CRISPR Typing Increases the Discriminatory Power of Streptococcus agalactiae Typing Methods

We explored the relevance of a Clustered regularly interspaced short palindromic repeats (CRISPR)-based genotyping tool for Streptococcus agalactiae typing and we compared this method to current molecular methods [multi locus sequence typing (MLST) and capsular typing]. To this effect, we developed two CRISPR marker schemes (using 94 or 25 markers, respectively). Among the 255 S. agalactiae isolates tested, 229 CRISPR profiles were obtained. The 94 and 25 markers made it possible to efficiently separate isolates with a high diversity index (0.9947 and 0.9267, respectively), highlighting a high discriminatory power, superior to that of both capsular typing and MLST (diversity index of 0.9017 for MLST). This method has the advantage of being correlated with MLST [through analysis of the terminal direct repeat (TDR) and ancestral spacers] and to possess a high discriminatory power (through analysis of the leader-end spacers recently acquired, which are the witnesses of genetic mobile elements encountered by the bacteria). Furthermore, this “one-shot” approach presents the benefit of much-reduced time and cost in comparison with MLST. On the basis of these data, we propose that this method could become a reference method for group B Streptococcus (GBS) typing.

Evolution and phenotypic characterization of whole HBV genome in compliant patients experiencing unexplained entecavir treatment failure

Entecavir treatment failure can be observed in compliant patients despite an absence of detectable resistance mutations by Pol/RT Sanger sequencing. We hypothesized that these unexplained treatment failures could rely on other mechanisms of viral resistance, especially on mutations selected outside of the Pol/RT domain. Partial virological response to entecavir was observed in three patients treated with immunosuppressive drugs, without selection of Pol/RT resistance mutations. Mutations selected in the whole HBV genome during entecavir treatment and potentially associated with resistance were searched for using deep sequencing and characterized using a phenotypic resistance assay. Mutations Q206K (pre-core/core), Q120K (pre-S1/pre-S2, T-cell epitope) and A300E (spacer domain) were selected during entecavir treatment in patient #1 but were not associated with an increased level of resistance to entecavir or an increase in HBV replication capacity. Core promoter mutations T1753G, A1762T and G1764A were present as major mutations before and after treatment in patient #1. HBs Ag immune escape mutations were present as major mutations before and after treatment in patients #2 (sK122R, sT126I, sP127S and sG145R) and #3 (sM133I). We demonstrated that PVR to entecavir does not require selection of any resistance mutation in the whole HBV genome. Our results demonstrate that major mutations can be selected outside of the Pol/RT domain before or during entecavir treatment. These mutations could contribute to entecavir treatment failure by other mechanisms than an increased level of resistance.

Serum IgG Concentrations in Adult Patients Experiencing Virus-Induced Severe Asthma Exacerbations

BACKGROUND

Patients experiencing severe asthma exacerbations have a poorer quality of life and an increase in morbidity and mortality. Viruses are frequently involved in asthma exacerbations.

OBJECTIVE

To determine the value of measuring serum IgG concentrations in asthma exacerbations and assess their link with viral infections in patients hospitalized for asthma.

METHODS

Patients hospitalized for asthma exacerbation were included in an observational study from January 1, 2015, to December 31, 2015. Serum IgG concentrations on admission were compared between patients with a positive upper airway viral sample and those with a negative viral sample.

RESULTS

Among the 82 patients included, those with positive viral nasopharyngeal samples (n = 40) presented with lower serum IgG concentrations during exacerbation than those with a negative viral sample (n = 42) (10.1 ± 2.3 g/L vs 11.5 ± 3.6 g/L; P < .05). The median concentration of serum IgG was lower in patients hospitalized for more than 3 days compared with those hospitalized for less than 3 days (10.0 g/L [8.2-12.4] vs 11.4 g/L [10.1-12.8]; P < .05) and in patients who received oral corticosteroid therapy for more than 5 days compared with those treated with oral steroids for less than 5 days (10.1 g/L [8.3-12.2] vs 11.6 g/L [10.0-13.8]; P < .05).

CONCLUSIONS

Serum IgG level was significantly lower when asthma exacerbations were associated with positive viral samples. The patients with lower serum IgG concentrations required longer hospitalizations and longer courses of steroids.

Exacerbation d’asthme et virus : quelles différences en fonction des zones climatiques ?

Introduction

Les exacerbations d’asthme correspondent à des aggravations rapides des symptômes respiratoires et sont responsables d’une morbidité et mortalité importantes. Les infections virales figurent parmi les causes les plus fréquentes des exacerbations mais les données épidémiologiques sont, dans leur grande majorité, issues de cohorte de pays tempérés. Peu de données sont disponibles dans les pays tropicaux malgré une augmentation de la prévalence de l’asthme dans ces régions ces dernières années.

Méthodes

Dans cette étude observationnelle réalisée sur l’année 2015, l’épidémiologie virale de patients adultes hospitalisés pour exacerbation d’asthme a été comparée entre la ville de Saint Pierre à la Réunion (climat tropical) et de Tours (climat tempéré). Un portage viral était recherché à l’entrée à l’hôpital par polymerase chain reaction (PCR) multiplex sur aspiration nasopharyngée. Seize virus ont été analysés : VRS A et B, rhinovirus, métapneumovirus, myxovirus influenzae A, H1N1, H5N1, parainfluenzae de 1 à 4, coronavirus 229E, NL63 et OC43, adénovirus, entérovirus. À la Réunion, le panel de virus recherché comprenait en plus coronavirus HKU1, bocavirus et paréchovirus.

Résultats

Au total, 100 patients ont été inclus dont 62 à Saint Pierre et 38 à Tours. La présence d’au moins un virus est retrouvé dans les aspirations naso-pharyngées chez 53 % des patients à Tours et 31 % des patients à Saint Pierre (p < 0,05). La répartition des virus diffère selon la géolocalisation. Le rhinovirus est l’espèce la plus fréquemment retrouvée dans les 2 groupes : soit 42 % des prélèvements à Saint Pierre et 30 % à Tours. On trouve de façon équivalente, entre les groupes, le virus influenza A dans 19 % des cas. Le classement diverge ensuite, l’entérovirus qui représente 19 % des aspirations naso-pharyngées à Tours n’est pas retrouvé à Saint Pierre. Inversement, le virus influenza H1N1 et le virus para-influenza identifiés dans 12 et 4 % des prélèvements à Saint Pierre sont absents à Tours. Les exacerbations semblent avoir une saisonnalité à Tours avec un pic en septembre et en hiver. Aucune saisonnalité n’est retrouvée sous le climat tropical de la Réunion.

Conclusion

La proportion de patients hospitalisés pour exacerbation d’asthme et ayant un prélèvement viral positif est plus faible en climat tropical qu’en climat tempéré. L’origine de ces exacerbations reste donc à déterminer. Il est nécessaire d’étudier spécifiquement en zone tropicale d’autres facteurs environnementaux comme les allergènes (moisissures…) ou les parasites.

Analysis of the type II-A CRISPR-Cas system of Streptococcus agalactiae reveals distinctive features according to genetic lineages

CRISPR-Cas systems (clustered regularly interspaced short palindromic repeats/CRISPR-associated proteins) are found in 90% of archaea and about 40% of bacteria. In this original system, CRISPR arrays comprise short, almost unique sequences called spacers that are interspersed with conserved palindromic repeats. These systems play a role in adaptive immunity and participate to fight non-self DNA such as integrative and conjugative elements, plasmids, and phages. In Streptococcus agalactiae, a bacterium implicated in colonization and infections in humans since the 1960s, two CRISPR-Cas systems have been described. A type II-A system, characterized by proteins Cas9, Cas1, Cas2, and Csn2, is ubiquitous, and a type I–C system, with the Cas8c signature protein, is present in about 20% of the isolates. Unlike type I–C, which appears to be non-functional, type II-A appears fully functional. Here we studied type II-A CRISPR-cas loci from 126 human isolates of S. agalactiae belonging to different clonal complexes that represent the diversity of the species and that have been implicated in colonization or infection. The CRISPR-cas locus was analyzed both at spacer and repeat levels. Major distinctive features were identified according to the phylogenetic lineages previously defined by multilocus sequence typing, especially for the sequence type (ST) 17, which is considered hypervirulent. Among other idiosyncrasies, ST-17 shows a significantly lower number of spacers in comparison with other lineages. This characteristic could reflect the peculiar virulence or colonization specificities of this lineage.