Whole-genome sequence of a stenotrophomonas maltophilia isolate from tap water in an intensive care unit

Here, we present a 4,508,936-bp complete genome sequence of Stenotrophomonas maltophilia strain HW002Y, which was isolated from the tap water in an intensive care unit at Sultan Ahmad Shah Medical Centre at the International Islamic University of Malaysia (Kuantan, Pahang, Malaysia). Sequencing was performed using a Nanopore Flongle flow cell

Identification of Cryptosporodium from Dairy Cattle in Pahang, Malaysia

Cryptosporidium, a protozoan parasite, can cause cryptosporidiosis which is a gastrointestinal disease that can infect humans and livestock. Cattle are the most common livestock that can be infected with this protozoan. This study was carried out to determine the prevalence of Cryptosporidium infection in cattle in Kuantan, Pahang, Malaysia and to find out the association between the occurrence of infection and 3 different ages of cattle (calves less than 1 year, yearling, and adult cattle). The samples were processed by using formol-ether concentration technique and stained by modified Ziehl Neelsen. The results showed that 15.9% (24/151) of cattle were positive for Cryptosporidium oocysts. The occurrence of Cryptosporidium in calves less than 1 year was the highest with the percentage of 20.0% (11/55) followed by yearling and adult cattle, with the percentage occurrence of 15.6 % (7/45) and 11.8% (6/51), respectively. There was no significant association between the occurrence and age of cattle and presence of diarrhea. Good management practices and proper hygiene management must be taken in order to reduce the infection. It is highly important to control the infection since infected cattle may serve as potential reservoirs of the infection to other animals and humans, especially animal handlers

Whole Genome Sequencing Analysis of Spike D614G Mutation Reveals Unique SARS-CoV-2 Lineages of B.1.524 and AU.2 in Malaysia

The SARS-CoV-2 has spread throughout the world since its discovery in China, and Malaysia is no exception. WGS has been a crucial approach in studying the evolution and genetic diversity of SARS-CoV-2 in the ongoing pandemic, and while an exceptional number of SARS-CoV-2 complete genomes have since been submitted to GISAID and NCBI, there is a scarcity of data from Malaysia. This study aims to report new Malaysian lineages responsible for the sustained spikes in COVID-19 cases during the third wave of the pandemic. Patients whose nasopharyngeal and oropharyngeal swabs were confirmed positive by real-time RT-PCR with Ct-value < 25 were chosen for WGS. The 10 SARS-CoV-2 isolates obtained were then sequenced, characterized and analyzed, including 1356 sequences of the dominant lineages of D614G variant currently circulating throughout Malaysia. The prevalence of clade GH and G formed strong ground of the discovery of two Malaysian lineages that caused sustained spikes of cases locally. Statistical analysis on the association of gender and age group with Malaysian lineages revealed a significant association (p < 0.05). Phylogenetic analysis revealed dispersion of 41 lineages, for which 22 lineages are still active. Mutational analysis observed unique G1223C missense mutation in Transmembrane Domain of Spike protein. Thus, calls for the large-scale WGS analysis of strains found around the world for greater understanding of viral evolution and genetic diversity especially in addressing the question of the effect of deleterious substitution mutation in transmembrane region of Spike protein

Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia

SARS-CoV-2 has spread throughout the world since its discovery in China, and Malaysia is no exception. WGS has been a crucial approach in studying the evolution and genetic diversity of SARS-CoV-2 in the ongoing pandemic. Despite considerable number of SARS-CoV-2 genome sequences have been submitted to GISAID and NCBI databases, there is still scarcity of data from Malaysia. This study aims to report new Malaysian lineages of the virus, responsible for the sustained spikes in COVID-19 cases during the third wave of the pandemic. Patients with nasopharyngeal and/or oropharyngeal swabs confirmed COVID-19 positive by real-time RT-PCR with CT value < 25 were chosen for WGS. The selected SARS-CoV-2 isolates were then sequenced, characterized and analyzed along with 986 sequences of the dominant lineages of D614G variants currently circulating throughout Malaysia. The prevalence of clade GH and G formed strong ground for the presence of two Malaysian lineages of AU.2 and B.1.524 that has caused sustained spikes of cases in the country. Statistical analysis on the association of gender and age group with Malaysian lineages revealed a significant association (p <0.05). Phylogenetic analysis revealed dispersion of 41 lineages, of these, 22 lineages are still active. Mutational analysis showed presence of unique G1223C missense mutation in transmembrane domain of the spike protein. For better understanding of the SARS-CoV-2 evolution in Malaysia especially with reference to the reported lineages, large scale studies based on WGS are warranted

Near-Complete Genome Sequences of Nine SARS-CoV-2 Strains Harboring the D614G Mutation in Malaysia

Here, we report the nearly complete genome sequences of nine severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with the D614G mutation. These viruses were detected from various infected individuals with different levels of severity from Pahang, Malaysia. In addition, this study described the presence of lineage B.1.351 as a type of variant of concern (VOC) and lineages B.1.466.2 and B.1.524 as local variants

Comparative study on protein expression of chicken heart between commercial broilers and indigenous chicken

Broiler chicken are produced by modern integrated poultry raising facilities and been chosen by the farmers due to their high feed-meat conversion ratio ability. This type of chicken is raised in condition which involves antibiotic feed in order to make the chicken gain weight faster and also healthier. Farmers have focused to maximize the production of meat in the shortest time to supply the demand of chicken in the market. However, they may have health issues caused by the fast growth, including sudden death syndrome, metabolic problems such as ascites, and leg problems such as lameness. To analyse the protein expression of chicken liver tissue between antibiotic and non-antibiotic treated chicken through second dimension gel electrophoresis. Protein extraction was carried out according to Zaman et. al. without any modification. The protein concentration of each sample was assayed using Bradford Assay, a Coomassie dye-binding method. A standard curve was generated with serial dilution of bovine serum albumin (BSA) to get the protein concentration of the sample. The protein sample for each replicates was prepared for in-gel rehydration with rehydration buffer such that the concentration of protein applied to each IPG (Immobilized pH Gradient) strip was 120 µg in rehydration buffer and with a total volume of 125 µL. Strip were carefully placed into the SDS-PAGE gel slightly above the well with the gel side facing out and such that the + 3-10 pH sign was on the left side. he gel was viewed using GS-800™ Calibrated Densitometer (Bio-Rad) using Quantity One 1D Analysis software version 4.5 and PDQuest 2D Analysis software (Bio-Rad). Spots of interest were identified using ExPASy SWISS-2DPAGE database (world-2dpage.expasy.org/swiss-2dpage/) as reference. The mean value of protein concentrations in broilers chicken and indigenous chicken heart tissues are 10.43 μg/μL and 11.06 μg/μL respectively. Three spots were identified which shows differential protein expression. First spot is near pH 4.0 with Mw 50-75 kDa which highly expressed in broilers compared to indigenous chicken; second spot is near pH 7.0 with Mw 10-15 kDa, which have a higher spot intensity in indigenous chicken compared to broiler; and third spot is at pH 6.0, Mw 25-37 kDa which expressed in broiler but absent in indigenous chicken. The possible candidates for protein spots which belong to spot i, ii and ii which might represent alpha-1-antitrypsin, myoglobin, and heat shock protein 27 (HSP27) respectively after comparing with HEART-2DPAGE database (http://userpage.chemie.fu-berlin.de/~pleiss/protein_all.html).The Alpha-1-antitrypsin (AAT) is a protease inhibitor that possesses anti-inflammatory and tissue-protective properties. AAT inhibits caspase-1 activity in the condition of inadequate blood supply (ischemia) in myocardium that will help the preservation of viable myocardium. The highly expressed AAT in commercial broilers might appear as a mechanism to overcome or reduce the common heart failure among broilers. Based on the result of 2D gel, the broiler’s heart contains lower concentration of myoglobin compared with indigenous chicken’s heart which is might be the key factor of common case of heart failure among broilers due to lack of oxygen supply by the red blood cells to the heart tissue. Heat Shock Protein (HSP) is expressed in response with the environmental stresses such as heat shock, hypoxia and water deprivation. The functions of the expression of HSP in cells are to adapt to environmental changes and survive from different type of injuries. From the gel, the HSP27 protein was expressed in broilers’ heart while not in the indigenous chicken’s heart. The expression of HSP27 protein in broiler gives signals that the broiler’s chicken heart is under the stress condition, which was assumed to be hypoxia. Thus, the expression of HSP27 in broiler’s heart might aid the cells to survive in the hypoxic condition

Suppression of non-albicans candida species (NAC) biofilm formation by probiotic Streptococcus salivarius

Introduction: Candida spp. are most common opportunistic pathogenic yeast that inhabit human oral cavity, epider­mis, gastrointestinal tract, and vagina leading to candidiasis. The transition of this yeast from commensal to potent pathogen is facilitated by numbers of virulence factors including biofilm formation. While most reports on candidi­asis are associated with formation Candida albicans biofilms, however, non-albicans Candida species prevalence is of growing concern. Recently, the use of probiotics as antifungal and antibiofilm has gained an increasing attention. As such, we aim to evaluate the inhibitory effect of monomicrobial and polymicrobial of Streptococcus Salivarius on six strains of NAC namely Candida dubliniensis, Candida glabrata, Candida krusei, Candida lusitanaei, Candida parapsilosis and Candida tropicalis. Methods: Antifungal activity of S. salivarius on NAC species was performed using well diffusion method on Mueller Hinton Agar (MHA) and the diameter of inhibition zone were assessed. For formation of monomicrobial biofilm, standardized cell suspensions of NAC species and probiotic Streptococcus salivarius were grown in RPMI or nutrient broth media at 37°C for 72 h. Meanwhile to study polymicrobial biofilm -of both NAC and 5. salivarius, similar protocol was employed by inoculating both microorganisms with a similar cell density as in monomicrobial. Finally, biofilrm formation was assessed through quantification of total biomass by crystal violet (CV) assay and the absorbance of adherent biofilm was measured in triplicate at 620nm. Results: Antifungal susceptibility testing of S. salivarius on all six NAC species discerned no zone of inhibition. Furthermore, our results showed variability of monomicrobial and polymicrobial biofilm biomass between NAC species and growth medium. All six polymicrobial NB-grown and RPMl-grown exhibited decreased of the biofilm formation. C. parapsilosis co-cultured with 5. salivarius in NB medium had shown lowest biofilm bio­mass by 75.51 + _1 .34% while in RPMI medium, C. lusitanaei demonstrated with most reduced biofilm biomass by 67.03+ _5. 19. Conclusion: Our study elucidated the antagonistic relationship between Streptococcus salivarius and non-albicans Candida by supressing the growth of polymicrobial biofilm and pseudohyphae/hyphae of NAC species

Intestinal parasitic infections among school children in Kuantan area

The intestinal parasitic infections are usually caused by helminths and protozoa that can lead to the public health problem such as acute and chronic diarrhea, dehydration and abdominal pain. Common factors that cause intestinal parasitic infection among school children are poor hygiene habits, overcrowding, drinking unsafe water and poor immnunity. Therefore, the study aimed to identify the presence of the protozoa and helminths among school children aged 10 years old from four different schools in Kuantan, Pahang. The informed consent form is given to parents before conducting this research. Only 62 school children were willing to participate in this study. The collected stool specimens were examined microscopically by direct smear for detecting the presence of helminths. Trichrome staining and modified Ziehl-Neelsen staining were performed to identify the presence of cysts and oocysts

Occurrence of helminths and coccidia from calves in a commercial farm in Kuantan, Pahang, Malaysia

Parasitic infections in cattle are considered one of the major problems in livestock industry causing morbidity and mortality. Hence, the study aimed to determine the occurrence of intestinal helminths and coccida from cattle in a commercial farm in Kuantan, Pahang between April to May 2015. The fecal samples were collected and examined using floatation and sedimentation methods. A total of 152 calves aged 1 year old and reared under intensive farm management were examined for helminths and coccidia. Results showed that 13 calves were infected with helminths which include Strongyle (7.24%) and followed by Strongyloides (1.32%). Meanwhile, 84 calves were infected with coccidia, Eimeria species (55.26%). From this result, Eimeria species were more dominant in calves than helminths. The present findings indicate that Eimeria species infection could be a problem of calves kept in crowding and under intensive management system. Hence, a better control and strategies should be implemented to control Eimeria species infection among calves

Whole-genome sequence of a stenotrophomonas maltophilia isolate from tap water in an intensive care unit

Here, we present a 4,508,936-bp complete genome sequence of Stenotrophomonas maltophilia strain HW002Y, which was isolated from the tap water in an intensive care unit at Sultan Ahmad Shah Medical Centre at the International Islamic University of Malaysia (Kuantan, Pahang, Malaysia). Sequencing was performed using a Nanopore Flongle flow cell