Cautionary tale of using 16S rRNA gene sequence similarity values in identification of human-associated bacterial species.

Modern bacterial taxonomy is based on a polyphasic approach that combines phenotypic and genotypic characteristics, including 16S rRNA sequence similarity. However, the 95 % (for genus) and 98.7 % (for species) sequence similarity thresholds that are currently recommended to classify bacterial isolates were defined by comparison of a limited number of bacterial species, and may not apply to many genera that contain human-associated species. For each of 158 bacterial genera containing human-associated species, we computed pairwise sequence similarities between all species that have names with standing in nomenclature and then analysed the results, considering as abnormal any similarity value lower than 95 % or greater than 98.7 %. Many of the current bacterial species with validly published names do not respect the 95 and 98.7 % thresholds, with 57.1 % of species exhibiting 16S rRNA gene sequence similarity rates ≥98.7 %, and 60.1 % of genera containing species exhibiting a 16S rRNA gene sequence similarity rate <95 %. In only 17 of the 158 genera studied (10.8 %), all species respected the 95 and 98.7 % thresholds. As we need powerful and reliable taxonomical tools, and as potential new tools such as pan-genomics have not yet been fully evaluated for taxonomic purposes, we propose to use as thresholds, genus by genus, the minimum and maximum similarity values observed among species.

Non-contiguous finished genome sequence and description of Collinsella massiliensis sp. nov.

Collinsella massiliensis strain GD3(T) is the type strain of Collinsella massiliensis sp. nov., a new species within the genus Collinsella. This strain, whose genome is described here, was isolated from the fecal flora of a 53-year-old French Caucasoid woman who had been admitted to intensive care unit for Guillain-Barré syndrome. Collinsella massiliensis is a Gram-positive, obligate anaerobic, non motile and non sporulating bacillus. Here, we describe the features of this organism, together with the complete genome sequence and annotation. The genome is 2,319,586 bp long (1 chromosome, no plasmid), exhibits a G+C content of 65.8% and contains 2,003 protein-coding and 54 RNA genes, including 1 rRNA operon.

Genome sequence and description of Bacteroides timonensis sp. nov.

Bacteroides timonensis strain AP1(T) (= CSUR P194 = DSM 26083) is the type strain of B. timonensis sp. nov. This strain, whose genome is described here, was isolated from the fecal flora of a 21-year-old French Caucasoid female who suffered from severe anorexia nervosa. Bacteroides timonensis is a Gram-negative, obligate anaerobic bacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 7,130,768 bp long genome (1 chromosome, no plasmid) exhibits a G+C content of 43.3% and contains 5,786 protein-coding and 59 RNA genes, including 2 rRNA genes.

Anti-hepatitis E virus antibody prevalence in French expatriate workers.

OBJECTIVE: The hepatitis E virus (HEV) is a leading cause of acute hepatitis in developing countries and an emerging pathogen in Europe. HEV seroprevalence has rarely been assessed in cohorts of travelers, and previous studies have reported a very low rate of exposure. We assessed HEV seroprevalence in French expatriate workers. METHODS: The prevalence of HEV IgG and IgM was assessed among 43 French expatriate workers using two commercial microplate enzyme immunoassays (Adaltis and Wantai). Additionally HEV IgG-positive sera were tested with an immunoblot assay (recomLine), while IgM-positive sera were tested with a rapid immunochromatographic assay (Assure). RESULTS: The prevalence of anti-HEV IgG was 3.7 times higher in French expatriates than in comparable blood donors from the same area. A discrepancy was evidenced between the HEV IgG results obtained by the Wantai and Adaltis assays (48.8% vs. 30.2%). CONCLUSIONS: Expatriation from France, including to areas not recognized as hyperendemic for HEV, may expose individuals to HEV infection. This issue warrants further study; in particular, serology should be compared before and after travel. The most sensitive Wantai serological assay should be used for epidemiological studies to obtain better insight into the epidemiology of HEV.

Discrepancy between anti-hepatitis E virus immunoglobulin G prevalence assessed by two assays in kidney and liver transplant recipients.

BACKGROUND: Hepatitis E virus (HEV) is an emerging clinical threat in Europe among kidney and liver-transplant recipients. The incidence and prevalence of HEV infection in this special population are poorly known. False-negative results have been observed for anti-HEV IgG detection in severely immunocompromized persons. Moreover, large discrepancies have been reported between rates of anti-HEV IgG detection in blood donors and hepatitis E cases. OBJECTIVES: To compare anti-HEV IgG and IgM prevalence using two different commercial microplate enzyme-immuno assays (MEIAs) (Adaltis and Wantai) in 64 kidney-/liver-transplant recipients. STUDY DESIGN: Serum samples tested in our routine clinical practice over the 12/2009-12/2011 period with Adaltis MEIAs were retrospectively tested using Wantai MEIAs. IgG-positive sera were further tested by an immunoblot while those found IgM-positive were further tested with an immunochromatography rapid test and for the presence of HEV RNA. RESULTS: Positive results on anti-HEV IgG testing were obtained for seven (10.9%) compared to 20 (31.3%) serum samples with Adaltis and Wantai assays, respectively (p=0.005). Then, 6/7 (86%) of the serum samples positive with Adaltis and 16/20 (80%) of those positive with Wantai were positive with the immunoblot. One patient with chronic HEV infection was IgG-negative with both MEIAs. Regarding anti-HEV IgM, Adaltis and Wantai assays were concordant for 97% of the serum samples, prevalence being 8% with both MEIAs. CONCLUSIONS: The accuracy of currently available commercial or in-house anti-HEV IgG MEIAs should be tested comparatively on a panel of serum samples collected from solid organ-transplant recipients, including some who experienced PCR-documented HEV infection.