Safety of reducing antibiotic prescribing in primary care: a mixed-methods study

Background

The threat of antimicrobial resistance has led to intensified efforts to reduce antibiotic utilisation, but serious bacterial infections are increasing in frequency.

Objectives

To estimate the risks of serious bacterial infections in association with lower antibiotic prescribing and understand stakeholder views with respect to safe antibiotic reduction.

Design

Mixed-methods research was undertaken, including a qualitative interview study of patient and prescriber views that informed a cohort study and a decision-analytic model, using primary care electronic health records. These three work packages were used to design an application (app) for primary care prescribers.

Data sources

The Clinical Practice Research Datalink.

Setting

This took place in UK general practices.

Participants

A total of 706 general practices with 66.2 million person-years of follow-up from 2002 to 2017 and antibiotic utilisation evaluated for 671,830 registered patients. The qualitative study included 31 patients and 30 health-care professionals from primary care.

Main outcome measures

Sepsis and localised bacterial infections.

Results

Patients were concerned about antimicrobial resistance and the side effects, as well as the benefits, of antibiotic treatment. Prescribers viewed the onset of sepsis as the most concerning potential outcome of reduced antibiotic prescribing. More than 40% of antibiotic prescriptions in primary care had no coded indication recorded across both Vision® and EMIS® practice systems. Antibiotic prescribing rates varied widely between general practices, but there was no evidence that serious bacterial infections were less frequent at higher prescribing practices (adjusted rate ratio for 20% increase in prescribing 1.03, 95% confidence interval 1.00 to 1.06; p = 0.074). The probability of sepsis was lower if an antibiotic was prescribed at an infection consultation, and the number of antibiotic prescriptions required to prevent one episode of sepsis (i.e. the number needed to treat) decreased with age. For those aged 0–4 years, the number needed to treat was 29,773 (95% uncertainty interval 18,458 to 71,091) in boys and 27,014 (95% uncertainty interval 16,739 to 65,709) in girls. For those aged > 85 years, the number needed to treat was 262 (95% uncertainty interval 236 to 293) in men and 385 (95% uncertainty interval 352 to 421) in women. Frailty was associated with a greater risk of sepsis and a smaller number needed to treat. For severely frail patients aged 55–64 years, the number needed to treat was 247 (95% uncertainty interval 156 to 459) for men and 343 (95% uncertainty interval 234 to 556) for women. At all ages, the probability of sepsis was greatest for urinary tract infection, followed by skin infection and respiratory tract infection. The numbers needed to treat were generally smaller for the period 2014–17, when sepsis was diagnosed more frequently. The results are available using an app that we developed to provide primary care prescribers with stratified risk estimates during infection consultations.

Limitations

Analyses were based on non-randomised comparisons. Infection episodes and antibiotic prescribing are poorly documented in primary care.

Conclusions

Antibiotic treatment is generally associated with lower risks, but the most serious bacterial infections remain infrequent even without antibiotic treatment. This research identifies risk strata in which antibiotic prescribing can be more safely reduced.

Future work

The software developed from this research may be further developed and investigated for antimicrobial stewardship effect.

Funding

This project was funded by the National Institute for Health Research (NIHR) Health Services and Delivery Research programme and will be published in full in Health Services and Delivery Research; Vol. 9, No. 9. See the NIHR Journals Library website for further project information.

Applying Artificial Intelligence Methods for the Estimation of Disease Incidence: The Utility of Language Models

Background: AI-driven digital health tools often rely on estimates of disease incidence or prevalence, but obtaining these estimates is costly and time-consuming. We explored the use of machine learning models that leverage contextual information about diseases from unstructured text, to estimate disease incidence.

Methods: We used a class of machine learning models, called language models, to extract contextual information relating to disease incidence. We evaluated three different language models: BioBERT, Global Vectors for Word Representation (GloVe), and the Universal Sentence Encoder (USE), as well as an approach which uses all jointly. The output of these models is a mathematical representation of the underlying data, known as “embeddings.” We used these to train neural network models to predict disease incidence. The neural networks were trained and validated using data from the Global Burden of Disease study, and tested using independent data sourced from the epidemiological literature.

Findings: A variety of language models can be used to encode contextual information of diseases. We found that, on average, BioBERT embeddings were the best for disease names across multiple tasks. In particular, BioBERT was the best performing model when predicting specific disease-country pairs, whilst a fusion model combining BioBERT, GloVe, and USE performed best on average when predicting disease incidence in unseen countries. We also found that GloVe embeddings performed better than BioBERT embeddings when applied to country names. However, we also noticed that the models were limited in view of predicting previously unseen diseases. Further limitations were also observed with substantial variations across age groups and notably lower performance for diseases that are highly dependent on location and climate.

Interpretation: We demonstrate that context-aware machine learning models can be used for estimating disease incidence. This method is quicker to implement than traditional epidemiological approaches. We therefore suggest it complements existing modeling efforts, where data is required more rapidly or at larger scale. This may particularly benefit AI-driven digital health products where the data will undergo further processing and a validated approximation of the disease incidence is adequate.

The impact of HIV infection on tuberculosis transmission in a country with low tuberculosis incidence: a national retrospective study using molecular epidemiology

BACKGROUND

HIV is known to increase the likelihood of reactivation of latent tuberculosis to active TB disease; however, its impact on tuberculosis infectiousness and consequent transmission is unclear, particularly in low-incidence settings.

METHODS

National surveillance data from England, Wales and Northern Ireland on tuberculosis cases in adults from 2010 to 2014, strain typed using 24-locus mycobacterial-interspersed-repetitive-units-variable-number-tandem-repeats was used retrospectively to identify clusters of tuberculosis cases, subdivided into 'first' and 'subsequent' cases. Firstly, we used zero-inflated Poisson regression models to examine the association between HIV status and the number of subsequent clustered cases (a surrogate for tuberculosis infectiousness) in a strain type cluster. Secondly, we used logistic regression to examine the association between HIV status and the likelihood of being a subsequent case in a cluster (a surrogate for recent acquisition of tuberculosis infection) compared to the first case or a non-clustered case (a surrogate for reactivation of latent infection).

RESULTS

We included 18,864 strain-typed cases, 2238 were the first cases of clusters and 8471 were subsequent cases. Seven hundred and fifty-nine (4%) were HIV-positive. Outcome 1: HIV-positive pulmonary tuberculosis cases who were the first in a cluster had fewer subsequent cases associated with them (mean 0.6, multivariable incidence rate ratio [IRR] 0.75 [0.65-0.86]) than those HIV-negative (mean 1.1). Extra-pulmonary tuberculosis (EPTB) cases with HIV were less likely to be the first case in a cluster compared to HIV-negative EPTB cases. EPTB cases who were the first case had a higher mean number of subsequent cases (mean 2.5, IRR (3.62 [3.12-4.19]) than those HIV-negative (mean 0.6). Outcome 2: tuberculosis cases with HIV co-infection were less likely to be a subsequent case in a cluster (odds ratio 0.82 [0.69-0.98]), compared to being the first or a non-clustered case.

CONCLUSIONS

Outcome 1: pulmonary tuberculosis-HIV patients were less infectious than those without HIV. EPTB patients with HIV who were the first case in a cluster had a higher number of subsequent cases and thus may be markers of other undetected cases, discoverable by contact investigations. Outcome 2: tuberculosis in HIV-positive individuals was more likely due to reactivation than recent infection, compared to those who were HIV-negative.

Peritonsillar Abscess and Antibiotic Prescribing for Respiratory Infection in Primary Care: A Population-Based Cohort Study and Decision-Analytic Model

PURPOSE

To quantify the risk of peritonsillar abscess (PTA) following consultation for respiratory tract infection (RTI) in primary care.

METHOD

A cohort study was conducted in the UK Clinical Practice Research Datalink including 718 general practices with 65,681,293 patient years of follow-up and 11,007 patients with a first episode of PTA. From a decision tree, Bayes theorem was employed to estimate both the probability of PTA following an RTI consultation if antibiotics were prescribed or not, and the number of patients needed to be treated with antibiotics to prevent 1 PTA.

RESULTS

There were 11,007 patients with PTA with age-standardized incidence of new episodes of PTA of 17.2 per 100,000 patient years for men and 16.1 for women; 6,996 (64%) consulted their practitioner in the 30 days preceding PTA diagnosis, including 4,243 (39%) consulting for RTI. The probability of PTA following an RTI consultation was greatest in men aged 15 to 24 years with 1 PTA in 565 (95% uncertainty interval 527 to 605) RTI consultations without antibiotics prescribed but 1 in 1,139 consultations (1,044 to 1,242) if antibiotics were prescribed. One PTA might be avoided for every 1,121 (975 to 1,310) additional antibiotic prescriptions for men aged 15 to 24 years and 926 (814 to 1,063) for men aged 25 to 34 years. The risk of PTA following RTI consultation was smaller and the number needed to treat higher at other ages and risks were lower in women than men.

CONCLUSIONS

The risk of PTA may be lower if antibiotics are prescribed for RTI but even in young men nearly 1,000 antibiotic prescriptions may be required to prevent 1 PTA case. We caution that lack of randomization and data standardization may bias estimates.

Probability of sepsis after infection consultations in primary care in the United Kingdom in 2002-2017: Population-based cohort study and decision analytic model

BACKGROUND

Efforts to reduce unnecessary antibiotic prescribing have coincided with increasing awareness of sepsis. We aimed to estimate the probability of sepsis following infection consultations in primary care when antibiotics were or were not prescribed.

METHODS AND FINDINGS

We conducted a cohort study including all registered patients at 706 general practices in the United Kingdom Clinical Practice Research Datalink, with 66.2 million person-years of follow-up from 2002 to 2017. There were 35,244 first episodes of sepsis (17,886, 51%, female; median age 71 years, interquartile range 57-82 years). Consultations for respiratory tract infection (RTI), skin or urinary tract infection (UTI), and antibiotic prescriptions were exposures. A Bayesian decision tree was used to estimate the probability (95% uncertainty intervals [UIs]) of sepsis following an infection consultation. Age, gender, and frailty were evaluated as association modifiers. The probability of sepsis was lower if an antibiotic was prescribed, but the number of antibiotic prescriptions required to prevent one episode of sepsis (number needed to treat [NNT]) decreased with age. At 0-4 years old, the NNT was 29,773 (95% UI 18,458-71,091) in boys and 27,014 (16,739-65,709) in girls; over 85 years old, NNT was 262 (236-293) in men and 385 (352-421) in women. Frailty was associated with greater risk of sepsis and lower NNT. For severely frail patients aged 55-64 years, the NNT was 247 (156-459) in men and 343 (234-556) in women. At all ages, the probability of sepsis was greatest for UTI, followed by skin infection, followed by RTI. At 65-74 years, the NNT following RTI was 1,257 (1,112-1,434) in men and 2,278 (1,966-2,686) in women; the NNT following skin infection was 503 (398-646) in men and 784 (602-1,051) in women; following UTI, the NNT was 121 (102-145) in men and 284 (241-342) in women. NNT values were generally smaller for the period from 2014 to 2017, when sepsis was diagnosed more frequently. Lack of random allocation to antibiotic therapy might have biased estimates; patients may sometimes experience sepsis or receive antibiotic prescriptions without these being recorded in primary care; recording of sepsis has increased over the study period.

CONCLUSIONS

These stratified estimates of risk help to identify groups in which antibiotic prescribing may be more safely reduced. Risks of sepsis and benefits of antibiotics are more substantial among older adults, persons with more advanced frailty, or following UTIs.

Risk factors for Epstein Barr virus-associated cancers: a systematic review, critical appraisal, and mapping of the epidemiological evidence

BACKGROUND

Epstein Barr Virus (EBV) infects 90%-95% of all adults globally and causes ~ 1% of all cancers. Differing proportions of Burkitt's lymphoma (BL), gastric carcinoma (GC), Hodgkin's lymphoma (HL) and nasopharyngeal carcinoma (NPC) are associated with EBV. We sought to systematically review the global epidemiological evidence for risk factors that (in addition to EBV) contribute to the development of the EBV-associated forms of these cancers, assess the quality of the evidence, and compare and contrast the cancers.

METHODS

MEDLINE, Embase and Web of Science were searched for studies of risk factors for EBV-associated BL, GC, HL and NPC without language or temporal restrictions. Studies were excluded if there was no cancer-free comparator group or where analyses of risk factors were inadequately documented. After screening and reference list searching, data were extracted into standardised spreadsheets and quality assessed. Due to heterogeneity, a narrative synthesis was undertaken.

RESULTS

9916 hits were retrieved. 271 papers were retained: two BL, 24 HL, one GC and 244 NPC. The majority of studies were from China, North America and Western Europe. Risk factors were categorised as dietary, environmental/non-dietary, human genetic, and infection and clinical. Anti-EBV antibody load was associated with EBV-associated GC and BL. Although the evidence could be inconsistent, HLA-A alleles, smoking, infectious mononucleosis and potentially other infections were risk factors for EBV-associated HL. Rancid dairy products; anti-EBV antibody and EBV DNA load; history of chronic ear, nose and/or throat conditions; herbal medicine use; family history; and human genetics were risk factors for NPC. Fresh fruit and vegetable and tea consumption may be protective against NPC.

CONCLUSIONS

Many epidemiological studies of risk factors in addition to EBV for the EBV-associated forms of BL, GC, HL and NPC have been undertaken, but there is a dearth of evidence for GC and BL. Available evidence is of variable quality. The aetiology of EBV-associated cancers likely results from a complex intersection of genetic, clinical, environmental and dietary factors, which is difficult to assess with observational studies. Large, carefully designed, studies need to be strategically undertaken to harmonise and clarify the evidence.

REGISTRATION

PROSPERO CRD42017059806.

Predictors of Epstein-Barr virus serostatus and implications for vaccine policy: A systematic review of the literature

BACKGROUND

Epstein-Barr virus (EBV) is an important human pathogen; it infects >90% people globally and is linked to infectious mononucleosis and several types of cancer. Vaccines against EBV are in development. In this study we present the first systematic review of the literature on risk factors for EBV infection, and discuss how they differ between settings, in order to improve our understanding of EBV epidemiology and aid the design of effective vaccination strategies.

METHODS

MEDLINE, Embase, and Web of Science were searched on 6th March 2017 for observational studies of risk factors for EBV infection. Studies were excluded if they were published before 2008 to ensure relevance to the modern day, given the importance of influencing future vaccination policies. There were no language restrictions. After title, abstract and full text screening, followed by checking the reference lists of included studies to identify further studies, data were extracted into standardised spreadsheets and quality assessed. A narrative synthesis was undertaken.

RESULTS

Seventy-seven papers met our inclusion criteria, including data from 31 countries. There was consistent evidence that EBV seroprevalence was associated with age, increasing throughout childhood and adolescence and remaining constant thereafter. EBV was generally acquired at younger ages in Asia than Europe/North America. There was also compelling evidence for an association between cytomegalovirus infection and EBV. Additional factors associated with EBV seroprevalence, albeit with less consistent evidence, included ethnicity, socioeconomic status, other chronic viral infections, and genetic variants of HLA and immune response genes.

CONCLUSIONS

Our study is the first systematic review to draw together the global literature on the risk factors for EBV infection and includes an evaluation of the quality of the published evidence. Across the literature, the factors examined are diverse. In Asia, early vaccination of infants would be required to prevent EBV infection. In contrast, in Western countries a vaccine could be deployed later, particularly if it has only a short duration of protection and the intention was to protect against infectious mononucleosis. There is a lack of high-quality data on the prevalence and age of EBV infection outside of Europe, North America and South-East Asia, which are essential for informing effective vaccination policies in these settings.

Serious bacterial infections and antibiotic prescribing in primary care: cohort study using electronic health records in the UK

OBJECTIVE

This study evaluated whether serious bacterial infections are more frequent at family practices with lower antibiotic prescribing rates.

DESIGN

Cohort study.

SETTING

706 UK family practices in the Clinical Practice Research Datalink from 2002 to 2017.

PARTICIPANTS

10.1 million registered patients with 69.3 million patient-years' follow-up.

EXPOSURES

All antibiotic prescriptions, subgroups of acute and repeat antibiotic prescriptions, and proportion of antibiotic prescriptions associated with specific-coded indications.

MAIN OUTCOME MEASURES

First episodes of serious bacterial infections. Poisson models were fitted adjusting for age group, gender, comorbidity, deprivation, region and calendar year, with random intercepts representing family practice-specific estimates.

RESULTS

The age-standardised antibiotic prescribing rate per 1000 patient-years increased from 2002 (male 423; female 621) to 2012 (male 530; female 842) before declining to 2017 (male 449; female 753). The median family practice had an antibiotic prescribing rate of 648 per 1000 patient-years with 95% range for different practices of 430-1038 antibiotic prescriptions per 1000 patient-years. Specific coded indications were recorded for 58% of antibiotic prescriptions at the median family practice, the 95% range at different family practices was from 10% to 75%. There were 139 759 first episodes of serious bacterial infection. After adjusting for covariates and the proportion of coded consultations, there was no evidence that serious bacterial infections were lower at family practices with higher total antibiotic prescribing. The adjusted rate ratio for 20% higher total antibiotic prescribing was 1.03, (95% CI 1.00 to 1.06, p=0.074).

CONCLUSIONS

We did not find population-level evidence that family practices with lower total antibiotic prescribing might have more frequent occurrence of serious bacterial infections overall. Improving the recording of infection episodes has potential to inform better antimicrobial stewardship in primary care.

Predictors of Epstein-Barr virus serostatus in young people in England

BACKGROUND

Epstein-Barr virus (EBV) is an important human pathogen which causes lifelong infection of > 90% people globally and is linked to infectious mononucleosis (arising from infection in the later teenage years) and several types of cancer. Vaccines against EBV are in development. In order to determine the most cost-effective public health strategy for vaccine deployment, setting-specific data on the age at EBV acquisition and risk factors for early infection are required. Such data are also important to inform mathematical models of EBV transmission that can determine the required target product profile of vaccine characteristics. We thus aimed to examine risk factors for EBV infection in young people in England, in order to improve our understanding of EBV epidemiology and guide future vaccination strategies.

METHODS

The Health Survey for England (HSE) is an annual, cross-sectional representative survey of households in England during which data are collected via questionnaires and blood samples. We randomly selected individuals who participated in the HSE 2002, aiming for 25 participants of each sex in each single year age group from 11 to 24 years. Stored samples were tested for EBV and cytomegalovirus (CMV) antibodies. We undertook descriptive and regression analyses of EBV seroprevalence and risk factors for infection.

RESULTS

Demographic data and serostatus were available for 732 individuals. EBV seroprevalence was strongly associated with age, increasing from 60.4% in 11-14 year olds throughout adolescence (68.6% in 15-18 year olds) and stabilising by early adulthood (93.0% in those aged 22-24 years). In univariable and multivariable logistic regression models, ethnicity was associated with serostatus (adjusted odds ratio for seropositivity among individuals of other ethnicity versus white individuals 2.33 [95% confidence interval 1.13-4.78]). Smoking was less strongly associated with EBV seropositivity.

CONCLUSIONS

By the age of 11 years, EBV infection is present in over half the population, although age is not the only factor associated with serostatus. Knowledge of the distribution of infection in the UK population is critical for determining future vaccination policies, e.g. comparing general versus selectively targeted vaccination strategies.

Tuberculosis infection and disease in people living with HIV in countries with low tuberculosis incidence

In countries with low tuberculosis (TB) incidence, TB is concentrated in vulnerable populations, including people living with the human immunodeficiency virus (PLHIV), who have a substantially greater risk of TB than people without HIV. We searched PubMed, EMBASE and Web of Science for studies evaluating the risk factors for latent tuberculous infection (LTBI) or active TB in PLHIV in countries with TB incidence 10 per 100 000 population. Due to the number of risk factors evaluated and heterogeneity in study designs, we present summary data and a narrative synthesis. We included 45 studies: 17 reported data on the risk factors for LTBI and 32 on active TB. Black, Asian or Hispanic ethnicity, birth or long-term residence in a country with high TB incidence, and HIV acquisition via injecting drug use (IDU) or heterosexual sex were strong predictors of both LTBI and active TB. History of contact, a greater degree of immunosuppression at diagnosis or higher viral load increased the TB risk. Early HIV diagnosis to allow timely initiation of antiretroviral therapy is essential for the prevention of TB in PLHIV. Screening and treating PLHIV for LTBI to reduce the risk of progression to active TB disease should also be considered to further reduce the burden of active TB in low TB incidence settings. Research to support the expansion of TB and HIV prevention and treatment globally is essential to eliminate TB in low-incidence settings.

Modelling the dynamics of EBV transmission to inform a vaccine target product profile and future vaccination strategy

Epstein-Barr virus (EBV) is one of the most common human viruses and the cause of pathologies such as infectious mononucleosis (IM) and certain cancers. No vaccine against EBV infection currently exists, but such vaccines are in development. Knowledge of how EBV is transmitted at the population level is critical to the development of target product profiles (TPPs) for such vaccines and future vaccination strategies. We present the first mathematical model of EBV transmission, parameterised using data from England, and use it to compare hypothetical prophylactic vaccines with different characteristics and the impact of vaccinating different age groups. We found that vaccine duration had more impact than vaccine efficacy on modelled EBV and IM prevalence. The age group vaccinated also had an important effect: vaccinating at a younger age led to a greater reduction in seroprevalence but an increase in IM cases associated with delayed infection. Vaccination had impact on cancer incidence only in the long run, because in England most EBV-related cancers arise in later life. Durability of protection should be a key factor to prioritise in EBV vaccine development and included in vaccine TPPs. These findings are timely and important for vaccine developers and policy-makers alike.

Quantifying the beliefs of key players in the UK sheep industry on the efficacy of two treatments for footrot

Clinical trials have demonstrated that sheep with footrot treated with parenteral and topical antibiotics without foot trimming (treatment A), cure faster than sheep treated with foot trimming and topical antibiotics (treatment B). We investigated how key players in the UK sheep industry recommended treating footrot, and tested whether reviewing the evidence surrounding treatment of footrot changed their beliefs. Eight key players attended a workshop to investigate their current practices, and their perceived efficacy of treatments, using probabilistic elicitation. At the start of the study, all participants recommended use of antibiotic injection but only four recommended not foot trimming feet with footrot. Initial beliefs in the difference in cure rate within five days of treatment ranged from 30 to 97% in favour of treatment A (true difference 60%); this heterogeneity reduced after reviewing the evidence. Participants who believed the cure rate differed by >60% over-estimated the cure rate of treatment A whilst participants who believed the difference was <60% over-estimated the efficacy of treatment B. During discussions, participants stated that parenteral antibiotics had always been recommended as a treatment for footrot but that the new research clarified when to use them. In contrast, it was highly novel to hear that foot trimming was detrimental to recovery, and key players and farmers are taking longer to accept this evidence. Three months after the workshop, two participants stated that they now placed greater emphasis on rapid individual antibiotic treatment of lame sheep and one was no longer recommending trimming feet.

Trends in, and factors associated with, HIV infection amongst tuberculosis patients in the era of anti-retroviral therapy: a retrospective study in England, Wales and Northern Ireland

BACKGROUND

HIV increases the progression of latent tuberculosis (TB) infection to active disease and contributed to increased TB in the UK until 2004. We describe temporal trends in HIV infection amongst patients with TB and identify factors associated with HIV infection.

METHODS

We used national surveillance data of all TB cases reported in England, Wales and Northern Ireland from 2000 to 2014 and determined HIV status through record linkage to national HIV surveillance. We used logistic regression to identify associations between HIV and demographic, clinical and social factors.

RESULTS

There were 106,829 cases of TB in adults (≥ 15 years) reported from 2000 to 2014. The number and proportion of TB patients infected with HIV decreased from 543/6782 (8.0%) in 2004 to 205/6461 (3.2%) in 2014. The proportion of patients diagnosed with HIV > 91 days prior to their TB diagnosis increased from 33.5% in 2000 to 60.2% in 2013. HIV infection was highest in people of black African ethnicity from countries with high HIV prevalence (32.3%), patients who misused drugs (8.1%) and patients with miliary or meningeal TB (17.2%).

CONCLUSIONS

There has been an overall decrease in TB-HIV co-infection and a decline in the proportion of patients diagnosed simultaneously with both infections. However, high rates of HIV remain in some sub-populations of patients with TB, particularly black Africans born in countries with high HIV prevalence and people with a history of drug misuse. Whilst the current policy of testing all patients diagnosed with TB for HIV infection is important in ensuring appropriate management of TB patients, many of these TB cases would be preventable if HIV could be diagnosed before TB develops. Improving screening for both latent TB and HIV and ensuring early treatment of HIV in these populations could help prevent these TB cases. British HIV Association guidelines on latent TB testing for people with HIV from sub-Saharan Africa remain relevant, and latent TB screening for people with HIV with a history of drug misuse, homelessness or imprisonment should also be considered.

Interpreting whole genome sequencing for investigating tuberculosis transmission: a systematic review

BACKGROUND

Whole genome sequencing (WGS) is becoming an important part of epidemiological investigations of infectious diseases due to greater resolution and cost reductions compared to traditional typing approaches. Many public health and clinical teams will increasingly use WGS to investigate clusters of potential pathogen transmission, making it crucial to understand the benefits and assumptions of the analytical methods for investigating the data. We aimed to understand how different approaches affect inferences of transmission dynamics and outline limitations of the methods.

METHODS

We comprehensively searched electronic databases for studies that presented methods used to interpret WGS data for investigating tuberculosis (TB) transmission. Two authors independently selected studies for inclusion and extracted data. Due to considerable methodological heterogeneity between studies, we present summary data with accompanying narrative synthesis rather than pooled analyses.

RESULTS

Twenty-five studies met our inclusion criteria. Despite the range of interpretation tools, the usefulness of WGS data in understanding TB transmission often depends on the amount of genetic diversity in the setting. Where diversity is small, distinguishing re-infections from relapses may be impossible; interpretation may be aided by the use of epidemiological data, examining minor variants and deep sequencing. Conversely, when within-host diversity is large, due to genetic hitchhiking or co-infection of two dissimilar strains, it is critical to understand how it arose. Greater understanding of microevolution and mixed infection will enhance interpretation of WGS data.

CONCLUSIONS

As sequencing studies have sampled more intensely and integrated multiple sources of information, the understanding of TB transmission and diversity has grown, but there is still much to be learnt about the origins of diversity that will affect inferences from these data. Public health teams and researchers should combine epidemiological, clinical and WGS data to strengthen investigations of transmission.