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  1. Article ; Online: Probing the in-vivo reservoir of latent tuberculosis infection.

    Lalvani, Ajit / Fenn, Joe / Pillay, Timesh D

    The Lancet. Microbe

    2021  Volume 2, Issue 6, Page(s) e226–e227

    MeSH term(s) HIV Infections ; Humans ; Latent Tuberculosis/diagnosis ; Mycobacterium tuberculosis
    Language English
    Publishing date 2021-03-31
    Publishing country England
    Document type Journal Article ; Comment
    ISSN 2666-5247
    ISSN (online) 2666-5247
    DOI 10.1016/S2666-5247(21)00080-X
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  2. Article: Progress in interferon-gamma release assay development and applications: an unfolding story of translational research.

    Lalvani, Ajit / Whitworth, Hilary S

    Annals of translational medicine

    2019  Volume 7, Issue Suppl 3, Page(s) S128

    Language English
    Publishing date 2019-09-25
    Publishing country China
    Document type Editorial ; Comment
    ZDB-ID 2893931-1
    ISSN 2305-5847 ; 2305-5839
    ISSN (online) 2305-5847
    ISSN 2305-5839
    DOI 10.21037/atm.2019.05.76
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  3. Article ; Online: Understanding How BCG Vaccine Protects Against Mycobacterium tuberculosis Infection: Lessons From Household Contact Studies.

    Lalvani, Ajit / Seshadri, Chetan

    The Journal of infectious diseases

    2019  Volume 221, Issue 8, Page(s) 1229–1231

    MeSH term(s) BCG Vaccine ; Humans ; Immunity, Innate ; Mycobacterium bovis/immunology ; Mycobacterium tuberculosis/immunology ; Tuberculosis/prevention & control
    Chemical Substances BCG Vaccine
    Language English
    Publishing date 2019-07-10
    Publishing country United States
    Document type Editorial ; Comment
    ZDB-ID 3019-3
    ISSN 1537-6613 ; 0022-1899
    ISSN (online) 1537-6613
    ISSN 0022-1899
    DOI 10.1093/infdis/jiz261
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  4. Article ; Online: fastlin: an ultra-fast program for Mycobacterium tuberculosis complex lineage typing.

    Derelle, Romain / Lees, John / Phelan, Jody / Lalvani, Ajit / Arinaminpathy, Nimalan / Chindelevitch, Leonid

    Bioinformatics (Oxford, England)

    2023  Volume 39, Issue 11

    Abstract: Summary: Fastlin is a bioinformatics tool designed for rapid Mycobacterium tuberculosis complex (MTBC) lineage typing. It utilizes an ultra-fast alignment-free approach to detect previously identified barcode single nucleotide polymorphisms associated ... ...

    Abstract Summary: Fastlin is a bioinformatics tool designed for rapid Mycobacterium tuberculosis complex (MTBC) lineage typing. It utilizes an ultra-fast alignment-free approach to detect previously identified barcode single nucleotide polymorphisms associated with specific MTBC lineages. In a comprehensive benchmarking against existing tools, fastlin demonstrated high accuracy and significantly faster running times.
    Availability and implementation: fastlin is freely available at https://github.com/rderelle/fastlin and can easily be installed using Conda.
    MeSH term(s) Mycobacterium tuberculosis/genetics ; Computational Biology ; Polymorphism, Single Nucleotide ; Software
    Language English
    Publishing date 2023-11-09
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1422668-6
    ISSN 1367-4811 ; 1367-4803
    ISSN (online) 1367-4811
    ISSN 1367-4803
    DOI 10.1093/bioinformatics/btad648
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  5. Article ; Online: Patient outcomes following emergency admission to hospital for COVID-19 compared with influenza: retrospective cohort study.

    Woodcock, Thomas / Greenfield, Geva / Lalvani, Ajit / Majeed, Azeem / Aylin, Paul

    Thorax

    2022  Volume 78, Issue 7, Page(s) 706–712

    Abstract: Background: We examine differences in posthospitalisation outcomes, and health system resource use, for patients hospitalised with COVID-19 during the UK's first pandemic wave in 2020, and influenza during 2018 and 2019.: Methods: This retrospective ... ...

    Abstract Background: We examine differences in posthospitalisation outcomes, and health system resource use, for patients hospitalised with COVID-19 during the UK's first pandemic wave in 2020, and influenza during 2018 and 2019.
    Methods: This retrospective cohort study used routinely collected primary and secondary care data. Outcomes, measured for 90 days follow-up after discharge were length of stay in hospital, mortality, emergency readmission and primary care activity.
    Results: The study included 5132 patients admitted to hospital as an emergency, with COVID-19 and influenza cohorts comprising 3799 and 1333 patients respectively. Patients in the COVID-19 cohort were more likely to stay in hospital longer than 10 days (OR 3.91, 95% CI 3.14 to 4.65); and more likely to die in hospital (OR 11.85, 95% CI 8.58 to 16.86) and within 90 days of discharge (OR 7.92, 95% CI 6.20 to 10.25). For those who survived, rates of emergency readmission within 90 days were comparable between COVID-19 and influenza cohorts (OR 1.07, 95% CI 0.89 to 1.29), while primary care activity was greater among the COVID-19 cohort (incidence rate ratio 1.30, 95% CI 1.23 to 1.37).
    Conclusions: Patients admitted for COVID-19 were more likely to die, more likely to stay in hospital for over 10 days and interact more with primary care after discharge, than patients admitted for influenza. However, readmission rates were similar for both groups. These findings, while situated in the context of the first wave of COVID-19, with the associated pressures on the health system, can inform health service planning for subsequent waves of COVID-19, and show that patients with COVID-19 interact more with healthcare services as well as having poorer outcomes than those with influenza.
    MeSH term(s) Humans ; Influenza, Human/epidemiology ; Influenza, Human/therapy ; Retrospective Studies ; Length of Stay ; Patient Readmission ; COVID-19/epidemiology ; Patient Discharge ; Hospitals ; Hospital Mortality
    Language English
    Publishing date 2022-07-27
    Publishing country England
    Document type Journal Article
    ZDB-ID 204353-1
    ISSN 1468-3296 ; 0040-6376
    ISSN (online) 1468-3296
    ISSN 0040-6376
    DOI 10.1136/thoraxjnl-2021-217858
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  6. Article ; Online: Evaluating the clinical impact of routine whole genome sequencing in tuberculosis treatment decisions and the issue of isoniazid mono-resistance.

    Park, Mirae / Lalvani, Ajit / Satta, Giovanni / Kon, Onn Min

    BMC infectious diseases

    2022  Volume 22, Issue 1, Page(s) 349

    Abstract: Background: The UK has implemented routine use of whole genome sequencing (WGS) in TB diagnostics. The WHO recommends addition of a fluoroquinolone for isoniazid mono-resistance, so early detection may be of use. The aim of this study was to describe ... ...

    Abstract Background: The UK has implemented routine use of whole genome sequencing (WGS) in TB diagnostics. The WHO recommends addition of a fluoroquinolone for isoniazid mono-resistance, so early detection may be of use. The aim of this study was to describe the clinical utility and impact of WGS on treatment decisions for TB in a low incidence high resource clinical setting. The clinical turnaround time (TAT) for WGS was analysed in comparison to TB PCR using Xpert MTB/RIF (Cepheid, Sunnyvale, CA) results where available and subsequent phenotypic drug susceptibility testing (DST) when required.
    Methods: This was a retrospective analysis of TB cases from January 2018 to March 2019 in London. Susceptibility and TAT by WGS, phenotypic DST, TB PCR using Xpert MTB/RIF were correlated to drug changes in order to describe the utility of WGS on treatment decisions on isoniazid mono-resistance in a low incidence high resource setting.
    Results: 189 TB cases were identified; median age 44 years (IQR 28-60), m:f ratio 112:77, 7 with HIV and 6 with previous TB. 80/189 cases had a positive culture and WGS result. 50/80 were fully sensitive to 1st line treatment on WGS, and the rest required additional DST. 20/80 cases required drug changes; 12 were defined by WGS: 8 cases had isoniazid mono-resistance, 2 had MDR-TB, 1 had isoniazid and pyrazinamide resistance and 1 had ethambutol resistance. The median TAT for positive culture was 16 days (IQR 12.5-20.5); for WGS was 35 days (IQR 29.5-38.75) and for subsequent DST was 86 days (IQR 69.5-96.75), resulting in non-WHO regimens for a median of 50.5 days (IQR 28.0-65.0). 9/12 has TB PCRs (Xpert MTB/RIF), with a median TAT of 1 day.
    Conclusion: WGS clearly has a substantial role in our routine UK clinical settings with faster turnaround times in comparison to phenotypic DST. However, the majority of treatment changes defined by WGS were related to isoniazid resistance and given the 1 month TAT for WGS, it would be preferable to identify isoniazid resistance more quickly. Therefore if resources allow, diagnostic pathways should be optimised by parallel use of WGS and new molecular tests to rapidly identify isoniazid resistance in addition to rifampicin resistance and to minimise delays in starting WHO isoniazid resistance treatment.
    MeSH term(s) Adult ; Antitubercular Agents/pharmacology ; Antitubercular Agents/therapeutic use ; Humans ; Isoniazid/pharmacology ; Isoniazid/therapeutic use ; Microbial Sensitivity Tests ; Mycobacterium tuberculosis/genetics ; Retrospective Studies ; Rifampin/therapeutic use ; Tuberculosis, Multidrug-Resistant/diagnosis ; Tuberculosis, Multidrug-Resistant/drug therapy ; Tuberculosis, Multidrug-Resistant/epidemiology ; Whole Genome Sequencing
    Chemical Substances Antitubercular Agents ; Isoniazid (V83O1VOZ8L) ; Rifampin (VJT6J7R4TR)
    Language English
    Publishing date 2022-04-07
    Publishing country England
    Document type Journal Article
    ZDB-ID 2041550-3
    ISSN 1471-2334 ; 1471-2334
    ISSN (online) 1471-2334
    ISSN 1471-2334
    DOI 10.1186/s12879-022-07329-y
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  7. Article ; Online: Reply to Fenton

    Bruni, Teresa / Lalvani, Ajit / Richeldi, Luca

    American journal of respiratory and critical care medicine

    2020  Volume 202, Issue 8, Page(s) 1192–1193

    MeSH term(s) Betacoronavirus ; COVID-19 ; Coronavirus Infections/epidemiology ; Humans ; Pandemics ; Pneumonia, Viral ; SARS-CoV-2 ; Telemedicine
    Keywords covid19
    Language English
    Publishing date 2020-08-13
    Publishing country United States
    Document type Letter ; Comment
    ZDB-ID 1180953-x
    ISSN 1535-4970 ; 0003-0805 ; 1073-449X
    ISSN (online) 1535-4970
    ISSN 0003-0805 ; 1073-449X
    DOI 10.1164/rccm.202008-3063LE
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  8. Article ; Online: A conceptual framework to accelerate the clinical impact of evolving research into long COVID.

    Kondratiuk, Alexandra L / Pillay, Timesh D / Kon, Onn Min / Lalvani, Ajit

    The Lancet. Infectious diseases

    2021  Volume 21, Issue 6, Page(s) 756–757

    MeSH term(s) Biomedical Research/statistics & numerical data ; Biomedical Research/trends ; COVID-19/complications ; COVID-19/epidemiology ; COVID-19/physiopathology ; Forecasting ; Humans ; Long Term Adverse Effects/physiopathology ; SARS-CoV-2 ; United Kingdom/epidemiology
    Language English
    Publishing date 2021-04-22
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2061641-7
    ISSN 1474-4457 ; 1473-3099
    ISSN (online) 1474-4457
    ISSN 1473-3099
    DOI 10.1016/S1473-3099(21)00136-5
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  9. Article ; Online: Telemedicine-enabled Accelerated Discharge of Patients Hospitalized with COVID-19 to Isolation in Repurposed Hotel Rooms.

    Bruni, Teresa / Lalvani, Ajit / Richeldi, Luca

    American journal of respiratory and critical care medicine

    2020  Volume 202, Issue 4, Page(s) 508–510

    MeSH term(s) Betacoronavirus ; COVID-19 ; Coronavirus Infections/epidemiology ; Coronavirus Infections/therapy ; Humans ; Pandemics ; Patient Discharge/trends ; Pneumonia, Viral/epidemiology ; Pneumonia, Viral/therapy ; Public Facilities/statistics & numerical data ; SARS-CoV-2 ; Telemedicine/methods
    Keywords covid19
    Language English
    Publishing date 2020-06-16
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 1180953-x
    ISSN 1535-4970 ; 0003-0805 ; 1073-449X
    ISSN (online) 1535-4970
    ISSN 0003-0805 ; 1073-449X
    DOI 10.1164/rccm.202004-1238OE
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  10. Article ; Online: Removing the handle of the Broad Street pump: measures to slow the spread of covid-19 in primary care teams.

    de Lusignan, Simon / Carlyon, Tamsin / Lalvani, Ajit

    BMJ (Clinical research ed.)

    2020  Volume 369, Page(s) m1841

    MeSH term(s) Betacoronavirus ; COVID-19 ; Coronavirus Infections ; Humans ; Pandemics ; Pneumonia, Viral ; Primary Health Care ; SARS-CoV-2
    Keywords covid19
    Language English
    Publishing date 2020-05-12
    Publishing country England
    Document type Letter ; Comment
    ZDB-ID 1362901-3
    ISSN 1756-1833 ; 0959-8154 ; 0959-8146 ; 0959-8138 ; 0959-535X ; 1759-2151
    ISSN (online) 1756-1833
    ISSN 0959-8154 ; 0959-8146 ; 0959-8138 ; 0959-535X ; 1759-2151
    DOI 10.1136/bmj.m1841
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