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

Mycobacterium abscessus comprises three subspecies: M. abscessus subsp. abscessus, M. abscessus subsp. bolletii, and M. abscessus subsp. massiliense. 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. An investigation was performed on isolates cultured from an Asian, predominantly non-CF population to explore the phylogenomic relationships within our population and compare it to global M. abscessus isolates. Whole-genome-sequencing was performed on M. abscessus isolates between 2017 and 2019. Bioinformatic analysis was performed to determine multi-locus-sequence-type, to establish the phylogenetic relationships between isolates, and to identify virulence and resistance determinants in these isolates. A total of 210 isolates were included, of which 68.5 % (144/210) were respiratory samples. These isolates consisted of 140 (66.6 %) M. abscessus subsp. massiliense, 67 (31.9 %) M. abscessus subsp. abscessus, and three (1.4 %) M. abscessus subsp. bolletii. Dominant sequence-types in our population were similar to those of global CF isolates, but SNP differences in our population were comparatively wider despite the isolates being from the same geographical region. ESX (ESAT-6 secretory) cluster three appeared to occur most commonly in ST4 and ST6 M. abscessus subsp. massiliense, but other virulence factors did not demonstrate an association with isolate subspecies or sample source. We demonstrate that although similar predominant sequence-types are seen in our patient population, cross-transmission is absent. The risk of patient-to-patient transmission appears to be largely limited to the vulnerable CF population, indicating infection from environmental sources remains more common than human-to-human transmission. Resistance and virulence factors are largely consistent across the subspecies with the exception of clarithromycin susceptibility and ESX-3.

In vitro susceptibility of Mycobacterium abscessus complex and feasibility of standardizing treatment regimens.

OBJECTIVES: To determine the in vitro susceptibility of members of the Mycobacterium abscessus complex to routinely tested antibiotics and to an extended antibiotic panel. METHODS: Non-duplicate isolates for which susceptibility testing results were available were included in this study. Retrospective laboratory records were reviewed, including tigecycline susceptibility results, and testing was performed with additional drugs, including vancomycin, dalbavancin, telavancin, oritavancin, rifabutin, delafloxacin, eravacycline, clofazimine and bedaquiline using broth microdilution (Sensititre, Thermo Fisher). RESULTS: A total of 218 M. abscessus complex isolates were included for retrospective review, of which 151 were respiratory isolates. Of these 218 isolates, 211 were available for additional testing with the extended antibiotic panel. Of these, 146 were respiratory isolates. One isolate had a vancomycin MIC of 2 mg/L and MICs of all other isolates were >8 mg/L. All isolates had MICs of >8 mg/L for oritavancin, dalbavancin and telavancin. One isolate had a delafloxacin MIC of 4 mg/L and MICs of all other isolates were >8 mg/L. The MIC50/MIC90s of rifabutin, tigecycline, eravacycline, clofazimine and bedaquiline were 16/32, 0.5/1, 0.12/0.25, 0.12/0.25 and 0.06/0.12 mg/L, respectively. CONCLUSIONS: In vitro activity was demonstrated for clofazimine, bedaquiline and eravacycline, indicating potential for inclusion as standardized therapy for M. abscessus complex infections.

Comparative Clinical Evaluation of the Roche Elecsys and Abbott Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Serology Assays for Coronavirus Disease 2019 (COVID-19).

CONTEXT.­: The use of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) serologic tests detects antibodies in the host, contributing to the identification of individuals who have been exposed to coronavirus disease 2019 (COVID-19). OBJECTIVE.­: To critically evaluate 2 commercially available SARS-CoV-2 serology tests. DESIGN.­: A total of 333 unique, nonduplicated serum samples obtained from COVID-19 patients (n = 170) and negative controls (n = 163) obtained before December 2019 were used in the study. Samples were tested on the Roche E411 and Abbott Architect i4000SR platforms, and results were correlated to reverse transcription polymerase chain reaction (PCR) results and clinical symptoms. RESULTS.­: There was a strong level of agreement in the qualitative results between both assays, with a Cohen κ value of .840, P < .001. The specificity for both Roche and Abbott were excellent at 100%. Roche exhibited marginally better performance in the 21 days or more group with a sensitivity of 90.6% (95% CI, 75.8%-96.8%) versus an Abbott sensitivity of 84.4% (95% CI, 68.3%-93.1%), as well as in the 14- to 20-day group with a sensitivity of 85.7% (95% CI, 65.4%-95.0%) versus an Abbott sensitivity of 81.0% (95% CI, 60.0%-92.3%). Less than 14 days of symptoms groups exhibited poor sensitivity at less than 50% for both assays. The areas under curve (± standard error) for Roche (0.894 ± 0.025, P < .001) and Abbott (0.884 ± 0.026, P < .001) were very similar. Potential confounders for negative serologic results include antiretroviral medication use and pauci-symptomatic patients. CONCLUSIONS.­: Specificities for high-throughput Roche and Abbott immunoassays are excellent, but users need to be cautious to interpret serologic test results after 14 days of symptoms to avoid false negatives.

Practical laboratory considerations amidst the COVID-19 outbreak: early experience from Singapore.

The coronavirus disease 2019 (COVID-19) is a zoonotic viral infection originating from Wuhan, China in December 2019. The World Health Organization has classified this pandemic as a global health emergency due to its virulent nature of transmission, which may lead to acute respiratory distress syndrome. Singapore's health ministry has responded with enhanced surveillance of COVID-19 for all suspected pneumonia cases, further increasing the volume of testing via real-time reverse transcription PCR, as well as samples necessitating stringent infectious control. Collectively, this has implications on the total testing process, laboratory operations and its personnel due to biosafety concerns. Turnaround time for routine testing may also be affected. The aim of this article is to present our tertiary institution's early experience with managing this emerging crisis and offer practical considerations for the preanalytical, analytical and postanalytical phases of laboratory testing in this cohort of patients.

Head-to-head evaluation on diagnostic accuracies of six SARS-CoV-2 serological assays.

In this study, we evaluated and compared six SARS-CoV-2 serology kits including the Abbott SARS-CoV-2 IgG assay, Beckman Access SARS-CoV-2 IgG assay, OCD Vitros OCD Anti-SARS-CoV-2 Total antibody assay, Roche Elecsys Anti SARS-CoV-2 assay, Siemens SARS-CoV-2 Total assay, and cPass surrogate viral neutralising antibody assay. A total of 336 non-duplicated residual serum samples that were obtained from COVID-19 confirmed patients (n=173) on PCR and negative controls (n=163) obtained pre-December 2019 before the COVID-19 pandemic were used for the study. These were concurrently analysed on the different immunoassay platforms and correlated with clinical characteristics. Our results showed all assays had specificity ranging from 99.3% to 100.0%. Overall sensitivity across all days of symptoms, in descending order were OCD (49.1%, 95% CI 41.8-56.5%), cPass (44.8%, 95% CI 37.5-52.3%), Roche (41.6%, 95% CI 34.5-49.0%), Siemens (39.9%, 95% CI 32.9-47.3%), Abbott (39.8%, 95% CI 32.9-47.3%) and Beckman (39.6%, 95% CI 32.5-47.3%). Testing after at least 14 days from symptom onset is required to achieve AUCs greater than 0.80. OCD and cPass performed the best in terms of sensitivity for >21 days symptoms with 93.3% (95% CI, 73.5-99.2%) and 96.7% (95% CI, 82.8-99.9%), respectively. Both also shared the greatest concordance, kappa 0.963 (95% CI 0.885-1.0), p<0.001, and had the lowest false negative rates. Serology results should be interpreted with caution in certain cases. False negatives were observed in a small number of individuals with COVID-19 on immunosuppressive therapy, pauci-symptomatic or who received antiretroviral therapy. In conclusion, all assays exhibited excellent specificity and total antibody assays with spike protein configurations generally outperformed nucleocapsid configurations and IgG assays in terms of diagnostic sensitivity.

Responding to COVID-19: how an academic infectious diseases division mobilized in Singapore.

BACKGROUND: On January 30, COVID-19 was declared a Public Health Emergency of International Concern-a week after Singapore's first imported case and 5 days before local transmission. The National University Hospital (NUH) is Singapore's third largest hospital with 1200 beds, heavy clinical workloads, and major roles in research and teaching. MAIN BODY: With memories of SARS still vivid, there was an urgent requirement for the NUH Division of Infectious Diseases to adapt-undergoing major reorganization to face rapidly changing priorities while ensuring usual essential services and standards. Leveraging on individual strengths, our division mobilized to meet the demands of COVID-19 while engaging in high-level coordination, strategy, and advocacy. We present our experience of the 60 days since the nation's first case. During this time, our hospital has managed 3030 suspect cases, including 1300 inpatients, 37 confirmed cases, and overseen 4384 samples tested for COVID-19. CONCLUSION: Complex hospital adaptations were supported by an unprecedented number of workflows and coordination channels essential to safe and effective operations. The actions we describe, aligned with international recommendations and emerging evidence-based best practices, may serve as a framework for other divisions and institutions facing the spread of COVID-19 globally.

Selective reporting of fluoroquinolone susceptibility as a stewardship measure is of marginal benefit.

A retrospective time series analysis was conducted to compare inpatient fluoroquinolone use when susceptibilities were masked and after susceptibilities were unmasked. Although inappropriate culture-directed prescriptions increased, overall fluoroquinolone usage decreased. Culture-directed therapy was a small part of fluoroquinolone usage; hence, efforts should target empiric use to reduce overall consumption.

Distinguishing Zika and Dengue Viruses through Simple Clinical Assessment, Singapore.

Dengue virus and Zika virus coexist in tropical regions in Asia where healthcare resources are limited; differentiating the 2 viruses is challenging. We showed in a case-control discovery cohort, and replicated in a validation cohort, that the diagnostic indices of conjunctivitis, platelet count, and monocyte count reliably distinguished between these viruses.

Evaluation of the Luminex ARIES HSV 1&2 Assay and Comparison with the FTD Neuro 9 and In-house Real-Time PCR Assays for Detecting Herpes Simplex Viruses.

BACKGROUND: Human herpes simplex virus type 1 (HSV-1) and type 2 (HSV-2) are responsible for a plethora of human diseases, of which cutaneous and mucocutaneous infections are the most prevalent. In its most severe form, HSV infection can cause meningitis/encephalitis. We compared the Luminex ARIES HSV 1&2 assay (Luminex Corp., Austin, TX, USA), an automated sample-to-result molecular solution, to two non-automated HSV DNA assays. METHODS: A total of 116 artificial controls were used to determine the analytical performance of the ARIES assay. Controls were prepared by spiking universal transport medium (UTM) and cerebrospinal fluid (CSF) samples from patients who tested negative for HSV by an in-house HSV-1 and -2 DNA assay with reference materials (SeraCare Life Sciences, MA, USA; ZeptoMetrix Corp., MA, USA). Another 117 clinical samples were then used to compare the clinical performance of the ARIES assay with those of an in-house assay and the FTD Neuro 9 assay (Fast Track Diagnostics, Junglinster, Luxembourg). RESULTS: The analytical sensitivity (95% limit of detection) of the ARIES assay was 318 copies/mL (UTM samples) and 935 copies/mL (CSF samples) for HSV-1 strain 96 and 253 copies/mL (UTM samples) and 821 copies/mL (CSF samples) for HSV-2 strain 09. No cross-reactivity was observed in samples spiked with 14 non-HSV microorganisms. Compared with the reference result (agreement between the in-house and FTD Neuro 9 results), the ARIES assay had overall concordance rates of 98.2% (111/113) and 100% (113/113) for HSV-1 and HSV-2, respectively. CONCLUSIONS: The ARIES assay appears to be an excellent alternative for rapid detection and differentiation of HSV in skin and genital infections, meningitis, and encephalitis.

Performance evaluation of Cepheid Xpert Norovirus kit with a user-modified protocol.

The Cepheid Xpert® Norovirus kit automates sample processing, nucleic acid extraction, and real-time reverse transcription polymerase chain reactions (RT-PCRs) to detect norovirus genogroups I (GI) and II (GII). Eighty-five stool samples collected between February 2015 and May 2017 were used to compare the performance of a user-modified Xpert assay against a clinically validated laboratory-developed test (LDT). Of the 85 samples, 54 were previously archived in -80°C freezer. The remaining 31 were fresh samples tested concurrently with the LDT. The results of all samples tested using the Xpert kit and LDT were found to be concordant, including 12 GI- and 42 GII-positive samples, 1 GI and GII coinfection, and 30 negative samples. Comparison of the assays showed perfect concordance with a kappa coefficient score of 1.00 (95%CI from 1.00 to 1.00). Of the 30 negative stool samples tested, three samples were positive for rotavirus detected using an immunochromatographic assay, with no cross-reactivity shown in both LDT and Xpert assays. In-run sample processing control of the Xpert assay for all negative samples tested showed no/minor inhibition. Compared to the LDT, the Xpert assay produced similar or better Ct values for detection. It also showed better mitigation of PCR inhibition in stool sample testing.

Whole genome analysis of cephalosporin-resistant Escherichia coli from bloodstream infections in Australia, New Zealand and Singapore: high prevalence of CMY-2 producers and ST131 carrying blaCTX-M-15 and blaCTX-M-27.

Objectives: To characterize MDR Escherichia coli from bloodstream infections (BSIs) in Australia, New Zealand and Singapore. Methods: We collected third-generation cephalosporin-resistant (3GC-R) E. coli from blood cultures in patients enrolled in a randomized controlled trial from February 2014 to August 2015. WGS was used to characterize antibiotic resistance genes, MLST, plasmids and phylogenetic relationships. Antibiotic susceptibility was determined using disc diffusion and Etest. Results: A total of 70 3GC-R E. coli were included, of which the majority were ST131 (61.4%). BSI was most frequently from a urinary source (69.6%), community associated (62.9%) and in older patients (median age 71 years). The median Pitt score was 1 and ICU admission was infrequent (3.1%). ST131 possessed more acquired resistance genes than non-ST131 (P = 0.003). Clade C1/C2 ST131 predominated (30.2% and 53.5% of ST131, respectively) and these were all ciprofloxacin resistant. All clade A ST131 (n = 6) were community associated. The predominant ESBL types were blaCTX-M (80.0%) and were strongly associated with ST131 (95% carried blaCTX-M), with the majority blaCTX-M-15. Clade C1 was associated with blaCTX-M-14 and blaCTX-M-27, whereas blaCTX-M-15 predominated in clade C2. Plasmid-mediated AmpC genes (mainly blaCMY-2) were frequent (17.1%) but were more common in non-ST131 (P < 0.001) isolates from Singapore and Brisbane. Two strains carried both blaCMY-2 and blaCTX-M. The majority of plasmid replicon types were IncF. Conclusions: In a prospective collection of 3GC-R E. coli causing BSI, community-associated Clade C1/C2 ST131 predominate in association with blaCTX-M ESBLs, although a significant proportion of non-ST131 strains carried blaCMY-2.

Imported Asymptomatic Bancroftian Filariasis Discovered from a Plasmodium vivax Infected Patient: A Case Report from Singapore.

Human lymphatic filariasis is a vector-borne disease mainly caused by the parasitic nematode Wuchereria bancrofti and transmitted worldwide within the tropical and subtropical regions. Singapore was once endemic for bancroftian filariasis but recent reports are scarce and the disease is nearly forgotten. The case report presented here reports the incidental hospital laboratory finding of an asymptomatic microfilaremia in a relapsing Plasmodium vivax imported case during a malaria treatment follow-up appointment. The parasite was identified by microscopy as W. bancrofti and retrospective investigation of the sample collected during malaria onset was found to be also positive. Additional confirmation was obtained by DNA amplification, sequencing, and phylogenetic analysis of the mitochondrial cox1 gene that further related the parasite to W. bancrofti strains from the Indian region. Considering the large proportion of asymptomatic filariasis with microfilaremia, the high number of migrants and travellers arriving from the surrounding endemic countries, and the common presence of local competent mosquito vectors, Singapore remains vulnerable to the introduction, reemergence, and the spread of lymphatic filariasis. This report brings out from the shadow the potential risk of lymphatic filariasis in Singapore and could help to maintain awareness about this parasitic disease and its public health importance.

Preliminary investigations into developing all-D Omiganan for treating Mupirocin-resistant MRSA skin infections.

Staphylococcus aureus is the primary pathogen responsible for the majority of human skin infections, and meticillin-resistant S. aureus (MRSA) currently presents a major clinical concern. The overuse of Mupirocin, the first-line topical antibacterial drug over 30 years, has led to the emergence of Mupirocin-resistant MRSA, creating a clinical concern. The antimicrobial peptide Omiganan was touted to be a promising antibacterial drug candidate due to its rapid membrane-disrupting bactericidal mode of action, entering clinical trials in 2005 as a topical gel to prevent catheter site infections. However, drug development ceased in 2009 due to a lack of efficacy. We postulate this to be due to proteolytic degradation caused by endogenous human skin proteases. Herein, we tested our hypothesis using Omiganan and its all-D enantiomer in a human skin protease stability assay, followed by anti-MRSA activity assay against of a panel of clinical MRSA isolates, a bactericidal/static determination and a time-kill assay to gauge all-D Omiganan's potential for further topical antibacterial drug development.

Cutaneous Emboli of Invasive Basidiomycosis in a Child With Aplastic Anemia.

Invasive fungal diseases are a significant cause of mortality among the immunocompromised. This report documents an unusual case of disseminated fungal infection in a child with severe aplastic anemia. The offending fungus, a Basidiomycete, is rarely known to cause human infections. The patient presented acutely with multiple purpuric skin lesions in various parts of the body. The skin biopsy revealed septated fungal hyphae embolized within small dermal blood vessels. Molecular sequencing indicated Earliella scabrosa as the likely organism. The clinical course of the infection was inexorable despite systemic antifungal treatment, resulting in mortality. The literature of human infections due to Basidiomycetes, the usefulness of histopathology in the early diagnosis of the infection, and possible treatment options are discussed.

A Successful Vancomycin-Resistant Enterococci Reduction Bundle at a Singapore Hospital.

We report a reduction in the vancomycin-resistant enterococci (VRE) rate from a peak of 1.5 cases per 1,000 admissions (95% confidence interval [CI], 1.0-2.1) in August 2012 to 0.5 per 1,000 admissions (95% CI: 0.3-1.0) by January 2015, associated with a bundle of interventions. Infect. Control Hosp. Epidemiol. 2015;37(1):107-109.