Whole-genome phylogenetic analysis of complex from clinical respiratory samples.

Unlabelled: The complex (MAC) is a common causative agent causing nontuberculous mycobacterial (NTM) pulmonary disease worldwide. Whole-genome sequencing was performed on a total of 203 retrospective MAC isolates from respiratory specimens. Phylogenomic analysis identified eight subspecies and species.

Deciphering epidemiology through culture-independent multiplex amplicon and metagenomic sequencing.

Unlabelled: Whooping cough (pertussis) has re-emerged despite high vaccine coverage in Australia and many other countries worldwide, partly attributable to genetic adaptation of the causative organism, to vaccines. Therefore, genomic surveillance has become essential to monitor circulating strains for these genetic changes. However, increasing uptake of PCR for the diagnosis of pertussis has affected the availability of cultured isolates for typing.

Emergence and genomic insights of non-pandemic O1 in Zhejiang, China.

It is well recognized that only O1 causes cholera pandemics. However, not all O1 strains cause pandemic-level disease. In this study, we analyzed non-pandemic O1 isolates from the 1960s to the 1990s from China and found that they fell into three lineages, one of which shared the most recent common ancestor with pandemic O1 strains.

Screening for extended-spectrum beta-lactamase in recreational beach waters in Singapore.

As part of Singapore's One Health antimicrobial resistance (AMR) management, this work was designed to understand the AMR burden in recreational beach waters using extended-spectrum beta-lactamase (ESBL-EC) as an indicator. A total of 90 water samples were collected from six different recreational beaches over three different time periods. Only 28/90 (31.

Genomic epidemiology and multilevel genome typing of .

causes pertussis (or whooping cough), a severe respiratory infectious disease in infants, although it can be prevented by whole cell and acellular vaccines. The recent pertussis resurgence in industrialised countries is partly attributed to pathogen adaptation to vaccines, while emergence of antimicrobial resistance, specifically to macrolides in China, has become a concern. Surveillance of current circulating and emerging strains is therefore vital to understand the risks they pose to public health.

Genomic epidemiology of human candidaemia isolates in a tertiary hospital.

Invasive candida infections are significant infections that may occur in vulnerable patients with high rates of mortality or morbidity. Drug-resistance rates also appear to be on the rise which further complicate treatment options and outcomes. The aims of this study were to describe the prevalence, molecular epidemiology, and genetic features of bloodstream isolates in a hospital setting.

Viable mpox virus in the environment of a patient room.

We conducted a prospective environmental surveillance study to investigate the air, surface, dust, and water contamination of a room occupied by a patient infected with mpox virus (MPXV) at various stages of the illness. The patient tested positive for MPXV from a throat swab and skin lesions. Environmental sampling was conducted in a negative pressure room with 12 unidirectional high efficiency particulate air filter (HEPA) air changes per hour and daily cleaning of the surfaces.

Field trial assessing the antimicrobial decontamination efficacy of gaseous ozone in a public bus setting.

The widespread COVID-19 pandemic caused by the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) necessitated measures aimed at preventing the spread of SARS-CoV-2. To mitigate the risk of fomite-mediated transmission, environmental cleaning and disinfection regimes have been widely implemented. However, conventional cleaning approaches such as surface wipe downs can be laborious and more efficient and effective disinfecting technologies are needed.

Genomic Epidemiology and Multilevel Genome Typing of Australian Salmonella enterica Serovar Enteritidis.

Salmonella enterica serovar Enteritidis is one of the leading causes of salmonellosis in Australia. In this study, a total of 568 Enteritidis isolates from two Australian states across two consecutive years were analyzed and compared to international strains, using the Enteritidis multilevel genome typing (MGT) database, which contained 40,390 publicly available genomes from 99 countries. The Australian Enteritidis isolates were divided into three phylogenetic clades (A, B, and C).

Genome Sequence of a Clinical Blood Isolate of Kodamaea ohmeri.

Kodamaea ohmeri is a rarely occurring yeast that can cause human infections. We describe the whole-genome sequence of a K. ohmeri clinical blood isolate.

MGTdb: a web service and database for studying the global and local genomic epidemiology of bacterial pathogens.

Multilevel genome typing (MGT) enables the genomic characterization of bacterial isolates and the relationships among them. The MGT system describes an isolate using multiple multilocus sequence typing (MLST) schemes, referred to as levels. Thus, for a new isolate, sequence types (STs) assigned at multiple precisely defined levels can be used to type isolates at multiple resolutions.

Epidemiological, Clinical, and Phylogenetic Characteristics of the First SARS-CoV-2 Transmission in a Nursing Home of Singapore: A Prospective Observational Investigation.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission has resulted in a significant burden among nursing home facilities globally. This prospective observational cohort study aims to define the potential sources of introduction and characteristics of SARS-CoV-2 transmission of the first nursing home facility in Singapore. An epidemiological serial point-prevalence survey of SARS-CoV-2 was conducted among 108 residents and 56 healthcare staff (HCS).

Molecular epidemiology and phylogenomic analysis of clinical isolates in an Asian population.

comprises three subspecies. These closely related strains are typically multi-drug-resistant and can cause difficult-to-treat infections. Dominant clusters of isolates with increased pathogenic potential have been demonstrated in pulmonary infections in the global cystic fibrosis (CF) population.

sp. nov., a new member of the complex, isolated from human clinical specimens.

and are the newest members of the complex. The number of clinical reports attributed to these new complex members is limited. In a retrospective clinical laboratory study conducted over a 4-month period investigating the prevalence of and , a total of 43 isolates were selected.

Factors influencing SARS-CoV-2 transmission and outbreak control measures in densely populated settings.

Starting with a handful of SARS-CoV-2 infections in dormitory residents in late March 2020, rapid transmission in their dense living environments ensued and by October 2020, more than 50,000 acute infections were identified across various dormitories in Singapore. The aim of the study is to identify combination of factors facilitating SARS-CoV-2 transmission and the impact of control measures in a dormitory through extensive epidemiological, serological and phylogenetic investigations, supported by simulation models. Our findings showed that asymptomatic cases and symptomatic cases who did not seek medical attention were major drivers of the outbreak.

Elucidation of global and national genomic epidemiology of serovar Enteritidis through multilevel genome typing.

serovar Enteritidis is a major cause of foodborne infections and outbreaks in humans. Effective surveillance and timely outbreak detection are essential for public health control. Multilevel genome typing (MGT) with multiple levels of resolution has been previously demonstrated as a promising tool for this purpose.