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Fulltext Genome sequence data of Bacillus sp. CCB-MMP212 isolated from Malaysian mangrove: A potential strain in arsenic resistance with ArsI, C•As lyase

Azami NA, Lau NS, Furusawa G

Data Brief, 2022 Dec;45:108597.
PMID: 36164294 DOI: 10.1016/j.dib.2022.108597

Bacillus sp. CCB-MMP212 is a Gram-positive bacterium isolated from mangrove sediment in Matang Perak, Malaysia (4.85496°E, 100.73495°N). Genome sequencing was performed using the Oxford Nanopore and Illumina platforms. The assembled genome was annotated using the rapid annotation subsystem technology server (RAST) (rast.nmpdr.org). The genome size of the Bacillus sp. CCB-MMP212 was 6,151,644 base pairs (bp) with a G+C content of 34.75%. The genome includes 6,311 coding sequences and 58 RNAs. The sequence has been deposited at Genbank with the accession number of JALDQE000000000. Interestingly, an arsenic resistance (ars) operon consisted of arsenic resistance operon repressor (arsR), ACR3 family arsenite efflux transporter (arsB), and arsenate reductase (arsC) genes were found in the genome. In addition, the arsenic inducible gene (arsI), which encoded a dioxygenase with C•As lyase activity, was also found in the ars operon. The enzyme is crucial for the methylation of methylarsonous acid [MAs(III)] and trivalent roxarsone [Rox(III)]. This dataset reveals the genetic ability of this strain in arsenic resistance. To the best of our knowledge, the arsI encoding C•As lyase is rarely reported within the genus Bacillus. Therefore, the dataset presented in this manuscript provides further insight into the arsenic resistance mechanisms of the genus Bacillus.
Fulltext Genes for degradation and utilization of uronic acid-containing polysaccharides of a marine bacterium Catenovulum sp. CCB-QB4

Furusawa G, Azami NA, Teh AH

PeerJ, 2021;9:e10929.
PMID: 33732545 DOI: 10.7717/peerj.10929

BACKGROUND: Oligosaccharides from polysaccharides containing uronic acids are known to have many useful bioactivities. Thus, polysaccharide lyases (PLs) and glycoside hydrolases (GHs) involved in producing the oligosaccharides have attracted interest in both medical and industrial settings. The numerous polysaccharide lyases and glycoside hydrolases involved in producing the oligosaccharides were isolated from soil and marine microorganisms. Our previous report demonstrated that an agar-degrading bacterium, Catenovulum sp. CCB-QB4, isolated from a coastal area of Penang, Malaysia, possessed 183 glycoside hydrolases and 43 polysaccharide lyases in the genome. We expected that the strain might degrade and use uronic acid-containing polysaccharides as a carbon source, indicating that the strain has a potential for a source of novel genes for degrading the polysaccharides.
METHODS: To confirm the expectation, the QB4 cells were cultured in artificial seawater media with uronic acid-containing polysaccharides, namely alginate, pectin (and saturated galacturonate), ulvan, and gellan gum, and the growth was observed. The genes involved in degradation and utilization of uronic acid-containing polysaccharides were explored in the QB4 genome using CAZy analysis and BlastP analysis.
RESULTS: The QB4 cells were capable of using these polysaccharides as a carbon source, and especially, the cells exhibited a robust growth in the presence of alginate. 28 PLs and 22 GHs related to the degradation of these polysaccharides were found in the QB4 genome based on the CAZy database. Eleven polysaccharide lyases and 16 glycoside hydrolases contained lipobox motif, indicating that these enzymes play an important role in degrading the polysaccharides. Fourteen of 28 polysaccharide lyases were classified into ulvan lyase, and the QB4 genome possessed the most abundant ulvan lyase genes in the CAZy database. Besides, genes involved in uronic acid metabolisms were also present in the genome. These results were consistent with the cell growth. In the pectin metabolic pathway, the strain had genes for three different pathways. However, the growth experiment using saturated galacturonate exhibited that the strain can only use the pathway related to unsaturated galacturonate.
Fulltext Genome Sequence of Vibrio sp. Strain CCB-PB317, Isolated from a Malaysian Mangrove, and Its Arsenic Resistance Mechanisms

Miswan N, Lau NS, Azami NA, Furusawa G

Microbiol Resour Announc, 2023 Jan 24;12(1):e0100022.
PMID: 36598229 DOI: 10.1128/mra.01000-22

Vibrio sp. strain CCB-PB317 with potential arsenic detoxification was isolated from a mangrove in Pulau Betong, Malaysia. Here, we report a draft genome sequence of strain CCB-PB317, which comprised 5,157,574 bp with a G+C content of 44.9%. The genome contains genes related to an arsenic resistance system coupled with glycolytic metabolism.
Characterisation and substrate binding modes of exopolygalacturonase PGQ1 from Saccharobesus litoralis

Azami NA, Lian MQ, Furusawa G, Teh AH

J Biomol Struct Dyn, 2023;41(22):12565-12571.
PMID: 36656114 DOI: 10.1080/07391102.2023.2167111

Among the enzymes required for the efficient utilisation of pectin is polygalacturonase. Saccharobesus litoralis harbours two polygalacturonases belonging to glycoside hydrolase family 28 (GH28). One of them, PGQ1, cleaved polygalacturonate exolytically at the non-reducing end into monomeric units. It was most active at 60 °C and pH 8, with Km and kcat values of 2.3 mg/ml and 6.4 s-1 respectively. Its homology model of a right-handed parallel β-helix core consisted of Asp297 as the general acid and either Asp276 or Asp298 as the general base. By inferring the substrate binding modes at the -1 and +1 subsites from known crystal structures, a hexagalacturonate could be docked into the highly electropositive binding cleft. Interestingly, while no residues were present in the vicinity to make up the +2 and +4 subsites, Arg361 and Arg430 could readily bind to the carboxyl groups of the galacturonates at the +3 and +5 subsites respectively. Structural comparison suggested that this binding pattern with missing subsites might be unique to closely related exopolygalacturonases. As S. litoralis grew much more slowly on extracellular galacturonate due to the lack of a transporter for the monosaccharide, PGQ1 probably functioned in the periplasm to help degrade oligopectates completely.Communicated by Ramaswamy H. Sarma.
Fulltext Dengue epidemic in Malaysia: Not a predominantly urban disease anymore

Muhammad Azami NA, Salleh SA, Neoh HM, Syed Zakaria SZ, Jamal R

BMC Res Notes, 2011;4:216.
PMID: 21714858 DOI: 10.1186/1756-0500-4-216

BACKGROUND:
Dengue infection has been an important and serious public health concern in Malaysia ever since its first reported case here in 1902. Nevertheless, to our knowledge, no nationwide investigation has been carried out to determine the actual magnitude of dengue endemicity in the Malaysian population. In this study, we describe a cross sectional seroepidemiology study of dengue IgG seroprevalence in the Malaysian adult population.

FINDINGS:
From 1000 subjects (35-74 years old), 91.6% subjects were found to be dengue seropositive. Age is found to be a significant risk factor associated with dengue seroposivity, where the seroprevalence increased with every 10 year increase in age. Nevertheless, gender and ethnicity did not have an effect. Interestingly, there were similar seroprevalence rates between urban and rural samples, showing that dengue is presently not confined to urban areas in Malaysia.

CONCLUSIONS:
High dengue IgG seropositivity found in the population is an indication that dengue might be endemic in Malaysia for a long time into the future. Public awareness, proper vector control and vigilant surveillance are critical to keep the infection rates low and to prevent outbreaks.
Fulltext Emergence of chikungunya seropositivity in healthy Malaysian adults residing in outbreak-free locations: chikungunya seroprevalence results from the Malaysian Cohort

Azami NA, Salleh SA, Shah SA, Neoh HM, Othman Z, Zakaria SZ, et al.

BMC Infect Dis, 2013;13:67.
PMID: 23379541 DOI: 10.1186/1471-2334-13-67

In 1998, Malaysia experienced its first chikungunya virus (CHIKV) outbreak in the suburban areas followed by another two in 2006 (rural areas) and 2008 (urban areas), respectively. Nevertheless, there is still a lack of documented data regarding the magnitude of CHIKV exposure in the Malaysian population. The aim of this study was to determine the extent of chikungunya virus infection in healthy Malaysian adults residing in outbreak-free locations.
Enhanced degradation of polyhydroxyalkanoates (PHAs) by newly isolated Burkholderia cepacia DP1 with high depolymerase activity

Azami NA, Wirjon IA, Kannusamy S, Teh AH, Abdullah AA

3 Biotech, 2017 May;7(1):75.
PMID: 28452023 DOI: 10.1007/s13205-017-0716-7

The contribution of microbial depolymerase has received much attention because of its potential in biopolymer degradation. In this study, the P(3HB) depolymerase enzyme of a newly isolated Burkholderia cepacia DP1 from soil in Penang, Malaysia, was optimized using response surface methodology (RSM). The factors affecting P(3HB) depolymerase enzyme production were studied using one-variable-at-a-time approach prior to optimization. Preliminary experiments revealed that the concentration of nitrogen source, concentration of carbon source, initial pH and incubation time were among the main factors influencing the enzyme productivity. An increase of 9.4 folds in enzyme production with an activity of 5.66 U/mL was obtained using optimal medium containing 0.028% N of di-ammonium hydrogen phosphate and 0.31% P(3HB-co-21%4HB) as carbon source at the initial pH of 6.8 for 38 h of incubation. Moreover, the RSM model showed great similarity between predicted and actual enzyme production indicating a successful model validation. This study warrants the ability of P(3HB) degradation by B. cepacia DP1 in producing higher enzyme activity as compared to other P(3HB) degraders being reported. Interestingly, the production of P(3HB) depolymerase was rarely reported within genus Burkholderia. Therefore, this is considered to be a new discovery in the field of P(3HB) depolymerase production.
Fulltext Hepatitis B and influenza vaccination coverage in healthcare workers, the elderly, and patients with diabetes in Malaysia

Muhammad Azami NA, Abdullah N, Kamalul Ariffin AS, Abdullah MS, Dauni A, Kamaruddin MA, et al.

Hum Vaccin Immunother, 2023 Dec 31;19(1):2170660.
PMID: 36728847 DOI: 10.1080/21645515.2023.2170660

Adult immunization remains to be a neglected issue in developing countries including Malaysia. This nationwide study determined the vaccination coverage of hepatitis B and influenza among Malaysia's healthcare workers (HCWs), the elderly (aged 60 y and above) and patients with diabetes, who are the participants of The Malaysia Cohort Program. The participants were categorized based on their occupation, age and medical history. Self-reported questionnaire was used to assess the participant's hepatitis B and influenza vaccination status. A Chi-square test and logistic regression analyses were performed to determine the risk factors associated with vaccination behavior. The hepatitis B vaccination coverage for healthcare workers, elderly, and patients with diabetes were 34.6%, 10.1% and 9.8%, respectively. The influenza vaccination coverage rates for healthcare workers, the elderly and patients with diabetes were 26.3%, 5.5% and 6.4%, respectively. The Chinese were more likely to be vaccinated against hepatitis B, while Malay was more likely to be vaccinated against influenza. Individuals with higher education and living in urban areas were more likely vaccinated than those with low education levels and who lived in rural areas. The low vaccination coverage for healthcare workers was alarming because hepatitis B and influenza were subsidized for the healthcare workers. The hepatitis B and influenza vaccination coverage among healthcare workers, elderly and patients with diabetes in Malaysia were low. Specific interventions such as educational and awareness programs should be conducted to increase the vaccination rate among adults, especially those at high risk.
Fulltext Seroprevalence of hepatitis B virus and hepatitis C virus infection among Malaysian population

Muhamad NA, Ab Ghani RM, Abdul Mutalip MH, Muhammad EN, Mohamad Haris H, Mohd Zain R, et al.

Sci Rep, 2020 12 03;10(1):21009.
PMID: 33273475 DOI: 10.1038/s41598-020-77813-5

Malaysia is a country with an intermediate endemicity for hepatitis B. As the country moves toward hepatitis B and C elimination, population-based estimates are necessary to understand the burden of hepatitis B and C for evidence-based policy-making. Hence, this study aims to estimate the prevalence of hepatitis B and C in Malaysia. A total of 1458 participants were randomly selected from The Malaysian Cohort (TMC) aged 35 to 70 years between 2006 and 2012. All blood samples were tested for hepatitis B and C markers including hepatitis B surface antigen (HBsAg), anti-hepatitis B core antibody (anti-HBc), antibodies against hepatitis C virus (anti-HCV). Those reactive for hepatitis C were further tested for HCV RNA genotyping. The sociodemographic characteristics and comorbidities were used to evaluate their associated risk factors. Descriptive analysis and multivariable analysis were done using Stata 14. From the samples tested, 4% were positive for HBsAg (95% CI 2.7-4.7), 20% were positive for anti-HBc (95% CI 17.6-21.9) and 0.3% were positive for anti-HCV (95% CI 0.1-0.7). Two of the five participants who were reactive for anti-HCV had the HCV genotype 1a and 3a. The seroprevalence of HBV and HCV infection in Malaysia is low and intermediate, respectively. This population-based study could facilitate the planning and evaluation of the hepatitis B and C control program in Malaysia.
Study name: The Malaysian Cohort (TMC) project
Fulltext COVID-19 in Malaysia: exposure assessment and prevention practices among healthcare workers at a teaching hospital

Muhammad Azami NA, Abdul Murad NA, Mohammed Nawi A, Salleh SA, Periyasamy P, Kori N, et al.

J Infect Dev Ctries, 2021 12 31;15(12):1816-1824.
PMID: 35044938 DOI: 10.3855/jidc.15277

INTRODUCTION: During the second wave of the coronavirus disease 19 (COVID-19) pandemic, Malaysia reported several COVID-19 clusters related to healthcare workers. Thus, addressing and understanding the risk of exposure in healthcare workers is important to prevent future infection and reduce secondary COVID-19 transmission within the healthcare settings. In this study, we aim to assess exposure and prevention practices against COVID-19 among healthcare workers at the Hospital Canselor Tuanku Muhriz, a university teaching hospital based in Kuala Lumpur, Malaysia.
METHODOLOGY: A total of 571 healthcare workers at COVID-19 and non-COVID-19 wards as well as the emergency department and laboratory staff at COVID-19 testing labs were recruited. The presence of novel human coronavirus (SARS-CoV-2) and IgM/IgG antibodies were confirmed in all healthcare workers. The healthcare workers responded to an online Google Forms questionnaire that evaluates demographic information and comorbidities, exposure and adherence to infection prevention and control measures against COVID-19. Descriptive analysis was performed using Statistical Package for the Social Sciences 24.0.
RESULTS: Three healthcare workers (0.5%) tested positive for SARS-CoV-2, while the remaining 568 (99.5%) were negative. All were negative for IgM and IgG antibodies during recruitment (day 1) and follow-up (day 15). More than 90% of the healthcare workers followed infection prevention and control practices recommendations regardless of whether they have been exposed to occupational risk for COVID-19.
CONCLUSIONS: The healthcare workers' high level of adherence to infection prevention practices at this hospital helped reduce and minimize their occupational exposure to COVID-19.
Detection of SARS-CoV-2 in Environment: Current Surveillance and Effective Data Management of COVID-19

Nadzirah S, Mohamad Zin N, Khalid A, Abu Bakar NF, Kamarudin SS, Zulfakar SS, et al.

Crit Rev Anal Chem, 2023 Jun 26.
PMID: 37358486 DOI: 10.1080/10408347.2023.2224433

Since diagnostic laboratories handle large COVID-19 samples, researchers have established laboratory-based assays and developed biosensor prototypes. Both share the same purpose; to ascertain the occurrence of air and surface contaminations by the SARS-CoV-2 virus. However, the biosensors further utilize internet-of-things (IoT) technology to monitor COVID-19 virus contamination, specifically in the diagnostic laboratory setting. The IoT-capable biosensors have great potential to monitor for possible virus contamination. Numerous studies have been done on COVID-19 virus air and surface contamination in the hospital setting. Through reviews, there are abundant reports on the viral transmission of SARS-CoV-2 through droplet infections, person-to-person close contact and fecal-oral transmission. However, studies on environmental conditions need to be better reported. Therefore, this review covers the detection of SARS-CoV-2 in airborne and wastewater samples using biosensors with comprehensive studies in methods and techniques of sampling and sensing (2020 until 2023). Furthermore, the review exposes sensing cases in public health settings. Then, the integration of data management together with biosensors is well explained. Last, the review ended with challenges to having a practical COVID-19 biosensor applied for environmental surveillance samples.

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