Assignment of provisionally named CDC group NO-1 strains derived from animal bite wounds and other clinical sources, to genera nova in the family Comamonadaceae: description of Vandammella animalimorsus gen. nov., sp. nov. and Franklinella schreckenbergeri gen. nov., sp. nov

CDC group non-oxidizer (NO)-1 is the provisional name designated in 1993 for phenotypically similar, Gram-stain-negative bacilli recovered primarily from human wound infections after animal bites. Otherwise, this group has been rarely alluded to in recent literature. CDC NO-1 strains had been described as non-motile, asaccharolytic, oxidase-negative, catalase-positive, nitrate-reducing bacilli, with predominate cellular fatty acids of C10 : 0 3OH, C16 : 1 ω7c, C16 : 0 and C18 : 1 ω7c. Only one 16S rRNA gene sequence deposited in NCBI (accession no. DQ054782) had been identified as CDC group NO-1 prior to this study. That sequence was closely related (>99 % identity) to sequences called ‘ Xenophilus species’ from canine (JN713339) and feline (KM461961) oral microbiomes as well as to sequences derived from human strains (this study). Some of the 11 isolates delineated here were recovered from human wound infections subsequent to cat/dog bites; others were from wounds (links to animal bites not described) and two were recovered from dialysates. After 16S rRNA and whole genome sequencing, the isolates were found to be most closely related to each other but fell into two distinct genera assignable to the family Comamonadaceae , provisionally discussed here as CDC group NO-1 and CDC group NO-1-like. The genomes of CDC group NO-1 isolates ranged from 3.08 to 3.38 MB with G+C contents of 65.08–66.92 %; genomes derived from CDC group NO-1-like strains were smaller, ranging from 2.72 to 2.82 Mb with G+C contents of 62.87–63.0 mol%. Based on a polyphasic study of these bacteria, we describe Vandammella animalimorsus gen. nov., sp. nov. and Franklinella schreckenbergeri gen. nov., sp. nov. for these clusters.

Corynebacterium hindlerae sp. nov., derived from a human granuloma, which forms black colonies and black halos on modified Tinsdale medium but is not closely related to Corynebacterium diphtheriae and related taxa

Corynebacterium diphtheriae, Corynebacterium belfantii, Corynebacterium rouxii, Corynebacterium ulcerans, Corynebacterium pseudotuberculosis and Corynebacterium silvaticum are the only taxa from among ~121 Corynebacterium species deemed potentially able to harbour diphtheria tox genes. Subsequently tox-gene bearing species may potentially produce diphtheria toxin, which is linked to fatal respiratory distress if a pharyngeal pseudomembrane is formed or toxaemia develops in those unimmunized or under-immunized. Detection of diphtheria toxin-producing species may also invoke a public health response and contact tracing. Recovery of such species from the respiratory tract or other contaminated sources such as non-healing ulcerative wounds are expedited by use of differential and selective media such as modified Tinsdale medium (MTM). This medium is supplemented with potassium tellurite, which supresses most normal flora present in contaminated specimens, as well as l-cystine and thiosulphate. Most diphtheria-tox-gene bearing species grow well on MTM, producing black colonies with a black halo around each colony. This is due to an ability to produce cystinase in the presence of tellurite, cystine and thiosulphate, resulting in black tellurium deposits being observed in the agar. Other Corynebacterium species may/may not be able to grow at all in the presence of tellurite but if able to grow, will have small beige or brownish colonies which do not exhibit black halos. We describe here an unusual non-tox-gene-bearing isolate, NML 93-0612^T, recovered from a human wrist granuloma, which produced black colonies with black halos on MTM agar but was otherwise distinguishable from Corynebacterium species which can bear tox genes. Distinctive features included its unusual colony morphology on MTM and sheep blood agar, by proteomic, biochemical and chemotaxonomic properties and by molecular methods. Its genome contained 2 680 694 bytes, a G+C content of 60.65 mol% with features consistent with the genus Corynebacterium and so represents a new species for which we propose the name Corynebacterium hindlerae sp. nov.

Pseudoxanthomonas winnipegensis sp. nov., derived from human clinical materials and recovered from cystic fibrosis and other patient types in Canada, and emendation of Pseudoxanthomonas spadix Young et al. 2007

Twelve isolates recovered from 10 cystic fibrosis/other patient types and a variety of clinical sources, were referred to Canada's National Microbiology Laboratory over 7 years. These were assignable to the genus Pseudoxanthomonas but were unidentifiable to species level. Patients included five males and five females from two geographically separated provinces, ranging in age from 2 months to 84 years. In contrast, most Pseudoxanthomonas species described to date have been derived from water, plants or contaminated soils. By 16S rRNA gene sequencing, the patient strains had ≥99.4 % similarity to each other but only 97.73-98.29 % to their closest relatives, Pseudoxanthomonas spadix or Pseudoxanthomonas helianthi. Bacteria were studied by whole genome sequencing using average nucleotide identity by Blastn, digital DNA-DNA hybridization, average amino acid identity, core genome and single nucleotide variant analyses, MALDI-TOF, biochemical and cellular fatty acid analyses, and by antimicrobial susceptibility testing. Bacterial structures were assessed using scanning and transmission electron microscopy. Strains were strict aerobes, yellowish-pigmented, oxidative, non-motile, Gram-stain-negative bacilli and generally unable to reduce nitrate. Strains were susceptible to most of the antibiotics tested; some resistance was observed towards carbapenems, several cephems and uniformly to nitrofurantoin. The single taxon group observed by 16S rRNA gene sequencing was supported by whole genome sequencing; genomes ranged in size from 4.36 to 4.73 Mb and had an average G+C content of 69.12 mol%. Based on this study we propose the name Pseudoxanthomonas winnipegensis sp. nov. for this cluster. Pseudoxanthomonas spadix DSM 18855^T, acquired for this study, was found to be non-motile phenotypically and by electron microscopy; we therefore propose the emendation of Pseudoxanthomonas spadix Young et al. 2007 to document that observation.

Enemella gen. nov., Enemella evansiae sp. nov., Enemella dayhoffiae sp. nov. and Parenemella sanctibonifatiensis gen. nov., sp. nov., novel taxa assignable to the family Propionibacteriaceae and derived from human clinical samples

Nine Gram-stain-positive cocci, coccobacilli or short, rod-shaped strains recovered from clinical sources from patients located in two Canadian provinces and one environmental source were extensively studied. Clinical sources included blood cultures, cerebral spinal fluid, lymph node, lung biopsy and peritoneal fluid. Through 16S rRNA gene and whole genome sequencing analyses, the strains were found to cluster into three groups, closest to but distinguished from other genera in the family Propionibacteriaceae. The genomes from these bacteria had high G+C content, ranging from 67.8-69.56 mol%, and genome sizes of 3.02-4.52 Mb. Biochemical and chemotaxonomic properties including branched-chain cellular fatty acids, l-lysine diaminopimelic acid (ll-DAP) and cell-wall type A3γ (ll-DAP-gly) containing ll-DAP, alanine, glycine and glutamic acid were found and so the strains were therefore deemed to be consistent with other new genera in this family. Based on this investigation, we propose Enemella gen. nov., Enemella evansiae sp. nov., Enemella dayhoffiae sp. nov. and Parenemella sanctibonifatiensis gen. nov., sp. nov. for these taxa. Misidentified taxon 'Ponticoccus gilvus' was found to be assignable to Enemella evansiae based on this study.

Vaginimicrobium propionicum gen. nov., sp. nov., a novel propionic acid bacterium derived from human vaginal discharge

A Gram-stain-positive anaerobic rod-shaped bacterium, designated strain Marseille-P3275^T, was isolated using culturomics from the vaginal discharge of healthy French woman. Marseille-P3275^T was non-motile and did not form spores. Cells had neither catalase nor oxidase activity. The major fatty acids were C_16 : 0 (29 %), C_18:1ω9 (18 %), and iso-C_15 : 0 (17 %). The genomic DNA G+C content was 50.64 mol%. The phylogenetic analysis based on 16S rRNA gene sequence indicated that Marseille-P3275^T was related to members of the family Propionibacteriaceae (between 90.32-92.92 % sequence similarity) with formation of a clade with the monospecific genus Propionimicrobium (type species Propionimicrobium lymphophilum). On the basis of these phylogenetic and phenotypic differences, Marseille-P3275^T was classified in a novel genus, Vaginimicrobium, as Vaginimicrobium propionicum gen. nov., sp. nov. The type strain is Marseille-P3275^T (=CSUR P3275^T=CECT 9677^T).

Corynebacterium godavarianum Jani et al. 2018 and Corynebacterium hadale Wei et al. 2018 are both later heterotypic synonyms of Corynebacterium gottingense Atasayar et al. 2017, proposal of an emended description of Corynebacterium gottingense Atasayar et al. 2017

Seven strains of an unidentifiable Corynebacterium species recovered from blood cultures, urine or cerebrospinal fluid over 26 years, closest to but differentiated from Corynebacterium imitans by 16S rRNA gene and partial rpoB gene sequencing, were studied. In November 2017, Atasayar et al. described a blood culture isolate as Corynebacterium gottingense sp. nov., which had >99 % similarity by 16S rRNA gene sequencing to the Canadian strains. In January 2018, Jani et al. described Corynebacterium godavarianum sp. nov., recovered from the Godavari River, India, which also had >99 % similarity by 16S/rpoB sequencing to the Canadian strains and C. gottingense. In May 2018, Wei et al. described Corynebacterium hadale recovered from hadopelagic water; this too had >99 % similarity by 16S rRNA gene sequencing to C. gottingense, C. godavarianum and the Canadian strains. C. gottingense DSM 103494^T and C. godavarianum LMG 29598^T were acquired and whole genome sequencing was performed (not previously done). Results were compared with genomes from C. hadale (GenBank accession NQMQ01) and the Canadian isolates. We found that these ten genomes formed a single taxon when compared using digital DNA-DNAhybridization, average nucleotide identity using blastn and average amino acid identity criteria but exhibited some subtle biochemical and chemotaxonomic differences. Heuristically, we propose that C. godavarianum and C. hadale are later heterotypic synonyms of, and the Canadian isolates are identifiable as, C. gottingense. We provide an emended description of Corynebacterium gottingense Atasayar et al. 2017; genomes ranged from 2.48 to 2.69 Mb (C. gottingense DSM 103494^T, 2.62 Mb) with G+C content of 65.1-65.6 mol% (WGS), recovered from clinical and environmental sites.

Description of Eikenella halliae sp. nov. and Eikenella longinqua sp. nov., derived from human clinical materials, emendation of Eikenella exigua Stormo et al. 2019 and emendation of the genus Eikenella to include species which are strict anaerobes

The Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK) group genus Eikenella contained a single species, Eikenella corrodens, for many years. In November 2019, Eikenella exigua was described after recovery from a brain abscess and blood culture in Norway. Coincidentally, characterization of 22 Gram-negative bacteria resembling Eikenella from 17 Canadian patients had been underway. Seven isolates from five patients were conclusively identifiable as E. corrodens. One (NML 120819) was deemed to represent a species of the genus Eikenella most closely related to E. corrodens. Fourteen isolates had 97.6 to 98.8% similarities to E. corrodens by 16S rRNA gene sequencing, forming three distinct groups by genome analyses. The largest contained ten anaerobic isolates from eight patients recovered from blood, brain, bone and other abscesses; upon re-evaluation, this group was found to be most consistent with E. exigua. A second facultatively anaerobic clade consisted of two ocular isolates from one patient and a sinus isolate from a second patient. The third taxon consisted of a single strictly anaerobic blood culture isolate. The novel taxa, like E. corrodens, were poorly reactive biochemically and difficult to discern from each other phenotypically and chemotaxonomically, including by cellular fatty acids. MALDI-TOF (Bruker) and whole-genome sequencing were used to further characterize isolates. Draft genomes for the strains had similar DNA G+C contents (55.38-58.53 mol%) while sizes varied from 1.82 Mb to 2.54 Mb. We propose here emendations of the genus Eikenella and the species Eikenella exigua, as well as describing Eikenella halliae sp. nov. NML 130454^T (=LMG 30894^T=NCTC 14180^T) and Eikenella longinqua sp. nov. NML 02-A-017^T (=LMG 30896^T=NCTC 14179^T), on the basis of these findings.

Emendation of the Genus Auritidibacter Yassin et al. 2011 and Auritidibacter ignavus Yassin et al. 2011 based on features observed from Canadian and Swiss clinical isolates and whole-genome sequencing analysis

Auritidibacter ignavus is a Gram-stain-positive bacillus derived from otorrhea. Four strains derived from ear discharges in Canada and Switzerland, with features consistent with but distinguishable from Auritidibacter ignavus IMMIB L-1656^T (accession number FN554542) by 16S rRNA gene sequencing (97.5 % similarity), were thought to represent a novel species of the genus Auritidibacter. Auritidibacter ignavus DSM 45359^T (=IMMIB L-1656^T) was acquired to compare with Canadian and Swiss strains by whole-genome sequencing (WGS). Unexpectedly, those isolates were observed to be consistent with A. ignavus DSM 45359^T by WGS (ANIb scores >98 %), MALDI-TOF (Bruker), cellular fatty acid analysis and biochemically (some differences were observed). A nearly full 16S rRNA gene sequence could not be readily prepared from A. ignavus DSM 45359^T, even after multiple attempts. A 16S rRNA gene chimeric consensus sequence created from the genome assembly of A. ignavus DSM 45359^T had only 97.5 % similarity to that of A. ignavus IMMIB L-1656^T, implying that 16S rRNA sequence accession number FN554542 could not be replicated. We concluded that our isolates of members of the genus Auritidibacter were consistent with A. ignavus DSM 45359^T, did not represent a novel species, and that the sequence corresponding to FN554542 was not reproducible. By WGS, A. ignavus DSM 45359^T had genome of 2.53×10⁶ bp with a DNA G+C content of 59.34%, while genomes of Canadian and Swiss isolates ranged from 2.47 to 2.59×10⁶ bp with DNA G+C contents of 59.3-59.52 %. A. ignavus NML 100628 (=NCTC 14178=LMG 30897) did not demonstrate a rodcoccus cycle. Emendation of Auritidibacter ignavus was proposed based on these results.

Ignatzschineria indica bacteremia in a patient with a maggot-infested heel ulcer: a case report and literature review

An elderly patient was admitted with sepsis to a community hospital. The individual was found to have a foot wound infested with maggots, and clinical evidence of cellulitis. A blood culture was positive on day 2 with Ignatzschineria indica . The patient was treated successfully with a combination of antibiotics and manual removal of the maggots. Poor living conditions were central to his presentation.

Propionibacterium ruminifibrarum sp. nov., isolated from cow rumen fibrous content

A novel propionate producing bacterium, strain JV5^T, was isolated from the rumen fibrous content of a Holstein Friesian dairy cow. Cells of strain JV5^T were Gram-stain-positive, non-motile and aerotolerant. Growth occurred between 35 and 45 °C, with an optimum at 39 °C. The pH range for growth was 6.5-8, with an optimum at pH 7. The 16S rRNA gene sequence of strain JV5^T was 98.4 and 96.5 % identical to those of Propionibacterium australiense DSM 15818^T and Propionibacterium acidifaciens DSM 21887^T, respectively. Genome wide average nucleotide identity and digital DNA-DNA hybridization values were 88.3 and 35.5 %, respectively, against P. australiense DSM 15818^T. The G+C content of strain JV5^T was 68.9  mol%. Strain JV5^T did not produce urease and was able to metabolize glutamate, but not aspartate and glycine. Strain JV5^T was able to ferment a range of substrates including certain simple and complex carbohydrates, sugar alcohols and amino acids. Chemotaxonomic analysis of strain JV5^T revealed the presence of meso-diamino pimelic acid isomers similar those found in P. australiense, but different from P. acidifaciens. The observed major (>10 %) cellular fatty acids in strain JV5^T (C18 : 1 ω9c, anteiso-C15 : 1, C16 : 0, C17 : 0 and C16 : 0 alcohol) were also different from those observed in P. australiense and P. acidifaciens. Based on these findings, a novel species is proposed within the genus Propionibacterium, Propionibacterium ruminifibrarum sp. nov. (type strain JV5^T=DSM 106771^T=TISTR 2629^T).

Criibacterium bergeronii gen. nov., sp. nov., a new member of the family Peptostreptococcaceae, isolated from human clinical samples

A rod-shaped, motile anaerobic bacterium, designated CCRI-22567T, was isolated from a vaginal sample of a woman diagnosed with bacterial vaginosis and subjected to a polyphasic taxonomic study. The novel strain was capable of growth at 30-42 °C (optimum, 42 °C), at pH 5.5-8.5 (optimum, pH 7.0-7.5) and in the presence of 0-1.5 % (w/v) NaCl (optimally at 0.5 % NaCl). The phylogenetic trees based on 16S rRNA gene sequences showed that strain CCRI-22567T forms a distinct evolutionary lineage independent of other taxa in the family Peptostreptococcaceae. Strain CCRI-22567T exhibited 90.1 % 16S rRNA gene sequence similarity to Peptoanaerobacter stomatis ACC19aT and 89.7 % to Eubacterium yurii subsp. schtitka ATCC 43716. The three closest organisms with an available whole genome were compared to strain CCRI-22567T for genomic relatedness assessment. The genomic average nucleotide identities (OrthoANIu) obtained with Peptoanaerobacter stomatis ACC19aT, Eubacterium yurii subsp. margaretiae ATCC 43715 and Filifactor alocis ATCC 35896T were 71.8, 70.3 and 69.6 %, respectively. Strain CCRI-22567T contained C18 : 1 ω9c and C18 : 1 ω9c DMA as the major fatty acids. The DNA G+C content of strain CCRI-22567T based on its genome sequence was 33.8 mol%. On the basis of the phylogenetic, chemotaxonomic and other phenotypic properties, strain CCRI-22567T is considered to represent a new genus and species within the family Peptostreptococcaceae, for which the name Criibacterium bergeronii gen. nov., sp. nov., is proposed. The type strain of Criibacterium bergeronii is CCRI-22567T (=LMG 31278T=DSM 107614T=CCUG 72594T).

Whole-Genome Sequences of Propionibacterium australiense NML (LCDC) 98A072T and NML (LCDC) 98A078, Associated with Granulomatous Bovine Lesions

Draft genome sequences of Propionibacterium australiense isolates NML 98A072^T and NML 98A078, derived from granulomatous lesions of infected bovines, were assembled and studied. Respectively, the genome sizes were 2.99 and 3.01 Mb, with G+C contents of 68.4% and 68.5%.

Draft genome sequences of Propionibacterium australiense isolates NML 98A072^T and NML 98A078, derived from granulomatous lesions of infected bovines, were assembled and studied. Respectively, the genome sizes were 2.99 and 3.01 Mb, with G+C contents of 68.4% and 68.5%.

Impact of cleaning monitoring combined with channel purge storage on elimination of Escherichia coli and environmental bacteria from duodenoscopes

BACKGROUND AND AIMS

We aimed to determine whether monitoring of duodenoscope cleaning by rapid adenosine triphosphate (ATP) combined with channel-purge storage could eliminate high-concern microorganisms.

METHODS

In a simulated-use study, suction channels, as well as lever recesses, from 2 duodenoscopes models and the unsealed elevator guidewire (EGW) channel from 1 of these 2 duodenoscopes (the other model has a sealed EGW) were perfused with ATS2015 containing approximately 8 Log₁₀ colony-forming units (CFU)/mL of both Enterococcus faecalis and Escherichia coli. Pump-assisted cleaning was monitored by rapid ATP testing. Duodenoscopes exceeding 200 relative light units (RLUs) were recleaned. Clean duodenoscopes were processed through an automated endoscope reprocessor and then stored in a channel-purge storage cabinet for 1 to 3 days. Cultures of EGW channel and instrument channel combined with the lever recess (IC-LR) were taken after storage. The impacts of extended cleaning and alcohol flush were evaluated.

RESULTS

E coli was reliably eliminated in IC-LR and EGW channels of 119 duodenoscope tests (59 with sealed EGW and 60 with nonsealed EGW). However, actionable levels of E faecalis and environmental bacteria persisted. Neither alcohol flush nor extended cleaning resulted in a reduction of actionable levels for these organisms. Identification of isolates indicated that residual organisms in duodenoscope channels were hardy Gram-positive bacteria (often spore formers) that likely originated from environmental sources.

CONCLUSIONS

These data indicate that high-concern Gram-negative bacteria but not E faecalis or environmental bacteria can be reliably eliminated by use of the manufacturer's instructions for reprocessing with ATP monitoring of cleaning and channel-purge storage conditions.

Clostridium neonatale sp. nov. linked to necrotizing enterocolitis in neonates and a clarification of species assignable to the genus Clostridium (Prazmowski 1880) emend. Lawson and Rainey 2016

A description of an outbreak of necrotizing enterocolitis among neonates, linked to the putative novel species Clostridium neonatale and assignable to the genus Clostridium, was previously reported in brief but that name had never been validly published (Alfa et al. Clin Inf Dis 2002;35:S101-S105). Features of this taxon group and its phylogenetic position with respect to contemporary species in the genus Clostridium were recently reviewed and still found to be unique. Therefore, we provide here a description based on biochemical, chemotaxonomic and antimicrobial susceptibility testing (AST), matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS, 16S rRNA gene sequencing as well as information obtained by whole genome sequencing (WGS) for strains 99A005^T and 99A006. Those two C. neonatale strains were essentially identical to each other, with genome sizes of 4 658 596-4 705 520 bp and G+C content of 28.4-28.5 mol% (WGS). AST inferred susceptibility to 14 antibiotics. MALDI-TOF spectra were unique and could potentially be used for identification. The type strain is (NML) LCDC 99A005^T [=ATCC BAA-265^T=CCUG 46077^T=St. Boniface Hospital 30686^T]. While performing this review, we found that the names of 24 validly published species assignable to the genus Clostridium had been omitted from the emended description of the genus (Lawson and Rainey Int J Syst Evol Microbiol 2016;66 :1009-1016). Those species are listed in brief here. Lastly, based on this review, we also propose that Eubacterium budayi, Eubacterium nitritogenes and Eubacterium combesii be transferred to the emended genus Clostridium, as Clostridium budayi comb. nov., Clostridium nitritogenes comb. nov. and Clostridium combesii comb. nov., respectively.

Characterization of isolates of Eisenbergiella tayi, a strictly anaerobic Gram-stain variable bacillus recovered from human clinical materials in Canada

Eisenbergiella gen. nov. was proposed in 2014 to describe an obligate anaerobic, structurally Gram-positive but Gram-stain-negative-appearing bacillus recovered from the blood culture of an elderly Israeli man. Here, we describe features for eight blood culture isolates as well one appendix-derived isolate, recovered from seven patients located in two Canadian provinces, which by 16S rRNA gene sequencing, were identifiable as Eisenbergiella tayi, the sole validly- named species in this genus. After whole genome sequencing, isolates were found to be essentially identical (96.8-98.7% identity) to each other and to E. tayi DSM 26961^T, after comparison using the ANIb tool and in silico DNA-DNA hydridization. All isolates were observed to have remarkably large genomes (7.1-8.3 Mb) with a G + C content of 46.5%-46.9%.

Dairy propionibacteria as probiotics: recent evidences

Nowdays there is evidence that dairy propionibacteria display probiotic properties, which as yet have been underestimated. The aim of this paper is to review the recent highlights of data representing the probiotic potential of dairy propionibacteria, studied both by general selection criteria (useful for all probiotic potentials), and by more specific and innovative approach. Dairy propionibacteria show a robust nature, that makes them able to overcome technological hurdles, allowing their future use in various fermented probiotic foods. In addition to the general selection criteria for probiotics in areas such as food safety, technological and digestive stress tolerance, many potential health benefits have been recently described for dairy propionibacteria, including, production of several active molecules and adhesion capability, that can mean a steady action in modulation of microbiota and of metabolic activity in the gut; their impact on intestinal inflammation, modulation of the immune system, potential modulation of risk factors for cancer development modulation of intestinal absorption.

Pulsed field gel electrophoresis for dairy propionibacteria

Pulsed field gel electrophoresis (PFGE) is a technique using alternating electric fields to migrate high molecular weight DNA fragments with a high resolution. This method consists of the digestion of bacterial chromosomal DNA with rare-cutting restriction enzymes and in applying an alternating electrical current between spatially distinct pairs of electrodes. DNA molecules migrate at different speeds according to the size of the fragments. Among other things, this technique is considered as the "gold standard" for genotyping, genetic fingerprinting, epidemiological studies, genome size estimation, and studying radiation-induced DNA damage and repair. This chapter describes a PFGE method that can be used to differentiate dairy propionibacteria.

Engineering propionibacteria as versatile cell factories for the production of industrially important chemicals: advances, challenges, and prospects

Propionibacteria are actinobacteria consisting of two principal groups: cutaneous and dairy. Cutaneous propionibacteria are considered primary pathogens to humans, whereas dairy propionibacteria are widely used in the food and pharmaceutical industries. Increasing attention has been focused on improving the performance of dairy propionibacteria for the production of industrially important chemicals, and significant advances have been made through strain engineering and process optimization in the production of flavor compounds, nutraceuticals, and antimicrobial compounds. In addition, genome sequencing of several propionibacteria species has been completed, deepening understanding of the metabolic and physiological features of these organisms. However, the metabolic engineering of propionibacteria still faces several challenges owing to the lack of efficient genome manipulation tools and the existence of various types of strong restriction-modification systems. The emergence of systems and synthetic biology provides new opportunities to overcome these bottlenecks. In this review, we first introduce the major species of propionibacteria and their properties and provide an overview of their functions and applications. We then discuss advances in the genome sequencing and metabolic engineering of these bacteria. Finally, we discuss systems and synthetic biology approaches for engineering propionibacteria as efficient and robust cell factories for the production of industrially important chemicals.

Extended characterization of Corynebacterium pyruviciproducens based on clinical strains from Canada and Switzerland

The species Corynebacterium pyruviciproducens was described in 2010 based on the features of a single strain. In this report, we describe the chemotaxonomic and phenotypic characteristics of 11 C. pyruviciproducens clinical strains isolated in Switzerland and Canada in comparison to the strain 06-17730(T). Heterogeneities within the type strain were found in the 16S rRNA gene and in biochemical markers. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) identification of this species could not be achieved since currently this bacterial species is not included in the corresponding database. Reliable identification is obtained only with sequence-based identification tools. Results of antimicrobial susceptibility testing of this species with an extended panel of antimicrobials are presented here for the first time.

Novel fastidious, partially acid-fast, anaerobic Gram-positive bacillus associated with abscess formation and recovered from multiple medical centers

We report a novel anaerobe causing abscess in four patients at three hospitals. In the clinical specimen, bacilli were branching, Gram positive, and acid fast. The organism grew slowly and was not identified by 16S rRNA sequencing. Our findings support the description of a new genus and species of the suborder Corynebacterineae.

Emendation of the description of the species Corynebacterium propinquum to include strains which produce urease

Corynebacterium propinquum is a Gram-positive rod occasionally recovered from clinical infections which, according to 16S rRNA gene sequencing, is most closely related (>99 % sequence similarity) to Corynebacterium pseudodiphtheriticum . The two species are very similar biochemically, commonly differentiated by a single test, the detection of urease, where strains of C. propinquum are described as being urease-non-producing and strains of C. pseudodiphtheriticum are described as urease-producing. In this study, historical and contemporary strains of C. propinquum and C. pseudodiphtheriticum from this laboratory were definitively characterized, which included use of rpoB sequencing. Urease-producing strains of C. propinquum as well as typical urease-non-producing isolates were identified after rpoB sequencing, with six of these being originally identified as C. pseudodiphtheriticum . Based on these observations, we propose emendation of the description of C. propinquum to include strains which produce urease. MALDI-TOF analysis may be a useful tool to differentiate these taxa. Existing commercial databases should be updated to include urease-positive strains of C. propinquum .

Isolation and characterization of Pigmentiphaga-like isolates from human clinical material

Species in the genus Pigmentiphaga are Gram-negative, catalase- and oxidase-positive rods derived exclusively to date from environmental sources. Features of strains most like Pigmentiphaga daeguensis or Pigmentiphaga kullae from a case of suppurative otitis media in a 6-year-old female post-transplant recipient and in a human stool sample are described.

Staphylococcus lugdunensis: low prevalence and clinical significance in a pediatric microbiology laboratory

Staphylococcus lugdunensis is reported to be a highly virulent coagulase-negative Staphylococcus species, but whether it is an important pediatric pathogen is uncertain. At our pediatric center, only 2.1% (7/347) of coagulase-negative Staphylococcus isolates were found to be S. lugdunensis, and only 1 isolate was considered possibly clinically significant.S. lugdunensis does not appear to be a common pathogen in children.

Enterococcus ureasiticus sp. nov. and Enterococcus quebecensis sp. nov., isolated from water

Three enterococcal isolates, CCRI-16620, CCRI-16986T and CCRI-16985T, originating from water were characterized using morphological, biochemical and molecular taxonomic methods. 16S rRNA gene sequence analysis classified all three strains in the Enterococcus faecalis species group. The phylogenetic tree of 16S rRNA gene sequences showed that the three isolates form two separate branches. The first branch is represented by strains CCRI-16620 and CCRI-16986T and the second branch by strain CCRI-16985T. Further sequence analysis of the housekeeping genes rpoA (encoding RNA polymerase α subunit), pheS (phenylalanyl-tRNA synthase), tufA (elongation factor Tu) and atpD (ATP synthase β-subunit) as well as the results of amplified fragment length polymorphism (AFLP) DNA fingerprinting and DNA–DNA hybridization experiments confirmed the distinct status of these strains. Moreover, biochemical tests allowed phenotypic differentiation of the strains from the other species of the E. faecalis species group. On the basis of the results obtained, the names Enterococcus ureasiticus sp. nov. (type strain CCRI-16986T = CCUG 59304T = DSM 23328T = LMG 26304T) and Enterococcus quebecensis sp. nov. (type strain CCRI-16985T = CCUG 59306T = DSM 23327T = LMG 26306T) are proposed for the two hitherto undescribed species.

Corynebacterium macginleyi conjunctivitis in Canada

This report describes for the first time Corynebacterium macginleyi as a cause of conjunctivitis in Canada, where menaquinone analysis was done as part of the strain characterization. This species is typically isolated from ocular surfaces of patients from Europe and Japan. The isolate was resistant to erythromycin and clindamycin.

Assignment of Brevibacterium stationis (ZoBell and Upham 1944) Breed 1953 to the genus Corynebacterium, as Corynebacterium stationis comb. nov., and emended description of the genus Corynebacterium to include isolates that can alkalinize citrate

Brevibacterium stationis ATCC 14403T, Corynebacterium ammoniagenes ATCC 6872 and two clinical isolates were found to form a single taxon group consistent with the genus Corynebacterium, designated here as Corynebacterium stationis comb. nov. The type strain of Corynebacterium stationis is ATCC 14403T =CCUG 43497T =CIP 104228T =DSM 20302T =NBRC 12144T =JCM 11611T =VKM B-1228T. These strains can utilize citrate; therefore, inclusion of C. stationis requires that the description of the genus Corynebacterium be amended to include citrate-positive strains.

Approaches to the study of the systematics of anaerobic, gram-negative, non-sporeforming rods: current status and perspectives

The present article gives an overview of recent taxonomic changes among the Gram-negative, anaerobic rods, briefly highlighting areas where the biology and ecology have a bearing on recent nomenclatorial changes. The focus is among the genera Bacteroides, Prevotella, Porphyromonas, Leptotrichia, Dysgonomonas, Fusobacterium and the Synergistes group and additionally demonstrates the value of conserved indels and group-specific proteins for identifying and circumscribing many of these taxa and the Bacteroidetes-Chlorobi species in general.

Propionibacterium acidifaciens sp. nov., isolated from the human mouth

Three strains of anaerobic, pleomorphic, Gram-positive-staining bacilli, which were isolated from human carious dentine, were subjected to a comprehensive range of phenotypic and genotypic tests and were found to comprise a homogeneous group. The strains were saccharolytic and produced acetic and propionic acids in large amounts, and succinic acid in moderate amounts, as the end products of fermentation. 16S rRNA gene and RpoB protein sequence analyses revealed that the strains constituted a novel group within the genus Propionibacterium, most closely related to Propionibacterium australiense but sharing only 8 % DNA-DNA relatedness with the type strain of that species. Therefore, a novel species, Propionibacterium acidifaciens sp. nov., is proposed to accommodate these strains. The DNA G+C content of the type strain is 70 mol%. The type strain is C3M_31(T) (=DSM 21887(T) =CCUG 57100(T)).

Clostridium lavalense sp. nov., a glycopeptide-resistant species isolated from human faeces

Two vancomycin-resistant, strictly anaerobic, Gram-positive, rod-shaped, spore-forming organisms (strains CCRI-9842(T) and CCRI-9929) isolated from human faecal specimens in Québec, Canada, and Australia were characterized using phenotypic, biochemical and molecular taxonomic methods. Pairwise analysis of the 16S rRNA gene sequences showed that both strains were closely related to each other genetically (displaying 99.2 % sequence similarity) and represented a previously unknown subline within the Clostridium coccoides rRNA group of organisms (rRNA cluster XIVa of the genus Clostridium). Strains CCRI-9842(T) and CCRI-9929 used carbohydrates as fermentable substrates, producing acetic acid as the major product of glucose metabolism. The novel strains were most closely related to Clostridium asparagiforme, Clostridium bolteae and Clostridium clostridioforme, but morphological, biochemical and phylogenetic studies demonstrated that they represent a previously unidentified species of the genus Clostridium. This was confirmed by the unique cellular fatty acid composition of strains CCRI-9842(T) and CCRI-9929. Therefore, on the basis of data from the polyphasic taxonomic analysis, it is proposed that strains CCRI-9842(T) and CCRI-9929 represent a novel species of the genus Clostridium, for which the name Clostridium lavalense sp. nov. is proposed. The type strain is CCRI-9842(T) (=CCUG 54291(T)=JCM 14986(T)=NML 03-A-015(T)).

Ruminococcus gauvreauii sp. nov., a glycopeptide-resistant species isolated from a human faecal specimen

A novel strictly anaerobic, vancomycin-resistant, Gram-positive coccus (strain CCRI-16,110(T)) was isolated from a human faecal specimen. This strain was characterized using morphological, biochemical and molecular taxonomic methods. The organism was unable to hydrolyse aesculin and failed to produce acid from cellobiose, d-lactose and alpha-raffinose. Acetic acid was the sole product of glucose fermentation by the organism. On the basis of 16S rRNA and tuf gene sequence comparison, strain CCRI-16,110(T) was most closely related to species of the genus Ruminococcus and formed a hitherto unknown sublineage within the Clostridium coccoides rRNA cluster of organisms (cluster XIVa). Based on phenotypic and phylogenetic evidence, a novel species, Ruminococcus gauvreauii sp. nov., is proposed. The type strain is CCRI-16,110(T) (=NML 060141(T) =CCUG 54,292(T) =JCM 14987(T)).

First report of isolation and characterization of Aurantimonas altamirensis from clinical samples

The genus Aurantimonas, proposed in 2003, encompasses four species from environmental sources, including Aurantimonas altamirensis, isolated from a cave wall in Spain. Here, we report what we believe are the first cases of the recovery of A. altamirensis from human clinical materials.

Legionella jordanis lower respiratory tract infection: case report and review

Legionella jordanis was first described in 1982 after isolation from environmental sources and is otherwise a very rare human pathogen. Here, we report the recovery of L. jordanis from a bronchoalveolar lavage specimen from a patient who presented with an indolent lower respiratory tract infection associated with constitutional symptoms. This case is the first culture-positive case of infection involving this species in Canada.

Comparison of amplified ribosomal DNA restriction analysis, peptidoglycan hydrolase and biochemical profiles for rapid dairy propionibacteria species identification

Species of dairy propionibacteria are used as cheese-ripening cultures as well as probiotics. However, no rapid identification methods are currently available. With this in mind, the present study compared three methods, (i) carbohydrate fermentation, (ii) ARDRA (amplified ribosomal DNA restriction analysis) and (iii) peptidoglycan hydrolase (PGH) activity profiles to improve the identification of Propionibacterium thoenii, Propionibacterium jensenii, Propionibacterium acidipropionici and Propionibacterium microaerophilum. The species Propionibacterium freudenreichii and Propionibacterium cyclohexanicum have previously been shown to be easily distinguishable from the other species. Principal component analysis of the carbohydrate fermentation profiles of 113 P. thoenii, P. jensenii, P. acidipropionici and P. microaerophilum strains correctly classified 85% of the strains based on the fermentation of seven carbohydrates. Regarding PGH profiles, optimized conditions of PGH-renaturing SDS-PAGE were applied to 34 of the strains. The PGH profiles of P. acidipropionici and P. microaerophilum were indistinguishable from one another, but were easily distinguished from P. jensenii and P. thoenii. However, four strains exhibited atypical profiles. Hence, in general, the PGH profiles were shown to be conserved within a species, with some exceptions. Four endonucleases were tested for ARDRA and the four species differentiated by combining the profiles obtained with MspI and HaeIII. P. freudenreichii and P. cyclohexanicum profiles were also performed but showed wide differences. Consequently, ARDRA was shown to be the most appropriate method for rapidly distinguishing strains of propionibacteria. Carbohydrate fermentation and peptidoglycan hydrolase activity profiles are useful as complementary identification tools, since about 15% of the 34 strains tested showed atypical profiles.

Total bacterial and species-specific 16S rDNA micro-array quantification of complex samples

AIMS

We describe a novel DNA-micro-array-based method that targets 16S rDNA to quantify changes in both the total bacterial DNA and the species-specific DNA composition.

METHODS AND RESULTS

Quantifications were achieved by combining competitive PCR for quantifying total bacterial DNA with quantification of species-specific DNA composition based on signature 16S rDNA sequences. We constructed 11 different probes, which were evaluated on 21 different strains, in addition to complex samples. The signals obtained with sequence-specific labelling of the probes corresponded well with what should be expected based on 16S rDNA phylogenetic reconstruction. The quantification of species-specific DNA composition showed that the micro-array approach could be used to accurately determine differential growth of bacteria in mixed samples. We analysed samples containing mixtures of Lactococcus lactis and different species of propionibacteria during a 2-week incubation period. Lactococcus lactis grew fast, reaching a maximum after 12 h, Propionibacterium acidipropionici and Propionibacterium freudenreichii reached a maximum after 48 h, whereas Propionibacterium jensenii showed a slow increase during the whole growth period. The 16S rDNA total bacterial DNA quantification was compared with real-time PCR, absorbance measurements (ABS600) and colony forming units (CFU).

CONCLUSION

The accuracy of the array approach was in the same range or better than the alternative techniques. The potential of the 16S rDNA micro-array method was further demonstrated using a liquid cheese model.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is to our knowledge the first time quantification of the total bacterial DNA and the species-specific DNA compositions of mixed populations have been achieved in the same assay.

Dialister micraerophilus sp. nov. and Dialister propionicifaciens sp. nov., isolated from human clinical samples

Seventeen anaerobic, Gram-negative, tiny coccobacilli were collected in France from various human clinical samples. Biochemical analyses as well as molecular studies, including 16S rRNA and dnaK gene sequencing, affiliated all the isolates to the genus Dialister. However, 16S rRNA and dnaK gene sequence similarities were below 95.2 and 79.7 %, respectively, when comparisons were performed with the currently described species Dialister pneumosintes and Dialister invisus. Two clusters consisting of 13 and four isolates could be differentiated. 16S rRNA- and dnaK-based phylogeny confirmed that these two clusters represent two novel and distinct lineages within the genus Dialister. Finally, phenotypic, genotypic and phylogenetic data supported the proposal of the two novel species Dialister micraerophilus sp. nov. (type strain ADV 04.01T=AIP 25.04T=CIP 108278T=CCUG 48837T) and Dialister propionicifaciens sp. nov. (type strain ADV 1053.03T=AIP 26.04T=CIP 108336T=CCUG 49291T). The G+C content of the DNA of the D. micraerophilus type strain is 36.3 mol%. On the basis of 16S rRNA gene sequence analysis, 11 isolates originating from Canada could also be affiliated to D. micraerophilus sp. nov., and were included in the species description.

Corynebacterium nigricans sp. nov.: proposed name for a black-pigmented Corynebacterium species recovered from the human female urogenital tract

Six independent isolates of an unusual black-pigmented Corynebacterium species (strains CN-1, CN-2, CN-3415, W70124, 91-0032, and 92-0360) were recovered from the human female urogenital tract. Four of the six source patients had complications of pregnancy, including spontaneous abortion, preterm labor, and low amniotic fluid volume at the time of the pathogen isolation. One isolate was recovered from a vaginal ulcer. All six strains yielded black-pigmented colonies on sheep blood agar, chocolate agar, and colistin-nalidixic acid agar after 24 to 48 h of incubation at 35 degrees C. The dry, adherent colonies pitted the agar surface. The cells were coccobacillary to rod-shaped, catalase positive, nonmotile, and nonlipophilic. Only five of six isolates were available for characterization. Biochemical and chemotaxonomic studies revealed that the strains belong to the genus Corynebacterium but differ from known corynebacterial species. Comparative 16S rRNA gene sequence analysis showed that the strains are closely related and form a new subline within the genus Corynebacterium. We propose the name Corynebacterium nigricans sp. nov. for this group of coryneforms. The type strain of Corynebacterium nigricans is CN-1. It is deposited in the American Type Culture Collection (assigned strain number ATCC 700975) and in the Institute Pasteur collection (assigned strain number CIP 107346).

Characteristics of rare or recently described corynebacterium species recovered from human clinical material in Canada

Nineteen new Corynebacterium species or taxa described since 1995 have been associated with human disease. We report the characteristics of 72 strains identified as or most closely resembling 14 of these newer, medically relevant Corynebacterium species or taxa, as well as describe in brief an isolate of Corynebacterium bovis, a rare pathogen for humans. The bacteria studied in this report were nearly all derived from human clinical specimens and were identified by a polyphasic approach. Most were characterized by nearly full 16S rRNA gene sequence analysis. Some isolates were recovered from previously unreported sources and exhibited unusual phenotypes or represented the first isolates found outside Europe. Products of fermentation, with emphasis on the presence or absence of propionic acid, were also studied in order to provide an additional characteristic with which to differentiate among phenotypically similar species.