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Article ; Online: Dataset of complete genome assembly and analysis of mycobacterium tuberculosis strain SIT745/EAI1-MYS

Mohammad Abdullah / Siti Suraiya / Suharni Mohamad / Azian Harun

Data in Brief, Vol 31, Iss , Pp 105949- (2020)

2020

Abstract: In this dataset, we report the genome assembly and data analysis of Mycobacterium tuberculosis strain SIT745/EAI1-MYS. Previously, this strain was isolated from a Malaysian patient with extra-pulmonary tuberculosis, and identification of this strain is ... ...

Abstract	In this dataset, we report the genome assembly and data analysis of Mycobacterium tuberculosis strain SIT745/EAI1-MYS. Previously, this strain was isolated from a Malaysian patient with extra-pulmonary tuberculosis, and identification of this strain is done by spoligotype patterns with fifteen known Shared International Type (SITs). Further analysis showed that this strain has a remarkable phylogeographical specificity for Malaysia. Based on the National Center for Biotechnology Information (NCBI) nucleotide database information, the complete genome consists of 150 contigs with various sequence lengths and was not assembled. In this assembly, the aforementioned contigs along with reference sequence from Mycobacterium tuberculosis strain H37Rv and Mycobacterium bovis strain AF2122/97 was used for gap closures, were assembled into a single circular chromosome length of approximately 4.42 Mega bases (Mb) with an average GC content of 65.6%. The single circular chromosome was shown to contain 4,009 protein-coding sequences, 3 ribosomal RNAs, 45 transfer RNAs, and 12 superclasses distributed with 277 subsystems which constitute nearly 1900 genes, respectively. The genome information will provide fundamental knowledge of this organism as well as insight for understanding genomic and proteomic profiling, phylogenetic relationship.
Keywords	Mycobacterium tuberculosis ; Genome assembly and annotations ; Phylogenetic analysis ; Comparative genomics ; Kelantan ; Malaysia ; Computer applications to medicine. Medical informatics ; R858-859.7 ; Science (General) ; Q1-390
Subject code	572
Language	English
Publishing date	2020-08-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Diagnostic detection of intended bacteria associated with respiratory tract infections among Kelantanese Malaysian Hajj pilgrims by a ready-to-use, thermostable multiplex PCR assay

Nik Mohd Noor Nik Zuraina / Habsah Hasan / Suharni Mohamad / Siti Suraiya

Saudi Journal of Biological Sciences, Vol 29, Iss 8, Pp 103349- (2022)

2022

Abstract: Bacterial respiratory tract infections (RTIs) are prone to be associated with serious health problems during the annual Hajj pilgrimage and are a public health concern due to the potential of pathogens transmission across continents. This study aimed to ... ...

Abstract	Bacterial respiratory tract infections (RTIs) are prone to be associated with serious health problems during the annual Hajj pilgrimage and are a public health concern due to the potential of pathogens transmission across continents. This study aimed to perform a diagnostic screening of intended bacteria associated with RTIs among Malaysian Hajj pilgrims by using a newly developed PCR assay. Expectorated sputum specimens (n = 202) and sociodemographic characteristics of the returning Hajj pilgrims were collected upon arrival in Kelantan, Malaysia. Diagnostic screening of bacterial respiratory pathogens was performed using a thermostabilized multiplex PCR assay in parallel with the sputum culture. Of the six intended bacteria: Haemophilus influenzae, Klebsiella pneumoniae, Mycobacterium tuberculosis, Pseudomonas aeruginosa, Staphylococcus aureus and Streptococcus pneumoniae, the sputum specimens were found positive for H. influenzae (n = 139), K. pneumoniae (n = 20), and S. pneumoniae (n = 19) by the multiplex PCR assay. The sensitivity, specificity, positive- and negative predictive values (PPV and NPV) of this assay were 100% (95% confidence interval (CI): 97.85% to 100.00%), 92.23% (95% CI: 85.27% to 96.59%), 95.51% (95% CI: 91.61% to 97.64%) and 100.00%, respectively. The accuracy of this assay was 97.07% (95% CI: 94.31% to 98.73%). Overall, H. influenzae was found to be the predominant organism in the pilgrims’ sputa by both molecular and microbial culture methods. The multiplex PCR assay would enable a simple, faster and reliable means for the massive screening of intended bacteria compared to the sputum culture, especially during the Hajj pilgrimage.
Keywords	Hajj ; Haemophilus influenzae ; Klebsiella pneumoniae ; Multiplex PCR ; Respiratory tract infections ; Biology (General) ; QH301-705.5
Subject code	572
Language	English
Publishing date	2022-08-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Dentin–Pulp Complex Response in Molars of Rats after Occlusal and Cervical Restorations with Conventional Glass Ionomer Cement and Nano-Hydroxyapatite Silica Glass Ionomer Cement

Fayez Hussain Niazi / Norhayati Luddin / Masitah Hayati Harun / Arshad Hasan / Thirumulu Ponnuraj Kannan / Suharni Mohamad / Amer Mahmood

Applied Sciences, Vol 13, Iss 3156, p

2023 Volume 3156

Abstract: The purpose of this in vivo study was to evaluate and compare the dentin–pulp complex response following occlusal and cervical restorations in rat molars restored with nano-hydroxyapatite silica glass ionomer cement (nano-HA-SiO 2 -GIC) and conventional ... ...

Abstract	The purpose of this in vivo study was to evaluate and compare the dentin–pulp complex response following occlusal and cervical restorations in rat molars restored with nano-hydroxyapatite silica glass ionomer cement (nano-HA-SiO 2 -GIC) and conventional glass ionomer cement (c-GIC). In total, 64 maxillary first molars of 32 male Wistar rats were restored using Fuji IX (c-GIC) and nano-HA-SiO 2 -GIC using a split-mouth design. Half of them were reserved for the occlusal type of restoration while the other half was for cervical restorations. After one week and one month, rats were euthanized and were stained with hematoxylin and eosin, Masson’s trichrome, and Brown and Brenn techniques for histological examination. Parameters such as disorganization of the pulp tissue, inflammatory cell infiltration, detection of bacteria, and tertiary dentin deposition were measured for each group. One week after sacrifice, the odontoblastic layer was disrupted, and moderate inflammation in the pulp area close to the cut dentin was observed in both types of restorations. Nano-HA-SiO 2 -GIC showed significantly superior properties when assessed based on tertiary dentin formation as compared to c-GIC. One month after sacrifice, there was no evidence of disruptions of the odontoblast layer, which exhibited a normal palisade appearance in both groups. In terms of inflammation, the pulp tissue recovered in almost all cases except one of c-GIC, but a few cases of the nano-HA-SiO 2 -GIC group still displayed mild-to-moderate inflammatory reactions, especially of the occlusal type. Both c-GIC and nano-HA-SiO 2 -GIC exhibited favorable responses in terms of biocompatibility. Nano-HA-SiO 2 -GIC exerted more inflammation but encouraged better tertiary dentin formation compared to c-GIC.
Keywords	dentin–pulp complex ; nano-HA-SiO 2 -GIC ; conventional GIC ; tertiary dentin deposition ; Technology ; T ; Engineering (General). Civil engineering (General) ; TA1-2040 ; Biology (General) ; QH301-705.5 ; Physics ; QC1-999 ; Chemistry ; QD1-999
Subject code	540
Language	English
Publishing date	2023-03-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Thermostable Heptaplex PCR Assay for the Detection of Six Respiratory Bacterial Pathogens

Nik Mohd Noor Nik Zuraina / Mohammed Dauda Goni / Khazani Nur Amalina / Habsah Hasan / Suharni Mohamad / Siti Suraiya

Diagnostics, Vol 11, Iss 753, p

2021 Volume 753

Abstract: A thermostabilized, multiplex polymerase chain reaction (mPCR) assay was developed in this study for the detection of six respiratory bacterial pathogens. Specific primers were designed for an internal amplification control (IAC) and six target sequences ...

Abstract	A thermostabilized, multiplex polymerase chain reaction (mPCR) assay was developed in this study for the detection of six respiratory bacterial pathogens. Specific primers were designed for an internal amplification control (IAC) and six target sequences from Klebsiella pneumoniae , Staphylococcus aureus , Streptococcus pneumoniae , Pseudomonas aeruginosa , Mycobacterium tuberculosis , and Haemophilus influenzae . The resultant seven-band positive amplification control (PAC) of this heptaplex PCR assay corresponded to 105 base pairs (bp) of IAC, 202 bp of K. pneumoniae , 293 bp of S. aureus , 349 bp of S. pneumoniae , 444 bp of P. aeruginosa , 505 bp of M. tuberculosis , and 582 bp of H. influenzae . Results found that 6% ( w / v ) of the stabilizer was optimum to preserve the functional conformation of Taq DNA polymerase enzyme. This assay was stable at ambient temperature for at least 6 months. The sensitivity and specificity of this assay were both 100% when testing on the intended target organisms ( n = 119) and non-intended species ( n = 57). The mPCR assay developed in this study enabled accurate, rapid, and simple detection of six respiratory bacteria.
Keywords	Klebsiella pneumoniae ; Staphylococcus aureus ; Streptococcus pneumoniae ; Pseudomonas aeruginosa ; Mycobacterium tuberculosis ; Haemophilus influenzae ; Medicine (General) ; R5-920
Subject code	572
Language	English
Publishing date	2021-04-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: RT-LAMP CRISPR-Cas12/13-Based SARS-CoV-2 Detection Methods

Kasturi Selvam / Mohamad Ahmad Najib / Muhammad Fazli Khalid / Suharni Mohamad / Fahreddin Palaz / Mehmet Ozsoz / Ismail Aziah

Diagnostics, Vol 11, Iss 1646, p

2021 Volume 1646

Abstract: Coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has attracted public attention. The gold standard for diagnosing COVID-19 is reverse transcription–quantitative polymerase chain ... ...

Abstract	Coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has attracted public attention. The gold standard for diagnosing COVID-19 is reverse transcription–quantitative polymerase chain reaction (RT-qPCR). However, RT-qPCR can only be performed in centralized laboratories due to the requirement for advanced laboratory equipment and qualified workers. In the last decade, clustered regularly interspaced short palindromic repeats (CRISPR) technology has shown considerable promise in the development of rapid, highly sensitive, and specific molecular diagnostic methods that do not require complicated instrumentation. During the current COVID-19 pandemic, there has been growing interest in using CRISPR-based diagnostic techniques to develop rapid and accurate assays for detecting SARS-CoV-2. In this work, we review and summarize reverse-transcription loop-mediated isothermal amplification (RT-LAMP) CRISPR-based diagnostic techniques for detecting SARS-CoV-2.
Keywords	COVID-19 ; SARS-CoV-2 ; RT-LAMP ; CRISPR ; Cas12 ; Cas13 ; Medicine (General) ; R5-920
Language	English
Publishing date	2021-09-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: The antibacterial efficacy of silver diamine fluoride (SDF) is not modulated by potassium iodide (KI) supplements

Nizam Abdullah / Farah Al Marzooq / Suharni Mohamad / Normastura Abd Rahman / Koippallil Gopalakrishnan Aghila Rani / Hien Chi Ngo / Lakshman Perera Samaranayake

PLoS ONE, Vol 15, Iss 11, p e

A study on in-situ plaque biofilms using viability real-time PCR with propidium monoazide.

2020 Volume 0241519

Abstract: Silver diamine fluoride (SDF) is commonly used to arrest caries lesions, especially in early childhood caries. Recently, it was suggested that SDF can be combined with potassium iodide (KI) to minimize the discoloration of demineralized dentine ... ...

Abstract	Silver diamine fluoride (SDF) is commonly used to arrest caries lesions, especially in early childhood caries. Recently, it was suggested that SDF can be combined with potassium iodide (KI) to minimize the discoloration of demineralized dentine associated with SDF application. However, the antibacterial efficacy of SDF alone or combined with KI on in-situ biofilm is unknown. Hence, we compared the anti-plaque biofilm efficacy of two different commercially available SDF solutions, with or without KI, using an in-situ biofilm, analysed using viability real-time PCR with propidium monoazide (PMA). Appliance-borne in-situ biofilm samples (n = 90) were grown for a period of 6 h in five healthy subjects who repeated the experiment on three separate occasions, using a validated, novel, intraoral device. The relative anti-biofilm efficacy of two SDF formulations; 38.0% Topamine (SDFT) and 31.3%, Riva Star (SDFR), KI alone, and KI in combination with SDFR (SDFR+KI) was compared. The experiments were performed by applying an optimized volume of the agents onto the biofilm for 1min, mimicking the standard clinical procedure. Afterwards the viability of the residual biofilm bacteria was quantified using viability real-time PCR with PMA, then the percentage of viable from total bacteria was calculated. Both SDF formulations (SDFT and SDFR) exhibited potent antibacterial activities against the in-situ biofilm; however, there was non-significant difference in their efficacy. KI alone did not demonstrate any antibacterial effect, and there was non-significant difference in the antibacterial efficacy of SDF alone compared to SDF with KI, (SDFT v SDFR/KI). Thus, we conclude that the antibacterial efficacy of SDF against plaque biofilms is not modulated by KI supplements. Viability real-time PCR with PMA was successfully used to analyze the viability of naturally grown oral biofilm; thus, the same method can be used to test the antimicrobial effect of other agents on oral biofilms in future research.
Keywords	Medicine ; R ; Science ; Q
Subject code	616
Language	English
Publishing date	2020-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Current State of COVID-19 Pandemic in Africa

Godwin Attah Obande / Ahmad Ibrahim Bagudo / Suharni Mohamad / Zakuan Zainy Deris / Azian Harun / Chan Yean Yean / Ismail Aziah / Kirnpal Kaur Banga Singh

International Journal of Environmental Research and Public Health, Vol 18, Iss 9968, p

Lessons for Today and the Future

2021 Volume 9968

Abstract: This study is a cross-sectional, observational analysis of the COVID-19 pandemic in Africa, to understand the progression of the disease across the continent. Published data on COVID-19 from 20 January 2020 to 21 June 2021 were obtained and analyzed. ... ...

Abstract	This study is a cross-sectional, observational analysis of the COVID-19 pandemic in Africa, to understand the progression of the disease across the continent. Published data on COVID-19 from 20 January 2020 to 21 June 2021 were obtained and analyzed. Case fatality ratios, as well as case growth rates and other indices were computed. On 21 June 2021, a total of 178,210,532 confirmed cases and 3,865,978 deaths had been recorded worldwide. While the Americas recorded the highest number of cases, Southern Africa recorded the majority of African cases. Fatality rate since from 20 February 2020 to 21 June 2021 was highest in the Americas (2.63%) and low in the South Eastern Asia region (1.39%), globally increasing from 2.17% at the end of January to 6.36% in May 2020 and decreasing to a range between 2.14% to 2.30% since January 2021. In Africa, the infection rate per 100,000 persons was up to 3090.18, while deaths per 100,000 and case fatality ratio were as high as 119.64 and 5.72%, respectively, among the 20 most-affected countries. The testing rate per million population was highest in Botswana (512,547.08). Fatality appears to be increasing in some regions of Africa. The rate of infection and fatality in Africa could still likely take an upward turn. Strict control measures are required, considering the continent’s weak healthcare systems.
Keywords	COVID-19 ; Africa ; SARS-CoV-2 ; coronavirus ; infection ; healthcare system ; Medicine ; R
Subject code	390
Language	English
Publishing date	2021-09-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: High frequency of Haemophilus influenzae associated with respiratory tract infections among Malaysian Hajj pilgrims.

Nik Zuraina, Nik M N / Sarimah, Abdullah / Suharni, Mohamad / Hasan, Habsah / Suraiya, Siti

Journal of infection and public health

2018 Volume 11, Issue 6, Page(s) 878–883

Abstract: Background: Overcrowding during the annual Hajj pilgrimage has been known to increase the risk of infectious diseases transmission. Despite the high prevalence of respiratory illness among Malaysian Hajj pilgrims, knowledge about the etiologic pathogens ...

Abstract	Background: Overcrowding during the annual Hajj pilgrimage has been known to increase the risk of infectious diseases transmission. Despite the high prevalence of respiratory illness among Malaysian Hajj pilgrims, knowledge about the etiologic pathogens is yet very limited. Thus, this study aimed to determine the spectrum of bacterial respiratory pathogens among the Hajj pilgrims returning to Malaysia in year 2016. Methods: Expectorated sputum specimens were collected from the Hajj pilgrims with symptomatic respiratory tract infections (RTIs). Subsequently, the bacterial pathogens were identified using the standard bacteriological culture method and Vitek II system. Results: This study indicated that 255 (87.33%) out of 292 cultured sputa were positive with at least one potential pathogenic bacteria. Out of 345 total bacterial isolates, 60% (n=207) were Haemophilus influenzae, which was associated with both single bacterium infection (132/173, 76.3%) and multiple bacterial infections (75/82, 91.5%). The other bacterial isolates included; Klebsiella pneumoniae (n=37, 10.7%), Moraxella catarrhalis (n=27, 7.8%), Haemophilus parainfluenzae (n=25, 7.2%), Streptococcus group G (n=18, 5.2%), Klebsiella spesies (n=16, 4.6%), Streptococcus pneumoniae (n=11, 3.2%) and few other organisms. Conclusion: High frequency of H. influenzae was isolated from Malaysian Hajj pilgrims, especially those with respiratory symptoms. Further study should evaluate the actual pathogenicity of the organism and the interactions between the respiratory microbiota towards developing effective prevention strategies of RTIs among the local pilgrims.
MeSH term(s)	Adult ; Aged ; Aged, 80 and over ; Bacteriological Techniques ; Cross-Sectional Studies ; Crowding ; Female ; Haemophilus Infections/epidemiology ; Haemophilus Infections/microbiology ; Haemophilus influenzae/isolation & purification ; Humans ; Malaysia/epidemiology ; Male ; Middle Aged ; Prevalence ; Religion ; Respiratory Tract Infections/epidemiology ; Respiratory Tract Infections/microbiology ; Sputum/microbiology ; Travel-Related Illness
Language	English
Publishing date	2018-08-07
Publishing country	England
Document type	Journal Article
ISSN	1876-035X
ISSN (online)	1876-035X
DOI	10.1016/j.jiph.2018.07.010
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: In-vitro antimicrobial effectiveness of herbal-based mouthrinses against oral microorganisms

Ju Ying Teh / Rabiah Rawi / Siti Suraiya Md Noor / Haslina Taib / Suharni Mohamad

Asian Pacific Journal of Tropical Biomedicine, Vol 5, Iss 5, Pp 370-

2015 Volume 374

Abstract: Objective: To evaluate the in vitro antimicrobial effectiveness of commercial herbal-based mouthrinses against oral microorganisms. Methods: A total of three mouthrinses (OX, Pesona and Watsons) were tested for their antimicrobial activity against six ... ...

Abstract	Objective: To evaluate the in vitro antimicrobial effectiveness of commercial herbal-based mouthrinses against oral microorganisms. Methods: A total of three mouthrinses (OX, Pesona and Watsons) were tested for their antimicrobial activity against six oral organisms, Streptococcus mutans (S. mutans), Streptococcus sobrinus (S. sobrinus), Lactobacillus salivarius (L. salivarius), Staphylococcus aureus (S. aureus), Pseudomonas aeruginosa (P. aeruginosa) and Candida albicans (C. albicans) by standard agar-disk diffusion assay. Oradex mouthrinse containing 0.12% chlorhexidine gluconate and sterile distilled water was served as positive and negative controls, respectively. Results: All mouthrinse formulations were effective in inhibiting the growth of S. mutans, S. sobrinus, L. salivarius and C. albicans. Among the tested mouthrinses, Pesona was the only effective mouthrinse against S. aureus and P. aeruginosa, similar to Oradex mouthrinse. Pesona mouthrinse formulation appears to be as effective as Oradex mouthrinse formulation to kill S. aureus and P. aeruginosa. Statistical analysis showed no significant difference among the tested formulations regarding their antimicrobial activities (P > 0.05). Conclusions: Pesona was not the only herbal mouthrinse effective in inhibiting the growth of S. mutans, S. sobrinus, L. salivarius and C. albicans in vitro. All tested formulations were effective against those strains. Our findings may serve as a guide for selecting a kind of herbal mouthrinses as well as providing information to the dental professionals about the efficacy of these products.
Keywords	Mouthrinses ; Chlorhexidine gluconate ; Antimicrobial properties ; Zones of inhibitions ; Arctic medicine. Tropical medicine ; RC955-962 ; Biology (General) ; QH301-705.5
Language	English
Publishing date	2015-05-01T00:00:00Z
Publisher	Wolters Kluwer Medknow Publications
Document type	Article ; Online
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Article ; Online: A Thermostabilized, One-Step PCR Assay for Simultaneous Detection of Klebsiella pneumoniae and Haemophilus influenzae

Nur Amalina Khazani / Nik Zuraina Nik Mohd Noor / Chan Yean Yean / Habsah Hasan / Siti Suraiya / Suharni Mohamad

Journal of Tropical Medicine, Vol

2017 Volume 2017

Abstract: Klebsiella pneumoniae and Haemophilus influenzae are two common pathogens associated with respiratory tract infections. The identification of these pathogens using conventional molecular diagnostic tests requires trained personnel, cold-chain ... ...

Abstract	Klebsiella pneumoniae and Haemophilus influenzae are two common pathogens associated with respiratory tract infections. The identification of these pathogens using conventional molecular diagnostic tests requires trained personnel, cold-chain transportation, and storage-dependance, which does not render them user-friendly. The aim of this study was to develop a thermostabilized, cold-chain-free, one-step multiplex PCR for simultaneous detection of K. pneumoniae and H. influenzae. The multiplex PCR assay was designed to amplify the php gene of K. pneumoniae (202 bp) and p6 gene of H. influenzae (582 bp). In addition, the specific primer to amplify glm gene of Helicobacter pylori (105 bp) was included as an internal amplification control. Subsequently, the designed primers and all PCR reagents were thermostabilized by lyophilization. The stability of the thermostabilized PCR was evaluated using the Q10 method. The sensitivity and specificity of performances for thermostabilized PCR were evaluated using 127 clinical isolates and were found to be 100% sensitive and specific. The thermostabilized PCR mix was found to be stable for 30 days and the Q10 accelerated stability was found to be 3.02 months. A cold-chain-free, PCR assay for easy, rapid, and simultaneous detection of K. pneumoniae and H. influenzae was successfully developed in this study.
Keywords	Arctic medicine. Tropical medicine ; RC955-962
Subject code	572
Language	English
Publishing date	2017-01-01T00:00:00Z
Publisher	Hindawi Limited
Document type	Article ; Online
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