Clinical and microbiological characteristics of non-tuberculous mycobacteria diseases in Singapore with a focus on pulmonary disease, 2012-2016.

BACKGROUND: Information on non-tuberculosis mycobacterial (NTM) diseases remains limited in Singapore and other Southeast Asian countries. This study aimed to delineate epidemiological and clinical features of pulmonary NTM disease. METHODS: A retrospective review was performed on all NTM isolates identified in Singapore General Hospital from 2012 to 2016 using the 2007 ATS/IDSA diagnostic criteria. RESULTS: A total of 2026 NTM isolates from 852 patients were identified. M. abscessus-chelonae group (1010, 49.9%) was the most commonly isolated and implicated in pulmonary NTM disease. Pulmonary cases (352, 76%) had the highest prevalence among patients diagnosed with NTM diseases (465/852, 54.6%) with no gender difference. Male patients were older (68.5 years, P = 0.014) with a higher incidence of chronic obstructive pulmonary disease (COPD) (23.6%, P < 0.001) and recurrent cough with phlegm production (51.6%, P = 0.035). In contrast, more female patients had bronchiectasis (50%, P < 0.001) and haemoptysis (37.6%, P = 0.042). Age and COPD were associated with multiple NTM species isolation per patient. CONCLUSIONS: M. abscessus-chelonae group was the commonest NTM species isolated in Singapore. Pulmonary NTM infection has the highest frequency with male and female patients associated with a higher incidence of COPD and bronchiectasis respectively. Age and COPD were associated with multiple NTM species isolation per patient.

Detection and characterisation of a sixth Candida auris clade in Singapore: a genomic and phenotypic study.

BACKGROUND: The emerging fungal pathogen Candida auris poses a serious threat to global public health due to its worldwide distribution, multidrug resistance, high transmissibility, propensity to cause outbreaks, and high mortality. We aimed to characterise three unusual C auris isolates detected in Singapore, and to determine whether they constitute a novel clade distinct from all previously known C auris clades (I-V). METHODS: In this genotypic and phenotypic study, we characterised three C auris clinical isolates, which were cultured from epidemiologically unlinked inpatients at a large tertiary hospital in Singapore. The index isolate was detected in April, 2023. We performed whole-genome sequencing (WGS) and obtained hybrid assemblies of these C auris isolates. The complete genomes were compared with representative genomes of all known C auris clades. To provide a global context, 3651 international WGS data from the National Center for Biotechnology Information (NCBI) database were included in a high-resolution single nucleotide polymorphism (SNP) analysis. Antifungal susceptibility testing was done and antifungal resistance genes, mating-type locus, and chromosomal rearrangements were characterised from the WGS data of the three investigated isolates. We further implemented Bayesian logistic regression models to classify isolates into known clades and simulate the automatic detection of isolates belonging to novel clades as their WGS data became available. FINDINGS: The three investigated isolates were separated by at least 37 000 SNPs (range 37 000-236 900) from all existing C auris clades. These isolates had opposite mating-type allele and different chromosomal rearrangements when compared with their closest clade IV relatives. The isolates were susceptible to all tested antifungals. Therefore, we propose that these isolates represent a new clade of C auris, clade VI. Furthermore, an independent WGS dataset from Bangladesh, accessed via the NCBI Sequence Read Archive, was found to belong to this new clade. As a proof-of-concept, our Bayesian logistic regression model was able to flag these outlier genomes as a potential new clade. INTERPRETATION: The discovery of a new C auris clade in Singapore and Bangladesh in the Indomalayan zone, showing a close relationship to clade IV members most commonly found in South America, highlights the unknown genetic diversity and origin of C auris, particularly in under-resourced regions. Active surveillance in clinical settings, along with effective sequencing strategies and downstream analysis, will be essential in the identification of novel strains, tracking of transmission, and containment of adverse clinical effects of C auris infections. FUNDING: Duke-NUS Academic Medical Center Nurturing Clinician Researcher Scheme, and the Genedant-GIS Innovation Program.

Clonal serotype 1c multidrug-resistant Shigella flexneri detected in multiple institutions by sentinel-site sequencing.

Shigella flexneri is a major diarrhoeal pathogen, and the emergence of multidrug-resistant S. flexneri is of public health concern. We report the detection of a clonal cluster of multidrug-resistant serotype 1c (7a) S. flexneri in Singapore in April 2022. Long-read whole-genome sequence analysis found five S. flexneri isolates to be clonal and harboring the extended-spectrum ß-lactamases bla CTX-M-15 and bla TEM-1. The isolates were phenotypically resistant to ceftriaxone and had intermediate susceptibility to ciprofloxacin. The S. flexneri clonal cluster was first detected in a tertiary hospital diagnostic laboratory (sentinel-site), to which the S. flexneri isolates were sent from other hospitals for routine serogrouping. Long-read whole-genome sequence analysis was performed in the sentinel-site near real-time in view of the unusually high number of S. flexneri isolates received within a short time frame. This study demonstrates that near real-time sentinel-site sequence-based surveillance of convenience samples can detect possible clonal outbreak clusters and may provide alerts useful for public health mitigations at the earliest possible opportunity.

Antimicrobial susceptibility profiles and species distribution of medically relevant Nocardia species: Results from a large tertiary laboratory in Australia.

OBJECTIVES: There are limited surveillance studies on the epidemiology and resistance rates ofNocardia spp. in Australia, particularly in the jurisdiction of New South Wales. This study aimed to investigate the species distribution and antimicrobial susceptibility of a large number of contemporary (2011-2016) clinical Nocardia spp. referred to a large tertiary hospital in Sydney, Australia. METHODS: A total of 270Nocardia spp. isolates identified to species level by dual-target gene sequencing were investigated. Antimicrobial susceptibility testing was performed using a Sensititre™ RAPMYCOI panel, with the minimum inhibitory concentration (MIC) range and geometric mean MIC obtained for each species and drug combination. Antimicrobial susceptibility profiles and species distribution were analysed. RESULTS: The respiratory system is the most affected site in nocardiosis. In this study, Nocardia nova complex was the most frequently isolated Nocardia spp. (n = 80; 29.6%), followed by Nocardia cyriacigeorgica (n = 61; 22.6%), Nocardia brasiliensis (n = 52; 19.3%) and Nocardia farcinica (n = 38; 14.1%). Of the tested isolates, 9.3% and 59.3% displayed resistance to trimethoprim/sulfamethoxazole (SXT) and imipenem, respectively. Nocardia farcinica accounted for the highest number of SXT-resistant isolates. High imipenem resistance in N. cyriacigeorgica is atypical to its drug pattern but has been reported elsewhere. All tested isolates remained susceptible to linezolid, with only 0.7% exhibiting resistance to amikacin. CONCLUSION: Linezolid and amikacin remain good empirical options for treatment of nocardiosis. Routine antimicrobial susceptibility testing ofNocardia is advisable with the detection of sulfonamide resistance and atypical antibiograms in this study.

An unusual case of Scedosporium apiospermum fungaemia in an immunocompetent patient with a left ventricular assist device and an implantable cardiac device.

Left ventricular assist device (LVAD)-related infections are a leading cause of morbidity and mortality, with fungal infections being particularly difficult to manage. We report a case of an immunocompetent 39-year-old male with an LVAD and an implantable cardiac device (ICD) who developed fatal Scedosporium apiospermum fungaemia. To the best of our knowledge, this is the first reported case of LVAD-related S. apiospermum fungaemia.

Metal 3D printing technology for functional integration of catalytic system.

Mechanical properties and geometries of printed products have been extensively studied in metal 3D printing. However, chemical properties and catalytic functions, introduced by metal 3D printing itself, are rarely mentioned. Here we show that metal 3D printing products themselves can simultaneously serve as chemical reactors and catalysts (denoted as self-catalytic reactor or SCR) for direct conversion of C1 molecules (including CO, CO2 and CH4) into high value-added chemicals. The Fe-SCR and Co-SCR successfully catalyze synthesis of liquid fuel from Fischer-Tropsch synthesis and CO2 hydrogenation; the Ni-SCR efficiently produces syngas (CO/H2) by CO2 reforming of CH4. Further, the Co-SCR geometrical studies indicate that metal 3D printing itself can establish multiple control functions to tune the catalytic product distribution. The present work provides a simple and low-cost manufacturing method to realize functional integration of catalyst and reactor, and will facilitate the developments of chemical synthesis and 3D printing technology.

Report of a Leprosy case in Singapore: an age-old disease not to be forgotten in developed countries with low-prevalence settings.

INTRODUCTION: Leprosy is rarely reported in developed countries with low-prevalence settings. Its diagnosis may be missed due to its low frequency in non-endemic regions, as well as its long incubation period. The report describes an imported leprosy case of a healthcare worker in Singapore. CASE PRESENTATION: A Filipino nursing personnel presented with a persistent non-tender erythematous plaque over his right upper back for many years despite topical treatment. He had the lesion before coming to Singapore but decided to seek medical consultation only after the lesion progressed with new erythematous papules developing over his face, trunk and upper limbs. Punch biopsies of skin lesions revealed fite-positive bacilli, which were identified to be Mycobacterium leprae by GenoType LepraeDR v1 assay (Hain LifeScience, Germany). No mutation was detected at rpoB (rifampicin), gyrA (ofloxacin) and folP1 (dapsone) gene targets. He was started on multi-drug therapy and responded to the treatment. The only prolonged close contact he had was his housemate who was screened and given a single dose of rifampicin as chemoprophylaxis. CONCLUSION: In non-endemic settings, awareness is crucial in diagnosing leprosy. The availability of molecular testing and multi-disciplinary management are essential in the confirmation and control of this disease of public health importance.

Epidemiology, risk factors, and outcomes of adult cutaneous non-tuberculous mycobacterial infection over a 10-year period in Singapore.

BACKGROUND: Unfamiliarity with the presentation, diagnostic process, and treatment of cutaneous non-tuberculous mycobacterium (NTM) infection leads to poorer outcomes. We describe our experience with managing cutaneous NTM infection in a regional hospital in Singapore from 2005 to 2014. METHODS: Adult patients with cutaneous NTM infections were identified through positive skin tissue cultures in this retrospective case series. We excluded patients younger than 21 years of age, patients whose care was transferred to another hospital, and patients with catheter-related infections. Data including demographic variables, as well as disease and treatment outcomes, were collected. We compared the data between patients with and without risk factors for immunosuppression to look for any significant difference. RESULTS: Fifty-eight cases were reviewed. Mycobacterium abscessus was the commonest organism isolated (51.7%), and abscesses or inflamed cysts were the most common presentation. Nineteen specimens (57.6%) showed suppurative or necrotizing granulomatous dermatitis on biopsy and acid-fast bacilli were identified in 2 of 21 histologic specimens (9.5%) stained for mycobacterium. Treatment included systemic antibiotics, surgery, or both. In total, 33 cases had clinical resolution while 25 cases were lost to follow-up. Our study was limited by the under-reporting of cases, bias due to data from a single center, and high dropout rates, thereby precluding a detailed assessment of treatment outcomes. CONCLUSIONS: A high index of suspicion is required to diagnose cutaneous NTM infection. Education of both patients and physicians will help to raise the level of awareness and reduce treatment delays.

Candida auris in Singapore: Genomic epidemiology, antifungal drug resistance, and identification using the updated 8.01 VITEKⓇ2 system.

OBJECTIVES: Candida auris (C. auris) has globally emerged as a multidrug-resistant pathogen. While it is known that there are four geographic clades, little is known about its genomic epidemiology in the Southeast Asian region. Laboratory identification can be challenging but the VITEKⓇ2 system (version 8.01 software) has recently updated its database to include C. auris. This study aimed to investigate the genomic epidemiology of C. auris isolated in Singapore and the susceptibility profiles in relation to ERG11 and FKS1 mutations. METHODS: Seven C. auris isolates from 2012-2018 were analysed using whole-genome sequencing, and antifungal susceptibility testing was performed. The performance of the updated VITEKⓇ2 system in identifying C. auris was also evaluated using these C. auris strains together with five closely related Candida species. RESULTS: Three clades were identified: South Asian (71.4%), South American (14.3%) and East Asian (14.3%). Local transmission was unlikely as there was no obviously identified cluster and most cases were likely to be imported at different time points following overseas hospitalisation exposure. Three isolates (42.9%) were multidrug-resistant. All South Asian strains were resistant to fluconazole and harboured ERG11 mutations, which were clade-specific. No FKS1 mutation was detected. The VITEKⓇ2 system was able to correctly identify most of the South Asian C. auris strains but misidentified the East Asian strain and gave a low discrimination result for the South American clade. CONCLUSION: This study showed that the introduction of C. auris into Singapore was possibly over multiple episodes and from different sources. The VITEKⓇ2 System version 8.01 software has limited abilities in identifying C .auris.

Evaluation of Enterococcus faecalis clinical isolates with 'penicillin-resistant, ampicillin-susceptible' phenotype as reported by Vitek-2 Compact system.

It has been recently reported that ampicillin susceptibility cannot accurately predict piperacillin and imipenem susceptibilities in penicillin-resistant, ampicillin-susceptible (Pen-R, Amp-S) Enterococcus faecalis isolates, contrary to the current Clinical and Laboratory Standards Institute (CLSI) recommendations. This has important therapeutic implications. Such isolates were noted after the use of Vitek-2 Compact system AST-GP67 susceptibility cards in a Singapore general hospital and they were increasing in numbers. The primary aim of this study was to evaluate these clinical isolates against microbroth dilution (MBD) technique and other commonly used antimicrobial susceptibility test (AST) methods for penicillin and ampicillin. The secondary aim was to evaluate whether ampicillin susceptibility could indeed be a reliable surrogate marker for piperacillin and imipenem susceptibilities in E. faecalis isolates that were confirmed Pen-R, Amp-S.From 2009 to 2013, a total of 49 isolates (5%) of 983 non-duplicate E. faecalis tested by Vitek-2 displayed the 'Pen-R, Amp-S' phenotype in a general hospital in Singapore. These were tested against MBD which was the reference method, Etest and disc diffusion for penicillin and ampicillin. Susceptibilities to piperacillin and imipenem were also tested using MBD. In addition, ß-lactamase production test was performed. Forty E. faecalis isolates with penicillin-susceptible, ampicillin-susceptible (Pen-S, Amp-S) phenotype were included for comparative purposes.The categorical agreement rate was 100% for all AST methods in ampicillin reporting for the 'Pen-R, Amp-S' group of E. faecalis isolates. However, a large number of isolates (46 isolates, 93.9%) fell into the major error category for penicillin testing by the Vitek-2 system. Penicillin minimum inhibitory concentrations (MICs) generated by the Vitek-2 system for the majority of these isolates were two doubling dilutions higher compared to those obtained by the reference test. The Etest method correlated well with the MBD method. Thirty-two isolates (65.3%) were in categorical agreement with the MBD method when tested by the disc diffusion method for penicillin. Only three E. faecalis isolates (6.1%) were confirmed to have the uncommon penicillin resistance phenotype, with two of them showing resistance to piperacillin and intermediate to imipenem. ß-lactamase production test was negative for all isolates. Among the Pen-S, Amp-S E. faecalis isolates, the categorical agreement was 100% for penicillin and ampicillin in all the tested methods.Enterococcus faecalis with 'Pen-R, Amp-S' phenotype reported by the Vitek-2 system using AST-GP67 susceptibility cards must be confirmed with a reference test, the Etest method being a good alternative. The Vitek-2 system generated higher penicillin MIC readings compared to MBD in this study. The actual prevalence of this uncommon penicillin resistance phenotype in E. faecalis was found to be low in this institution. More studies are required to confirm the reliability of ampicillin as a surrogate marker for piperacillin and imipenem susceptibilities in these isolates.

An Outbreak of Community Associated Methicillin Resistant Staphylococcus aureus Subtype USA300 at an International School in Singapore.

Community associated methicillin-resistant Staphylococcus aureus (CA-MRSA) subtype USA300 remains relatively well confined within North American shores. Between August and November 2010, a large international school in Singapore recorded 27 skin and soft tissue infections, 8 of which were confirmed USA 300. This study reports the outbreak investigation and the interventions instituted.