Nanopore Sequencing Discloses Compositional Quality of Commercial Probiotic Feed Supplements.

The market for the application of probiotics as a livestock health improvement supplement has increased in recent years. However, most of the available products are quality-controlled using low-resolution techniques and un-curated databases, resulting in misidentification and incorrect product labels. In this work, we deployed two workflows and compared results obtained by full-length 16S rRNA genes (16S) and metagenomic (Meta) data to investigate their reliability for the microbial composition of both liquid and solid forms of animal probiotic products using Oxford Nanopore long-read-only (without short-read).

Full-Length 16S rRNA Gene Amplicon and Metagenome Taxonomic Profiling of Beneficial Microbes in Poultry and Swine Probiotic Product.

Analysis of feed supplements can highlight microbial diversity and the prevalence of antimicrobial resistance (AMR), allowing users to monitor the safety of their animals. The 16S amplicon and metagenomic data generated by nanopore sequencing revealed that was the dominant prokaryote, and AMR genes were detected in the animal probiotic products.

Long-Read 16S rRNA Amplicon and Metagenomic Data of Swine Feed-Additive Probiotics Product.

Swine feed-additive probiotics products play a major role in swine performance and welfare by promoting gut health. Here, we present two types of data, including a full-length 16S rRNA amplicon sequence data and a long-read metagenomic sequence data obtained from the same commercial probiotic product.

Antimicrobial Resistance in Swine Fecal Specimens Across Different Farm Management Systems.

Antimicrobial use in agricultural animals is known to be associated with increases in antimicrobial resistance. Most prior studies have utilized culture and susceptibility testing of select organisms to document these phenomena. In this study we aimed to detect 66 antimicrobial resistance (AMR) genes for 10 antimicrobial agent classes directly in swine fecal samples using our previously developed antimicrobial resistance TaqMan array card (AMR-TAC) across three different swine farm management systems.

Clinical Characteristics and Treatment Outcomes for Patients Infected with Mycobacterium haemophilum.

Mycobacterium haemophilum is a nontuberculous mycobacterium that can infect immunocompromised patients. Because of special conditions required for its culture, this bacterium is rarely reported and there are scarce data for long-term outcomes. We conducted a retrospective study at Siriraj Hospital, Bangkok, Thailand, during January 2012-September 2017.

Genotypic antimicrobial resistance assays for use on E. coli isolates and stool specimens.

Antimicrobial resistance (AMR) is an emerging public health problem and methods for surveillance are needed. We designed 85 sequence-specific PCR reactions to detect 79 genes or mutations associated with resistance across 10 major antimicrobial classes, with a focus on E. coli.

Clinical outcome and laboratory markers for predicting disease activity in patients with disseminated opportunistic infections associated with anti-interferon-γ autoantibodies.

Background: Clinical courses and treatment outcomes are largely unknown in patients with adult-onset immunodeficiency associated with anti-interferon-gamma autoantibodies due to the fact that it was recently recognized and anti-IFN-γ auto-Abs detection is not widely available.

Methods And Findings: Non-HIV-infected adult patients with detectable anti-IFN-γ auto-Abs diagnosed and followed at Siriraj Hospital, Bangkok, Thailand during January 2013 to November 2016 were prospectively studied. At each follow-up visit, patients were classified as stable or active disease according to symptoms and signs, and all proven OIs were recorded.

Diagnosis of feline filariasis assisted by a novel semi-automated microfluidic device in combination with high resolution melting real-time PCR.

Background: The diagnosis of filariasis traditionally relies on the detection of circulating microfilariae (mf) using Giemsa-stained thick blood smears. This approach has several limitations. We developed a semi-automated microfluidic device to improve and simplify the detection of filarial nematodes.

d-Cycloserine Pharmacokinetics/Pharmacodynamics, Susceptibility, and Dosing Implications in Multidrug-resistant Tuberculosis: A Faustian Deal.

Background: d-cycloserine is used to treat multidrug-resistant tuberculosis. Its efficacy, contribution in combination therapy, and best clinical dose are unclear, also data on the d-cycloserine minimum inhibitory concentration (MIC) distributions is scant.

Methods: We performed a systematic search to identify pharmacokinetic and pharmacodynamic studies performed with d-cycloserine.

Molecular Evidence of Rickettsia in Human and Dog Blood in Bangkok.

Rickettsia spp. has been detected in dog fleas in Bangkok, Thailand. With the intent of collecting evidence to confirm the presence of rickettsioses in dogs and to assess the level of associated potential for accidental human infection, human buffy coat from patients with fever of unknown origin (n = 168), whole blood samples from dogs (n = 353), and 19 flea groups from our dog sample population were studied during the 2012 to 2014 study period.

Correction: Prevalence and extent of heteroresistance by next generation sequencing of multidrug-resistant tuberculosis.

[This corrects the article DOI: 10.1371/journal.pone.

Prevalence and extent of heteroresistance by next generation sequencing of multidrug-resistant tuberculosis.

Amplicon-based Next Generation Sequencing (NGS) is an emerging method for Mycobacterium tuberculosis drug susceptibility testing (DST) but has not been well described. We examined 158 clinical multidrug-resistant M. tuberculosis isolates via NGS of 11 resistance-associated gene regions covering 3519 nucleotides.

Performance of TaqMan array card to detect TB drug resistance on direct specimens.

Culture based phenotypic drug susceptibility testing (DST) for Mycobacterium tuberculosis (TB) is time consuming therefore rapid genotypic methods are increasingly being utilized. We previously developed and evaluated on TB isolates a rapid genotypic TaqMan array card (TAC) that detects mutations in several resistance-associated genes using dozens of primer pairs, probes, and high resolution melt analysis, with >96% accuracy versus Sanger sequencing. In this study we examined the performance of TAC on sputum, comparing results between 71 paired sputum and TB isolates of which 62 were MDR-TB.

Factors associated with acquired Anti IFN- γ autoantibody in patients with nontuberculous mycobacterial infection.

Background: The clinical syndrome of disseminated nontuberculous mycobacterial (NTM) infection in patients who were previously healthy is now well recognized to be associated with an acquired autoantibody to Interferon gamma (Anti IFN- γ autoantibody). However, the risk factors of this syndrome remain unknown.

Method: We performed an unmatched case control study among patients with NTM diseases who were diagnosed and treated at Siriraj Hospital, Bangkok, Thailand.

Epidemiology, Clinical Characteristics, Sites of Infection and Treatment Outcomes of Mucocutaneous Candidiasis Caused by Non-Albicans Species of Candida at a Dermatologic Clinic.

Background: Increasing numbers of mucocutaneous infection due to non-albicans species of Candida (N-CA) had been reported. Laboratory based studies showed multidrug resistance in N-CA population.

Objective: Demonstrate epidemiology, clinical characteristics, sites of infection, and treatment outcomes of mucocutaneous candidiasis caused by N-CA at a dermatologic clinic, including statistical evaluation data between N-CA and C.

PREVALENCE AND FACTORS ASSOCIATED WITH MULTIDRUG-RESISTANT TUBERCULOSIS AT SIRIRAJ HOSPITAL, BANGKOK, THAILAND.

The objective of this study was to determine the prevalence and factors associated with multidrug-resistant tuberculosis (MDR-TB) at Siriraj Hospital, Bangkok, Thailand. We conducted a retrospective unmatched case-control study of patients clinically diagnosed and microbiologically confirmed to have tuber- culosis (TB) at Siriraj Hospital from 2010 to 2012. Patient characteristics, clinical data, microbiological findings, outcomes and drug susceptibilities were recorded.

Comparison and development of pyrazinamide susceptibility testing methods for tuberculosis in Thailand.

Pyrazinamide (PZA) plays a critical role in shortening tuberculosis treatment duration and in treating multi-drug resistant tuberculosis (MDR-TB). The standard phenotypic MGIT PZA susceptibility testing method is imperfect because it is slow and has potential for false resistance. In this study, we evaluated 2 different phenotypic-based methods, quantitative real-time PCR (qPCR) phage assay, and MTT assay, as well as genotypic sequencing.

Rapid Differentiation of Filariae in Unstained and Stained Paraffin-Embedded Sections by a High-Resolution Melting Analysis PCR Assay.

Background: Apart from infection with human filariae, zoonotic filariasis also occurs worldwide, and the numbers of cases have been increasing steadily. Diagnosis of intact filariae in tissues or organs depends on histological identification. The morphology of parasites in tissue-embedded sections is poor and shows high levels of homoplasy.

HLA-DRB1 and HLA-DQB1 Are Associated with Adult-Onset Immunodeficiency with Acquired Anti-Interferon-Gamma Autoantibodies.

Recently a newly identified clinical syndrome of disseminated non-tuberculous mycobacterial diseases (with or without other opportunistic infections in adult patients who were previously healthy, has been recognized in association with an acquired autoantibody to interferon-gamma. This syndrome is emerging as an important cause of morbidity and mortality, especially among people of Asian descent. Trigger for the production of this autoantibody remains unknown, but genetic factors are strongly suspected to be involved.

Integrated microfluidic card with TaqMan probes and high-resolution melt analysis to detect tuberculosis drug resistance mutations across 10 genes.

Unlabelled: Genotypic methods for drug susceptibility testing of Mycobacterium tuberculosis are desirable to speed the diagnosis and proper therapy of tuberculosis (TB). However, the numbers of genes and polymorphisms implicated in resistance have proliferated, challenging diagnostic design. We developed a microfluidic TaqMan array card (TAC) that utilizes both sequence-specific probes and high-resolution melt analysis (HRM), providing two layers of detection of mutations.

Clinical features and outcomes of isoniazid mono-resistant pulmonary tuberculosis.

Objective: To determine the characteristics of pulmonary tuberculosis (TB) patients harbored organisms with isoniazid mono-resistant drug susceptibility pattern.

Material And Method: A retrospective review of medical records for all culture-proven adult pulmonary TB patients in Siriraj Hospital between July 2009 and July 2011 was conducted. Demographic data, clinical presentations, and radiological characteristics were recorded and compared between isoniazid mono-resistant and other-resistant groups.

Multi-probe real-time PCR identification of four common Candida species in blood culture broth.

We developed a single-tube real-time polymerase chain reaction (PCR) assay with multiple hybridization probes for detecting Candida albicans, C. tropicalis, C. glabrata, and C.

Use of mycobacteriophage quantitative PCR on MGIT broths for a rapid tuberculosis antibiogram.

Phenotypic culture-based drug susceptibility testing (DST) for Mycobacterium tuberculosis is a valuable tool to identify four to six active drugs for individualized multidrug-resistant (MDR) tuberculosis (TB) regimens. Current culture-based methods are slow, however; therefore, we evaluated a rapid mycobacteriophage-based quantitative PCR (qPCR) assay for use directly on M. tuberculosis-positive MGIT broths.

A high resolution melting real time PCR for mapping of filaria infection in domestic cats living in brugian filariosis-endemic areas.

We present here a real time PCR with high resolution melting (HRM) analysis for determining the prevalence and distribution of filarial species in domestic cats residing in brugian filariosis endemic areas of Narathiwat province, Thailand. Filarial species can be clearly distinguished in a single well using a single pair of primers. Blood samples were taken from a total of 2039 domestic cats living in endemic areas.

Pyrazinamide susceptibility testing of Mycobacterium tuberculosis by high resolution melt analysis.

Pyrazinamide (PZA) plays the important role in shortening the tuberculosis treatment period and in treating MDR-TB. Phenotypic PZA susceptibility methods are limited because they require specialized acidified media, which increases costs and complexity. In this study we developed a genotypic high resolution melt (HRM) analysis technique to detect pncA mutations associated with PZA resistant Mycobacterium tuberculosis.