Whole genome sequencing-based identification of human tuberculosis caused by animal-lineage Mycobacterium orygis

Mycobacterium orygis and its unseen impact: re-evaluating zoonotic tuberculosis in animal and human populations

Globally, the incidence and burden of zoonotic tuberculosis (zTB) in humans are underestimated. Earlier, it was considered that Mycobacterium bovis (M. bovis) was the sole etiology of zTB; however, novel zoonotic species of mycobacteria, namely, Mycobacterium orygis (M. orygis), is also implicated and often neglected pathogen, which necessitates more attention. M. orygis has been recently included under the members of the Mycobacterium tuberculosis complex (MTBC), and it shares genetic similarities with other members of this complex. M. orygis can cause tuberculosis (TB) in animals and humans. This bacterium is harbored by a wide range of host species; however, the exact host spectrum is not well understood. In recent years, M. orygis has received considerable interest due to its frequent isolation in zTB infections that often originated from tuberculosis-endemic countries than non-endemic countries. Therefore, the zoonotic potential of this bacterium highlights the importance of "One Health" approaches in understanding its possible routes of transmission, reservoir, ecology, and pathogenicity. Moreover, the occurrence of M. orygis in tuberculosis-endemic countries with limited resources poses further challenges in disease surveillance and identification, emphasizing the significance of collaborative measures across multiple sectors to monitor and control its spread. This review focuses on the current knowledge of M. orygis and underscores the importance of this neglected pathogen, which has potential impacts on both human and animal health.

Emergence of Mycobacterium orygis: novel insights into zoonotic reservoirs and genomic epidemiology

Tuberculosis (TB), caused by members of the Mycobacterium tuberculosis complex (MTBC), is a significant global health threat, with millions of cases diagnosed annually and an annual death toll exceeding 1.6 million. Zoonotic TB (zTB), transmitted between animals and humans, remains poorly understood and difficult to control. This narrative review examined current evidence of the emergence and transmission pathways of Mycobacterium orygis, a recently defined member of MTBC. The structured searches for published literature and genome sequence with relevant metadata were conducted using NCBI PubMed and GenBank, respectively. Population diversity was investigated using phylogenomic analysis. Despite significant gaps in current laboratory diagnostic capacity for TB, M. orygis has been documented in 14 countries from 5 continents across 17 host species. Many cases (≈40%) were diagnosed around The Subcontinent and associated with a diverse range of mammalian hosts. In India, zTB due to M. orygis appeared to be more prevalent than disease associated with M. bovis (another zoonotic member of the MTBC). The whole genome sequencing of M. orygis isolates highlighted high diversity associated with different ecological niches. The increasing world-wide prevalence of M. orygis, especially in Asia, highlighted its emergence as a significant pathogen with zoophilic and anthropophilic potential. The reviewed evidence suggested multiple transmission pathways between humans and domesticated and wild mammalian hosts. Enhanced TB laboratory diagnostics and surveillance are imperative for mitigating the spread of zTB including one caused by M. orygis in areas of established and currently unrecognized endemicity.

Characterization of Mycobacterium orygis, Mycobacterium bovis, and Mycobacterium caprae Infections in Humans in Western Canada

Epidemiologic research on zoonotic tuberculosis historically used Mycobacterium bovis as a surrogate measure; however, increased reports of human tuberculosis caused by other animal-associated Mycobacterium tuberculosis complex members like Mycobacterium orygis necessitates their inclusion. We performed a retrospective cohort study including persons infected with any animal-lineage M tuberculosis complex species in Alberta, Canada, from January 1995 to July 2021, identifying 42 patients (20 M bovis, 21 M orygis, 1 M caprae). Demographic, epidemiologic, and clinical characteristics were compared against persons with culture-confirmed M tuberculosis infection. The proportion of culture-positive infections caused by M orygis increased continuously from 2016 to 2020. Significantly more females at a higher median age were impacted by M orygis, with all patients originating from South Asia. Mycobacterium bovis caused significantly more extrapulmonary disease and disproportionately impacted young females, particularly those pregnant or postpartum. All infections were acquired abroad. These findings can aid in developing targeted public health interventions.

Draft genome sequences of clinical Mycobacterium canettii strains in Canada

Mycobacterium canettii is a rare pathogen causing tuberculosis in humans and presents a risk to public health. Here, we report the genome sequences of two M. canettii strains. The genomes will assist in creating sequence-based tools for M. canettii and serve as references for identification, surveillance, and epidemiological investigations.

Evaluation of Whole Genome Sequencing-Based Predictions of Antimicrobial Resistance to TB First Line Agents: A Lesson from 5 Years of Data

Phenotypic susceptibility testing of the Mycobacterium tuberculosis complex (MTBC) isolate requires culture growth, which can delay rapid detection of resistant cases. Whole genome sequencing (WGS) and data analysis pipelines can assist in predicting resistance to antimicrobials used in the treatment of tuberculosis (TB). This study compared phenotypic susceptibility testing results and WGS-based predictions of antimicrobial resistance (AMR) to four first-line antimicrobials-isoniazid, rifampin, ethambutol, and pyrazinamide-for MTBC isolates tested between the years 2018-2022. For this 5-year retrospective analysis, the WGS sensitivity for predicting resistance for isoniazid, rifampin, ethambutol, and pyrazinamide using Mykrobe was 86.7%, 100.0%, 100.0%, and 47.8%, respectively, and the specificity was 99.4%, 99.5%, 98.7%, and 99.9%, respectively. The predictive values improved slightly using Mykrobe corrections applied using TB Profiler, i.e., the WGS sensitivity for isoniazid, rifampin, ethambutol, and pyrazinamide was 92.31%, 100%, 100%, and 57.78%, respectively, and the specificity was 99.63%. 99.45%, 98.93%, and 99.93%, respectively. The utilization of WGS-based testing addresses concerns regarding test turnaround time and enables analysis for MTBC member identification, antimicrobial resistance prediction, detection of mixed cultures, and strain genotyping, all through a single laboratory test. WGS enables rapid resistance detection compared to traditional phenotypic susceptibility testing methods using the WHO TB mutation catalog, providing an insight into lesser-known mutations, which should be added to prediction databases as high-confidence mutations are recognized. The WGS-based methods can support TB elimination efforts in Canada and globally by ensuring the early start of appropriate treatment, rapidly limiting the spread of TB outbreaks.

Genomic Characterization of IS6110 Insertions in Mycobacterium orygis

Mycobacterium orygis, a subspecies of the Mycobacterium tuberculosis complex (MTBC), has emerged as a significant concern in the context of One Health, with implications for zoonosis or zooanthroponosis or both. MTBC strains are characterized by the unique insertion element IS6110, which is widely used as a diagnostic marker. IS6110 transposition drives genetic modifications in MTBC, imparting genome plasticity and profound biological consequences. While IS6110 insertions are customarily found in the MTBC genomes, the evolutionary trajectory of strains seems to correlate with the number of IS6110 copies, indicating enhanced adaptability with increasing copy numbers. Here, we present a comprehensive analysis of IS6110 insertions in the M. orygis genome, utilizing ISMapper, and elucidate their genetic consequences in promoting successful host adaptation. Our study encompasses a panel of 67 paired-end reads, comprising 11 isolates from our laboratory and 56 sequences downloaded from public databases. Among these sequences, 91% exhibited high-copy, 4.5% low-copy, and 4.5% lacked IS6110 insertions. We identified 255 insertion loci, including 141 intragenic and 114 intergenic insertions. Most of these loci were either unique or shared among a limited number of isolates, potentially influencing strain behavior. Furthermore, we conducted gene ontology and pathway analysis, using eggNOG-mapper 5.0, on the protein sequences disrupted by IS6110 insertions, revealing 63 genes involved in diverse functions of Gene Ontology and 45 genes participating in various KEGG pathways. Our findings offer novel insights into IS6110 insertions, their preferential insertion regions, and their impact on metabolic processes and pathways, providing valuable knowledge on the genetic changes underpinning IS6110 transposition in M. orygis.

Whole genome sequencing and comparative genomics of Mycobacterium orygis isolated from different animal hosts to identify specific diagnostic markers

Introduction

Mycobacterium orygis, a member of MTBC has been identified in higher numbers in the recent years from animals of South Asia. Comparative genomics of this important zoonotic pathogen is not available which can provide data on the molecular difference between other MTBC members. Hence, the present study was carried out to isolate, whole genome sequence M. orygis from different animal species (cattle, buffalo and deer) and to identify molecular marker for the differentiation of M. orygis from other MTBC members.

Methods

Isolation and whole genome sequencing of M. orygis was carried out for 9 samples (4 cattle, 4 deer and 1 buffalo) died due to tuberculosis. Comparative genomics employing 53 genomes (44 from database and 9 newly sequenced) was performed to identify SNPs, spoligotype, pangenome structure, and region of difference.

Results

M. orygis was isolated from water buffalo and sambar deer which is the first of its kind report worldwide. Comparative pangenomics of all M. orygis strains worldwide (n= 53) showed a closed pangenome structure which is also reported for the first time. Pairwise SNP between TANUVAS_2, TANUVAS_4, TANUVAS_5, TANUVAS_7 and NIRTAH144 was less than 15 indicating that the same M. orygis strain may be the cause for infection. Region of difference prediction showed absence of RD7, RD8, RD9, RD10, RD12, RD301, RD315 in all the M. orygis analyzed. SNPs in virulence gene, PE35 was found to be unique to M. orygis which can be used as marker for identification.

Conclusion

The present study is yet another supportive evidence that M. orygis is more prevalent among animals in South Asia and the zoonotic potential of this organism needs to be evaluated.