Facklamia miroungae sp. nov., from a juvenile southern elephant seal (Mirounga leonina)

Facklamia lactis sp. nov., isolated from raw milk

Two strains of a Gram-staining-positive species were isolated from German bulk tank milk. On the basis of their 16S rRNA sequences they were affiliated to the genus Facklamia but could not be assigned to any species with a validly published name. Facklamia miroungae ATCC BAA-466^T (97.3 % 16S rRNA sequence similarity), Facklamia languida CCUG 37842^T (96.9 %), and Facklamia hominis CCUG 36813^T (96.6 %) are the closest relatives. In the 16S rRNA phylogeny and in the core-genome phylogeny strains WS 5301^T and WS 5302 form a well-supported, separate lineage. Pairwise average nucleotide identity calculated using MUMmer (ANIm) between WS 5301^T and type strains of other Facklamia species is well below the species cut-off (95 %) and ranges from 83.4 to 87.7 %. The DNA G+C content of the type strain is 36.4 mol% and the assembly size of the genome is 2.2 Mb. Cells of WS 5301^T are non-motile, non-endospore-forming, oxidase-negative, catalase-negative and facultatively anaerobic cocci. The fastidious species grows at 10-40 °C and with up to 7.0 % (w/v) NaCl in BHI supplemented with 5 g l^-1 yeast extract. Major polar lipids are phosphatidylglycerol, diphosphatidylglycerol and two glycolipids. Predominant fatty acids are C_16 : 1ω9c and C_18 : 1ω9c. On the basis of their genomic, physiological and chemotaxonomic characteristics the strains examined in this study represent the same, hitherto unknown species. We propose the name Facklamia lactis sp. nov. for which WS 5301^T (=DSM 111018^T=LMG 31861^T) is the type strain and WS 5302 (=DSM 111019=LMG 31862) is an additional strain of this novel species.

Reclassification of Facklamia ignava, Facklamia sourekii and Facklamia tabacinasalis as Falseniella ignava gen. nov., comb. nov., Hutsoniella sourekii gen. nov., comb. nov., and Ruoffia tabacinasalis gen. nov., comb. nov., and description of Ruoffia halotolerans sp. nov., isolated from hypersaline Inland Sea of Qatar

A Gram-stain-positive, non-pigmented, coccus-shaped, facultatively anaerobic and α-hemolytic bacterium designated as INB8^T was isolated from a hypersaline marine water sample collected at the Inland Sea of Qatar. The isolate was able to grow at 25-40 °C (optimum, 30 °C), at pH 5-11 and with 2-8% NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain INB8^T was placed within the family Aerococcaceae with the highest sequence similarity to Facklamia tabacinasalis CCUG 30090^T (99.5%), followed by Facklamia hominis CCUG 36813^T (93.9%), Facklamia sourekii Y17312^T (93.8%), Facklamia ignava CCUG 37419^T (93.6%), Facklamia miroungae CCUG 42728^T (93.5%), Suicoccus acidiformans ZY16052^T (93.5%), Facklamia languida CCUG 37842^T (93.2%), Ignavigranum ruoffiae (93.1%), and Dolosicoccus paucivorans DSM 15742^T (90.8%). Average nucleotide identity and digital DNA-DNA hybridization values between strain INB8^T and F. tabacinasalis CCUG 30090^T were determined to be 94.5% and 58.9% respectively, confirming strain INB8^T represents a novel species. The major fatty acids were C_14:0, C_16:0, C_18:0 and C_18:1 ω9c_. The G + C content of strain INB8^T determined from the genome was 36.3 mol%. Based on the phylogenetic, chemotaxonomic and phenotypic information, it is proposed that Facklamia tabacinasalis should be reclassified as Ruoffia tabacinasalis, Facklamia ignava be reclassified as Falseniella ignava, and Facklamia sourekii be reclassified Hutsoniella sourekii. It is further proposed that strain INB8^T should be classified as a species of the genus Ruoffia for which the name Ruoffia halotolerans sp. nov. is proposed. The type strain is INB8^T (= LMG 30291^T = CCUG 70701^T = QCC/B60/17^T).

Facklamia hominis bacteremia after transurethral resection of the prostate: a case report

Background

Transurethral resection of the prostate (TUR-P) is one of the most frequent routine procedures in urology. Because of the semisterile environment, postoperative infections, including sepsis, are a common complication, with Escherichia coli, Klebsiella spp., Proteus mirabilis or Enterococcus faecalis as frequently isolated pathogens. Facklamia hominis is a gram-positive, facultatively anaerobic, alpha-hemolytic, catalase-negative coccus that was first described in 1997. To date, only a few cases of infectious complications have been described. We report the first case of postoperative bacteremia due to Facklamia hominis after TUR-P.

Case presentation

An 82-year-old man developed fever only a few hours after elective TUR-P because of benign prostate syndrome. After cultivation of blood cultures, antibiotic therapy with ceftriaxone was intravenously administered and changed to oral cotrimoxazole before discharge of the afebrile patient. One anaerobic blood culture revealed Facklamia hominis. Under antibiotic therapy, the patient remained afebrile and showed no signs of infections during follow-up.

Conclusions

Fever and bacteremia are frequent complications after TUR-P. This study is the first report of Facklamia hominis in a postoperative blood culture after TUR-P. To date, there are only a few reports of patients with infectious complications and isolation of Facklamia hominis in various patient samples. Because Facklamia hominis resembles viridans streptococci on blood agar analysis, this pathogen may often be misidentified. In this case identification of Facklamia hominis was possible with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. It has been postulated that Facklamia hominis might be a facultative pathogen and that its incidence will increase in the future.

Performance and Application of 16S rRNA Gene Cycle Sequencing for Routine Identification of Bacteria in the Clinical Microbiology Laboratory

This review provides a state-of-the-art description of the performance of Sanger cycle sequencing of the 16S rRNA gene for routine identification of bacteria in the clinical microbiology laboratory. A detailed description of the technology and current methodology is outlined with a major focus on proper data analyses and interpretation of sequences. The remainder of the article is focused on a comprehensive evaluation of the application of this method for identification of bacterial pathogens based on analyses of 16S multialignment sequences. In particular, the existing limitations of similarity within 16S for genus- and species-level differentiation of clinically relevant pathogens and the lack of sequence data currently available in public databases is highlighted. A multiyear experience is described of a large regional clinical microbiology service with direct 16S broad-range PCR followed by cycle sequencing for direct detection of pathogens in appropriate clinical samples. The ability of proteomics (matrix-assisted desorption ionization-time of flight) versus 16S sequencing for bacterial identification and genotyping is compared. Finally, the potential for whole-genome analysis by next-generation sequencing (NGS) to replace 16S sequencing for routine diagnostic use is presented for several applications, including the barriers that must be overcome to fully implement newer genomic methods in clinical microbiology. A future challenge for large clinical, reference, and research laboratories, as well as for industry, will be the translation of vast amounts of accrued NGS microbial data into convenient algorithm testing schemes for various applications (i.e., microbial identification, genotyping, and metagenomics and microbiome analyses) so that clinically relevant information can be reported to physicians in a format that is understood and actionable. These challenges will not be faced by clinical microbiologists alone but by every scientist involved in a domain where natural diversity of genes and gene sequences plays a critical role in disease, health, pathogenicity, epidemiology, and other aspects of life-forms. Overcoming these challenges will require global multidisciplinary efforts across fields that do not normally interact with the clinical arena to make vast amounts of sequencing data clinically interpretable and actionable at the bedside.

Vaginisenegalia massiliensis gen. nov., sp. nov., a new bacterium isolated from the vagina flora and its taxono-genomic description

Strain Marseille-P5643T was isolated from a vaginal sample of a healthy Senegalese woman. It is an anaerobic Gram-negative, rod-shaped bacterium. Strain Marseille-P5643T exhibits 93.7% similarity levels with the Facklamia hominis strain ATCC 700628T, the phylogenetically closest related species with standing in nomenclature. The draft genome size of strain Marseille-P5643T is 1.79 Mb with 39.0 mol% of G+C content. We propose here the creation of Vaginisenegalia massiliensis gen. nov., sp. nov., as a new bacterial genus from the phylum Firmicutes.

Suicoccus acidiformans gen. nov., sp. nov., isolated from a sick pig

A Gram-stain-positive, non-spore-forming, catalase-positive and facultatively anaerobic coccus, designated ZY16052^T, was isolated from mesenteric lymph nodes of a sick piglet in Kunming, Yunnan Province, PR China and its taxonomic position was studied by following a polyphasic approach. Optimal growth was observed at 37 °C, pH 8.0 and 2 % NaCl (w/v) on Columbia agar. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain ZY16052^T formed a separated evolutionary lineage from recognized genera of the family Aerococcaceae and shared low similarity to its closest related species Facklamiasourekii (93.8 %) and Ignavigranum ruoffiae (93.4 %). Phylogenetic analysis based on the housekeeping gene recA indicated that strain ZY16052^T represented a deep and distinct evolutionary lineage, and was well separated from all genera in the family Aerococcaceae, with very low sequence similarity(≤73.2 %). Sequence analysis based on the housekeeping gene rpoA indicated that strain ZY16052^T shared very low similarity ≤77.0 % to related genera. The genomic OrthoANI values between strain ZY16052^T and type species of related genera in the family Aerococcaceae and species in the genus Facklamia were ≤67.77 and ≤68.11 %, respectively. The genomic G+C content was 42.3 mol%. The predominant fatty acids (>5 %) were C16 : 0, C18 : 1ω9c, C14 : 0 and summed feature 5 (C18 : 2ω6,9c and/or C18 : 0 ante). The major polar lipids were digalactosyldiacylglycerol, phosphatidylglycerol, diacylglycerols, triacylglycerol and phosphatidic acid. The peptidoglycan contained the amino acids lysine, glycine, alanine and glutamic acid, which is characteristic of peptidoglycan type A1a. Based on the phylogenetic and phenotypic evidence, we propose that the unknown bacterium be classified as Suicoccus acidiformans gen. nov., sp. nov. The type strain of Suicoccus acidiformans is ZY16052^T (=CCTCC AB 2017017^T=DSM 105755^T).

Ignavigranum ruoffiae, a rare pathogen that caused a skin abscess

Introduction

Ignavigranum ruoffiae is an extremely rare cause of human infections.

Case presentation

An 83-year-old male with a painless, ten-day-old, erythematous skin abscess on his left flank, which had showed a purulent discharge for 48 h, was admitted to the Emergency service. He was treated with cephalexin, disinfection with Codex water and spray of rifampicin. Five days later, surgical drainage of the abscess was proposed due to the torpid evolution of the patient. Samples were taken for culture, and antibiotic treatment with trimethoprim-sulfamethoxazole was established. The patient returned after 10 days showing healing of the abscess. Microbiological studies showed a few Gram-positive cocci present as single cells and short chains that grew after 72 h of incubation at 35 °C with CO₂ on 5 % sheep blood agar. Colonies presented a strong sauerkraut odour. Initial biochemical test results were negative for catalase, aesculin and bile-aesculin, and positive for pyrrolidonyl arylamidase, leucine aminopeptidase and growth in 6.5 % NaCl broth, which prompted the preliminary identification of Facklamia species or I. ruoffiae. The positive result for arginine deamination and negative result for hippurate hydrolysis, failure to produce acid from mannitol, sucrose, sorbitol or trehalose, plus the distinctive sauerkraut odour identified the organism as I. ruoffiae. The phenotypic identification was confirmed by 16S rRNA gene sequence analysis. The strain seemed to be susceptible to the antimicrobials tested but had decreased susceptibility to carbapenems.

Conclusion

This case provides more insights into the phenotypic characteristics and antimicrobial resistance profile of I. ruoffiae.

Facklamia Species as an Underrecognized Pathogen

Facklamia species are a rarely reported etiology of clinical infection with few cases described in literature. However, the prevalence of infection may be underestimated due to challenges in species identification. We describe 3 cases of Facklamia species bacteremia and the unique microbiologic aspects inherent to this genus that make it particularly challenging to identify. In addition, given the unique susceptibility profile of Facklamia species, we discuss the importance of fully identifying this organism when it is a suspected as a pathogen, to optimize therapy based on its distinct antibiotic resistance profile.

Facklamia Species and Streptococcus pneumoniae Meningitis: A Case Report and Review of the Literature

Facklamia sp are Gram-positive cocci that are often mistaken for viridans streptococci, but they rarely cause invasive disease. In this report, we describe a case of mixed Facklamia sp and Streptococcus pneumoniae meningitis in an immunocompetent host with sinusitis. This case demonstrates that Facklamia sp may be part of normal human flora but can be associated with invasive disease.

Case report: first report of a prosthetic joint infection caused by Facklamia hominis

Facklamia spp. are gram-positive cocci first described in 1997. They are α-hemolytic, facultative anaerobes, catalase-negative cocci, resembling viridians streptococci on 5% sheep blood agar. Facklamia hominis is, by far, the most common species of the 6 so far described, and it is thought that its natural habitat is the female genital tract. Four previous human infections with Facklamia spp. have been documented. We report the first case of a chronic prosthetic joint infection caused by F. hominis and its successful treatment by a 2-stage exchange procedure to eradicate the infection. This is also the first osteoarticular infection reported. The clinical implications are discussed.

Identification of Facklamia sourekii from a Lactating Cow

A gram-positive, catalase-negative, facultatively anaerobic coccus was isolated from a lactating cow with hematuria and urodynia in Japan. The isolate was identified by 16S rRNA gene sequence analysis as Facklamia sourekii. The biochemical and culture characteristics of the isolate were well consistent with those of F. sourekii type strain. Since all F. sourekii strains reported so far were isolated from human clinical specimens, this is the first reported case of F. sourekii isolated from veterinary clinical specimen.

What happened to the streptococci: overview of taxonomic and nomenclature changes

Since the division of the Streptococcus genus into enterococci, lactococci, and streptococci in 1984, many changes in the nomenclature and taxonomy of the Streptococcus genus have taken place. The application of genetic comparisons has improved the proper classification of the different species. The Lancefield system of serogrouping the streptococci by the expression of beta-hemolysis on blood agar plates is still very useful for the identification of streptococci for patient management. The Lancefield grouping system cannot be used in itself for accurate identification of specific beta-hemolytic species, but it can be a useful part of the identification procedure. Except for identification of the "Streptococcus bovis group" of species and Streptococcus suis, Lancefield grouping is of little value in identification of the non-beta-hemolytic streptococci and related genera. In fact, identification of the non-beta-hemolytic species is problematic for conventional as well as commercially available identification procedures. A combination of conventional tests and specific chromogenic tests suggested by several investigators is presented and discussed. Tables are included that suggest tests and procedures to guide investigators attempting to identify all the species.