Fatal nosocomial MDR TB identified through routine genetic analysis and whole-genome sequencing

The role of whole genome sequencing in identifying occupational tuberculosis among healthcare workers: two case reports

In this case report, we present case reports for two nurses, both working in departments of respiratory medicine, who developed tuberculosis (TB). For each individual case, whole genome sequencing (WGS) revealed only one specific match within a genomic distance of <6 single-nucleotide polymorphisms. The subsequent epidemiological investigations confirmed that both nurses had relevant exposures to their corresponding match 1139 and 1704 days before presenting with TB symptoms, respectively. Twenty-two studies were identified that reported using genotyping to identify occupational transmission of Mycobacterium tuberculosis to healthcare workers. Only two studies applied WGS, both conducted in resource-rich countries, comparable to the present Danish investigation. When comparing the two WGS studies to the other studies that used older genotyping techniques, WGS provided a higher resolution and much more detailed information. Consequently, the epidemiological investigations were more straightforward. In conclusion, WGS is a powerful tool for determining whether M. tuberculosis transmission is occupational as demonstrated for the two cases in this study.

Reducing the risk of tuberculosis transmission for HCWs in high incidence settings

Globally, tuberculosis (TB) is a leading cause of death from a single infectious agent. Healthcare workers (HCWs) are at increased risk of hospital-acquired TB infection due to persistent exposure to Mycobacterium tuberculosis (Mtb) in healthcare settings. The World Health Organization (WHO) has developed an international system of infection prevention and control (IPC) interventions to interrupt the cycle of nosocomial TB transmission. The guidelines on TB IPC have proposed a comprehensive hierarchy of three core practices, comprising: administrative controls, environmental controls, and personal respiratory protection. However, the implementation of most recommendations goes beyond minimal physical and organisational requirements and thus cannot be appropriately introduced in resource-constrained settings and areas of high TB incidence. In many low- and middle-income countries (LMICs) the lack of knowledge, expertise and practice on TB IPC is a major barrier to the implementation of essential interventions. HCWs often underestimate the risk of airborne Mtb dissemination during tidal breathing. The lack of required expertise and funding to design, install and maintain the environmental control systems can lead to inadequate dilution of infectious particles in the air, and in turn, increase the risk of TB dissemination. Insufficient supply of particulate respirators and lack of direction on the re-use of respiratory protection is associated with unsafe working practices and increased risk of TB transmission between patients and HCWs. Delayed diagnosis and initiation of treatment are commonly influenced by the effectiveness of healthcare systems to identify TB patients, and the availability of rapid molecular diagnostic tools. Failure to recognise resistance to first-line drugs contributes to the emergence of drug-resistant Mtb strains, including multidrug-resistant and extensively drug-resistant Mtb. Future guideline development must consider the social, economic, cultural and climatic conditions to ensure that recommended control measures can be implemented in not only high-income countries, but more importantly low-income, high TB burden settings. Urgent action and more ambitious investments are needed at both regional and national levels to get back on track to reach the global TB targets, especially in the context of the COVID-19 pandemic.

Extensive global movement of multidrug-resistantM. tuberculosis strains revealed by whole-genome analysis

Background

While the international spread of multidrug-resistant (MDR) Mycobacterium tuberculosis strains is an acknowledged public health threat, a broad and more comprehensive examination of the global spread of MDR-tuberculosis (TB) using whole-genome sequencing has not yet been performed.

Methods

In a global dataset of 5310 M. tuberculosis whole-genome sequences isolated from five continents, we performed a phylogenetic analysis to identify and characterise clades of MDR-TB with respect to geographic dispersion.

Results

Extensive international dissemination of MDR-TB was observed, with identification of 32 migrant MDR-TB clades with descendants isolated in 17 unique countries. Relatively recent movement of strains from both Beijing and non-Beijing lineages indicated successful global spread of varied genetic backgrounds. Migrant MDR-TB clade members shared relatively recent common ancestry, with a median estimate of divergence of 13–27 years. Migrant extensively drug-resistant (XDR)-TB clades were not observed, although development of XDR-TB within migratory MDR-TB clades was common.

Conclusions

Application of genomic techniques to investigate global MDR migration patterns revealed extensive global spread of MDR clades between countries of varying TB burden. Further expansion of genomic studies to incorporate isolates from diverse global settings into a single analysis, as well as data sharing platforms that facilitate genomic data sharing across country lines, may allow for future epidemiological analyses to monitor for international transmission of MDR-TB. In addition, efforts to perform routine whole-genome sequencing on all newly identified M. tuberculosis, like in England, will serve to better our understanding of the transmission dynamics of MDR-TB globally.

A screening strategy for latent tuberculosis in healthcare workers: Cost-effectiveness and budget impact of universal versus targeted screening

OBJECTIVE

To evaluate the clinical, cost-efficiency, and budgetary implications of universal versus targeted latent tuberculosis infection (LTBI) screening strategies among healthcare workers (HCWs) in an intermediate tuberculosis (TB)-burden country.

DESIGN

Pragmatic cost-effectiveness and budget impact analysis using decision-analytic modeling.

SETTING

A tertiary-care hospital in Singapore.

METHODS

We compared 7 potentially implementable LTBI screening programs including universal and targeted strategies with different screening frequencies. Feasible targeting methods included stratification by country of origin (a proxy for risk of prior TB exposure) and by high-risk occupation. The clinical and financial consequences of each strategy were estimated relative to "no screening" (current practice) and compared to locally appropriate cost-effectiveness thresholds. All analyses were conducted from the hospital's perspective over a 3-year time horizon, based on the typical hospital planning period. Parameter uncertainties were accounted for using sensitivity analyses.

RESULTS

In our model, relative to current practice, screening new international hires and triennial screening of existing high-risk workers is most cost-effective (US$58 per quality adjusted life year [QALY]) and decreases active TB cases from 19 to 14. Screening all new hires combined with triennial universal screening, with or without annual high-risk screening or annual universal screening, reduced active TB to a range of 19 to 6 cases, but these strategies are less cost-effective and require substantially higher expenditures.

CONCLUSIONS

Targeted LTBI screening for HCWs can be highly cost-effective for hospitals in settings similar to Singapore. More inclusive screening strategies (including regular universal screening) can yield better outcomes but are less efficient and may even be unaffordable.

Mycobacterium tuberculosis Whole Genome Sequences From Southern India Suggest Novel Resistance Mechanisms and the Need for Region-Specific Diagnostics

Background.

India is home to 25% of all tuberculosis cases and the second highest number of multidrug resistant cases worldwide. However, little is known about the genetic diversity and resistance determinants of Indian Mycobacterium tuberculosis, particularly for the primary lineages found in India, lineages 1 and 3.

Methods.

We whole genome sequenced 223 randomly selected M. tuberculosis strains from 196 patients within the Tiruvallur and Madurai districts of Tamil Nadu in Southern India. Using comparative genomics, we examined genetic diversity, transmission patterns, and evolution of resistance.

Results.

Genomic analyses revealed (11) prevalence of strains from lineages 1 and 3, (11) recent transmission of strains among patients from the same treatment centers, (11) emergence of drug resistance within patients over time, (11) resistance gained in an order typical of strains from different lineages and geographies, (11) underperformance of known resistance-conferring mutations to explain phenotypic resistance in Indian strains relative to studies focused on other geographies, and (11) the possibility that resistance arose through mutations not previously implicated in resistance, or through infections with multiple strains that confound genotype-based prediction of resistance.

Conclusions.

In addition to substantially expanding the genomic perspectives of lineages 1 and 3, sequencing and analysis of M. tuberculosis whole genomes from Southern India highlight challenges of infection control and rapid diagnosis of resistant tuberculosis using current technologies. Further studies are needed to fully explore the complement of diversity and resistance determinants within endemic M. tuberculosis populations.

"Who has to do it at the end of the day? Programme officials or hospital authorities?" Airborne infection control at drug resistant tuberculosis (DR-TB) centres of Karnataka, India: a mixed-methods study

Background

Drug resistant tuberculosis (DR-TB) centers admit patients with DR-TB for initiation of treatment and thereby concentrate the patients under one setting. It becomes imperative to assess the compliance of DR-TB centres to national airborne infection control (AIC) guidelines and explore the provider perspectives into reasons for unsatisfactory compliance.

Methods

This mixed methods study (triangulation design) was carried out across all the six DR-TB centers of Karnataka state, India, between November 2016 and April 2017. Non-participant observation using a structured format was carried out at the DR-TB wards (n = 6), outpatient departments (n = 6), patient waiting areas outside outpatient departments (n = 6) and culture and drug susceptibility testing laboratories (n = 3). Structured interviews of admitted patients (n = 30) were done to assess the knowledge on cough hygiene and sputum disposal. Key informant interviews (KIIs) of health care providers (n = 20) were done. Manual descriptive content analysis was done to analyse the transcripts of KIIs.

Results

The findings related to compliance in non-participant observation were corroborated by KIIs. All the laboratories were consistently implementing the AIC guidelines. Compliance to hand hygiene, wet mopping and ventilation measures were satisfactory in four or more DR-TB wards. The non-availability of N95 masks in wards as well as outpatient departments was staggering. Sputum disposal without prior disinfection and the lack of display materials on cough hygiene and patient education was common. Patient fast tracking in outpatient department waiting areas and visitor restrictions in wards were lacking. Trainings on AIC measures were uncommon. About half and one-third of patients admitted had satisfactory knowledge regarding sputum disposal and situations demanding mask respectively. The reasons for unsatisfactory compliance to AIC guidelines were poor coordination between programme and hospital authorities leading to lack of ownership; ineffective or non-existent infection control committees; vacant posts of medical officers; and attitudes of health care delivery staff.

Conclusion

Compliance with AIC guidelines in DR-TB centers of Karnataka was sub-optimal. The reasons identified require urgent attention of the programme managers and hospital authorities.

Electronic supplementary material

The online version of this article (10.1186/s13756-017-0270-4) contains supplementary material, which is available to authorized users.

Exposed, but Not Protected: More Is Needed to Prevent Drug-Resistant Tuberculosis in Healthcare Workers and Students

"Occupational MDR-TB"  …  "XDR-TB"  …  "Treatment-induced hearing loss": 3 life-changing messages imparted over the phone. Three personal accounts are shared highlighting the false belief held by many healthcare workers (HCWs) and students in low-resource settings-that they are immune to tuberculosis despite high levels of occupational tuberculosis exposure. This misconception reflects a lack of awareness of tuberculosis transmission and disease risk, compounded by the absence of accurate occupational tuberculosis estimates. As the global problem of drug-resistant (DR) tuberculosis evolves, HCWs are increasingly infected and suffer considerable morbidity and mortality from occupational DR tuberculosis disease. Similarly, healthcare students are emerging as a vulnerable and unprotected group. There is an urgent need for improved detection, vaccines, preventive therapy, treatment, and support for affected HCWs and those they care for, as well as destigmatization of all forms of tuberculosis. Finally, efforts to protect HCWs and prevent DR tuberculosis transmission by universal implementation of tuberculosis infection control measures should be prioritized.

Risk of Tuberculosis Infection and Disease for Health Care Workers: An Updated Meta-Analysis

Background

Tuberculosis (TB) remains a major challenge to global health. Healthcare workers (HCWs) appear to be at increased risk of TB compared with the general population, despite efforts to scale up infection control and reduce nosocomial TB transmission. This review aims to provide an updated estimate of the occupational risk of latent TB infection (LTBI) and active TB among HCWs compared with the general population.

Methods

A systematic review was performed to identify studies published over the last 10 years reporting TB prevalence or incidence among HCWs and a control group. Pooled effect estimates were calculated to determine the risk of infection.

Results

Twenty-one studies met the inclusion criteria, providing data on 30961 HCWs across 16 countries. Prevalence of LTBI among HCWs was 37%, and mean incidence rate of active TB was 97/100000 per year. Compared with the general population, the risk of LTBI was greater for HCWs (odds ratio [OR], 2.27; 95% confidence interval [CI], 1.61–3.20), and the incidence rate ratio for active TB was 2.94 (95% CI, 1.67–5.19). Comparing tuberculin skin test and interferon-gamma release assay, OR for LTBI was found to be 1.72 and 5.61, respectively.

Conclusions

The overall risk of both LTBI and TB to HCWs continues to be significantly higher than that of the general population, consistent with previous findings. This study highlights the continuing need for improvements in infection control and HCW screening programs.

The Evolution of Strain Typing in the Mycobacterium tuberculosis Complex

Tuberculosis (TB) is a contagious disease with a complex epidemiology. Therefore, molecular typing (genotyping) of Mycobacterium tuberculosis complex (MTBC) strains is of primary importance to effectively guide outbreak investigations, define transmission dynamics and assist global epidemiological surveillance of the disease. Large-scale genotyping is also needed to get better insights into the biological diversity and the evolution of the pathogen. Thanks to its shorter turnaround and simple numerical nomenclature system, mycobacterial interspersed repetitive unit-variable-number tandem repeat (MIRU-VNTR) typing, based on 24 standardized plus 4 hypervariable loci, optionally combined with spoligotyping, has replaced IS6110 DNA fingerprinting over the last decade as a gold standard among classical strain typing methods for many applications. With the continuous progress and decreasing costs of next-generation sequencing (NGS) technologies, typing based on whole genome sequencing (WGS) is now increasingly performed for near complete exploitation of the available genetic information. However, some important challenges remain such as the lack of standardization of WGS analysis pipelines, the need of databases for sharing WGS data at a global level, and a better understanding of the relevant genomic distances for defining clusters of recent TB transmission in different epidemiological contexts. This chapter provides an overview of the evolution of genotyping methods over the last three decades, which culminated with the development of WGS-based methods. It addresses the relative advantages and limitations of these techniques, indicates current challenges and potential directions for facilitating standardization of WGS-based typing, and provides suggestions on what method to use depending on the specific research question.

Genotypic characterization of drug resistant Mycobacterium tuberculosis in Quebec, 2002-2012

Background

The increasing emergence of drug-resistant tuberculosis presents a threat to the effective control of tuberculosis (TB). Rapid detection of drug-resistance is more important than ever to address this scourge. The purpose of this study was to genotypically characterize the first-line antitubercular drug-resistant isolates collected over 11 years in Quebec.

Results

The main mutations found in our resistant strains collection (n = 225) include: the S315T substitution in katG (50.2 %), the -15 C/T mutation in the inhA promoter (29 %); the S531L substitution in rpoB (43 %); the deletion 8 bp 446 / + R140S in pncA (72.9 %); the M306I (35.7 %) and M306V (21.4 %) substitutions in embB. Ten of the mutations in katG and 4 mutations identified in pncA were previously undescribed.

Conclusion

Screening of mutations conferring resistance to first-line antituberculous drugs using DNA-sequencing approach seems to be feasible and would drastically shorten the time to determine the resistance profile compared to the proportion method.

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.