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Genomic surveillance is crucial for tracking emergence and spread of novel variants of pathogens, such as SARS-CoV-2, to inform public health interventions and to enforce control measures. However, in some settings especially in low- and middle- income counties, where sequencing platforms are limited, only certain patients get to be selected for sequencing surveillance. Here, we show that patients with multiple comorbidities potentially harbour SARS-CoV-2 with higher mutation rates and thus deserve more attention for genomic surveillance. The relationship between the patient comorbidities, and type of amino acid mutations was assessed. Correlation analysis showed that there was a significant tendency for mutations to occur within the ORF1a region for patients with higher number of comorbidities. Frequency analysis of the amino acid substitution within ORF1a showed that nsp3 P822L of the PLpro protease was one of the highest occurring mutations. Using molecular dynamics, we simulated that the P822L mutation in PLpro represents a system with lower Root Mean Square Deviation (RMSD) fluctuations, and consistent Radius of gyration (Rg), Solvent Accessible Surface Area (SASA) values—indicate a much stabler protein than the wildtype. The outcome of this study will help determine the relationship between the clinical status of a patient and the mutations of the infecting SARS-CoV-2 virus. [ABSTRACT FROM AUTHOR]

Introduction: The World Health Organization (WHO) declared COVID-19 outbreak as a world pandemic on 12th March 2020. Diagnosis of suspected cases is confirmed by nucleic acid assays with real-time PCR, using respiratory samples. Serology tests are comparatively easier to perform, but their utility may be limited by the performance and the fact that antibodies appear later during the disease course. We aimed to describe the performance data on serological assays for COVID-19. Materials and Methods: A review of multiple reports and kit inserts on the diagnostic performance of rapid tests from various manufacturers that are commercially available were performed. Only preliminary data are available currently. Results: From a total of nine rapid detection test (RDT) kits, three kits offer total antibody detection, while six kits offer combination SARS-CoV-2 IgM and IgG detection in two separate test lines. All kits are based on colloidal gold-labeled immunochromatography principle and one-step method with results obtained within 15 minutes, using whole blood, serum or plasma samples. The sensitivity for both IgM and IgG tests ranges between 72.7% and 100%, while specificity ranges between 98.7% to 100%. Two immunochromatography using nasopharyngeal or throat swab for detection of COVID-19 specific antigen are also reviewed. Conclusions: There is much to determine regarding the value of serological testing in COVID-19 diagnosis and monitoring. More comprehensive evaluations of their performance are rapidly underway. The use of serology methods requires appropriate interpretations of the results and understanding the strengths and limitations of such tests. [ABSTRACT FROM AUTHOR]

Introduction: Infant hepatitis B vaccination was introduced into the Expanded Programme on Immunisation (EPI) in Malaysia in 1989. This study aimed to investigate seroprevalence of hepatitis B among UKM pre-clinical medical students, born between 1991 and 1995, and had their infant vaccination more than 20 years ago. Materials and Methods: A prospective, cross-sectional study involving 352 students, comprising 109 (31.0%) males and 243 (69.0%) females. Blood specimens were tested for anti-HBs, where levels of ≥10 mIU/mL was considered reactive and protective. Students with non-reactive levels were given a 20 μg HBV vaccine booster. Anti-HBs levels were tested six weeks after the first booster dose. Those with anti-HBs <10 mIU/mL were then given another two booster doses, at least one month apart. Anti-HBs levels were tested six weeks after the third dose. Results: Ninety-seven students (27.6%) had anti-HBs ranging from 10 to >1000 mIU/ mL while 255 (72.4%) had anti-HBs <10 mIU/mL. After one booster dose, 208 (59.1%) mounted anti-HBs ≥10 mIU/mL. Among the remaining 47 (13.3%), all except two students (0.6%) responded following completion of three vaccination doses. They were negative for HBsAg and anti-HBcore antibody, thus regarded as non-responders. Conclusions: Anti-HBs levels waned after 20 years post-vaccination, where more than 70% were within non-reactive levels. For healthcare workers, a booster dose followed by documenting anti-HBs levels of ≥10 mIU/mL may be recommended, to guide the management of post-exposure prophylaxis. Pre-booster anti-HBs testing may not be indicated. Serological surveillance is important in long-term assessment of HBV vaccination programs. No HBV carrier was detected. [ABSTRACT FROM AUTHOR]

Periodical surveillance on nosocomial pathogens is important for antimicrobial stewardship and infection control. The first methicillin-resistant Staphylococcus aureus (MRSA) molecular surveillance in Hospital Canselor Tuanku Muhriz (HCTM), a Malaysian teaching hospital, was performed in 2009. The dominant clone was identified as an MRSA carrying SCCmec type III-SCCmercury with ccrC and sea+cna toxin genes. In this study, we report the findings of the second HCTM MRSA surveillance carried out in 2017, after an interval of 8 years. Antibiotic susceptibility testing, SCCmec, toxin gene, and spa typing were performed for 222 MRSA strains isolated in 2017. Most strains were resistant to ciprofloxacin, erythromycin, clindamycin, cefoxitin, and penicillin (n = 126, 56.8%), belong to SCCmec type IV (n = 205, 92.3%), spa type t032 (n = 160, 72.1%) and harboured seg+sei toxin genes (n = 172, 77.5%). There was significant association between resistance of the aforementioned antibiotics with SCCmec type IV (p < 0.05), t032 (p < 0.001), and seg+sei carriage (p < 0.05). Results from this second MRSA surveillance revealed the occurrence of clonal replacement in HCTM during an interval of not more than 8 years. Investigation of the corresponding phenotype changes in this new dominant MRSA clone is currently on-going. [ABSTRACT FROM AUTHOR]

Bacterial culture and biochemical testing (CBtest) have been the cornerstone of pathogen identification in the diagnostic microbiology laboratory. With the advent of Sanger sequencing and later, next-generation sequencing, 16S rRNA next-generation sequencing (16SNGS) has been proposed to be a plausible platform for this purpose. Nevertheless, usage of the 16SNGS platform has both advantages and limitations. In addition, transition from the traditional methods of CBtest to 16SNGS requires procurement of costly equipment, timely and sustainable maintenance of these platforms, specific facility infrastructure and technical expertise. All these factors pose a challenge for middle-income countries, more so for countries in the lower middle-income range. In this review, we describe the basis for CBtest and 16SNGS, and discuss the limitations, challenges, advantages and future potential of using 16SNGS for bacterial pathogen identification in diagnostic microbiology laboratories of middle-income countries. [ABSTRACT FROM AUTHOR]

Draft genome sequences were obtained for four methicillin-resistant Staphylococcus aureus (MRSA) strains isolated from various wards of the Hospital Canselor Tuanku Muhriz (HCTM), Kuala Lumpur, Malaysia, in 2017. Using different bioinformatics tools, we annotated the draft genomes and identified multiple antimicrobial resistance genes.