Emergence and spread of a human-transmissible multidrug-resistant nontuberculous mycobacterium

Comparative survival of environmental and clinical Mycobacterium abscessus isolates in a variety of diverse host cells

Aims

Mycobacterium abscessus subsp. abscessus (MABS) is an emerging, opportunistic pathogen found globally in freshwater biofilms and soil. Typically, isolates are treated as a uniform group of organisms and very little is known about their comparative survival in healthy host cells. We posit that environmentally‐ and clinically derived isolates, show differential infectivity in immune cells and resistance to innate defenses.

Methods and Results

Six MABS isolates were tested including three water biofilm/soil and three sputum‐derived isolates. A clinical MABS type strain and an environmental isolate of Arthrobacter were also included. MABS counts were significantly higher compared to Arthrobacter after co‐culture with Acanthamoeba lenticulata, BEAS‐2B epithelial cells, alveolar macrophages and the THP‐1 macrophage cell line. A rough sputum‐derived MABS isolate emerged as an isolate with higher virulence compared to others tested, as both a pellicle and cord former, survivor in the human cell models tested, inducer of high and prolonged production of pro‐inflammatory cytokines, and the capacity to evade LL‐37.

Conclusions

Findings support intraspecies variation between MABS isolates.

Significance and Impact of the Study

These data indicate subversion of host immune defenses by environmental and clinical MABS isolates is nuanced and maybe isolate dependent, providing new information regarding the pathogenesis of NTM infections.

Non-tuberculous Mycobacterial Infection of the Musculoskeletal System Detected at Two Tertiary Medical Centres in Henan, China, 2016-2020

Non-tuberculous mycobacterial (NTM) infection of the musculoskeletal system is rare but poses a grave threat to public health. These infections yield non-specific symptoms that remain undetected until the development of the later stages of the disease. In this study, we performed a retrospective review of 25 cases of musculoskeletal NTM infection at two tertiary medical centres over a 5-year period to determine the clinical features and improve the current clinical diagnosis and treatment. The most common mycobacterial species detected were Mycobacterium fortuitum in eleven patients, Mycobacterium abscessus in eight patients, Mycobacterium houstonense in three patients, Mycobacterium avium in two patients, and Mycobacterium smegmatis in one patient. The sites of infection included the limbs and joints, most commonly the knee (ten patients) and foot (six patients). The median duration from the onset of symptoms to diagnosis was 2.5 months (0.8-13.5 months). Deep sinus tracts extending to the surgical site were observed in 60% of the patients (15/25), and granulomatous inflammation and granulomatous inflammation with necrosis occurred in 60% of the patients (15/25). All patients underwent surgical treatment for infection control, and all patients, except one, received antimycobacterial therapy based on drug sensitivity assays. The median duration of the antimicrobial chemotherapy was 5 months (range: 3-20 months). At the final follow-up, 24 patients presented with absence of recurrence and one patient succumbed owing to heart failure after debridement. Our findings highlight the importance of vigilance and improvements in the diagnostic methods for musculoskeletal NTM infection. Aggressive surgical treatment and antimycobacterial drug treatment can help achieve satisfactory results.

Genome reorganization during emergence of host-associated Mycobacterium abscessus

Mycobacterium abscessus is a rapid growing, free-living species of bacterium that also causes lung infections in humans. Human infections are usually acquired from the environment; however, dominant circulating clones (DCCs) have emerged recently in both M. abscessus subsp. massiliense and subsp. abscessus that appear to be transmitted among humans and are now globally distributed. These recently emerged clones are potentially informative about the ecological and evolutionary mechanisms of pathogen emergence and host adaptation. The geographical distribution of DCCs has been reported, but the genomic processes underlying their transition from environmental bacterium to human pathogen are not well characterized. To address this knowledge gap, we delineated the structure of M. abscessus subspecies abscessus and massiliense using genomic data from 200 clinical isolates of M. abscessus from seven geographical regions. We identified differences in overall patterns of lateral gene transfer (LGT) and barriers to LGT between subspecies and between environmental and host-adapted bacteria. We further characterized genome reorganization that accompanied bacterial host adaptation, inferring selection pressures acting at both genic and intergenic loci. We found that both subspecies encode an expansive pangenome with many genes at rare frequencies. Recombination appears more frequent in M. abscessus subsp. massiliense than in subsp. abscessus, consistent with prior reports. We found evidence suggesting that phage are exchanged between subspecies, despite genetic barriers evident elsewhere throughout the genome. Patterns of LGT differed according to niche, with less LGT observed among host-adapted DCCs versus environmental bacteria. We also found evidence suggesting that DCCs are under distinct selection pressures at both genic and intergenic sites. Our results indicate that host adaptation of M. abscessus was accompanied by major changes in genome evolution, including shifts in the apparent frequency of LGT and impacts of selection. Differences were evident among the DCCs as well, which varied in the degree of gene content remodelling, suggesting they were placed differently along the evolutionary trajectory toward host adaptation. These results provide insight into the evolutionary forces that reshape bacterial genomes as they emerge into the pathogenic niche.

[Mycobacterium abscessus, a model of resistance to multiple antibiotic classes]

Mycobacterium abscessus is an environmental fast-growing, non-tuberculous mycobacterium responsible for severe lung infections, especially in patients with underlying lung disorders such as cystic fibrosis. The standard chemotherapy combines a b-lactam (imipenem or cefoxitin), an aminoglycoside (amikacin) and a macrolide (clarithromycin or azithromycin). However, resistance of this bacterium to most antibiotic classes, including nearly all anti-tubercular drugs, leads frequently to treatment failure and considerably reduces the therapeutic arsenal available to the clinician. A comprehensive understanding of the innate and acquired resistance mechanisms is thus necessary to counteract M. abscessus lung infections.

Population Genomics of Mycobacterium abscessus from U.S. Cystic Fibrosis Care Centers

Rationale:Mycobacterium abscessus is a significant threat to individuals with cystic fibrosis (CF) because of innate drug resistance and potential transmission between patients. Recent studies described global dominant circulating clones of M. abscessus, but detailed genomic surveys have not yet been described for the United States. Objectives: We examined the genetic diversity of respiratory M. abscessus isolates from U.S. patients with CF and evaluated the potential for transmission events within CF Care Centers. Methods: Whole-genome sequencing was performed on 558 M. abscessus isolates from 266 patients with CF attending 48 CF Care Centers in 28 U.S. states as part of a nationwide surveillance program. U.S. isolates were also compared with 64 isolate genomes from 13 previous studies to evaluate the prevalence of recently described dominant circulating clones. Results: More than half of study patients with CF and M. abscessus had isolates within four dominant clones; two clones of M. abscessus subspecies (subsp.) abscessus (MAB) and two clones of M. abscessus subsp. massiliense (MMAS). Acquired drug resistance mutations for aminoglycosides and macrolides were rare in the isolate population, and they were not significantly enriched in dominant clones compared with unclustered isolates. For a subset of 55 patients, there was no relationship between dominant clones and diagnosis of active lung disease (P = 1.0). Twenty-nine clusters of genetically similar MAB isolates and eight clusters of genetically similar MMAS isolates were identified. Overall, 28 of 204 (14%) patients with MAB and 15 of 64 (23%) patients with MMAS had genetically isolates similar to those of at least one other patient at the same CF Care Center. Genetically similar isolates were also found between 60 of 204 (29%) patients with MAB and 19 of 64 (30%) patients with MMAS from different geographic locations. Conclusions: Our study reveals the predominant genotypes of M. abscessus and frequency of shared strains between patients in U.S. CF Care Centers. Integrated epidemiological and environmental studies would help to explain the widespread presence of dominant clones in the United States, including the potential for broad distribution in the environment. Single site studies using systematic, evidence-based approaches will be needed to establish the contributions of health care-associated transmission versus shared environmental exposures.

Molecular epidemiology and phylogenomic analysis of Mycobacterium abscessus clinical isolates in an Asian population

Mycobacterium abscessus comprises three subspecies: M. abscessus subsp. abscessus, M. abscessus subsp. bolletii, and M. abscessus subsp. massiliense. These closely related strains are typically multi-drug-resistant and can cause difficult-to-treat infections. Dominant clusters of isolates with increased pathogenic potential have been demonstrated in pulmonary infections in the global cystic fibrosis (CF) population. An investigation was performed on isolates cultured from an Asian, predominantly non-CF population to explore the phylogenomic relationships within our population and compare it to global M. abscessus isolates. Whole-genome-sequencing was performed on M. abscessus isolates between 2017 and 2019. Bioinformatic analysis was performed to determine multi-locus-sequence-type, to establish the phylogenetic relationships between isolates, and to identify virulence and resistance determinants in these isolates. A total of 210 isolates were included, of which 68.5 % (144/210) were respiratory samples. These isolates consisted of 140 (66.6 %) M. abscessus subsp. massiliense, 67 (31.9 %) M. abscessus subsp. abscessus, and three (1.4 %) M. abscessus subsp. bolletii. Dominant sequence-types in our population were similar to those of global CF isolates, but SNP differences in our population were comparatively wider despite the isolates being from the same geographical region. ESX (ESAT-6 secretory) cluster three appeared to occur most commonly in ST4 and ST6 M. abscessus subsp. massiliense, but other virulence factors did not demonstrate an association with isolate subspecies or sample source. We demonstrate that although similar predominant sequence-types are seen in our patient population, cross-transmission is absent. The risk of patient-to-patient transmission appears to be largely limited to the vulnerable CF population, indicating infection from environmental sources remains more common than human-to-human transmission. Resistance and virulence factors are largely consistent across the subspecies with the exception of clarithromycin susceptibility and ESX-3.

Nontuberculous mycobacteria in cystic fibrosis

PURPOSE OF REVIEW

Nontuberculous mycobacteria (NTM) are challenging infections among people with cystic fibrosis (pwCF) as the source, modes of transmission, and best practices for diagnosis and treatment are not known. Investigators have defined aspects of NTM infection that are unique to the CF population, as well as features shared with other conditions at risk. This review describes recent advances in our understanding of NTM infection among pwCF.

RECENT FINDINGS

The presence of dominant circulating clones of Mycobacterium abscessus within the CF community worldwide continue to be described, as well as pathogen phenotypes that could evoke greater environmental fitness and infectivity. The risk of direct or indirect transmission between pwCF remains an active focus of investigation, with divergent findings and conclusions reached in a site-specific fashion. Derived largely from studies in non-CF populations, new clinical guidelines are now available. A wide variety of agents are in preclinical development or early phase trials with promising findings, and new therapeutic targets have been identified as our understanding of the complex biology of NTM continues to expand.

SUMMARY

Significant challenges remain in the fight against NTM, however, recent advances in our understanding of the genetics, epidemiology and pathophysiology of pulmonary NTM infection in pwCF are leading efforts to improve clinical care.

The key factors contributing to the risk, diagnosis and treatment of non-tuberculous mycobacterial opportunistic infections

The incidence and prevalence of diseases caused by non-tuberculous mycobacteria (NTM) have been steadily increasing worldwide. NTM are environmental saprophytic organisms; however, a few strains are known to produce diseases in humans affecting pulmonary and extra-pulmonary sites. Although the environment is a major source of NTM infection, recent studies have shown that person-to-person dissemination could be an important transmission route for these microorganisms. Structural and functional lung defects and immunodeficiency are major risk factors for acquiring NTM infections. Diagnosis of NTM diseases is very complex owing to the necessity of distinguishing between a true pathogen and an environmental contaminant. Identification at the species level is critical due to differences in the antibiotic susceptibility patterns of various NTM strains. Such identification is mainly achieved by molecular methods; additionally, mass spectrometry (e.g., MALDI-TOF) is useful for NTM species determination. Natural resistance of NTM species to a wide spectrum of antibiotics makes prescribing treatment for NTM diseases very difficult. NTM therapy usually takes more than one year and requires multi-drug regimens, yet the outcome often remains poor. Therefore, alternatives to antibiotic therapy treatment methods is an area under active exploration. NTM infections are an active global health problem imposing the necessity for better diagnostic tools and more effective treatment methods.

Genomic Analysis of a Hospital-Associated Outbreak of Mycobacterium abscessus: Implications on Transmission

Whole genome sequencing (WGS) has recently been used to investigate acquisition of Mycobacterium abscessus (MABC). Investigators have reached conflicting conclusions about the meaning of genetic distances for interpretation of person-to-person transmission. Existing genomic studies were limited by a lack of WGS from environmental MABC isolates. In this study, we retrospectively analyzed the core and accessory genomes of 26 M. abscessus subsp. abscessus (MAA) isolates collected over seven years. Clinical isolates (n=22) were obtained from a large hospital-associated outbreak of MAA, the outbreak hospital before or after the outbreak, a neighboring hospital, and two outside laboratories. Environmental MAA isolates (n=4) were obtained from outbreak hospital water outlets. Phylogenomic analysis of study isolates revealed three clades with pairwise genetic distances ranging from 0-135 single nucleotide polymorphisms (SNPs). Compared to a reference environmental outbreak isolate, all seven clinical outbreak isolates and the remaining three environmental isolates had highly similar core and accessory genomes, differing by up to 7 SNPs and a median of 1.6% accessory genes, respectively. Although genomic comparisons of 15 non-outbreak clinical isolates revealed greater heterogeneity, five (33%) isolates had fewer than 20 SNPs compared to the reference environmental isolate, including two unrelated outside laboratory isolates with less than 4% accessory genome variation. Detailed genomic comparisons confirmed environmental acquisition of outbreak isolates of MAA. SNP distances alone, however, did not clearly differentiate the mechanism of acquisition of outbreak versus non-outbreak isolates. We conclude that successful investigation of MAA clusters requires molecular and epidemiologic components, ideally complemented by environmental sampling.

Whole Genome Sequencing in the Management of Non-Tuberculous Mycobacterial Infections

Infections caused by non-tuberculous mycobacteria (NTM) have been a public health problem in recent decades and contribute significantly to the clinical and economic burden globally. The diagnosis of infections is difficult and time-consuming and, in addition, the conventional diagnostics tests do not have sufficient discrimination power in species identification due to cross-reactions and not fully specific probes. However, technological advances have been made and the whole genome sequencing (WGS) method has been shown to be an essential part of routine diagnostics in clinical mycobacteriology laboratories. The use of this technology has contributed to the characterization of new species of mycobacteria, as well as the identification of gene mutations encoding resistance and virulence factors. Sequencing data also allowed to track global outbreaks of nosocomial NTM infections caused by M. abscessus complex and M. chimaera. To highlight the utility of WGS, we summarize recent scientific studies on WGS as a tool suitable for the management of NTM-induced infections in clinical practice.

Comparative Genomics of Mycobacterium avium Complex Reveals Signatures of Environment-Specific Adaptation and Community Acquisition

Nontuberculous mycobacteria, including those in the Mycobacterium avium complex (MAC), constitute an increasingly urgent threat to global public health. Ubiquitous in soil and water worldwide, MAC members cause a diverse array of infections in humans and animals that are often multidrug resistant, intractable, and deadly. MAC lung disease is of particular concern and is now more prevalent than tuberculosis in many countries, including the United States. Although the clinical importance of these microorganisms continues to expand, our understanding of their genomic diversity is limited, hampering basic and translational studies alike. Here, we leveraged a unique collection of genomes to characterize MAC population structure, gene content, and within-host strain dynamics in unprecedented detail. We found that different MAC species encode distinct suites of biomedically relevant genes, including antibiotic resistance genes and virulence factors, which may influence their distinct clinical manifestations. We observed that M. avium isolates from different sources—human pulmonary infections, human disseminated infections, animals, and natural environments—are readily distinguished by their core and accessory genomes, by their patterns of horizontal gene transfer, and by numerous specific genes, including virulence factors. We identified highly similar MAC strains from distinct patients within and across two geographically distinct clinical cohorts, providing important insights into the reservoirs which seed community acquisition. We also discovered a novel MAC genomospecies in one of these cohorts. Collectively, our results provide key genomic context for these emerging pathogens and will facilitate future exploration of MAC ecology, evolution, and pathogenesis.

IMPORTANCE Members of the Mycobacterium avium complex (MAC), a group of mycobacteria encompassing M. avium and its closest relatives, are omnipresent in natural environments and emerging pathogens of humans and animals. MAC infections are difficult to treat, sometimes fatal, and increasingly common. Here, we used comparative genomics to illuminate key aspects of MAC biology. We found that different MAC species and M. avium isolates from different sources encode distinct suites of clinically relevant genes, including those for virulence and antibiotic resistance. We identified highly similar MAC strains in patients from different states and decades, suggesting community acquisition from dispersed and stable reservoirs, and we discovered a novel MAC species. Our work provides valuable insight into the genomic features underlying these versatile pathogens.

Pulmonary nontuberculous mycobacterial infections and environmental factors: A review of the literature

BACKGROUND

Pulmonary nontuberculous mycobacterial (pNTM) infection is mainly acquired through the inhalation of bioaerosols. Nevertheless, behavioural restrictions are rarely given by clinicians to susceptible populations, in part because the available guidelines for pNTM management emphasize more diagnosis and treatment than prevention. Aim of this review is to clarify if pNTM prevention should routinely include recommendations about risk reducing behaviors.

METHODS

We used PubMed as biomedical database. We limited our search to the publication period 2000 to 2020 with selected keyword combinations including "nontuberculous mycobacteria", "water", "soil", and "exposure". Titles and abstract of selected articles were systematically screened. Articles were included in the analysis if they were published under free access through the digital library of the University of Brescia (Italy), and provided full text either in English, French, German or Italian. Articles were excluded if the topic was beyond the aim of our study. Finally, we selected 20 articles.

RESULTS

Studies disagree in identifying the type of aerosol posing the highest risk for the development of pNTM infection. In the retrieved publications the colonization of household niches has been associated with a higher risk of pNTM disease, such as in the exposure to shower aerosols. Considering the non-household settings, the exposure to aerosols in indoor swimming and the higher soil exposure (>2 h/week) seem to correlate with a higher risk to develop pNTM disease. According to our findings, randomized behavioural intervention studies are missing.

CONCLUSIONS

Stringent scientific evidence is missing to formulate recommendations on behavioural risk reduction for pNTM.

RNA-sequencing elucidates drug-specific mechanisms of antibiotic tolerance and resistance in M. abscessus

Mycobacterium abscessus is an opportunistic pathogen notorious for its resistance to most classes of antibiotics and low cure rates. M. abscessus carries an array of mostly unexplored defense mechanisms. A deeper understanding of antibiotic resistance and tolerance mechanisms is pivotal in development of targeted therapeutic regimens. We provide the first description of all major transcriptional mechanisms of tolerance to all antibiotics recommended in current guidelines, using RNA sequencing-guided experiments. M. abscessus ATCC 19977 bacteria were subjected to subinhibitory concentrations of clarithromycin (CLR), amikacin (AMK), tigecycline (TIG), cefoxitin (FOX), and clofazimine (CFZ) for 4 and 24 h, followed by RNA sequencing. To confirm key mechanisms of tolerance suggested by transcriptomic responses, we performed time-kill kinetic analysis using bacteria after preexposure to CLR, AMK, or TIG for 24 h and constructed isogenic knockout and knockdown strains. To assess strain specificity, pan-genome analysis of 35 strains from all three subspecies was performed. Mycobacterium abscessus shows both drug-specific and common transcriptomic responses to antibiotic exposure. Ribosome-targeting antibiotics CLR, AMK, and TIG elicit a common response characterized by upregulation of ribosome structural genes, the WhiB7 regulon and transferases, accompanied by downregulation of respiration through NuoA-N. Exposure to any of these drugs decreases susceptibility to ribosome-targeting drugs from multiple classes. The cytochrome bd-type quinol oxidase contributes to CFZ tolerance in M. abscessus, and the sigma factor sigH but not antisigma factor MAB_3542c is involved in TIG resistance. The observed transcriptomic responses are not strain-specific, as all genes involved in tolerance, except erm(41), are found in all included strains.

Dissemination of Mycobacterium abscessus via global transmission networks

Mycobacterium abscessus, a multidrug-resistant nontuberculous mycobacterium, has emerged as a major pathogen affecting people with cystic fibrosis (CF). Although originally thought to be acquired independently from the environment, most individuals are infected with one of several dominant circulating clones (DCCs), indicating the presence of global transmission networks of M. abscessus. How and when these clones emerged and spread globally is unclear. Here, we use evolutionary analyses of isolates from individuals both with and without CF to reconstruct the population history, spatiotemporal spread and recent transmission networks of the DCCs. We demonstrate synchronous expansion of six unrelated DCCs in the 1960s, a period associated with major changes in CF care and survival. Each of these clones has spread globally as a result of rare intercontinental transmission events. We show that the DCCs, but not environmentally acquired isolates, exhibit a specific smoking-associated mutational signature and that current transmission networks include individuals both with and without CF. We therefore propose that the DCCs initially emerged in non-CF populations but were then amplified and spread through the CF community. While individuals with CF are probably the most permissive host, non-CF individuals continue to play a key role in transmission networks and may facilitate long-distance transmission.

Epidemiology of Mycobacterium abscessus in England: an observational study

BACKGROUND

Mycobacterium abscessus has emerged as a significant clinical concern following reports that it is readily transmissible in health-care settings between patients with cystic fibrosis. We linked routinely collected whole-genome sequencing and health-care usage data with the aim of investigating the extent to which such transmission explains acquisition in patients with and without cystic fibrosis in England.

METHODS

In this retrospective observational study, we analysed consecutive M abscessus whole-genome sequencing data from England (beginning of February, 2015, to Nov 14, 2019) to identify genomically similar isolates. Linkage to a national health-care usage database was used to investigate possible contacts between patients. Multivariable regression analysis was done to investigate factors associated with acquisition of a genomically clustered strain (genomic distance <25 single nucleotide polymorphisms [SNPs]).

FINDINGS

2297 isolates from 906 patients underwent whole-genome sequencing as part of the routine Public Health England diagnostic service. Of 14 genomic clusters containing isolates from ten or more patients, all but one contained patients with cystic fibrosis and patients without cystic fibrosis. Patients with cystic fibrosis were equally likely to have clustered isolates (258 [60%] of 431 patients) as those without cystic fibrosis (322 [63%] of 513 patients; p=0·38). High-density phylogenetic clusters were randomly distributed over a wide geographical area. Most isolates with a closest genetic neighbour consistent with potential transmission had no identifiable relevant epidemiological contacts. Having a clustered isolate was independently associated with increasing age (adjusted odds ratio 1·14 per 10 years, 95% CI 1·04-1·26), but not time spent as an hospital inpatient or outpatient. We identified two sibling pairs with cystic fibrosis with genetically highly divergent isolates and one pair with closely related isolates, and 25 uninfected presumed household contacts with cystic fibrosis.

INTERPRETATION

Previously identified widely disseminated dominant clones of M abscessus are not restricted to patients with cystic fibrosis and occur in other chronic respiratory diseases. Although our analysis showed a small number of cases where person-to-person transmission could not be excluded, it did not support this being a major mechanism for M abscessus dissemination at a national level in England. Overall, these data should reassure patients and clinicians that the risk of acquisition from other patients in health-care settings is relatively low and motivate future research efforts to focus on identifying routes of acquisition outside of the cystic fibrosis health-care-associated niche.

FUNDING

The National Institute for Health Research, Health Data Research UK, The Wellcome Trust, The Medical Research Council, and Public Health England.

Genetic diversification of persistent Mycobacterium abscessus within cystic fibrosis patients

Mycobacterium (M.) abscessus infections in Cystic Fibrosis (CF) patients cause a deterioration of lung function. Treatment of these multidrug-resistant pathogens is associated with severe side-effects, while frequently unsuccessful. Insight on M. abscessus genomic evolvement during chronic lung infection would be beneficial for improving treatment strategies. A longitudinal study enrolling 42 CF patients was performed at a CF center in Berlin, Germany, to elaborate phylogeny and genomic diversification of in-patient M. abscessus. Eleven of the 42 CF patients were infected with M. abscessus. Five of these 11 patients were infected with global human-transmissible M. abscessus cluster strains. Phylogenetic analysis of 88 genomes from isolates of the 11 patients excluded occurrence of M. abscessus transmission among members of the study group. Genome sequencing and variant analysis of 30 isolates from 11 serial respiratory samples collected over 4.5 years from a chronically infected patient demonstrated accumulation of gene mutations. In total, 53 genes exhibiting non-synonymous variations were identified. Enrichment analysis emphasized genes involved in synthesis of glycopeptidolipids, genes from the embABC (arabinosyltransferase) operon, betA (glucose-methanol-choline oxidoreductase) and choD (cholesterol oxidase). Genetic diversity evolved in a variety of virulence- and resistance-associated genes. The strategy of M. abscessus populations in chronic lung infection is not clonal expansion of dominant variants, but to sustain simultaneously a wide range of genetic variants facilitating adaptation of the population to changing living conditions in the lung. Genomic diversification during chronic infection requires increased attention when new control strategies against M. abscessus infections are explored.

Challenges of diagnosing and treating non-tuberculous mycobacterial pulmonary disease [NTM-PD]: A case series

Non-tuberculous mycobacterial pulmonary disease (NTM-PD) may simulate Pulmonary Tuberculosis (PTB) in its clinical and radiological expression posing a diagnostic dilemma and challenge to the treating physician, especially in high TB prevalent countries. Though recent emerging data indicates inter-human transmission, infection with non-tuberculous mycobacteria (NTM) is commonly acquired from the environmental sources [1]. NTM can produce disease not only in immunocompromised populations but also in healthy individuals leading to significant morbidity and mortality [2]. Unlike PTB, NTM-PD is usually difficult to confirm and speciate in resource limited clinical settings and high TB endemic countries due to non-availability, poor accessibility and affordability to a specific culture facility. Apart from diagnostic challenges, adverse drug effects with treatment leading to non-adherence are another vexing problem. We present here case descriptions of four patients of NTM-PD, confirmed by culture isolates, one was a rapid grower and the other three were slow growers. All four patients were treated with available guideline-based treatment protocols and followed up.

Clinical course of peritoneal dialysis-related peritonitis due to non-tuberculosis mycobacterium - A single centre experience spanning 20 years

BACKGROUND

Peritoneal dialysis (PD)-related peritonitis caused by non-tuberculous mycobacteria (NTM) are difficult to diagnose, is associated with significant morbidity and mortality, and clinical course remains unclear. We determined the prevalence and clinical course of peritonitis caused by these organisms through our kidney registry over 20-year period.

METHOD

We reviewed all patients with NTM peritonitis identified in our tertiary centre between July 2000 and July 2020. The demographic characteristics, microbiological and clinical outcomes were examined.

RESULT

Among 27 patients identified, 20 patients presented with abdominal pain and all had cloudy peritoneal fluid. Twenty-one cases had concomitant exit site infection and 14 cases had prior antibiotic use. The majority of the cases are caused by Mycobacterium chelonae (37%) and Mycobacterium fortuitum (29.7%), with most being resistant to fluoroquinolones (59.3%) and cefoxitin (73.1%). They are all sensitive to amikacin otherwise. None of the cases achieve primary response at day 10 and 20 cases resulted in Tenckhoff catheter removal. Only two of them were able to resume PD. Eight patients died in our cohort. The presence of exit site infection, the use of prior antibiotics and topical disinfectants did not associate with a poorer outcome.

CONCLUSION

NTM peritonitis remains difficult to treat and often with a delay in diagnosis. Refractory peritonitis with negative culture and a poor response to standard antibiotics should raise a possibility of NTM infection and prompt catheter removal and an expert with experience treating NTM infections should be consulted.

Clinical Whole Genome Sequencing for Clarithromycin and Amikacin Resistance Prediction and Subspecies Identification of Mycobacterium abscessus

Mycobacterium abscessus infections are an emerging health care concern in patients with chronic pulmonary diseases, leading to high morbidity and mortality. One major challenge is resistance to clarithromycin, a cornerstone antibiotic with high efficacy. Therefore, treatment is primarily guided by phenotypic susceptibility results of clarithromycin, which requires extended incubation to assess for inducible resistance. Resistance mechanisms for clarithromycin include induction of erm(41) and mutations in the 23S rRNA gene (rrl). In addition, mutations in the 16S rRNA encoding gene (rrs) can confer high-level amikacin resistance, another essential drug in the treatment of M. abscessus infections. Herein, we developed a clinical whole genome sequencing (WGS) assay for clarithromycin resistance based on rrl and erm(41) gene sequences and amikacin resistance based on the rrs sequence in M. abscessus, as well as subspecies identification. Genotypic-based predictions were determined for 104 isolates from 68 patients. The overall accuracy of genotypic prediction for clarithromycin compared with phenotypic susceptibility results was 100% (95% CI, 96.45%-100%). For amikacin, we also obtained 100% accuracy (95% CI, 96.52%-100%). The high concordance between the genotypic and phenotypic results demonstrates that a WGS-based assay can be used in a clinical laboratory for determining resistance to clarithromycin and amikacin in M. abscessus isolates. WGS can also provide subspecies identification and high-definition phylogenetic information for more accurate M. abscessus strain typing.

Global phylogenomic analyses of Mycobacterium abscessus provide context for non cystic fibrosis infections and the evolution of antibiotic resistance

Mycobacterium abscessus (MAB) is an emerging pathogen that leads to chronic lung infections. To date, the global population structure of non-cystic fibrosis (CF) MAB and evolutionary patterns of drug resistance emergence have not been investigated. Here we construct a global dataset of 1,279 MAB whole genomes from CF or non-CF patients. We utilize whole genome analysis to assess relatedness, phylogeography, and drug resistance evolution. MAB isolates from CF and non-CF hosts are interspersed throughout the phylogeny, such that the majority of dominant circulating clones include isolates from both populations, indicating that global spread of MAB clones is not sequestered to CF contexts. We identify a large clade of M. abscessus harboring the erm(41) T28C mutation, predicted to confer macrolide susceptibility in this otherwise macrolide-resistant species. Identification of multiple evolutionary events within this clade, consistent with regain of wild type, intrinsic macrolide resistance, underscores the critical importance of macrolides in MAB.

Mycobacterium abscessus is an emerging infection that usually affects patients with structural lung diseases such as cystic fibrosis (CF). Here, the authors use phylogenetic analyses to demonstrate close relationships between isolates from CF and non-CF patients and identify antibiotic resistance markers.

Tap Water Avoidance Decreases Rates of Hospital-onset Pulmonary Nontuberculous Mycobacteria

We analyzed the impact of a hospital tap water avoidance protocol on respiratory isolation of nontuberculous mycobacteria (NTM). After protocol implementation, hospital-onset episodes of respiratory NTM isolation on high-risk units decreased from 41.0 to 9.9 episodes per 10 000 patient-days (incidence rate ratio, 0.24; 95% confidence interval, .17-.34; P < .0001).

Genomic characterization of sporadic isolates of the dominant clone of Mycobacterium abscessus subspecies massiliense

Recent studies have characterized a dominant clone (Clone 1) of Mycobacterium abscessus subspecies massiliense (M. massiliense) associated with high prevalence in cystic fibrosis (CF) patients, pulmonary outbreaks in the United States (US) and United Kingdom (UK), and a Brazilian epidemic of skin infections. The prevalence of Clone 1 in non-CF patients in the US and the relationship of sporadic US isolates to outbreak clones are not known. We surveyed a reference US Mycobacteria Laboratory and a US biorepository of CF-associated Mycobacteria isolates for Clone 1. We then compared genomic variation and antimicrobial resistance (AMR) mutations between sporadic non-CF, CF, and outbreak Clone 1 isolates. Among reference lab samples, 57/147 (39%) of patients with M. massiliense had Clone 1, including pulmonary and extrapulmonary infections, compared to 11/64 (17%) in the CF isolate biorepository. Core and pan genome analyses revealed that outbreak isolates had similar numbers of single nucleotide polymorphisms (SNPs) and accessory genes as sporadic US Clone 1 isolates. However, pulmonary outbreak isolates were more likely to have AMR mutations compared to sporadic isolates. Clone 1 isolates are present among non-CF and CF patients across the US, but additional studies will be needed to resolve potential routes of transmission and spread.

Non-tuberculous mycobacteria: a disease beyond TB and preparedness in India

BACKGROUND AND METHODS

Fifty-six Indian studies on NTM diseases were selected between 1981 and 2020 from various electronic databases (PubMed, EMBASE, Medline, BIOSIS preview, and Scopus) for systematic review.

RESULTS

NTM isolation rates increased from 0.9% between 2001 and 2010 to 1.6% between 2011 and 2020. Prevalence of NTM-pulmonary disease (NTM-PD) among presumptive-TB patients in India was 1.1% (395/34,829). M. avium complex (MAC) (19%) was most commonly isolated from pulmonary specimens followed by M. chelonae (10%), M. fortuitum (9.8%), and M. abscessus (8.8%). M. fortuitum (35.5%), M. chelonae (23.6%) and M. abscessus (15%) were frequently reported from extra-pulmonary specimens. Patients with NTM-PD were mostly treated with a macrolide-based three-drug regimen. Clarithromycin-based-drug regimen in combination with amikacin, ciprofloxacin and several other drugs (rifampicin, imipenem, ofloxacin, linezolid, azithromycin) was used for treatment of EP-NTM. Median duration of the treatment in NTM-PD was 12 months, (6-18 months) whereas it was 6 months (3.1-8.7 months) in EP-NTM. Treatment was successful in 45% (19/42) of NTM-PD patients and 75% (93/124) of EP-NTM patients.

CONCLUSION

It is concluded from this review that most Indian studies have published laboratory data on NTM isolation and speciation and lacked information on clinical, microbiological and radiological correlation and treatment outcome details. Future studies should address these issues while publishing on NTM diseases.

MAB_2355c Confers Macrolide Resistance in Mycobacterium abscessus by Ribosome Protection

Macrolide resistance is always a concern when treating Mycobacterium abscessus infections. MAB_2355c was identified previously as a possible new factor that confers the intrinsic resistance of 194 clinical M. abscessus isolates to clarithromycin. Herein, the potential mechanism by which MAB_2355c exerts macrolide resistance was explored by bioinformatics analysis, MAB_2355c cloning and protein purification, ATP hydrolysis assay, gene knockout and complementation, antibiotic sensitivity, and transcription-translation assays. MAB_2355c is a putative ATP-binding cassette F (ABC-F) family protein. Purified MAB_2355c protein exhibits ATP hydrolysis activity, which can be inhibited by ribosome-targeting antibiotics. MAB_2355c mRNA expression is upregulated more significantly after exposure to macrolides than after exposure to other ribosome-targeting antibiotics. MAB_2355c deleted strains showed increased sensitivity to macrolides, which was reduced by MAB_2355c complementation. Finally, MAB_2355c rescued the transcription and translation activities affected by macrolides in vitro. These findings suggest that MAB_2355c confers the resistance of M. abscessus to macrolides by ribosome protection, thus complementing other known resistance mechanisms.

Nontuberculous Mycobacteria in Humans, Animals, and Water in Zambia: A Systematic Review

Nontuberculous mycobacteria (NTM) are environmental opportunistic pathogens of humans and animals that are emerging with a serious public health impact particularly in individuals with Acquired Immunodeficiency Syndromes. Recent scientific evidence is shifting from NTMs being known as traditional environmental organisms to serious pathogenic organisms in both animals and humans. In humans, factors attributable to this rise have been linked mainly to Human Immunodeficiency Virus and Acquired Immunodeficiency Syndrome pandemic. In recent years there has been an increase in multidrug resistant Tuberculosis in Zambia and it is thought that NTMs could possibly be the cause. This study was therefore formulated to review available information on the prevalence of NTM in humans, animals and the environment, species distribution, zoonotic potential and public health importance in Zambia. This review was conducted in accordance with PRISMA guidelines. A literature search was done in PubMed and Google scholar using predefined search terms such as ‘nontuberculous mycobacteria’, ‘atypical mycobacteria’, ‘mycobacteria other than mycobacterium tuberculosis’ and ‘Zambia’, in combination with Boolean operators (AND, OR). This particular systematic review draws findings based on literature search between 2000 and 2020. Through literature search 243 papers were identified, 23 duplicates were identified and removed and 206 articles were excluded as they did not meet the inclusion criteria. The full text of the remaining 14 articles were considered for this review. The overall prevalence of NTM in humans was 24.39%, in water 21.5%, in animals 16.05% of which the prevalence in cattle was 14.81% and Kafue Lechwe 1.23%. Mycobacterium intracellulare was the most common isolated nontuberculous mycobacteria in humans and cattle while Mycobacterium gordonae was the most common in water, and Mycobacterium stomatepiae sp Nov in Kafue Lechwe. Nontuberculous mycobacteria are an emerging public health threat in Zambia both in humans and animals and this calls for the need for molecular information on the zoonotic transmission of nontuberculous mycobacteria. Increased awareness of nontuberculous mycobacteria diseases among clinicians and laboratory personnel is crucial for patient management and an essential step for facilitating the identification of nontuberculous mycobacteria species in laboratories.

Increased Virulence of Outer Membrane Porin Mutants of Mycobacterium abscessus

Chronic pulmonary infections caused by non-tuberculous mycobacteria of the Mycobacterium abscessus complex (MABSC) are emerging as a global health problem and pose a threat to susceptible individuals with structural lung disease such as cystic fibrosis. The molecular mechanisms underlying the pathogenicity and intrinsic resistance of MABSC to antibiotics remain largely unknown. The involvement of Msp-type porins in the virulence and biocide resistance of some rapidly growing non-tuberculous mycobacteria and the finding of deletions and rearrangements in the porin genes of serially collected MABSC isolates from cystic fibrosis patients prompted us to investigate the contribution of these major surface proteins to MABSC infection. Inactivation by allelic replacement of the each of the two Msp-type porin genes of M. abscessus subsp. massiliense CIP108297, mmpA and mmpB, led to a marked increase in the virulence and pathogenicity of both mutants in murine macrophages and infected mice. Neither of the mutants were found to be significantly more resistant to antibiotics. These results suggest that adaptation to the host environment rather than antibiotic pressure is the key driver of the emergence of porin mutants during infection.

Racemization-free synthesis of Nα-2-thiophenoyl-phenylalanine-2-morpholinoanilide enantiomers and their antimycobacterial activity

Nα-2-thiophenoyl-d-phenylalanine-2-morpholinoanilide (MMV688845, IUPAC: N-(1-((2-morpholinophenyl)amino)-1-oxo-3-phenylpropan-2-yl)thiophene-2-carboxamide) from the Pathogen Box^® library (Medicines for Malaria Ventures, MMV) is a promising lead compound for antimycobacterial drug development. Two straightforward synthetic routes to the title compound starting from phenylalanine or its Boc-protected derivative are reported. Employing Boc-phenylalanine as starting material and the T3P^® and PyBOP^® amide coupling reagents enables racemization-free synthesis, avoiding the need for subsequent separation of the enantiomers. The crystal structure of the racemic counterpart gives insight into the molecular structure and hydrogen bonding interactions in the solid state. The R-enantiomer of the title compound (derived from d-phenylalanine) exhibits activity against non-pathogenic and pathogenic mycobacterial strains, whereas the S-enantiomer is inactive. Neither of the enantiomers and the racemate of the title compound shows cytotoxicity against various mammalian cells.

Species-Specific Interferon-Gamma Release Assay for the Diagnosis of Mycobacterium abscessus Complex Infection

Mycobacterium abscessus complex (MABC) infection has a devastating impact on the course of cystic fibrosis (CF) and non-CF lung disease. Diagnosis of MABC pulmonary disease is challenging, and current diagnostic approaches lack accuracy, especially in CF. In this study, we aimed to establish an MABC-specific interferon-γ release assay to detect host immune responses to MABC and improve diagnostics of MABC infection by the detection of antigen-specific T cells. Four species-specific proteins of MABC were overexpressed in an Escherichia coli expression system. Purified proteins were used to stimulate peripheral blood mononuclear cells of study subjects in an ELISpot assay. Interferon-γ response of 12 subjects with established diagnosis of MABC infection (10 CF and two non-CF) was compared with 35 controls (22 CF and 13 non-CF) distributed to three control groups, 17 CF subjects without NTM infection, nine subjects with NTM infection other than MABC, and nine subjects with tuberculosis. Cellular in vitro responses in the MABC group were stronger than in the control groups, especially toward the protein MAB_0405c (39 vs. 4 spots per 300,000 PBMC, p = 0.004; data represent mean values) in all patients and also in the subgroup of CF subjects (39 spots vs. 1 spot, p = 0.003). Receiver operating characteristic curve analysis indicated that spot numbers of at least 20 were highly predictive of MABC infection (all patients: area under curve 0.773, sensitivity 58%, and specificity 94%; CF patients: area under curve 0.818, sensitivity 60%, and specificity 100%). In conclusion, we identified MAB_0405c as a protein that may stimulate MABC-specific interferon-γ secretion and may add to the diagnosis of MABC infection in affected patients.

In vitro susceptibility of Mycobacterium abscessus complex and feasibility of standardizing treatment regimens

OBJECTIVES

To determine the in vitro susceptibility of members of the Mycobacterium abscessus complex to routinely tested antibiotics and to an extended antibiotic panel.

METHODS

Non-duplicate isolates for which susceptibility testing results were available were included in this study. Retrospective laboratory records were reviewed, including tigecycline susceptibility results, and testing was performed with additional drugs, including vancomycin, dalbavancin, telavancin, oritavancin, rifabutin, delafloxacin, eravacycline, clofazimine and bedaquiline using broth microdilution (Sensititre, Thermo Fisher).

RESULTS

A total of 218 M. abscessus complex isolates were included for retrospective review, of which 151 were respiratory isolates. Of these 218 isolates, 211 were available for additional testing with the extended antibiotic panel. Of these, 146 were respiratory isolates. One isolate had a vancomycin MIC of 2 mg/L and MICs of all other isolates were >8 mg/L. All isolates had MICs of >8 mg/L for oritavancin, dalbavancin and telavancin. One isolate had a delafloxacin MIC of 4 mg/L and MICs of all other isolates were >8 mg/L. The MIC50/MIC90s of rifabutin, tigecycline, eravacycline, clofazimine and bedaquiline were 16/32, 0.5/1, 0.12/0.25, 0.12/0.25 and 0.06/0.12 mg/L, respectively.

CONCLUSIONS

In vitro activity was demonstrated for clofazimine, bedaquiline and eravacycline, indicating potential for inclusion as standardized therapy for M. abscessus complex infections.

Genome-Wide Essentiality Analysis of Mycobacterium abscessus by Saturated Transposon Mutagenesis and Deep Sequencing

Mycobacterium abscessus is an emerging opportunistic human pathogen that naturally resists most major classes of antibiotics, making infections difficult to treat. Thus far, little is known about M. abscessus physiology, pathogenesis, and drug resistance. Genome-wide analyses have comprehensively catalogued genes with essential functions in Mycobacterium tuberculosis and Mycobacterium avium subsp. hominissuis (here, M. avium) but not in M. abscessus. By optimizing transduction conditions, we achieved full saturation of TA insertion sites with Himar1 transposon mutagenesis in the M. abscessus ATCC 19977^T genome, as confirmed by deep sequencing prior to essentiality analyses of annotated genes and other genomic features. The overall densities of inserted TA sites (85.7%), unoccupied TA sites (14.3%), and nonpermissive TA sites (8.1%) were similar to results in M. tuberculosis and M. avium. Of the 4,920 annotated genes, 326 were identified as essential, 269 (83%) of which have mutual homology with essential M. tuberculosis genes, while 39 (12%) are homologous to genes that are not essential in M. tuberculosis and M. avium, and 11 (3.4%) only have homologs in M. avium. Interestingly, 7 (2.1%) essential M. abscessus genes have no homologs in either M. tuberculosis or M. avium, two of which were found in phage-like elements. Most essential genes are involved in DNA replication, RNA transcription and translation, and posttranslational events to synthesize important macromolecules. Some essential genes may be involved in M. abscessus pathogenesis and antibiotics response, including certain essential tRNAs and new short open reading frames. Our findings will help to pave the way for better understanding of M. abscessus and benefit development of novel bactericidal drugs against M. abscessus. IMPORTANCE Limited knowledge regarding Mycobacterium abscessus pathogenesis and intrinsic resistance to most classes of antibiotics is a major obstacle to developing more effective strategies to prevent and mitigate disease. Using optimized procedures for Himar1 transposon mutagenesis and deep sequencing, we performed a comprehensive analysis to identify M. abscessus genetic elements essential for in vitro growth and compare them to similar data sets for M. tuberculosis and M. avium subsp. hominissuis. Most essential M. abscessus genes have mutual homology with essential M. tuberculosis genes, providing a foundation for leveraging available knowledge from M. tuberculosis to develop more effective drugs and other interventions against M. abscessus. A small number of essential genes unique to M. abscessus deserve further attention to gain insights into what makes M. abscessus different from other mycobacteria. The essential genes and other genomic features such as short open reading frames and noncoding RNA identified here will provide useful information for future study of M. abscessus pathogenicity and new drug development.

Activity of Oritavancin and Its Synergy with Other Antibiotics against Mycobacterium abscessus Infection In Vitro and In Vivo

Background: Pulmonary disease caused by Mycobacterium abscessus (M. abscessus) spreads around the world, and this disease is extremely difficult to treat due to intrinsic and acquired resistance of the pathogen to many approved antibiotics. M. abscessus is regarded as one of the most drug-resistant mycobacteria, with very limited therapeutic options. Methods: Whole-cell growth inhibition assays was performed to screen and identify novel inhibitors. The IC₅₀ of the target compounds were tested against THP-1 cells was determined to calculate the selectivity index, and then time–kill kinetics assay was performed against M. abscessus. Subsequently, the synergy of oritavancin with other antibiotics was evaluated by using checkerboard method. Finally, in vivo efficacy was determined in an immunosuppressive murine model simulating M. abscessus infection. Results: We have identified oritavancin as a potential agent against M. abscessus. Oritavancin exhibited time-concentration dependent bactericidal activity against M. abscessus and it also displayed synergy with clarithromycin, tigecycline, cefoxitin, moxifloxacin, and meropenem in vitro. Additionally, oritavancin had bactericidal effect on intracellular M. abscessus. Oritavancin significantly reduced bacterial load in lung when it was used alone or in combination with cefoxitin and meropenem. Conclusions: Our in vitro and in vivo assay results indicated that oritavancin may be a viable treatment option against M. abscessus infection.

Photocross-Linked Antimicrobial Amino-Siloxane Elastomers

Mechanically robust bulk antimicrobial polymers are one way to address disease transmission via contaminated surfaces. Here, we demonstrate the visible light photo-oxidative cross-linking of amine-containing PDMS using a single-component, solvent-free system where amines have a dual role as antimicrobial functionalities and cross-linking sites. Rose Bengal, a xanthene dye used as a fluorescent stain, is thermally reacted with the polymer to give a solvent-free liquid siloxane that can generate reactive singlet oxygen upon aerobic green light irradiation, coupling the amine functionalities into imine cross-links. Photorheological experiments demonstrate that light intensity is the largest kinetic factor in the photo-oxidative curing of these polymers. Room temperature irradiation under an ambient atmosphere results in free-standing elastic materials with mechanical properties that depend on the amount of Rose Bengal present. An ultimate elongation strain of 117% and Young's modulus of 2.15 MPa were observed for the highest dye loading, with both mechanical properties found to be higher than those for the same solution-based dye amounts. We demonstrate that the solvent-free nature of the material can be exploited to generate 3D structures using low-temperature deposition as well as direct-write patterning and photolithography on glass substrates. The antimicrobial activity was investigated, with the cross-linked material demonstrating greater efficacy against E. coli (Gram negative) compared with MRSA (Gram positive) bacterial strains and inducing complete cell lysis of incubated CHO-K1 mammalian cells, demonstrating applicability as a mechanically robust single-component antimicrobial elastomer.

Stepwise pathogenic evolution of Mycobacterium abscessus

Although almost all mycobacterial species are saprophytic environmental organisms, a few, such as Mycobacterium tuberculosis, have evolved to cause transmissible human infection. By analyzing the recent emergence and spread of the environmental organism M. abscessus through the global cystic fibrosis population, we have defined key, generalizable steps involved in the pathogenic evolution of mycobacteria. We show that epigenetic modifiers, acquired through horizontal gene transfer, cause saltational increases in the pathogenic potential of specific environmental clones. Allopatric parallel evolution during chronic lung infection then promotes rapid increases in virulence through mutations in a discrete gene network; these mutations enhance growth within macrophages but impair fomite survival. As a consequence, we observe constrained pathogenic evolution while person-to-person transmission remains indirect, but postulate accelerated pathogenic adaptation once direct transmission is possible, as observed for M. tuberculosis Our findings indicate how key interventions, such as early treatment and cross-infection control, might restrict the spread of existing mycobacterial pathogens and prevent new, emergent ones.

Rapid macrolide and amikacin resistance testing for Mycobacterium abscessus in people with cystic fibrosis

Introduction. Mycobacterium abscessus complex (MABSC) is an environmental organism and opportunistic pathogen. MABSC pulmonary infections in people with cystic fibrosis are of growing clinical concern. Resistance data guide the use of macrolides and amikacin in MABSC pulmonary disease treatment. MABSC can acquire resistance against macrolides or amikacin via 23S or 16S rRNA gene mutations, respectively.Gap Statement. Current culture-based methods for MABSC detection and antibiotic resistance characterization are typically prolonged, limiting their utility to directly inform treatment or clinical trials. Culture-independent molecular methods may help address this limitation.Aim. To develop real-time PCR assays for characterization of key 23S or 16S rRNA gene mutations associated with constitutive resistance in MABSC.Methodology. We designed two real-time PCR assays to detect the key 23S and 16S rRNA gene mutations. The highly conserved nature of rRNA genes was a major design challenge. To reduce potential cross-reactivity, primers included non-template bases and targeted single-nucleotide polymorphisms unique to MABSC. We applied these assays, as well as a previously developed real-time PCR assay for MABSC detection, to 968 respiratory samples from people with cystic fibrosis. The results from the molecular methods were compared to those for gold standard culture methods and 23S and 16S rRNA gene sequencing.Results.The real-time PCR MABSC detection assay provided a sensitivity of 83.8 % and a specificity of 97.8 % compared to culture. The results from the real-time PCR resistance detection assays were mostly concordant (>77.4 %) with cultured isolate sequencing. The real-time PCR resistance detection assays identified several samples harbouring both resistant and susceptible MABSC, while culture-dependent methods only identified susceptible MABSC in these samples.Conclusion. Using the molecular methods described here, results for health care providers or researchers could be available days or weeks earlier than is currently possible via culture-based antibiotic susceptibility testing.

Population genomics provides insights into the evolution and adaptation to humans of the waterborne pathogen Mycobacterium kansasii

Mycobacterium kansasii can cause serious pulmonary disease. It belongs to a group of closely-related species of non-tuberculous mycobacteria known as the M. kansasii complex (MKC). Here, we report a population genomics analysis of 358 MKC isolates from worldwide water and clinical sources. We find that recombination, likely mediated by distributive conjugative transfer, has contributed to speciation and on-going diversification of the MKC. Our analyses support municipal water as a main source of MKC infections. Furthermore, nearly 80% of the MKC infections are due to closely-related M. kansasii strains, forming a main cluster that apparently originated in the 1900s and subsequently expanded globally. Bioinformatic analyses indicate that several genes involved in metabolism (e.g., maintenance of the methylcitrate cycle), ESX-I secretion, metal ion homeostasis and cell surface remodelling may have contributed to M. kansasii's success and its ongoing adaptation to the human host.

Investigation of two cases of Mycobacterium chelonae infection in haemato-oncology patients using whole-genome sequencing and a potential link to the hospital water supply

BACKGROUND

Haemato-oncology patients are at increased risk of infection from atypical mycobacteria such as Mycobacterium chelonae which are commonly found in both domestic and hospital water systems.

AIMS

To describe the investigation and control measures following two patient cases of M. chelonae and positive water samples in the study hospital.

METHODS

Water testing was undertaken from outlets, storage tanks and mains supply. Whole-genome sequencing (WGS) was used to compare patient and positive water samples. The subsequent infection control measures implemented are described.

FINDINGS

The WGS results showed two main populations of M. chelonae within the group of sampled isolates. The results showed that the patient strains were unrelated to each other, but that the isolate from one patient was closely related to environmental samples from water outlets, supporting nosocomial acquisition.

CONCLUSIONS

WGS was used to investigate two patient cases of M. chelonae and positive water samples from a hospital water supply. Relevant control measures and the potential for chemical dosing of water systems to enhance proliferation of atypical mycobacteria are discussed.

Non tuberculous mycobacteria pulmonary disease: patients and clinicians working together to improve the evidence base for care

Non-tuberculous mycobacterial pulmonary disease is on the rise globally. It is often missed, and causes significant morbidity and even mortality. Here, members of a clinical research network and a patient support group discuss some of the current key issues in NTM management. In addition to the need for research into epidemiology, immunology and treatment, we recommend greater use of patient and clinician networks to: (i) educate primary and secondary care clinicians to develop a high index of suspicion when investigating and treating at risk populations. (ii) promote a multidisciplinary team. (iii) promote shared patient-clinician decision making throughout care. (iv) incorporate use of patient self-report measures to assess progress and outcomes. (v) increase education of patients on their illness and its management. (vi) recruit patients into research projects and registries to improve the clinical evidence base. (vii) increase co-production of research with key stakeholders such as patients and their families, using expert patients and patient groups. (viii) understand more about the psychological, social and economic consequences of the disease.

Phage Therapy for Mycobacterium Abscessus and Strategies to Improve Outcomes

Members of Mycobacterium abscessus complex are known for causing severe, chronic infections. Members of M. abscessus are a new "antibiotic nightmare" as one of the most resistant organisms to chemotherapeutic agents. Treatment of these infections is challenging due to the either intrinsic or acquired resistance of the M. abscessus complex to the available antibiotics. Recently, successful phage therapy with a cocktail of three phages (one natural lytic phage and two engineered phages) every 12 h for at least 32 weeks has been reported against a severe case of the disseminated M. abscessus subsp. massiliense infection, which underlines the high value of phages against drug-resistant superbugs. This report also highlighted the limitations of phage therapy, such as the absence of lytic phages with a broad host-range against all strains and subspecies of the M. abscessus complex and also the risk of phage resistant bacteria over treatment. Cutting-edge genomic technologies have facilitated the development of engineered phages for therapeutic purposes by introducing new desirable properties, changing host-range and arming the phages with additional killing genes. Here, we review the available literature and suggest new potential solutions based on the progress in phage engineering that can help to overcome the present limitations of M. abscessus treatment.

The double-edged sword of Tregs in M tuberculosis, M avium, and M absessus infection

Immunity against different Mycobacteria species targeting the lung requires distinctly different pulmonary immune responses for bacterial clearance. Many parameters of acquired and regulatory immune responses differ quantitatively and qualitatively from immunity during infection with Mycobacteria species. Nontuberculosis Mycobacteria species (NTM) Mycobacterium avium- (M avium), Mycobacterium abscessus-(M abscessus), and the Mycobacteria species Mycobacterium tuberculosis-(Mtb). Herein, we discuss the potential implications of acquired and regulatory immune responses in the context of animal and human studies, as well as future directions for efforts to treat Mycobacteria diseases.

Antimicrobial susceptibility profiles of Mycobacterium abscessus complex isolates from respiratory specimens in Shanghai, China

OBJECTIVES

The aim of this study was to compare the antibiotic susceptibility profiles of Mycobacterium abscessus complex (MABC) isolates and to investigate the relationship between susceptibility profiles and genetic mechanisms of macrolide resistance.

METHODS

More than 200 isolates collected from respiratory specimens between 2014 and 2018 were randomly analysed in this study. Minimum inhibitory concentrations (Mics) of ten potential antimicrobial agents were determined by the microplate alamarBlue assay.

RESULTS

We identified 43 MABC isolates, including 32 M. abscessus subsp. abscessus (M. abscessus) (6 from immunocompromised patients) and 11 M. abscessus subsp. massiliense (M. massiliense). The majority of MABC isolates were susceptible to amikacin (96.9% and 100.0% for M. abscessus and M. massiliense, respectively), linezolid (96.9% and 100.0%, respectively), cefoxitin (100.0% and 100.0%, respectively), imipenem (90.6% and 72.7%, respectively) and tobramycin (90.6% and 72.7%, respectively). The resistance rates to clarithromycin and doxycycline in isolates of M. abscessus (68.8% and 100.0%) were significantly higher than those in isolates of M. massiliense (18.2% and 63.6%) (P < 0.05), whereas the percentage of tobramycin-resistant isolates among M. abscessus (9.4%) was significantly lower than among M. massiliense (27.3%) (P = 0.007). Sequencing analyses showed significant differences between erm(41) of M. abscessus and M. massiliense.

CONCLUSION

Mycobacterium abscessus is the dominant pathogen of pulmonary MABC infections in our hospital. Aminoglycosides (amikacin and tobramycin), β-lactams (cefoxitin and imipenem) and linezolid exhibited potent inhibitory activity against MABC in vitro. The erm(41) gene may be a promising marker to predict macrolide susceptibility for M. abscessus.

Drug Resistance in Nontuberculous Mycobacteria: Mechanisms and Models

The genus Mycobacteria comprises a multitude of species known to cause serious disease in humans, including Mycobacterium tuberculosis and M. leprae, the responsible agents for tuberculosis and leprosy, respectively. In addition, there is a worldwide spike in the number of infections caused by a mixed group of species such as the M. avium, M. abscessus and M. ulcerans complexes, collectively called nontuberculous mycobacteria (NTMs). The situation is forecasted to worsen because, like tuberculosis, NTMs either naturally possess or are developing high resistance against conventional antibiotics. It is, therefore, important to implement and develop models that allow us to effectively examine the fundamental questions of NTM virulence, as well as to apply them for the discovery of new and improved therapies. This literature review will focus on the known molecular mechanisms behind drug resistance in NTM and the current models that may be used to test new effective antimicrobial therapies.

Glycopeptidolipid Genotype Correlates With the Severity of Mycobacterium abscessus Lung Disease

BACKGROUND

Smooth and rough colony morphotypes of Mycobacterium abscessus are associated with virulence, but some isolates form both smooth and rough colonies, impeding successful morphotype identification. Reportedly, smooth/rough morphotypes are also related to the glycopeptidolipid (GPL) genotype. However, the accuracy of GPL genotyping to discriminate morphotypes and the relationship between GPL genotype and clinical characteristics of M abscessus lung disease have not been verified.

METHODS

A retrospective analysis of colony morphology, GPL genotype, and clinical data from 182 patients with M abscessus lung disease was conducted.

RESULTS

Of 194 clinical isolates, 126 (65.0%), 15 (7.7%), and 53 (27.3%) exhibited rough, smooth, and mixed colony morphotypes, respectively. Glycopeptidolipid genotyping indicated that 86.7% (13 of 15) of smooth isolates belonged to the GPL-wild type (WT) group, whereas 98.4% (124 of 126) of rough isolates belonged to the GPL-mutant type (MUT) group. Therefore, GPL genotyping accurately distinguished between smooth and rough morphotypes. Mixed colony morphotypes were also divided into GPL-WT (18.9%) and GPL-MUT (81.1%) groups. Further analysis revealed that patients infected with the GPL-MUT group presented with significantly worse baseline clinical characteristics and exacerbated episodes of lung disease.

CONCLUSIONS

Glycopeptidolipid genotyping accurately distinguishes smooth and rough colony morphotypes. Patients infected with the GPL-MUT genotype exhibit worse clinical characteristics and are at a higher risk of exacerbated lung disease.

A novel DNA chromatography method to discriminate Mycobacterium abscessus subspecies and macrolide susceptibility

Background

The clinical impact of infection with Mycobacterium (M.) abscessus complex (MABC), a group of emerging non-tuberculosis mycobacteria (NTM), is increasing. M. abscessus subsp. abscessus/bolletii frequently shows natural resistance to macrolide antibiotics, whereas M. abscessus subsp. massiliense is generally susceptible. Therefore, rapid and accurate discrimination of macrolide-susceptible MABC subgroups is required for effective clinical decisions about macrolide treatments for MABC infection. We aimed to develop a simple and rapid diagnostic that can identify MABC isolates showing macrolide susceptibility.

Methods

Whole genome sequencing (WGS) was performed for 148 clinical or environmental MABC isolates from Japan to identify genetic markers that can discriminate three MABC subspecies and the macrolide-susceptible erm(41) T28C sequevar. Using the identified genetic markers, we established PCR based- or DNA chromatography-based assays. Validation testing was performed using MABC isolates from Taiwan.

Finding

We identified unique sequence regions that could be used to differentiate the three subspecies. Our WGS-based phylogenetic analysis indicated that M. abscessus carrying the macrolide-susceptible erm(41) T28C sequevar were tightly clustered, and identified 11 genes that were significantly associated with the lineage for use as genetic markers. To detect these genetic markers and the erm(41) locus, we developed a DNA chromatography method that identified three subspecies, the erm(41) T28C sequevar and intact erm(41) for MABC in a single assay within one hour. The agreement rate between the DNA chromatography-based and WGS-based identification was 99·7%.

Interpretation

We developed a novel, rapid and simple DNA chromatography method for identification of MABC macrolide susceptibility with high accuracy.

Funding

AMED, JSPS KAKENHI

Longitudinal non-cystic fibrosis trends of pulmonary Mycobacterium abscessus disease from 2010 to 2017: spread of the "globally successful clone" in Asia

BACKGROUND

Mycobacterium abscessus (MAB) has emerged as the predominant pulmonary non-tuberculous mycobacterial pathogen in parts of Asia, including Taiwan. The reasons for the significant increase in MAB infections in the non-cystic fibrosis (CF) populations are poorly understood. The study aimed to elucidate whether this increase is related to the spread of the globally successful clone of MAB.

METHODS

We performed multilocus sequence typing of 371 nonduplicated MAB pulmonary isolates from 371 patients sampled between 2010-2017 at seven hospitals across Taiwan.

RESULTS

In total, 183 (49.3%) isolates were M. abscessus subsp. abscessus (MAB-a), 187 (50.4%) were M. abscessus subsp. massiliense (MAB-m), and 1 (0.3%) was M. abscessus subsp. bolletii (MAB-b). MAB-a sequence type (ST)1 (23.7%) and ST127 (3.8%), followed by MAB-m ST48 (16.2%), ST117 (15.1%), ST23 (8.6%) were most common overall. Of MAB-a strains, 50 (27.3%) belonged to novel STs and 38 (10.2%) were singleton strains, while of MAB-m strains, only 10 (5.3%) were novel and 8 (2.2%) were singletons. From 2010 to 2017, the frequency of the historically dominant ST1 declined from 28.6% to 22.5%, whereas the recently emerged globally successful clonal cluster 3, ST23 and ST48, increased from 14.3% to 40.0%.

CONCLUSIONS

The dominance of ST1 particularly in the last 2 years of this study appears to be declining, while ST23, reported in outbreaks among CF and post-surgical cohorts across the Americas and Europe, alongside the closely related ST48, is present among non-CF populations in Taiwan. These trends need to be confirmed with further ongoing studies to track the molecular epidemiology of clinical MAB isolates worldwide.

Antimicrobial Susceptibility and Phylogenetic Relations in a German Cohort Infected with Mycobacterium abscessus

Mycobacterium abscessus is a highly antibiotic-resistant opportunistic pathogen causing clinically challenging infections in patients with preexisting lung diseases or under immunosuppression. Hence, reliable antibiotic susceptibility data are required for effective treatment. Aims of this study were to investigate (i) the congruence of genotypic and phenotypic antimicrobial susceptibility testing, (ii) the relationship between resistance profile and clinical course, and (iii) the phylogenetic relations of M. abscessus in a German patient cohort. A total of 39 isolates from 29 patients infected or colonized with M. abscessus underwent genotypic and phenotypic drug susceptibility testing. Clinical data were correlated with susceptibility data. Phylogenetic analysis was performed by means of whole-genome sequencing (WGS) and single-nucleotide polymorphism (SNP) analysis. Macrolide resistance was mainly mediated by functional Erm(41) methyltransferases (T28 sequevars) in M. abscessus subsp. abscessus (n = 25) and M. abscessus subsp. bolletii (n = 2). It was significantly associated with impaired culture conversion (P = 0.02). According to the core SNP phylogeny, we identified three clusters of closely related isolates with SNP distances below 25. Representatives of all circulating global clones (Absc. 1, Absc. 2, and Mass. 1) were identified in our cohort. However, we could not determine evidence for in-hospital interhuman transmission from clinical data. In our patient cohort, we identified three M. abscessus clusters with closely related isolates and representatives of the previously described international clusters but no human-to-human in-hospital transmission. Macrolide and aminoglycoside susceptibility data are critical for therapeutic decision-making in M. abscessus infections.

Non-Tuberculous Mycobacteria Interference with BCG-Current Controversies and Future Directions

The global tuberculosis (TB) epidemic caused by the bacterial pathogen Mycobacterium tuberculosis (M.tb) continues unabated. The Mycobacterium bovis bacillus Calmette–Guérin (BCG) vaccination is widely utilized worldwide to protect against infection with M.tb. BCG vaccine protection against TB has had widely varying results for reasons that are not well understood. BCG vaccine interference by non-tuberculosis (NTM) mycobacterial species has been implicated as the potential cause of reduced BCG vaccine efficacy against M.tb. Ongoing efforts to develop new vaccines for TB requires a thorough understanding of the effect of NTM exposure on BCG vaccine efficacy, which may ultimately be a critical determinant of success. We reviewed the conflicting reports on whether NTM interferes with the BCG vaccine, potential explanations to help resolve the controversy, and strategies for developing better animal models. Further studies are needed to longitudinally track the effects of NTM exposure on BCG vaccine-induced host-protective anti-TB immunity.