Insights on Mycobacterium leprae Efflux Pumps and Their Implications in Drug Resistance and Virulence

Drug resistance in Mycobacterium leprae is assumed to be due to genetic alterations in the drug targets and reduced cell wall permeability. However, as observed in Mycobacterium tuberculosis, drug resistance may also result from the overactivity of efflux systems, which is mostly unexplored. In this perspective, we discuss known efflux pumps involved in M. tuberculosis drug resistance and virulence and investigate similar regions in the genome of M. leprae. In silico analysis reveals that the major M. tuberculosis efflux pumps known to be associated with drug resistance and virulence have been retained during the reductive evolutionary process that M. leprae underwent, e.g., RND superfamily, the ABC transporter BacA, and the MFS P55. However, some are absent (DinF, MATE) while others are derepressed (Mmr, SMR) in M. leprae reflecting the specific environment where M. leprae may live. The occurrence of several multidrug resistance efflux transporters shared between M. leprae and M. tuberculosis reveals potential implications in drug resistance and virulence. The conservation of the described efflux systems in M. leprae upon genome reduction indicates that these systems are potentially required for its intracellular survival and lifestyle. They potentially are involved in M. leprae drug resistance, which could hamper leprosy treatment success. Studying M. leprae efflux pumps as new drug targets is useful for future leprosy therapeutics, enhancing the global efforts to eradicate endemic leprosy, and prevent the emergence of drug resistance in afflicted countries

Using comparative genomics to better understand mycobacterial infections

Les infections à mycobactéries comprennent la tuberculose et la lèpre, encore endémiques dans de nombreux pays, et les infections dites à « mycobactéries non-tuberculeuses (MNT) » qui sont des infections respiratoires et extra-respiratoires, opportunistes ou iatrogènes. Nous avons réalisé une étude de génomique comparative des mycobactéries autres que celles de la tuberculose, qui elle, est mieux connue. Nous nous sommes intéressés aux aspects phylogénétiques et à l’évolution des génomes au cours de l’infection. La première partie est consacrée à Mycobacterium leprae avec l’étude des souches isolées à Madagascar. Nous avons montré qu’elles appartiennent à un génotype très particulier (nommé 1D-Malagasy), ce qui permet de discuter l’histoire « moléculaire » de la lèpre sur l’île. Nous avons aussi comparé les gènes codant les pompes d’efflux de M. leprae avec ceux bien décrits de M. tuberculosis, ce qui a permis de montrer les points de divergence de ces espèces pour ces gènes importants. Dans une seconde partie, nous avons exploré la génomique des MNT dans le cadre d’enquêtes épidémiologiques réalisées suite à des cas groupés d’infections. Lors de l’épidémie mondiale d’infections post-opératoires sous circulation extra-corporelle (CEC), l’étude des souches de M. chimaera, issues des patients et des générateurs thermiques de CEC, a confirmé la spécificité génomique de la souche épidémique, tout en observant une certaine diversité du cluster. Enfin, l’étude génomique comparative de souches de M. marinum et M. chelonae isolées lors d’infections iatrogènes a permis d’infirmer ou de confirmer le mode de contamination dans ces différents cas. En conclusion, l’étude de génomique comparative des mycobactéries nous a permis de mieux caractériser les évolutions du génome de M. leprae et de diverses MNT par rapport aux infections, que ce soit sur un temps long, avec l’exemple de la diffusion de M. leprae à Madagascar, ou sur un temps plus court, lors d’enquêtes épidémiologiques à la recherche de la source d’une contamination.Mycobacteria infections include tuberculosis and leprosy, still endemic in many countries, and infections due to non-tuberculous mycobacteria (NTM) which are opportunist or iatrogenic, respiratory and extra-respiratory infections. Our work focused on comparative genomics of mycobacteria other than Mycobacterium tuberculosis, already investigated. We distinguished phylogenetic aspects and genome evolution during infection. The first part is devoted to M. leprae by analyzing strains isolated in Madagascar, that were shown to harbor a particular genotype (named 1D-Malagasy). This analysis allows discussing the molecular history of leprosy on this 400 kilometer long island. We also compared the genes encoding M. leprae efflux pumps with those well described from M. tuberculosis, which showed how those two species diverged for these important genes. In a second part, we explored the genomics of NTM in the context of epidemiological investigations carried out following iatrogenic human infections. The first investigation was the worldwide outbreak of disseminated M. chimaera infections following open-heart surgery with heater cooler units (HCU). The study of M. chimaera strains from patients and HCU confirmed the genomic specificity of the epidemic strain, while we still observed pertinent variations within isolates grouped in the same cluster. Finally, comparative genomic studies of M. marinum and M. chelonae strains isolated during different episodes of iatrogenic infections confirmed or ruled out the mode of contamination. In conclusion, comparative genomics of mycobacteria allowed to better characterize the evolution of the genome of M. leprae and of various NTM, whether over a long time scale, with the example of the diffusion of M. leprae in Madagascar, as well as over a shorter period, as during epidemiological investigations in search of the source of contamination

The SARS-CoV-2 B.1.351 lineage (VOC β) is outgrowing the B.1.1.7 lineage (VOC α) in some French regions in April 2021

International audienceTo assess SARS-CoV-2 variants spread, we analysed 36,590 variant-specific reverse-transcription-PCR tests performed on samples from 12 April–7 May 2021 in France. In this period, contrarily to January–March 2021, variants of concern (VOC) β (B.1.351 lineage) and/or γ (P.1 lineage) had a significant transmission advantage over VOC α (B.1.1.7 lineage) in Île-de-France (15.8%; 95% confidence interval (CI): 15.5–16.2) and Hauts-de-France (17.3%; 95% CI: 15.9–18.7) regions. This is consistent with VOC β’s immune evasion abilities and high proportions of prior-SARS-CoV-2-infected persons in these regions

Rapid spread of the SARS-CoV-2 Delta variant in some French regions, June 2021

International audienceWe analysed 9,030 variant-specific RT-PCR tests performed on SARS-CoV-2-positive samples collected in France between 31 May and 21 June 2021. This analysis revealed rapid growth of the Delta variant in three of the 13 metropolitan French regions and estimated a +79% (95% confidence interval: 52–110%) transmission advantage compared with the Alpha variant. The next weeks will prove decisive and the magnitude of the estimated transmission advantages of the Delta variant could represent a major challenge for public health authorities

Detecting Rapid Spread of SARS-CoV-2 Variants, France, January 26–February 16, 2021

International audienceVariants of severe acute respiratory syndrome coronavirus 2 raise concerns regarding the control of coronavirus disease epidemics. We analyzed 40,000 specific reverse transcription PCR tests performed on positive samples during January 26–February 16, 2021, in France. We found high transmission advantage of variants and more advanced spread than anticipated

SARS-CoV-2 variants of concern are associated with lower RT-PCR amplification cycles between January and March 2021 in France

International audienceSARS-CoV-2 variants raise concern regarding the mortality caused by COVID-19 epidemics. We analyse 88,375 cycle amplication (Ct) values from variant-specic RT-PCR tests performed between January 26 and March 13, 2021. We estimate that on March 12, nearly 85% of the infections were caused by the Alpha variant and that its transmission advantage over wild type strains was between 38 and 44%. We also nd that tests positive for Alpha and Beta/Gamma variants exhibit signicantly lower cycle threshold (Ct) values

Cause analysis of an infection in facelift surgery due to<em> Mycobacterium chelonae</em>

International audienceWe report a post-facelift infection due to Mycobacterium chelonae. An environmental strain recovered from the water supply network of the surgical clinic and the clinical strains were considered non-differentiable using whole genome sequencing. After the unhealed wound's exposure to M. chelonae while showering early at the clinic after surgery, a lasting exposure of the colonized wound to the warm and moist working conditions of a bakery may have been favorable to the infection's development

Mycobacterium chimaera genomics with regard to epidemiological and clinical investigations conducted for the open-chest post-surgical Mycobacterium chimaera infections outbreak

International audiencePost-surgical infections due to Mycobacterium chimaera appeared as a novel nosocomial threat in 2015, with a worldwide outbreak due to contaminated heater-cooler units used in open chest surgery. We report the results of investigations conducted in France including whole genome sequencing comparison of patient and HCU isolates.MethodsWe sought M. chimaera infection cases from 2010 onwards through national epidemiological investigations in healthcare facilities performing cardiopulmonary bypass together with a survey on good practices and systematic heater-cooler unit microbial analyses. Clinical and HCU isolates were subjected to whole genome sequencing analyzed with regards to the reference outbreak strain Zuerich-1.ResultsOnly two clinical cases were shown to be related to the outbreak, although 23% (41/175) heater-cooler units were declared positive for M. avium complex. Specific measures to prevent infection were applied in 89% (50/56) healthcare facilities although only 14% (8/56) of them followed the manufacturer maintenance recommendations. Whole genome sequencing comparison showed that the clinical isolates and 72% (26/36) of heater-cooler unit isolates belonged to the epidemic cluster. Within clinical isolates, 5 to 9 non-synonymous single nucleotide polymorphisms were observed, among which an in vivo mutation in a putative efflux pump gene observed in a clinical isolate obtained for one patient under antimicrobial treatment.ConclusionsCases of post-surgical M. chimaera infections were declared to be rare in France, although heater-cooler units were contaminated as in other countries. Genomic analyses confirmed the connection to the outbreak and identified specific single nucleotide polymorphisms, including one suggesting fitness evolution in vivo

Prise en charge de première intention du couple infertile : mise à jour des RPC 2010 du CNGOF

Objective: To update the 2010 CNGOF clinical practice guidelines for the first-line management of infertile couples.Materials and methods: Five major themes (first-line assessment of the infertile woman, first-line assessment of the infertile man, prevention of exposure to environmental factors, initial management using ovulation induction regimens, first-line reproductive surgery) were identified, enabling 28 questions to be formulated using the Patients, Intervention, Comparison, Outcome (PICO) format. Each question was addressed by a working group that had carried out a systematic review of the literature since 2010, and followed the Grading of Recommendations Assessment, Development and Evaluation (GRADE®) methodology to assess the quality of the scientific data on which the recommendations were based. These recommendations were then validated during a national review by 40 national experts.Results: The fertility work-up is recommended to be prescribed according to the woman's age: after one year of infertility before the age of 35 and after 6months after the age of 35. A couple's initial infertility work-up includes a single 3D ultrasound scan with antral follicle count, assessment of tubal permeability by hysterography or HyFOSy, anti-Mullerian hormone assay prior to assisted reproduction, and vaginal swabbing for vaginosis. If the 3D ultrasound is normal, hysterosonography and diagnostic hysteroscopy are not recommended as first-line procedures. Chlamydia trachomatis serology does not have the necessary performance to predict tubal patency. Post-coital testing is no longer recommended. In men, spermogram, spermocytogram and spermoculture are recommended as first-line tests. If the spermogram is normal, it is not recommended to check the spermogram. If the spermogram is abnormal, an examination by an andrologist, an ultrasound scan of the testicles and hormonal test are recommended. Based on the data in the literature, we are unable to recommend a BMI threshold for women that would contraindicate medical management of infertility. A well-balanced Mediterranean-style diet, physical activity and the cessation of smoking and cannabis are recommended for infertile couples. For fertility concern, it is recommended to limit alcohol consumption to less than 5 glasses a week. If the infertility work-up reveals no abnormalities, ovulation induction is not recommended for normo-ovulatory women. If intrauterine insemination is indicated based on an abnormal infertility work-up, gonadotropin stimulation and ovulation monitoring are recommended to avoid multiple pregnancies. If the infertility work-up reveals no abnormality, laparoscopy is probably recommended before the age of 30 to increase natural pregnancy rates. In the case of hydrosalpinx, surgical management is recommended prior to ART, with either salpingotomy or salpingectomy depending on the tubal score. It is recommended to operate on polyps>10mm, myomas 0, 1, 2 and synechiae prior to ART. The data in the literature do not allow us to systematically recommend asymptomatic uterine septa and isthmoceles as first-line surgery.Conclusion: Based on strong agreement between experts, we have been able to formulate updated recommendations in 28 areas concerning the initial management of infertile couples

Population Genomics of Mycobacterium leprae Reveals a New Genotype in Madagascar and the Comoros

Human settlement of Madagascar traces back to the beginning of the first millennium with the arrival of Austronesians from Southeast Asia, followed by migrations from Africa and the Middle East. Remains of these different cultural, genetic, and linguistic legacies are still present in Madagascar and other islands of the Indian Ocean. The close relationship between human migration and the introduction and spread of infectious diseases, a well-documented phenomenon, is particularly evident for the causative agent of leprosy, Mycobacterium leprae. In this study, we used whole-genome sequencing (WGS) and molecular dating to characterize the genetic background and retrace the origin of the M. leprae strains circulating in Madagascar (n = 30) and the Comoros (n = 3), two islands where leprosy is still considered a public health problem and monitored as part of a drug resistance surveillance program. Most M. leprae strains (97%) from Madagascar and Comoros belonged to a new genotype as part of branch 1, closely related to single nucleotide polymorphism (SNP) type 1D, named 1D-Malagasy. Other strains belonged to the genotype 1A (3%). We sequenced 39 strains from nine other countries, which, together with previously published genomes, amounted to 242 genomes that were used for molecular dating. Specific SNP markers for the new 1D-Malagasy genotype were used to screen samples from 11 countries and revealed this genotype to be restricted to Madagascar, with the sole exception being a strain from Malawi. The overall analysis thus ruled out a possible introduction of leprosy by the Austronesian settlers and suggests a later origin from East Africa, the Middle East, or South Asia