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.

Methicillin-resistant Staphylococcus aureus (MRSA) is a successful pathogen that has achieved global dissemination, with high prevalence rates in Southeast Asia. A huge diversity of clones has been reported in this region, with MRSA ST239 being the most successful lineage. Nonetheless, description of MRSA genotypes circulating in the Southeast Asia region has, until now, remained poorly compiled. In this review, we aim to provide a better understanding of the molecular epidemiology and distribution of MRSA clones in 11 Southeast Asian countries: Singapore, Malaysia, Thailand, Vietnam, Cambodia, Lao People’s Democratic Republic (PDR), Myanmar, Philippines, Indonesia, Brunei Darussalam, and Timor-Leste. Notably, while archaic multidrug-resistant hospital-associated (HA) MRSAs, such as the ST239-III and ST241-III, were prominent in the region during earlier observations, these were then largely replaced by the more antibiotic-susceptible community-acquired (CA) MRSAs, such as ST22-IV and PVL-positive ST30-IV, in recent years after the turn of the century. Nonetheless, reports of livestock-associated (LA) MRSAs remain few in the region.

Background: Gargling had been reported to have significant roles in the prevention and treatment of respiratory tract infections. The purpose of this study was to assess the ability of regular gargling to eliminate SARS-CoV-2 in the oropharynx and nasopharynx. Methodology: This pilot, open labeled, randomized, parallel study compared the effect of 30 seconds, 3 times/day gargling using 1% povidone-iodine (PVP-I), essential oils and tap water on SARS-CoV-2 viral clearance among COVID-19 patients in a tertiary hospital in Kuala Lumpur. Progress was monitored by day 4,6 and 12 PCR (Ct value), gargling and symptoms diary as well as clinical observations. Results: Five confirmed Stage 1 COVID-19 patients were recruited for each arm. The age range was from 22 to 56 years old. The majority were males. Two respondents had co-morbidities, which were asthma and obesity. Viral clearance was achieved at day 6 in 100%, 80%, 20% and 0% for 1% PVP-I, essential oils, tap water and control group respectively. Analysis of 1% PVP-I group versus control group showed significant p-value for comparison of PCR results on Day 4, Day 6 and Day 12. Conclusions: This preliminary study showed that gargling with 1% PVP-I and essential oils show great potential to be part of the treatment and management of Stage 1 COVID-19. Larger studies are required to ascertain the benefit of gargling for different stages of COVID-19 patients. This study was registered in clinicaltrial.gov ( NCT04410159 ).

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.