Epidemiological and genomic determinants of tuberculosis outbreaks in First Nations communities in Canada

Reporting practices for genomic epidemiology of tuberculosis: a systematic review of the literature using STROME-ID guidelines as a benchmark

BACKGROUND

Pathogen genomics have become increasingly important in infectious disease epidemiology and public health. The Strengthening the Reporting of Molecular Epidemiology for Infectious Diseases (STROME-ID) guidelines were developed to outline a minimum set of criteria that should be reported in genomic epidemiology studies to facilitate assessment of study quality. We evaluate such reporting practices, using tuberculosis as an example.

METHODS

For this systematic review, we initially searched MEDLINE, Embase Classic, and Embase on May 3, 2017, using the search terms "tuberculosis" and "genom* sequencing". We updated this initial search on April 23, 2019, and also included a search of bioRxiv at this time. We included studies in English, French, or Spanish that recruited patients with microbiologically confirmed tuberculosis and used whole genome sequencing for typing of strains. Non-human studies, conference abstracts, and literature reviews were excluded. For each included study, the number and proportion of fulfilled STROME-ID criteria were recorded by two reviewers. A comparison of the mean proportion of fulfilled STROME-ID criteria before and after publication of the STROME-ID guidelines (in 2014) was done using a two-tailed t test. Quasi-Poisson regression and tobit regression were used to examine associations between study characteristics and the number and proportion of fulfilled STROME-ID criteria. This study was registered with PROSPERO, CRD42017064395.

FINDINGS

976 titles and abstracts were identified by our primary search, with an additional 16 studies identified in bioRxiv. 114 full texts (published between 2009 and 2019) were eligible for inclusion. The mean proportion of STROME-ID criteria fulfilled was 50% (SD 12; range 16-75). The proportion of criteria fulfilled was similar before and after STROME-ID publication (51% [SD 11] vs 46% [14], p=0·26). The number of criteria reported (among those applicable to all studies) was not associated with impact factor, h-index, country of affiliation of senior author, or sample size of isolates. Similarly, the proportion of criteria fulfilled was not associated with these characteristics, with the exception of a sample size of isolates of 277 or more (the highest quartile). In terms of reproducibility, 100 (88%) studies reported which bioinformatic tools were used, but only 33 (33%) reported corresponding version numbers. Sequencing data were available for 86 (75%) studies.

INTERPRETATION

The reporting of STROME-ID criteria in genomic epidemiology studies of tuberculosis between 2009 and 2019 was low, with implications for assessment of study quality. The considerable proportion of studies without bioinformatics version numbers or sequencing data available highlights a key concern for reproducibility.

Dispersal of Mycobacterium tuberculosis Driven by Historical European Trade in the South Pacific

Mycobacterium tuberculosis (Mtb) is a globally distributed bacterial pathogen whose population structure has largely been shaped by the activities of its obligate human host. Oceania was the last major global region to be reached by Europeans and is the last region for which the dispersal and evolution of Mtb remains largely unexplored. Here, we investigated the evolutionary history of the Euro-American L4.4 sublineage and its dispersal to the South Pacific. Using a phylodynamics approach and a dataset of 236 global Mtb L4.4 genomes we have traced the origins and dispersal of L4.4 strains to New Zealand. These strains are predominantly found in indigenous Māori and Pacific people and we identify a clade of European, likely French, origin that is prevalent in indigenous populations in both New Zealand and Canada. Molecular dating suggests the expansion of European trade networks in the early 19th century drove the dispersal of this clade to the South Pacific. We also identify historical and social factors within the region that have contributed to the local spread and expansion of these strains, including recent Pacific migrations to New Zealand and the rapid urbanization of Māori in the 20th century. Our results offer new insight into the expansion and dispersal of Mtb in the South Pacific and provide a striking example of the role of historical European migrations in the global dispersal of Mtb.

Effects of Host, Sample, and in vitro Culture on Genomic Diversity of Pathogenic Mycobacteria

Mycobacterium tuberculosis (M. tb), an obligate human pathogen and the etiological agent of tuberculosis (TB), remains a major threat to global public health. Comparative genomics has been invaluable for monitoring the emergence and spread of TB and for gaining insight into adaptation of M. tb. Most genomic studies of M. tb are based on single bacterial isolates that have been cultured for several weeks in vitro. However, in its natural human host, M. tb comprises complex, in some cases massive bacterial populations that diversify over the course of infection and cannot be wholly represented by a single genome. Recently, enrichment via hybridization capture has been used as a rapid diagnostic tool for TB, circumventing culturing protocols and enabling the recovery of M. tb genomes directly from sputum. This method has further applicability to the study of M. tb adaptation, as it enables a higher resolution and more direct analysis of M. tb genetic diversity within hosts with TB. Here we analyzed genomic material from M. tb and Mycobacterium bovis populations captured directly from sputum and from cultured samples using metagenomic and Pool-Seq approaches. We identified effects of sampling, patient, and sample type on bacterial genetic diversity. Bacterial genetic diversity was more variable and on average higher in sputum than in culture samples, suggesting that manipulation in the laboratory reshapes the bacterial population. Using outlier analyses, we identified candidate bacterial genetic loci mediating adaptation to these distinct environments. The study of M. tb in its natural human host is a powerful tool for illuminating host pathogen interactions and understanding the bacterial genetic underpinnings of virulence.

Molecular degree of perturbation of plasma inflammatory markers associated with tuberculosis reveals distinct disease profiles between Indian and Chinese populations

Tuberculosis (TB) is a chronic inflammatory disease caused by Mycobacterium tuberculosis infection which causes tremendous morbidity and mortality worldwide. Clinical presentation of TB patients is very diverse and disease heterogeneity is associated with changes in biomarker signatures. Here, we compared at the molecular level the extent of individual inflammatory perturbation of plasma protein and lipid mediators associated with TB in patients in China versus India. We performed a cross-sectional study analyzing the overall degree of inflammatory perturbation in treatment-naïve pulmonary TB patients and uninfected individuals from India (TB: n = 97, healthy: n = 20) and China (TB: n = 100, healthy: n = 11). We employed the molecular degree of perturbation (MDP) adapted to plasma biomarkers to examine the overall changes in inflammation between these countries. M. tuberculosis infection caused a significant degree of molecular perturbation in patients from both countries, with higher perturbation detected in India. Interestingly, there were differences in biomarker perturbation patterns and the overall degree of inflammation. Patients with severe TB exhibited increased MDP values and Indian patients with this condition exhibited even higher degree of perturbation compared to Chinese patients. Network analyses identified IFN-α, IFN-β, IL-1RI and TNF-α as combined biomarkers that account for the overall molecular perturbation in the entire study population. Our results delineate the magnitude of the systemic inflammatory perturbation in pulmonary TB and reveal qualitative changes in inflammatory profiles between two countries with high disease prevalence.