Multilocus sequence analysis and rpoB sequencing of Mycobacterium abscessus (sensu lato) strains

Mycobacterium abscessus, Mycobacterium bolletii, and Mycobacterium massiliense (Mycobacterium abscessus sensu lato) are closely related species that currently are identified by the sequencing of the rpoB gene. However, recent studies show that rpoB sequencing alone is insufficient to discriminate between these species, and some authors have questioned their current taxonomic classification. We studied here a large collection of M. abscessus (sensu lato) strains by partial rpoB sequencing (752 bp) and multilocus sequence analysis (MLSA). The final MLSA scheme developed was based on the partial sequences of eight housekeeping genes: argH, cya, glpK, gnd, murC, pgm, pta, and purH. The strains studied included the three type strains (M. abscessus CIP 104536(T), M. massiliense CIP 108297(T), and M. bolletii CIP 108541(T)) and 120 isolates recovered between 1997 and 2007 in France, Germany, Switzerland, and Brazil. The rpoB phylogenetic tree confirmed the existence of three main clusters, each comprising the type strain of one species. However, divergence values between the M. massiliense and M. bolletii clusters all were below 3% and between the M. abscessus and M. massiliense clusters were from 2.66 to 3.59%. The tree produced using the concatenated MLSA gene sequences (4,071 bp) also showed three main clusters, each comprising the type strain of one species. The M. abscessus cluster had a bootstrap value of 100% and was mostly compact. Bootstrap values for the M. massiliense and M. bolletii branches were much lower (71 and 61%, respectively), with the M. massiliense cluster having a fuzzy aspect. Mean (range) divergence values were 2.17% (1.13 to 2.58%) between the M. abscessus and M. massiliense clusters, 2.37% (1.5 to 2.85%) between the M. abscessus and M. bolletii clusters, and 2.28% (0.86 to 2.68%) between the M. massiliense and M. bolletii clusters. Adding the rpoB sequence to the MLSA-concatenated sequence (total sequence, 4,823 bp) had little effect on the clustering of strains. We found 10/120 (8.3%) isolates for which the concatenated MLSA gene sequence and rpoB sequence were discordant (e.g., M. massiliense MLSA sequence and M. abscessus rpoB sequence), suggesting the intergroup lateral transfers of rpoB. In conclusion, our study strongly supports the recent proposal that M. abscessus, M. massiliense, and M. bolletii should constitute a single species. Our findings also indicate that there has been a horizontal transfer of rpoB sequences between these subgroups, precluding the use of rpoB sequencing alone for the accurate identification of the two proposed M. abscessus subspecies.

Phylogenetic approach reveals that virus genotype largely determines HIV set-point viral load

HIV virulence, i.e. the time of progression to AIDS, varies greatly among patients. As for other rapidly evolving pathogens of humans, it is difficult to know if this variance is controlled by the genotype of the host or that of the virus because the transmission chain is usually unknown. We apply the phylogenetic comparative approach (PCA) to estimate the heritability of a trait from one infection to the next, which indicates the control of the virus genotype over this trait. The idea is to use viral RNA sequences obtained from patients infected by HIV-1 subtype B to build a phylogeny, which approximately reflects the transmission chain. Heritability is measured statistically as the propensity for patients close in the phylogeny to exhibit similar infection trait values. The approach reveals that up to half of the variance in set-point viral load, a trait associated with virulence, can be heritable. Our estimate is significant and robust to noise in the phylogeny. We also check for the consistency of our approach by showing that a trait related to drug resistance is almost entirely heritable. Finally, we show the importance of taking into account the transmission chain when estimating correlations between infection traits. The fact that HIV virulence is, at least partially, heritable from one infection to the next has clinical and epidemiological implications. The difference between earlier studies and ours comes from the quality of our dataset and from the power of the PCA, which can be applied to large datasets and accounts for within-host evolution. The PCA opens new perspectives for approaches linking clinical data and evolutionary biology because it can be extended to study other traits or other infectious diseases.

Molecular epidemiology reveals long-term changes in HIV type 1 subtype B transmission in Switzerland

Sequence data from resistance testing offer unique opportunities to characterize the structure of human immunodeficiency virus (HIV) infection epidemics.

Implementation of raltegravir in routine clinical practice: selection criteria for choosing this drug, virologic response rates, and characteristics of failures

Raltegravir (RAL) achieved remarkable virologic suppression rates in randomized-clinical trials, but today efficacy data and factors for treatment failures in a routine clinical care setting are limited.

Randomized controlled study demonstrating failure of LPV/r monotherapy in HIV: the role of compartment and CD4-nadir

Long-term side-effects and cost of HIV treatment motivate the development of simplified maintenance. Monotherapy with ritonavir-boosted lopinavir (LPV/r-MT) is the most widely studied strategy. However, efficacy of LPV/r-MT in compartments remains to be shown.

Because someone has recommended it - Patients’ reasons for choosing acupuncture or qigong

Question: Recent research has indicated a considerable contribution of placebo effects to the outcome of acupuncture treatments: especially patients’ expectations seem to have an influence [1] and [2]. In this context it is important to better understand the patient–practitioner relationship. The aim of this study was to investigate why patients in Switzerland choose acupuncture or qigong, and what they expect from the treatment and the practitioners [3]. Methods: A qualitative survey with open questions was performed among 38 patients newly enrolled for treatment in 7 different practices for Traditional Chinese Medicine ((TCM); 6 practices for acupuncture, 1 for qigong). Questions aimed to identify reasons for choosing TCM, knowledge about its range of indications, and patients’ expectations towards method and therapist. Answers were categorised and analysed by frequency. Results: The most common reasons for choosing TCM were recommendation by acquaintances, the idea of trying a new treatment and the perception of TCM as being a gentle method. The majority of respondents had poor knowledge about the range of conditions to be treated with TCM: pain of the musculoskeletal system, headaches and chronic problems were considered as main indications. Surprisingly, gynaecological or gastro-intestinal diseases were not mentioned by the respondents. Practitioners were expected to have professional competence, provide information, empathy and understanding. Conclusions: The most striking result of this survey was the fact that patients knew very little about TCM and its indications. Thus, more precise information about TCM and other complementary methods should be offered to the general public, which would help patients to decide whether to consider TCM for the treatment of their disease. And, on the other hand, for the therapists it is important to better understand and respond to patients’ expectations in order to achieve better treatment results. The results of this qualitative survey were briefly discussed with the participating practitioners, who found them remarkable and support further quantitative studies. We plan to further investigate this topic. References 1. J. Pariente, P. White, R.S.J. Frackowiak, G. Lewith. Neuroimage, 25 (2005), pp. 1161–1167 2. M. Karst, D. Schneidewind, D. Scheinichen. Forsch Komplementmed, 17 (2010), pp. 21–27 3. S.D. Klein. Dt Ztschr f Akup, 52 (2009), pp. 18–23