Non-human sources of Mycobacterium tuberculosis

Tackling Drug-Resistant Tuberculosis: New Challenges from the Old Pathogen Mycobacterium tuberculosis

Antibiotics have played a crucial role in the reduction in the incidence of TB globally as evidenced by the fact that before the mid-20th century, the mortality rate within five years of the onset of the disease was 50%. The use of antibiotics has eliminated TB as a devastating disease, but the challenge of resistance to anti-TB drugs, which had already been described at the time of the introduction of streptomycin, has become a major global issue in disease management. Mismanagement of multidrug-resistant tuberculosis (MDR-TB) cases, resulting from intermittent drug use, prescription errors, and non-compliance of patients, has been identified as a critical risk factor for the development of extensively drug-resistant tuberculosis (XDR-TB). Antimicrobial resistance (AMR) in TB is a multi-factorial, complex problem of microbes evolving to escape antibiotics, the gradual decline in antibiotic development, and different economic and social conditions. In this review, we summarize recent advances in our understanding of how Mycobacterium tuberculosis evolves drug resistance. We also highlight the importance of developing shorter regimens that rapidly reach bacteria in diverse host environments, eradicating all mycobacterial populations and preventing the evolution of drug resistance. Lastly, we also emphasize that the current burden of this ancient disease is driven by a combination of complex interactions between mycobacterial and host factors, and that only a holistic approach that effectively addresses all the critical issues associated with drug resistance will limit the further spread of drug-resistant strains throughout the community.

Risk factors of tuberculosis in Mizoram: First report of the possible role of water source

BACKGROUND

Various risk factors of tuberculosis have been studied across the globe, but these may be altered over time and can be specific to geographical regions and there is not much information available from Northeastern region of India. This study aims to investigate the various risk factors of tuberculosis and analyze the presence of any less-established risk factors.

METHODS

A total of 400 TB cases and 840 healthy controls were interviewed from December 2017 - June 2020. Logistic regression model was used to analyze associated risk factors. Patients were categorized into pulmonary and extrapulmonary TB.

RESULTS

Clinical presentation such as fever, cough, weight loss, chest pain and night sweats were more prominent among pulmonary TB patients. The most common mode of diagnosis among pulmonary and extrapulmonary TB were GeneXpert and X-ray, respectively. Tuberculosis was found to be strongly prevalent among patients from lower socio-economic status, less educated, unemployed and improper housing condition. Other risk factors associated were alcohol consumption, neighbours with TB, travel history, no BCG vaccine, mass gathering, and non-ideal weight. An interesting less-established risk factor that demands attention is the source of water supply (p-0.017, OR-2.313, CI: 1.160-4.613), which was significant in this study.

CONCLUSION

Our data suggests that apart from all the well-established risk factors for TB, water supply might play a crucial role towards the transmission of TB, since proper hospital waste water treatment is yet to be adopted in Mizoram, Northeast India. From a public health standpoint, this highlights the need for further research in this area.

Evidence, Challenges, and Knowledge Gaps Regarding Latent Tuberculosis in Animals

Mycobacterium bovis and other Mycobacterium tuberculosis complex (MTBC) pathogens that cause domestic animal and wildlife tuberculosis have received considerably less attention than M. tuberculosis, the primary cause of human tuberculosis (TB). Human TB studies have shown that different stages of infection can exist, driven by host-pathogen interactions. This results in the emergence of heterogeneous subpopulations of mycobacteria in different phenotypic states, which range from actively replicating (AR) cells to viable but slowly or non-replicating (VBNR), viable but non-culturable (VBNC), and dormant mycobacteria. The VBNR, VBNC, and dormant subpopulations are believed to underlie latent tuberculosis (LTB) in humans; however, it is unclear if a similar phenomenon could be happening in animals. This review discusses the evidence, challenges, and knowledge gaps regarding LTB in animals, and possible host-pathogen differences in the MTBC strains M. tuberculosis and M. bovis during infection. We further consider models that might be adapted from human TB research to investigate how the different phenotypic states of bacteria could influence TB stages in animals. In addition, we explore potential host biomarkers and mycobacterial changes in the DosR regulon, transcriptional sigma factors, and resuscitation-promoting factors that may influence the development of LTB.

Mycobacterium tuberculosis sensu stricto in African Apes, What Is Its True Health Impact?

Since the Symposium on Mycobacterial Infections of Zoo Animals held at the National Zoological Park, Smithsonian Institution in 1976, our understanding of tuberculosis (TB) in non-domestic animals has greatly expanded. Throughout the past decades, this knowledge has resulted in improved zoo-habitats and facilities design, stricter biosecurity measures, and advanced diagnostic methods, including molecular techniques, that have significantly decreased the number of clinical disease caused by Mycobacterium tuberculosis in apes under human care settings. In the other hand, exponential growth of human populations has led to human encroachment in wildlife habitat which has resulted in increased inter-species contact and recurrent conflict between humans and wild animals. Although it is widely accepted that non-human primates are susceptible to M. tb infection, opinions differ with regard to the susceptibility to develop disease amongst different taxa. Specifically, some authors suggest that African apes are less susceptible to clinical tuberculosis than other species of primates. The aim of this review article is to evaluate the current scientific literature to determine the actual health impact of disease caused by Mycobacterium tuberculosis and more specifically Mycobacterium tuberculosis sensu stricto in African apes. The literature review included literature databases: Web of Science, Pubmed, Scopus, Wiley, Springer and Science direct, without temporal limit and proceedings of annual conferences in the field of wildlife health. Our general inclusion criteria included information about serological, molecular, pathological (macroscopic and/or microscopic), and clinical evidence of TB in African apes; while our, our more stringent inclusion selection criteria required that in addition to a gross pathology, a molecular test confirmed Mycobacterium tuberculosis sensu stricto as the cause of disease or death. We identified eleven reports of tuberculosis in African apes; of those, only four reports met the more stringent selection criteria that confirmed M. tb sensu stricto in six individuals. All reports that confirmed M. tb sensu stricto originated from zoological collections. Our review suggests that there is little evidence of disease or mortality caused by M. tb in the different species of African apes both under human care and free ranging populations. Additional studies are needed in free-ranging, semi-captive populations (sanctuaries) and animals under human care (zoos and rescue centers) to definitely conclude that this mycobacteria has a limited health effect in African ape species.

Zoonotic pathogens survey in free-living long-tailed macaques in Thailand

Long-tailed macaques (Macaca fascicularis) are known to harbour a variety of infectious pathogens, including zoonotic species. Long-tailed macaques and humans coexist in Thailand, which creates potential for interspecies pathogen transmission. This study was conducted to assess the presence of B virus, Mycobacterium spp., simian foamy virus (SFV), hepatitis B virus (HBV), and Plasmodium spp. in 649 free-living Thai long-tailed macaques through polymerase-chain reaction. DNA of SFV (56.5%), HBV (0.3%), and Plasmodium spp. (2.2%) was detected in these macaques, whereas DNA of B virus and Mycobacterium spp. was absent. SFV infection in long-tailed macaques is broadly distributed in Thailand and is correlated with age. The HBV sequences in this study were similar to HBV sequences from orangutans. Plasmodium spp. DNA was identified as P. inui. Collectively, our results indicate that macaques can carry zoonotic pathogens, which have a public health impact. Surveillance and awareness of pathogen transmission between monkeys and humans are important.

Molecular surveillance of tuberculosis-causing mycobacteria in wastewater

The surveillance of tuberculosis infections has largely depended on clinical diagnostics and hospitalization data. The advancement in molecular methods creates an opportunity for the adoption of alternative surveillance systems, such as wastewater-based epidemiology. This study presents the use of conventional and advanced polymerase chain reaction techniques (droplet digital PCR) to determine the occurrence and concentration of total mycobacteria and members of the Mycobacterium tuberculosis complex (MTBC) in treated and untreated wastewater. Wastewater samples were taken from three wastewater treatment plants (WWTPs) in the city of Durban, South Africa, known for a high burden of TB/MDR-TB due to HIV infections. All untreated wastewater samples contained total mycobacteria and MTBC at varying percentages per WWTP studied. Other members of the MTBC related to tuberculosis infection in animals, M. bovis and M. caprae were also detected. The highest median concentration detected in untreated wastewater was up to 4.9 (±0.2) Log10 copies/ml for total mycobacteria, 4.0 (±0.85) Log10 copies/ml for MTBC, 3.9 (±0.54) Log10 copies/ml for M. tuberculosis, 2.7 (±0.42) Log10 copies/ml for M. africanum, 4.0 (±0.29) Log10 copies/ml for M. bovis and 4.5 (±0.52) Log10 copies/ml for M. caprae. Lower concentrations were detected in the treated wastewater, with a statistically significant difference (P-value ≤ 0.05) in concentrations observed. The log reduction achieved for these bacteria in the respective WWTPs was not statistically different, indicating that the treatment configuration did not have an impact on their removal. The detection of M. africanum in wastewater from South Africa shows that it is possible that some of the TB infections in the community could be caused by this mycobacterium. This study, therefore, highlights the potential of wastewater-based epidemiology for monitoring tuberculosis infections.

Molecular detection of Mycobacterium tuberculosis sensu stricto in the soil of Niger

Mycobacterium tuberculosis (MTB) complex is comprising of pathogenic mycobacteria responsible for human and animal tuberculosis, a major public health problem in Niger. Although infected individuals are paramount sources of contamination, nevertheless alternative, neglected sources may play some role in minority forms of the infection. Accordingly, we investigated the presence of Mycobacterium tuberculosis complex in soil samples in Niger. A total of 103 soil samples were collected in six different areas in Niger in October and November 2018 and April and May 2020 from residential areas of tuberculosis patients. Screening PCR targeting M. tuberculosis complex CRISPR-Csm4 and Xpert MTB/RIF Ultra assay were applied to detect the M. tuberculosis complex. M. tuberculosis DNA was positively detected in five of 103 (5/103; 4.8%) soil samples (Dosso: one sample, Zinder: one sample and Niamey: three samples) using the CRISPR-Csm4 system. CRISPR-Csm4 gene sequence identified four M. tuberculosis sensu stricto (may be lineages 1, 3 or 4) and one M. tuberculosis L2 lineage (Beijing). Moreover, the five positive samples were confirmed by Xpert MTB/RIF Ultra assay as rifampicin-susceptible M. tuberculosis complex strains. However, culture remained negative after 42 days. In this study, we announced for the first time the presence of M. tuberculosis sensu stricto in the soil of Niger. Moreover, these detected lineages were identical to the dominant M. tuberculosis lineages in patients. The presence of common lineages of M. tuberculosis between the soil and human highlight the risk of transmission from the soil to human.

The puzzle of the evolutionary natural history of tuberculosis

Several pieces of the puzzle of the natural history of tuberculosis are assembled in this review to illustrate the potential reservoirs and sources of the Mycobacterium tuberculosis complex (MTBC) mycobacteria, their transmission to animals and humans, and their fate in populations, in a co-evolutionary perspective. Millennia-old companions of mammalian and human populations, MTBC are detected in the soil, in which they infect and survive within vegetative amoebae and cysts, except for Mycobacterium canettii. Never detected in the sphere of plants, they are transmissible by transcutaneous, digestive and respiratory routes and cause an infection of the lymphatic system with secondary dissemination in most tissues, in which they determine a specific and non-pathognomonic granulomatous inflammatory reaction; in which MTBC survives in dormant form irrespective of MTBC species and mammalian species; indicating that the current epidemiology in mammalian populations is essentially governed by the probabilities of contact between mammalian species and MTBC species. Individual variabilities in clinical expression of tuberculosis are related to MTBC species, strain and inoculum; host genetic factors; acquired modulations of the inflammatory response; and probably human microbiota. This review of the literature suggests an evolutionary natural history of telluric environmental mycobacteria, satellites of unicellular eukaryotes, transmissible to mammals via the digestive and then respiratory tracts, in which they determine a fatal contagious infection that is primarily lymphatic and a quiescence-mimicking encysted form. This review opens perspectives for microbiological and translational medical research.

Evolutionary Genetics of Mycobacterium tuberculosis and HIV-1: "The Tortoise and the Hare"

The already enormous burden caused by Mycobacterium tuberculosis and Human Immunodeficiency Virus type 1 (HIV-1) alone is aggravated by co-infection. Despite obvious differences in the rate of evolution comparing these two human pathogens, genetic diversity plays an important role in the success of both. The extreme evolutionary dynamics of HIV-1 is in the basis of a robust capacity to evade immune responses, to generate drug-resistance and to diversify the population-level reservoir of M group viral subtypes. Compared to HIV-1 and other retroviruses, M. tuberculosis generates minute levels of genetic diversity within the host. However, emerging whole-genome sequencing data show that the M. tuberculosis complex contains at least nine human-adapted phylogenetic lineages. This level of genetic diversity results in differences in M. tuberculosis interactions with the host immune system, virulence and drug resistance propensity. In co-infected individuals, HIV-1 and M. tuberculosis are likely to co-colonize host cells. However, the evolutionary impact of the interaction between the host, the slowly evolving M. tuberculosis bacteria and the HIV-1 viral "mutant cloud" is poorly understood. These evolutionary dynamics, at the cellular niche of monocytes/macrophages, are also discussed and proposed as a relevant future research topic in the context of single-cell sequencing.

Detection of Mycobacterium tuberculosis complex infection in Asian elephants (Elephas maximus) using an interferon gamma release assay in a captive elephant herd

Tuberculosis is highly contagious disease that can be transmitted between humans and animals. Asian elephants (Elephas maximus) in captivity live in close contact with humans in many Asian countries. In this study, we developed an interferon gamma release assay (IGRA) for elephant TB detection using antigens from the MTB complex (MTBC) and nontuberculous mycobacteria (NTM) as stimulating antigens (PPD, ESAT6, CFP10) to elicit a cell-mediated immune response (CMIR). The developed assay was applied to an elephant herd of more than 60 animals in Thailand, and the results were compared with those obtained through serological detection. IGRA has sufficient sensitivity for detecting elephant interferon gamma (eIFNγ) from specific antigen-stimulated PBMCs. Among 60 animals tested, 20 samples (33.3%) showed negative results for both MTBC and NTM infection. Eighteen samples (30%) showed positive responses against PPD from M. bovis and/or ESAT6 and CFP10, indicating MTBC infection. In contrast, only 15.6% showed seropositivity in a commercial serological test kit for elephant TB. The discrepancies between serological and CMIR highlight that the two methods may detect different stages of elephant TB. Therefore, employing both tests may enable them to complement each other in correctly identifying elephants that have been exposed to MTBC.

Synergy between Th1 and Th2 responses during Mycobacterium tuberculosis infection: A review of current understanding

Induction of Th1 (cell-mediated) immunity and associated production of IFN-γ by CD4+ T cells has been widely used as a marker of protective immunity against tuberculosis (TB). This is based on two assumptions. The first is the widely accepted view that Mycobacterium tuberculosis (Mtb), the causative agent of TB is an obligate intracellular pathogen, and the second is based on the Th1/Th2 paradigm, which posits that polarization of CD4+ T cells into type1 (cell-mediated) and type 2 (humoral) is central for proper induction of protective immunity against pathogens. However, almost all licensed vaccines currently in use are primarily anti-body based whether intracellular or extra-cellular. In addition, converging data from both animal models and humans indicate that the production of IFN-γ alone is not sufficient to confer protection against TB. In addition, a substantial body of the literature suggests that, in addition to Th1 cells, antibody classes and sub-classes are protective against TB. In a recent study, we have shown that there is a synergy between IFN-γ (cell-mediated) and IgA (humoral) in human population in an endemic setting. In this review, current data from both animal and human studies that support mixed Th1 and Th2 responses that are protective against Mtb and other pathogens are presented.

A New Phylogenetic Framework for the Animal-Adapted Mycobacterium tuberculosis Complex

Tuberculosis (TB) affects humans and other animals and is caused by bacteria from the Mycobacterium tuberculosis complex (MTBC). Previous studies have shown that there are at least nine members of the MTBC infecting animals other than humans; these have also been referred to as ecotypes. However, the ecology and the evolution of these animal-adapted MTBC ecotypes are poorly understood. Here we screened 12,886 publicly available MTBC genomes and newly sequenced 17 animal-adapted MTBC strains, gathering a total of 529 genomes of animal-adapted MTBC strains. Phylogenomic and comparative analyses confirm that the animal-adapted MTBC members are paraphyletic with some members more closely related to the human-adapted Mycobacterium africanum Lineage 6 than to other animal-adapted strains. Furthermore, we identified four main animal-adapted MTBC clades that might correspond to four main host shifts; two of these clades are hypothesized to reflect independent cattle domestication events. Contrary to what would be expected from an obligate pathogen, MTBC nucleotide diversity was not positively correlated with host phylogenetic distances, suggesting that host tropism in the animal-adapted MTBC seems to be driven by contact rates and demographic aspects of the host population rather by than host relatedness. By combining phylogenomics with ecological data, we propose an evolutionary scenario in which the ancestor of Lineage 6 and all animal-adapted MTBC ecotypes was a generalist pathogen that subsequently adapted to different host species. This study provides a new phylogenetic framework to better understand the evolution of the different ecotypes of the MTBC and guide future work aimed at elucidating the molecular mechanisms underlying host range.

Studies of nonhuman primates: key sources of data on zoonoses and microbiota

The genetic and morphologic similarities between primates and humans means that much information obtained from primates may be applied to humans, and vice versa. However, habitat loss, hunting and the continued presence of humans have a negative effect on the biology and behaviour of almost all nonhuman primates. Noninvasive methods such as stool collection are among the safest alternative ways to study the multiple aspects of the biology of primates. Many epidemiologic issues (e.g. pathogen detection, microbiota studies) may be easily studied using stool samples from primates. Primates are undoubtedly among the first candidates suspected of becoming the source of one of the next emerging epidemic of zoonotic origin, as has already been observed with HIV, malaria and monkeypox. The Institut Hospitalo-Universitaire Méditerranée Infection in Marseille actively participates in the study, mostly epidemiologic, of nonhuman primates, using mostly stool samples.

The History of In Vivo Tuberculin Testing in Bovines: Tuberculosis, a "One Health" Issue

Tuberculosis (TB) is more than 3 million years old thriving in multiple species. Ancestral Mycobacterium tuberculosis gave rise to multiple strains including Mycobacterium bovis now distributed worldwide with zoonotic transmission happening in both directions between animals and humans. M. bovis in milk caused problems with a significant number of deaths in children under 5 years of age due largely to extrapulmonary TB. This risk was effectively mitigated with widespread milk pasteurization during the twentieth century, and fewer young children were lost to TB. Koch developed tuberculin in 1890 and recognizing the possibility of using tuberculin to detect infected animals the first tests were quickly developed. Bovine TB (bTB) control/eradication programmes followed in the late nineteenth century/early twentieth century. Many scientists collaborated and contributed to the development of tuberculin tests, to refining and optimizing the production and standardization of tuberculin and to determining test sensitivity and specificity using various methodologies and injection sites. The WHO, OIE, and EU have set legal standards for tuberculin production, potency assay performance, and intradermal tests for bovines. Now, those using tuberculin tests for bTB control/eradication programmes rarely, see TB as a disease. Notwithstanding the launch of the first-ever roadmap to combat zoonotic TB, many wonder if bTB is actually a problem? Is there a better way of dealing with bTB? Might alternative skin test sites make the test “better” and easier to perform? Are all tuberculins used for testing equally good? Why have alternative “better” tests not been developed? This review was prompted by these types of questions. This article attempts to succinctly summarize the data in the literature from the late nineteenth century to date to show why TB, and zoonotic TB specifically, was and still is important as a “One Health” concern, and that the necessity to reduce the burden of zoonotic TB, to save lives and secure livelihoods is far too important to await the possible future development of novel diagnostic assays for livestock before renewing efforts to eliminate it. Consequently, it is highly probable that the tuberculin skin test will remain the screening test of choice for farmed livestock for the considerable future.

Inverse correlation between salt tolerance and host-adaptation in mycobacteria

BACKGROUND

The genus Mycobacterium includes host-adapted organisms regarded as obligate and opportunistic pathogens and environmental organisms. Factors contributing to this wide range of adaptations are poorly known.

RESULTS

We studied the salt tolerance of 46 Mycobacterium species of medical interest. Representative strains of the Mycobacterium tuberculosis complex, Mycobacterium avium complex, Mycobacterium chelonae-abscessus complex, Mycobacterium ulcerans, Mycobacterium marinum, Mycobacterium lentiflavum, Mycobacterium fortuitum and Mycobacterium conceptionense were inoculated on Middlebrook 7H10 medium supplemented with 0-10% sodium chloride. Colonies were counted after 2-4 week incubation at the appropriate 30-37 °C temperature depending on the tested strain. Further comparative genomics was done on 15 Mycobacterium strains representing the spectrum of salt-tolerance of mycobacteria. Based on the results the different species were grouped according to their salt tolerance into a "salt-sensitive" group (growth up to ≤3% salt) containing the M. tuberculosis complex, Mycobacterium chelonae, Mycobacterium lentiflavum, Mycobacterium ulcerans and Mycobacterium marinum; a "salt-intermediate" group (growth between 4 and 6% salt) comprising Mycobacterium avium, Mycobacterium intracellulare, Mycobacterium chimaera and a "salt-resistant" group (growth up to >6%) comprising Mycobacterium homonissuis, Mycobacterium bolettii, Mycobacterium fortuitum and Mycobacterium conceptionense. Genomic analysis revealed that 290 genes were unique to species belonging to the salt-sensitive group; and that 15% were annotated as being functionally associated with the ESX secretion systems Pro-Glu and Pro-Pro-Glu family proteins.

CONCLUSIONS

In this work we found an inverse correlation between salt tolerance and host adaptation. We thus propose that salinity is one of the multiple factors determining the ecological niches of mycobacteria.

Smooth Tubercle Bacilli: Neglected Opportunistic Tropical Pathogens

Smooth tubercle bacilli (STB) including “Mycobacterium canettii” are members of the Mycobacterium tuberculosis complex (MTBC), which cause non-contagious tuberculosis in human. This group comprises <100 isolates characterized by smooth colonies and cordless organisms. Most STB isolates have been obtained from patients exposed to the Republic of Djibouti but seven isolates, including the three seminal ones obtained by Georges Canetti between 1968 and 1970, were recovered from patients in France, Madagascar, Sub-Sahara East Africa, and French Polynesia. STB form a genetically heterogeneous group of MTBC organisms with large 4.48 ± 0.05 Mb genomes, which may link Mycobacterium kansasii to MTBC organisms. Lack of inter-human transmission suggested a yet unknown environmental reservoir. Clinical data indicate a respiratory tract route of contamination and the digestive tract as an alternative route of contamination. Further epidemiological and clinical studies are warranted to elucidate areas of uncertainty regarding these unusual mycobacteria and the tuberculosis they cause.

EVALUATION OF DIAGNOSTIC ACCURACY OF THE COMPARATIVE TUBERCULIN SKIN TEST IN REHABILITANT BORNEAN ORANGUTANS (PONGO PYGMAEUS)

The tuberculin skin test (TST) has been the mainstay of tuberculosis (TB) testing in primates for decades, but its interpretation in orangutans (Pongo spp.) is challenging, because many animals react strongly, without evidence of infection with Mycobacterium tuberculosis complex. One explanation is cross-reactivity with environmental nontuberculous mycobacteria (NTM). The use of a comparative TST (CTST), comparing reactivity to avian (representing NTM) and bovine (representing tuberculous mycobacteria) tuberculins aids in distinguishing cross-reactivity due to sensitization by NTM from shared antigens. The specificity of the TST can be increased with the use of CTST. We considered three interpretations of the TST in rehabilitant Bornean orangutans ( Pongo pygmaeus ) using avian purified protein derivative (APPD; 25,000 IU/ml) and two concentrations of bovine purified protein derivative (BPPD; 100,000 and 32,500 IU/ml). The tests were evaluated for their ability to identify accurately seven orangutans previously diagnosed with and treated for TB from a group of presumed negative individuals (n = 288 and n = 161 for the two respective BPPD concentrations). BPPD at 32,500 IU/ml had poor diagnostic capacity, whereas BPPD at 100,000 IU/ml performed better. The BPPD-only interpretation had moderate sensitivity (57%) and poor specificity (40%) and accuracy (41%). The comparative interpretation at 72 hr had similar sensitivity (57%) but improved specificity (95%) and accuracy (94%). However, best results were obtained by a comparative interpretation incorporating the 48- and 72-hr scores, which had good sensitivity (86%), specificity (95%) and accuracy (95%). These data reinforce recommendations that a CTST be used in orangutans and support the use of APPD at 25,000 IU/ml and BPPD at 100,000 IU/ml. The highest score at each site from the 48- and 72-hr checks should be considered the result for that tuberculin. If the bovine result is greater than the avian result, the animal should be considered a TB suspect.

Looking in amoebae as a source of mycobacteria

Mycobacteria exhibit various relationships with amoebae, ranging from the killing of one partner by the other one, to amoebae hosting mycobacteria in trophozoites and cysts. This observation indicates that poorly described biological factors affect the relationships, including mycobacterial cell-wall glycolipids and the size of the mycobacteria. Experimental observations indicate that a majority of environmental, opportunistic mycobacteria but also obligate pathogens including Mycobacterium tuberculosis, Mycobacterium leprae and Mycobacterium ulcerans are inter-amoebal organisms. Amoebae may give opportunities for genetic exchanges between mycobacteria, sympatric intra-amoebal organisms and the amoebae themselves. Amoebae clearly protect opportunistic mycobacterial pathogens during their environmental life but their role for obligate mycobacterial infection remains to be established. Accordingly, water was the source for emerging, community-acquired and health care-associated infection with amoeba-resisting mycobacteria of the Mycobacterium avium, Mycobacterium abscessus and Mycobacterium fortuitum groups, among others. Amoebae are organisms where mycobacteria can be found and, accordingly, amoeba co-culture can be used for the isolation of mycobacteria from environmental and clinical specimens. Looking in amoebae may help recovering new species of mycobacteria.

Long-term survival of tuberculosis complex mycobacteria in soil

While there is evidence for the persistence of Mycobacterium bovis in soil, there are no reports for the other Mycobacterium tuberculosis complex (MTC) mycobacteria. Here, soil was inoculated with 108 c.f.u. g−1 M. tuberculosis, M. bovis and M. canettii and subcultured monthly for 12 months. The pathogenicity of mycobacterial colonies, identified by using matrix-assisted laser desorption/ionization time of flight mass spectrometry, was assessed in a mouse model. Moreover, mice were fed with food that contained 16.7 % M. tuberculosis-contaminated soil. The three tested MTC species survived in soil for 12 months with a final inoculum of 2×103 c.f.u. g−1 for M. tuberculosis, 150 c.f.u. g−1 for M. bovis and 2×104 c.f.u. g−1 for M. canettii. In an experiment that included negative controls, all (5/5) mice inoculated with such M. tuberculosis and M. canettii developed 0.03–0.3 granulomas mm−2 in their lungs and spleen and grew mycobacteria; five mice that were inoculated with M. bovis from soil did not develop granulomas but grew mycobacteria. Furthermore, 0.2–0.4 granulomas mm−2 were observed in the lungs and spleen of 3/5 mice fed with M. tuberculosis-contaminated soil in the presence of two negative control mice. M. tuberculosis grew in the stomach, intestine, spleen and lung in 5/5 challenged mice, whereas the negative controls remained M. tuberculosis-free (P = 0.008, Fisher exact test). This study provides clear evidence that MTC mycobacteria survive in soil, and that M. tuberculosis remains virulent while in the soil, outside its hosts, for extended periods of time.