Rapid, culture-free detection of carbapenem-resistant Klebsiella pneumoniae in a case of bloodstream infection using genomics.

Timely diagnosis and treatment of sepsis is a major challenge faced by critical care specialists around the world. The traditional blood culture methods have a significant turnaround time which delays targeted therapy leading to poor prognosis. In the current study, we highlight the clinical utility of a genomics solution for diagnosis and management of bloodstream infections by combining the real-time DNA sequencing of Oxford Nanopore Technology with an automated genomic data analysis software.

Whole-genome sequencing of clinical isolates from tuberculosis patients in India: real-world data indicates a high proportion of pre-XDR cases.

Unlabelled: Treatment decisions for tuberculosis (TB) in the absence of full drug-susceptibility data can result in amplifying resistance and may compromise treatment outcomes. Genomics of () from clinical samples enables detection of drug resistance to multiple drugs. We performed whole-genome sequencing (WGS) for 600 clinical samples from patients with tuberculosis to identify the drug-resistance profile and mutation spectrum.

An integrated method for targeted Oxford Nanopore sequencing and automated bioinformatics for the simultaneous detection of bacteria, fungi, and ARG.

Aims: The use of metagenomics for pathogen identification in clinical practice has been limited. Here we describe a workflow to encourage the clinical utility and potential of NGS for the screening of bacteria, fungi, and antimicrobial resistance genes (ARGs).

Methods And Results: The method includes target enrichment, long-read sequencing, and automated bioinformatics.

Genomic revolution: Transforming tuberculosis diagnosis and treatment with the use of Whole Genome Sequencing - A consensus statement.

Tuberculosis (TB) is a preventable, treatable, and curable disease. However, in 2020, 9∙9 million people were estimated to have developed tuberculosis, and 1.5 million people were estimated to have died from it.

Development of a PNA-DiSc based portable absorbance platform for the detection of pathogen nucleic acids.

We report the development of a portable absorption (PortAbs)-based pathogen nucleic acid detection system using peptide nucleic acid (PNA) and a cyanine dye, DiSc(5). When the dye binds to the PNA-DNA hybrid, it results in a characteristic ∼110 nm shift in the dye absorbance, which we measure using PortAbs. The protocol involves amplification of the target DNA, PNA-DNA hybridization and dye complexing steps followed by absorption measurement.

Whole-genome sequencing of presumptive MDR-TB isolates from a tertiary healthcare setting in Mumbai.

Objectives: Whole-genome sequencing (WGS) of Mycobacterium tuberculosis (MTB), proven to be a better alternative when compared with the combined sensitivity and specificity of all other modalities for diagnosis of tuberculosis (TB), aids epidemiological surveillance investigations by combining the current research with diagnostics. This study was conducted to identify and resolve operational challenges in performing WGS-based drug resistance testing (DRT) for MTB in a TB culture and drug susceptibility testing (DST) laboratory. Three critical, non-redundant steps for WGS-based DRT were tested: viz.

The coevolution of large and small terminases of bacteriophages is a result of purifying selection leading to phenotypic stabilization.

Genome packaging in many dsDNA phages requires a series of precisely coordinated actions of two phage-coded proteins, namely, large terminase (TerL) and small terminase (TerS) with DNA and ATP, and with each other. Despite the strict functional conservation, TerL and TerS homologs exhibit large sequence variations. We investigated the sequence variability across eight phage types and observed a coevolutionary framework wherein the genealogy of TerL homologs mirrored that of the corresponding TerS homologs.

Upregulation of miR-101 during Influenza A Virus Infection Abrogates Viral Life Cycle by Targeting mTOR Pathway.

Micro RNAs (miRNAs) are a class of small non-coding single-stranded RNA, which play an important role in modulating host-Influenza A virus (IAV) crosstalk. The interplay between influenza and miRNA interaction is defined by a plethora of complex mechanisms, which are not fully understood yet. Here, we demonstrate that in IAV infected A549 cells, a synchronous increase was observed in the expression of mTOR up to 24 hpi and significant downregulation at 48 hpi.

Giant viral genomic signatures in the previously reported gut metagenomes of pre-school children in rural India.

A recent study by Ghosh et al. compared the gut microbiomes of 20 preschool children from India and found an association between the gut microbiome and the nutritional status of the child. Here, we explored these metagenomes for the presence of genomic signatures of prokaryotic and eukaryotic viruses.

Genomic and metagenomic signatures of giant viruses are ubiquitous in water samples from sewage, inland lake, waste water treatment plant, and municipal water supply in Mumbai, India.

We report the detection of genomic signatures of giant viruses (GVs) in the metagenomes of three environment samples from Mumbai, India, namely, a pre-filter of a household water purifier, a sludge sample from wastewater treatment plant (WWTP), and a drying bed sample of the same WWTP. The de novo assembled contigs of each sample yielded 700 to 2000 maximum unique matches with the GV genomic database. In all three samples, the maximum number of reads aligned to Pandoraviridae, followed by Phycodnaviridae, Mimiviridae, Iridoviridae, and other Megaviruses.

Author Correction: Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis.

In the version of this article initially published, the URL listed for TubercuList was incorrect. The correct URL is https://mycobrowser.epfl.

Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis.

To characterize the genetic determinants of resistance to antituberculosis drugs, we performed a genome-wide association study (GWAS) of 6,465 Mycobacterium tuberculosis clinical isolates from more than 30 countries. A GWAS approach within a mixed-regression framework was followed by a phylogenetics-based test for independent mutations. In addition to mutations in established and recently described resistance-associated genes, novel mutations were discovered for resistance to cycloserine, ethionamide and para-aminosalicylic acid.

The number of genes encoding repeat domain-containing proteins positively correlates with genome size in amoebal giant viruses.

Curiously, in viruses, the virion volume appears to be predominantly driven by genome length rather than the number of proteins it encodes or geometric constraints. With their large genome and giant particle size, amoebal viruses (AVs) are ideally suited to study the relationship between genome and virion size and explore the role of genome plasticity in their evolutionary success. Different genomic regions of AVs exhibit distinct genealogies.

Deregulation of Genes Associated with Alternate Drug Resistance Mechanisms in Mycobacterium tuberculosis.

Alternate mechanisms of drug resistance involving intrinsic defense pathways play an important role in development of drug resistance. Deregulation of drug efflux, cellular metabolism, and DNA repair have been indicated to have effect on drug tolerance and persistence. Here we chose eight genes from these pathways to investigate their association with development of multidrug resistance (MDR).

Whole genome sequencing of clinical strains of Mycobacterium tuberculosis from Mumbai, India: A potential tool for determining drug-resistance and strain lineage.

Amplification of drug resistance in Mycobacterium tuberculosis (M.tb) and its transmission are significant barriers in controlling tuberculosis (TB) globally. Diagnostic inaccuracies and delays impede appropriate drug administration, which exacerbates primary and secondary drug resistance.

Complete genome sequence of Kurlavirus, a novel member of the family Marseilleviridae isolated in Mumbai, India.

The complete genome sequence of Kurlavirus, a new member of the family Marseilleviridae is reported. The Kurlavirus genome was found to encode a remarkable complement of genes homologous to those of other members of the family Marseilleviridae. Interestingly, the Kurlavirus genome contains 71 fewer ORFs than that of Marseillevirus, even though their genome sizes are comparable.

Same-Day Diagnostic and Surveillance Data for Tuberculosis via Whole-Genome Sequencing of Direct Respiratory Samples.

Routine full characterization of is culture based, taking many weeks. Whole-genome sequencing (WGS) can generate antibiotic susceptibility profiles to inform treatment, augmented with strain information for global surveillance; such data could be transformative if provided at or near the point of care. We demonstrate a low-cost method of DNA extraction directly from patient samples for WGS.

Isolation and complete genome sequencing of Mimivirus bombay, a Giant Virus in sewage of Mumbai, India.

We report the isolation and complete genome sequencing of a new Mimiviridae family member, infecting Acanthamoeba castellanii, from sewage in Mumbai, India. The isolated virus has a particle size of about 435 nm and a 1,182,200-bp genome. A phylogeny based on the DNA polymerase sequence placed the isolate as a new member of the Mimiviridae family lineage A and was named as Mimivirus bombay.

Complete Genome Sequence of a New Megavirus Family Member Isolated from an Inland Water Lake for the First Time in India.

We report here the isolation and complete genome sequencing of a large double-stranded DNA virus, Powai Lake megavirus, for the first time from India. The isolation of a large DNA virus with genome size >1 Mb from India further attests to the prevalence of Giant viruses in different environmental niches.

Kinetics of recA and recX induction in drug-susceptible and MDR clinical strains of Mycobacterium tuberculosis.

Objectives: To investigate and compare the expression of recA and recX, components of the SOS pathway, following rifampicin treatment in drug-susceptible and MDR clinical strains of Mycobacterium tuberculosis.

Methods: Strains (M. tuberculosis and Mycobacterium smegmatis) were subjected to rifampicin- and mitomycin-induced stress for 36 h followed by RNA extraction.

The use and significance of a research networking system.

Background: Universities have begun deploying public Internet systems that allow for easy search of their experts, expertise, and intellectual networks. Deployed first in biomedical schools but now being implemented more broadly, the initial motivator of these research networking systems was to enable easier identification of collaborators and enable the development of teams for research.

Objective: The intent of the study was to provide the first description of the usage of an institutional research "social networking" system or research networking system (RNS).

Open Research Networking Gadgets (ORNG).

In 2009, UCSF embarked on a journey to utilize industry-backed application standards to extend our research networking tool of choice, Profiles, into a software platform. The goal of this work was to bring extended data and functionality to our researchers' online environment and make it easier to share independently-developed software innovations with others. We used the OpenSocial standard to achieve these ends.

Global transcriptional profiling of longitudinal clinical isolates of Mycobacterium tuberculosis exhibiting rapid accumulation of drug resistance.

The identification of multidrug resistant (MDR), extensively and totally drug resistant Mycobacterium tuberculosis (Mtb), in vulnerable sites such as Mumbai, is a grave threat to the control of tuberculosis. The current study aimed at explaining the rapid expression of MDR in Directly Observed Treatment Short Course (DOTS) compliant patients, represents the first study comparing global transcriptional profiles of 3 pairs of clinical Mtb isolates, collected longitudinally at initiation and completion of DOTS. While the isolates were drug susceptible (DS) at onset and MDR at completion of DOTS, they exhibited identical DNA fingerprints at both points of collection.

MIRU-VNTR profiles of three major Mycobacterium tuberculosis spoligotypes found in western India.

We performed 12 loci MIRU-VNTR on 327 Mycobacterium tuberculosis (Mtb) isolates belonging to three major spoligotypes MANU1, CAS1_Delhi and Beijing from Mumbai, western India and two proximal rural locations. Complete allele and drug susceptibility data was available for 232 isolates. These included 143 MANU1 (ST100), 65 CAS1_Delhi (ST26) and 24 Beijing (ST1) isolates.