and their compounds' potential as effective agents against bacteria, fungi, and viruses. It is hoped that the integration of EO applications in this work can be used to consider EO for future clinical applications.

Matched MeSH terms: Communicable Diseases/microbiology
Evaluation of the Atlas Helicobacter pylori stool antigen test for diagnosis of infection in adult patients

Osman HA, Hasan H, Suppian R, Bahar N, Hussin NS, Rahim AA, et al.

Asian Pac J Cancer Prev, 2014;15(13):5245-7.
PMID: 25040982

BACKGROUND: Helicobacter pylori (H. pylori) is one of the most important causes of dyspepsia and gastric cancer and diagnosis can be made by invasive or non-invasive methods. The Atlas Helicobacter pylori antigen test is a new rapid non-invasive method which is simple to conduct. The aim of this study was to determine its sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV) and accuracy.
MATERIALS AND METHODS: This prospective study was conducted between July 2012 and December 2013. Stool samples of 59 dyspeptic patients who underwent upper endoscopy were evaluated for H. pylori stool antigen.
RESULTS: From the 59 patients who participated in this study, there were 36 (61%) males and 23 (39%) females. H. pylori was diagnosed in 24 (40.7%) gastric biopsies, 22 (91.7 %) of these being positive for the Atlas H. pylori antigen test. The sensitivity, specificity, PPV, NPV and accuracy were 91.7%, 100%, 100%, 94.6% and 96.6% respectively.
CONCLUSIONS: The Atlas H. pylori antigen test is a new non-invasive method which is simple to perform and avails reliable results in a few minutes. Thus it can be the best option for the diagnosis of H. pylori infection due to its high sensitivity and specificity.

Matched MeSH terms: Communicable Diseases/microbiology