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Publications (39)
Klebsiella pneumoniae is a common opportunistic pathogen in humans, often associated with both virulence and antimicrobial resistance (AMR) phenotypes. K. pneumoniae have a highly plastic genome and can act as a vehicle for disseminating genetic information. Aiming to assess the impact of the human-animal-environment interface on AMR dissemination...
Background
Klebsiella pneumoniae is a common opportunistic pathogen known for having virulent and antimicrobial resistance (AMR) phenotypes. In addition to accumulating AMR and virulence genes, K. pneumoniae serves as a vehicle for broadly disseminating these elements into other species. Here, we applied genomic surveillance in a one-health framewo...
Respiratory infections are the major cause of death from infectious disease worldwide. Multiplexed diagnostic approaches are essential as many respiratory viruses have indistinguishable symptoms. We created self-assembled DNA nanobait that can simultaneously identify multiple short RNA targets. The nanobait approach relies on specific target select...
Salmonella enterica Typhi ( S . Typhi) and Paratyphi A ( S . Paratyphi A) are the causative agents of enteric fever, a systemic human disease with a burden of 300 000 cases per year in India. The majority of enteric fever cases are associated with S . Typhi, resulting in a paucity of data regarding S . Paratyphi A, specifically with respect to geno...
The Global Typhoid Genomics Consortium was established to bring together the typhoid research community to aggregate and analyse Salmonella enterica serovar Typhi (Typhi) genomic data to inform public health action. This analysis, which marks twenty-one years since the publication of the first Typhi genome, represents the largest Typhi genome seque...
Salmonella Paratyphi A, the primary etiology of paratyphoid, is estimated to cause 3.4 million infections annually, worldwide. With rising antimicrobial resistance and no licensed vaccines, genomic surveillance is key to track and monitor transmission, but there is currently no reliable genotyping framework for this pathogen. Here, we sequence 817...
Background
Hypervirulent variants of Klebsiella pneumoniae (HvKp) were typically associated with a broadly antimicrobial susceptible clone of sequence type (ST) 23 at the time of its emergence. Concerningly, HvKp is now also emerging within multidrug-resistant (MDR) clones, including ST11, ST15, and ST147. MDR-HvKp either carry both the virulence a...
Background:
Salmonella enterica serovar Typhi (S. Typhi), the causative agent of Typhoid fever, is transmitted faecal-orally. Some typhoid sufferers shed S. Typhi beyond convalescence, but culturing stool following every case is impractical. Here we hypothesised that serology might direct testing and identify shedding after a typhoid outbreak.
Meth...
Background: Typhoid and paratyphoid fever (enteric fever) is a common cause of non-specific febrile infection in adults and children presenting to health care facilities in low resource settings such as the South Asia. A 7-day course of a single oral antimicrobial such as ciprofloxacin, cefixime, or azithromycin is commonly used for its treatment....
Respiratory infections are the major cause of death from infectious disease worldwide. The clinical presentation of many respiratory viruses is indistinguishable; therefore, diagnostic approaches that can identify multiple pathogens are essential for patient management. We aimed to address this challenge with self-assembled DNA nanobait that can si...
Genomics, combined with population mobility data, used to map importation and spatial spread of SARS-CoV-2 in high-income countries has enabled the implementation of local control measures. Here, to track the spread of SARS-CoV-2 lineages in Bangladesh at the national level, we analysed outbreak trajectory and variant emergence using genomics, Face...
Background
The clinical response to ceftriaxone in patients with typhoid fever is significantly slower than with ofloxacin, despite infection with Salmonella enterica serovar Typhi (S. Typhi) isolates with similar susceptibilities (MIC 0.03–0.12 mg/L). The response to ofloxacin is slower if the isolate has intermediate susceptibility (MIC 0.25–1.0...
Background
New data streams are being used to track the pandemic of SARS-CoV-2, including genomic data which provides insights into patterns of importation and spatial spread of the virus, as well as population mobility data obtained from mobile phones. Here, we analyse the emergence and outbreak trajectory of SARS-CoV-2 in Bangladesh using these n...
Hypervirulent K. pneumoniae (HvKp) is typically associated with ST23 clone; however, hvKp is also emerging from clones ST11, ST15 and ST147, which are also multi-drug resistant (MDR). Here, we aimed to characterise nine novel MDR hvKp isolates harbouring mosaic plasmids simultaneously carrying antimicrobial resistance (AMR) and virulence genes. Nin...
Background: Diarrhoeal disease remains a common cause of illness and death in children <5 years of age. Faecal-oral infection by Shigella spp. causing bacillary dysentery is a leading cause of moderate-to-severe diarrhoea, particularly in low and middle-income countries. In Southeast Asia, S. sonnei predominates and infections are frequently resist...
We previously observed a substantial burden of cryptococcal meningitis in Vietnam atypically arising in individuals who are uninfected with human immunodeficiency virus (HIV). This disease was associated with a single genotype of Cryptococcus neoformans (sequence type [ST]5), which was significantly less common in HIV-infected individuals. Aiming t...
We previously observed a substantial burden of cryptococcal meningitis in Vietnam atypically arising in HIV-uninfected individuals. This disease was associated with a single genotype of Cryptococcus neoformans (Sequence Type (ST)5), which was significantly less common in HIV-infected individuals. Aiming to compare the phenotypic characteristics of...
The number of controlled human infection models (CHIMs) conducted worldwide has increased considerably in recent years, although few have been conducted in low and middle-income countries (LMICs), where infectious diseases have the greatest burden. Recently Oxford University Clinical Research Unit (OUCRU) in Ho Chi Minh City (HCMC) started developi...
Objectives:
We assessed the impact of MALDITOF-MS on the timeliness of optimal antimicrobial therapy through a parallel-arm randomised controlled trial in two hospitals in Vietnam.
Methods:
We recruited patients with a pathogen (bacterial or fungal) cultured from a normally sterile sample. Samples were randomly assigned (1:1) to identification b...
Investments in newer diagnostics and antimicrobial treatments are critical to improve management of enteric fever in South Asia, say Christopher Parry and colleagues. © Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to.
Background
Salmonella serovars Typhi (S. Typhi) and Paratyphi A (S. Paratyphi A), the causative agents of enteric fever, have been routinely isolated organisms from the blood of febrile patients in the Kathmandu Valley since the early 1990s. Susceptibility against commonly used antimicrobials for treating enteric fever has gradually changed through...
The annual distribution of blood culture results.
Annual counts (A) and percentages (B) of Salmonella-positive cultures, cultures positive for other bacteria, negative cultures and contamination in all blood cultures taken between 1992 and 2014.
(EPS)
Autocorrelation function of Salmonella cases.
Autocorrelation function (ACF) for monthly time series for Salmonella (Tyhi, Paratyphi and spp) (A), S. Typhi (B) and S. Paratyphi (C). One lag represents one year divided in 12 months.
(EPS)
The annual distribution of Salmonella-positive cultures.
Percentage of Salmonella-positive cultures among all positive cultures from 1992 to 2014. Symbol size is proportional to the number of positive cultures. A linear regression trend-line (blue) and confidence interval (shaded) are overlaid from 2002 to 2014 to illustrate the decline in the prop...
Microbiology laboratory report on Salmonella spp from April 1992 to December 2014 from Patan Hospital.
(CSV)
Shigella flexneri is the most common cause of bacterial dysentery in low-income countries. Despite this, S. flexneri remains largely unexplored from a genomic standpoint and is still described using a vocabulary based on serotyping reactions developed over half-a-century ago. Here we combine whole genome sequencing with geographical and temporal da...
This paper describes a rapid, high-throughput flow-through membrane immunoassay (FMIA) platform. A nitrocellulose membrane was spotted in an array format with multiple capture and control reagents for each sample detection area, and assay steps were carried out by sequential aspiration of sample and reagents through each detection area using a 96-w...
Combination antifungal therapy (amphotericin B deoxycholate and flucytosine) is the recommended treatment for cryptococcal meningitis but has not been shown to reduce mortality, as compared with amphotericin B alone. We performed a randomized, controlled trial to determine whether combining flucytosine or high-dose fluconazole with high-dose amphot...
DAPC cluster analysis.
(PDF)
Simulated and observed spatial genetic correlation.
(PDF)
Linkage disequilibrium.
(PDF)
Analysis of P. marneffei – bamboo rat species overlap.
(PDF)
Dispersal kernel effects on spatial genetic correlation.
(PDF)
Distribution of markers and within contig recombination.
(PDF)
Mating associated genes detected in P. marneffei.
(PDF)
Detection of putative recombinant isolates.
(PDF)
In vitro and in vivo co-inoculation.
(PDF)
Molecular genetic approaches typically detect recombination in microbes regardless of assumed asexuality. However, genetic data have shown the AIDS-associated pathogen Penicillium marneffei to have extensive spatial genetic structure at local and regional scales, and although there has been some genetic evidence that a sexual cycle is possible, thi...
