Evolution of anaerobe susceptibility testing in the United States

Paraphocaeicola brunensis gen. nov., sp. nov., Carrying Two Variants of nimB Resistance Gene from Bacteroides fragilis, and Caecibacteroides pullorum gen. nov., sp. nov., Two Novel Genera Isolated from Chicken Caeca

Three difficult-to-cultivate, strictly anaerobic strains, AN20^T, AN421^T, and AN502, were analyzed within a project studying possible probiotics for newly hatched chickens. Phylogenetic analyses showed that strains AN20^T, AN421^T, and AN502 formed two well-separated phylogenetic lineages in all phylogenetic and phylogenomic trees comprising members of the family Bacteroidaceae. Comparison to reference genomes of type species Bacteroides fragilis NCTC 9343^T, Phocaeicola abscessus CCUG 55929^T, and Capsularis zoogleoformans ATCC 33285^T showed low relatedness based on the calculated genome-to-genome distance and orthologous average nucleotide identity. Analysis of fatty acid profiles showed iso-C_15:0, anteiso-C_15:0, C_16:0, C_18:1ω9c, and iso-C_17:0 3OH as the major fatty acids for all three strains and additionally C_16:0 3OH for AN421^T and AN502. A specific combination of respiratory quinones different from related taxa was found in analyzed strains, MK-5 plus MK-11 in strain AN20^T and MK-5 plus MK-10 in strains AN421^T and AN502. Strains AN421^T and AN502 harbor complete CRISPR loci with CRISPR array, type II-C, accompanied by a set of cas genes (cas9, cas1, and cas2) in close proximity. Interestingly, strain AN20^T was found to harbor two copies of nimB gene with >95% similarity to nimB of B. fragilis, suggesting a horizontal gene transfer between these taxa. In summary, three isolates characterized in this study represent two novel species, which we proposed to be classified in two novel genera of the family Bacteroidaceae, for which the names Paraphocaeicola brunensis sp. nov. (AN20^T = CCM 9041^T = DSM 111154^T) and Caecibacteroides pullorum sp. nov. (AN421^T= CCM 9040^T = DSM 111155^T) are proposed.

IMPORTANCE This study represents follow-up research on three difficult-to-cultivate anaerobic isolates originally isolated within a project focused on strains that are able to stably colonize newly hatched chickens, thus representing possible probiotics. This project is exceptional in that it successfully isolates several miscellaneous strains that required modified and richly supplemented anaerobic media, as information on many gut-colonizing bacteria is based predominantly on metagenomic studies. Superior colonization of newly hatched chickens by Bacteroides spp., Phocaeicola spp., or related taxa can be considered of importance for development of future probiotics. Although different experiments can also be performed with provisionally characterized isolates, precise taxonomical definition is necessary for subsequent broad communication. The aim of this study is therefore to thoroughly characterize these isolates that represent novel genera and precisely determine their taxonomic position among related taxa to facilitate further research and communication involving these strains.

A case of uterine endometritis caused by Atopobium vaginae

Although Atopobium vaginae has been reported as a causative organisms in patients with bacterial vaginosis and/or tubo-ovarian abscess, clinical significance of Atopobium species has not been defined to date. Here we report the case of uterine endometritis caused by A. vaginae.

Antimicrobial resistance in Bacteroides spp.: occurrence and dissemination

Bacteroides spp. organisms, though important human commensals, are also opportunistic pathogens when they escape the colonic milieu. Resistance to multiple antibiotics has been increasing in Bacteroides spp. for decades, and is primarily due to horizontal gene transfer of a plethora of mobile elements. The mechanistic aspects of conjugation in Bacteroides spp. are only now being elucidated at a functional level. There appear to be key differences between Bacteroides spp. and non-Bacteroides spp. conjugation systems that may contribute to promiscuous gene transfer within and from this genus. This review summarizes the mechanisms of action and resistance of antibiotics used to treat Bacteroides spp. infections, and highlights current information on conjugation-based DNA exchange.

Anaerobic microbiology in 198 cases of pleural empyema: a Bulgarian study

The aim of the study was to evaluate the incidence of anaerobic bacteria in 198 patients with pleural empyema and the susceptibility of isolates to eight antibacterial agents. Isolates were identified by the Crystal anaerobes identification system, API System rapid ID 32 A and/or routine methods. Susceptibility was tested by Sceptor MIC system for anaerobic bacteria and limited agar dilution method. Anaerobic bacteria were found in 74.2% of the patients and included 247 strains within 21 genera. The predominant anaerobes were Gram-positive anaerobic cocci (52 isolates), Fusobacterium (51), microaerophilic streptococci (24), Prevotella (19) and Bacteroides species (11). Common species/groups were Fusobacterium nucleatum (in 27.2% of specimens yielding anaerobes), Micromonas micros (8.2%), Finegoldia magna (7.5%), Bacteroides fragilis group (6.8%), Peptostreptococcus anaerobius (6.1%) and F. necrophorum (5.4%). No resistance to chloramphenicol and ampicillin/sulbactam was detected. The susceptibility rates of Gram-negative anaerobic isolates to penicillin, cefoxitin, clindamycin, clarithromycin, metronidazole and tetracycline were 63.8%, 90.2%, 87.8%, 58.6%, 98.8% and 71%, and those of Gram-positive anaerobes were 79.2%, 100%, 84.3%, 68.4%, 41.9% and 75%, respectively. The wide diversity of isolated anaerobic genera and species and the susceptibility patterns of the isolates emphasize the role of the anaerobic microbiology in cases of pleural empyema.

Tuboovarian abscess caused by Atopobium vaginae following transvaginal oocyte recovery

A 39-year-old woman with tubarian sterility fell ill with acute pelvic inflammatory disease 2 months after transvaginal oocyte recovery. Laparotomy revealed a large tuboovarian abscess, from which Atopobium vaginae, an anaerobic gram-positive coccoid bacterium of hitherto unknown clinical significance, was isolated. The microbial etiology and the risk of pelvic infections following transvaginal punctures are discussed.