Pediatric asthma comprises different phenotypic clusters with unique nasal microbiotas

BACKGROUND

Pediatric asthma is the most common chronic childhood disease in the USA, currently affecting ~ 7 million children. This heterogeneous syndrome is thought to encompass various disease phenotypes of clinically observable characteristics, which can be statistically identified by applying clustering approaches to patient clinical information. Extensive evidence has shown that the airway microbiome impacts both clinical heterogeneity and pathogenesis in pediatric asthma. Yet, so far, airway microbiotas have been consistently neglected in the study of asthma phenotypes. Here, we couple extensive clinical information with 16S rRNA high-throughput sequencing to characterize the microbiota of the nasal cavity in 163 children and adolescents clustered into different asthma phenotypes.

RESULTS

Our clustering analyses identified three statistically distinct phenotypes of pediatric asthma. Four core OTUs of the pathogenic genera Moraxella, Staphylococcus, Streptococcus, and Haemophilus were present in at least 95% of the studied nasal microbiotas. Phyla (Proteobacteria, Actinobacteria, and Bacteroidetes) and genera (Moraxella, Corynebacterium, Dolosigranulum, and Prevotella) abundances, community composition, and structure varied significantly (0.05 < P ≤ 0.0001) across asthma phenotypes and one of the clinical variables (preterm birth). Similarly, microbial networks of co-occurrence of bacterial genera revealed different bacterial associations across asthma phenotypes.

CONCLUSIONS

This study shows that children and adolescents with different clinical characteristics of asthma also show different nasal bacterial profiles, which is indicative of different phenotypes of the disease. Our work also shows how clinical and microbial information could be integrated to validate and refine asthma classification systems and develop biomarkers of disease.

Bacterial biogeography of adult airways in atopic asthma

BACKGROUND

Perturbations to the composition and function of bronchial bacterial communities appear to contribute to the pathophysiology of asthma. Unraveling the nature and mechanisms of these complex associations will require large longitudinal studies, for which bronchoscopy is poorly suited. Studies of samples obtained by sputum induction and nasopharyngeal brushing or lavage have also reported asthma-associated microbiota characteristics. It remains unknown, however, whether the microbiota detected in these less-invasive sample types reflect the composition of bronchial microbiota in asthma.

RESULTS

Bacterial microbiota in paired protected bronchial brushings (BB; n = 45), induced sputum (IS; n = 45), oral wash (OW; n = 45), and nasal brushings (NB; n = 27) from adults with mild atopic asthma (AA), atopy without asthma (ANA), and healthy controls (HC) were profiled using 16S rRNA gene sequencing. Though microbiota composition varied with sample type (p < 0.001), compositional similarity was greatest for BB-IS, particularly in AAs and ANAs. The abundance of genera detected in BB correlated with those detected in IS and OW (r median [IQR] 0.869 [0.748-0.942] and 0.822 [0.687-0.909] respectively), but not with those in NB (r = 0.004 [- 0.003-0.011]). The number of taxa shared between IS-BB and NB-BB was greater in AAs than in HCs (p < 0.05) and included taxa previously associated with asthma. Of the genera abundant in NB, only Moraxella correlated positively with abundance in BB; specific members of this genus were shared between the two compartments only in AAs. Relative abundance of Moraxella in NB of AAs correlated negatively with that of Corynebacterium but positively with markers of eosinophilic inflammation in the blood and BAL fluid. The genus, Corynebacterium, trended to dominate all NB samples of HCs but only half of AAs (p = 0.07), in whom abundance of this genus was negatively associated with markers of eosinophilic inflammation.

CONCLUSIONS

Induced sputum is superior to nasal brush or oral wash for assessing bronchial microbiota composition in asthmatic adults. Although compositionally similar to the bronchial microbiota, the microbiota in induced sputum are distinct, reflecting enrichment of oral bacteria. Specific bacterial genera are shared between the nasal and the bronchial mucosa which are associated with markers of systemic and bronchial inflammation.

Characterization of the upper and lower respiratory tract microbiota in Piedmontese calves

BACKGROUND

The microbiota of the bovine upper respiratory tract has been recently characterized, but no data for the lower respiratory tract are available. A major health problem in bovine medicine is infectious bronchopneumonia, the most common respiratory syndrome affecting cattle. With this study, we used 16S rRNA gene sequencing to characterize and compare the microbial community composition of the upper and lower respiratory tracts in calves.

RESULTS

The microbiota of the upper (nasal swab [NS]) and the lower (trans-tracheal aspiration [TTA]) respiratory tracts of 19 post-weaned Piedmontese calves with (8/19) and without (11/19) clinical signs of respiratory disease, coming from six different farms, was characterized by 16S rRNA gene metabarcoding. A total of 29 phyla (29 in NS, 21 in TTA) and 305 genera (289 in NS, 182 in TTA) were identified. Mycoplasma (60.8%) was the most abundant genus identified in both the NS (27.3%) and TTA (76.7%) samples, followed by Moraxella (16.6%) in the NS and Pasteurella (7.3%) in the TTA samples. Pasteurella multocida (7.3% of total operational taxonomic units [OTUs]) was the most abundant species in the TTA and Psychrobacter sanguinis (1.1% of total OTUs) in the NS samples. Statistically significant differences between the NS and the TTA samples were found for both alpha (Shannon index, observed species, Chao1 index, and Simpson index; P = 0.001) and beta (Adonis; P = 0.001) diversity. Comparison of the NS and TTA samples by farm origin and clinical signs revealed no statistical difference (P > 0.05), except for farm origin for the NS samples when compared by the unweighted UniFrac metric (P = 0.05).

CONCLUSIONS

Using 16S rRNA gene sequencing, we characterized the microbiota of the upper and lower respiratory tracts of calves, both healthy individuals and those with clinical signs of respiratory disease. Our results suggest that environmental factors may influence the composition of the upper airway microbiota in cattle. While the two microbial communities (upper and lower airways) differed in microbial composition, they shared several OTUs, suggesting that the lung microbiota may be a self-sustaining, more homogeneous ecosystem, influenced by the upper respiratory tract microbiota.

Differentiation of Moraxella Bovoculi sp. nov. from other Coccoid Moraxellae by the Use of Polymerase Chain Reaction and Restriction Endonuclease Analysis of Amplified DNA

Moraxella oris was historically the only coccoid Moraxella identified in cultures of ocular fluid from cattle with infectious bovine keratoconjunctivitis (IBK) and could be morphologically and biochemically differentiated from Moraxella bovis. Moraxella bovoculi sp. nov. is a recently characterized Moraxella isolated from ulcerated eyes of calves with IBK in northern California in 2002. Like Moraxella ovis, M. bovoculi sp. nov. is a gram-negative coccus/diplococcus. All 18 original isolates of M. bovoculi sp. nov. possessed phenylalanine deaminase (PADase) activity and could therefore be differentiated from M. ovis and M. bovis. During the characterization of 44 additional isolates of hemolytic gram-negative cocci that were cultured from ulcerated eyes of IBK-affected calves, 2 PADase-negative isolates were identified that could not be differentiated biochemically from M. ovis; however, the DNA sequence of the 16S-23S intergenic spacer region (ISR) of the isolates matched the 16S-23S ISR DNA sequence of M. bovoculi sp. nov. To facilitate the identification of PADase-negative moraxellae, a polymerase chain reaction (PCR) coupled with restriction enzyme digestion analysis of amplified DNA was developed. Amplification of the 16S-23S ISR followed by AfaI digestion of amplified DNA could differentiate M. bovoculi sp. nov. from M. ovis and other moraxellae. The DNA sequence analysis of the amplified 16S-23S ISR from the 42 PADase-positive isolates of hemolytic gram-negative cocci indicated that all were M. bovoculi sp. nov. and all possessed an AfaI site. A PCR coupled with restriction analysis of amplified DNA can aid in identifying M. bovoculi sp. nov.

Molecular and phenotypic analysis of Moraxella spp. associated with infectious bovine keratoconjunctivitis in Uruguay

Infectious bovine keratoconjunctivitis (IBK) is a common ocular disease of cattle, which is generally thought to be caused by Moraxella bovis. However, a recently characterized Moraxella, M. bovoculi, has been isolated from animals with IBK. The aim of this study was to identify and characterize strains of Moraxella spp. obtained from IBK cases in different geographic locations within Uruguay. Ribosomal gene sequencing indicated that there were two groups of isolates that showed homology with either M. bovis or M. bovoculi. Phylogenetic analysis confirmed the presence of two species as the isolates grouped in different branches of the dendrogram. Conventional biochemical characterization did not distinguish between the species; only 9/25 isolates which had genetic homology with M. bovoculi showed any differences in biochemistry.

The microbial flora associated with oral carcinomas

OBJECTIVE

Changes in the microbial flora on the oral mucosa after cancerous alteration may lead to both local and systemic infections. In this study, we assessed the microbial flora associated with the surfaces of oral squamous cell carcinoma. A comparative evaluation of these microbial contents was made with that of the contralateral healthy mucosa and control (healthy) mucosa. We also assessed the microbial flora from the saliva culture in subjects with oral squamous cell carcinoma and healthy controls.

METHOD AND MATERIALS

The case control study was made up of 30 subjects with oral squamous cell carcinoma as the study group; 30 healthy age-, sex-, habit-, and dentition-matched subjects served as the control group. In the study group, microbial samples were collected from the carcinoma site, contralateral healthy mucosa, and saliva, whereas in the control group, samples were collected from the healthy mucosa and saliva. These samples were stored on ice and subsequently transported to the laboratory in 2 mL of thioglycollate transport media, where the microbial cultures were carried out.

RESULTS

Oral squamous cell carcinoma sites harbor significantly more microbial flora (bacteria and yeasts) compared to those of healthy mucosa (control group). The microbial flora predominantly isolated from the carcinoma site were Streptococcus species, Staphylococcus species, Moraxella species, Enterococcus feacalis, Aerobic spore bearers, Klebsiella species, Citrobacter species, Proteus species, Pseudomonas species, and Candida albicans. The median number of colony forming units (CFU)/mL at carcinoma sites (3.85 x 105 CFU/mL) was significantly higher than that of the healthy mucosa (0.571 x 105 CFU/mL; P = .0000, Wilcoxon nonparametric test). Similarly, in saliva of carcinoma subjects, the median number of CFU/mL (2.408 x 105 CFU/mL) was significantly higher than that of saliva in control subjects (0.78 x 105 CFU/mL; P = .0000, Wilcoxon nonparametric test).

CONCLUSION

The present study clearly indicates that the subjects with oral squamous cell carcinoma harbor significantly more microbial flora. Emphasis has to be given to preventing microbial flora in the oral cavity and treating these patients with appropriate antimicrobial agents, thus reducing their morbidity.

Moraxella lacunata: A rare cause of infective endocarditis

We describe the first case of Moraxella lacunata definite native valve endocarditis in a patient with previously normal mitral valves. The disease was complicated with embolizations of the brain and spleen. After 6 weeks of antimicrobial treatment, valvular replacement was performed. The clinical course and diagnostic findings suggest that Moraxella lacunata possesses high aggressiveness leading to progressive valvular destruction and embolizations.

Moraxella bovoculi sp. nov., isolated from calves with infectious bovine keratoconjunctivitis

Eighteen isolates of a Gram-negative coccus (strain 237T) were cultured from the eyes of dairy and beef calves affected with infectious bovine keratoconjunctivitis (IBK; ‘pinkeye’) in northern California, USA, during summer 2002. These isolates had near full-length (1397 bp) 16S rRNA gene sequences that clustered into three groups with 99.9 % sequence similarity. On the basis of 16S rRNA gene sequence, the isolates were most closely associated with Moraxella bovis and Moraxella ovis in clade I of the classical moraxellae. Biochemically, the novel isolates could be distinguished from the other members of the genus Moraxella isolated from animals on the basis of phenylalanine deaminase activity. The results of partial sequence analysis of six housekeeping genes, the 16S–23S rRNA gene interspacer region and partial 23S rRNA gene provide strong support for the inclusion of these isolates in a novel taxon, for which the name Moraxella bovoculi sp. nov. is proposed. The type strain is strain 237T (=ATCC BAA-1259T=CCUG 52049T).

Recovery of Moraxella ovis from the bovine respiratory tract and differentiation of Moraxella species by tDNA-intergenic spacer PCR

The purpose of the present study was to identify Moraxella (M.)--like organisms recovered from calves suffering from respiratory disease down to species level by means of tDNA-intergenic spacer length polymorphism analysis (tDNA-PCR), and to perform antimicrobial susceptibility testing of these isolates using an agar dilution technique. A total of 16 isolates originating from 12 unrelated occasions were identified as Moraxella ovis, and tDNA fingerprinting showed clear delineation from other Moraxella species. The minimal inhibitory concentrations (in microg/mL) for 90% of the investigated isolates were < or =0.03 for ampicillin; 0.25 for ceftiofur; 0.5 for oxytetracycline; 8 for gentamicin; 64 for spectinomycin; 0.5/9.5 for the combination trimethoprim-sulfonamides; 4 for erythromycin; 8 for tilmicosin; 1 for florfenicol and 0.125 for enrofloxacin.

Transfer of the misnamed [Alysiella] sp. IAM 14971 (=ATCC 29468) to the genus Moraxella as Moraxella oblonga sp. nov

Phylogenetic analysis based on 16S rRNA gene sequences revealed that [Alysiella] sp. IAM 14971 (=ATCC 29468) is closely related to the genus Moraxella of the γ-Proteobacteria (96–97 % similarity). The newly obtained phenotypic data also indicate that [Alysiella] sp. IAM 14971 is distinct from the genus Alysiella and similar to the genus Moraxella. On the basis of these results, the strain should be classified in the genus Moraxella, as Moraxella oblonga sp. nov. The type strain is IAM 14971T (=ATCC 29468T).

Bacteriological investigation of infectious keratoconjunctivitis in Norwegian sheep

Contagious keratoconjunctivitis is a rather common disease in Norwegian sheep. Since the knowledge of its aetiology is limited, the present study was performed to determine the microorganisms involved. Local veterinarians throughout the country collected conjunctival swabs from both sick (n = 43) and healthy (n = 42) sheep on 15 farms with outbreaks of ovine keratoconjunctivitis, and further from healthy sheep (n = 50) on 17 farms not showing any signs of conjunctival disease. All samples were cultivated for bacteria and mycoplasma.

Listeria monocytogenes was isolated from 3 cases (1%) in one single herd. Staphylococcus aureus (5%), Corynebacterium spp. (2%) and Escherichia coli (4%) were isolated only in herds with keratoconjunctivitis, but from both sick and healthy animals. Moraxella (Branhamella) ovis was isolated from 28% of sampled animals in affected herds and from 10% of sampled animals in healthy herds. The corresponding numbers for Moraxella spp. were 9%/12%, for Pseudomonas spp. 7%/8%, for Staphylococcus spp. 22%/22%, for Bacillus spp. 12%/14%, for Micrococcus spp. 6%/2% and for Streptococcus/Enterococcus spp. 2%/2%. Mycoplasma conjunctivae was isolated from 16 animals with keratoconjunctivitis (37%) and from 3 animals without clinical signs (7%) in farms with keratoconjunctivitis. In farms without clinical signs of keratoconjunctivitis, M. conjunctivae was isolated in 4 animals (8%).

To our knowledge, this is the first time M. conjunctivae has been isolated in Norway. Other predisposing agents found were Moraxella (Branhamella) ovis and Listeria monocytogenes. The etiological importance of different microorganisms in ovine keratoconjunctivitis seems to vary; some are probably only present as secondary invaders. Other possible causes of ovine keratoconjunctivitis in Norway, such as Chlamydia psittaci, remain to be investigated.

Mucoid nitrate-negative Moraxella nonliquefaciens from three patients with chronic lung disease

Mucoid strains of Moraxella nonliquefaciens were recovered from the sputa of three indigenous Australians with chronic lung disease. These atypical strains failed to reduce nitrate, and one strain produced beta-lactamase. While the mucoid phenotype of M. nonliquefaciens has rarely been reported, the mucoid nitrate-negative biovar has never been previously reported.

Presumed endocarditis caused by BRO beta-lactamase-producing Moraxella lacunata in an infant with Fallot's tetrad

A case of presumed endocarditis caused by Moraxella lacunata in a 15-month-old male infant with Fallot's tetrad is described. This infection may have occurred as the result of transmission of this organism between the father and his son. This is the first report of BRO beta-lactamase-producing M. lacunata causing presumed endocarditis.

Bacteremia due to Moraxella atlantae in a cancer patient

A gram-negative alkaline phosphatase- and pyrrolidone peptidase-positive rod-shaped bacterium (CCUG 45702) was isolated from two aerobic blood cultures from a female cancer patient. No identification could be reached using phenotypic techniques. Amplification of the tRNA intergenic spacers revealed fragments with lengths of 116, 133, and 270 bp, but no such pattern was present in our reference library. Sequencing of the 16S rRNA gene revealed its identity as Moraxella atlantae, a species isolated only rarely and published only once as causing infection. In retrospect, the phenotypic characteristics fit the identification as M. atlantae (formerly known as CDC group M-3). Comparative 16S rRNA sequence analysis indicates that M. atlantae, M. lincolnii, and M. osloensis might constitute three separate genera within the MORAXELLACEAE: After treatment with amoxicillin-clavulanic acid for 2 days, fever subsided and the patient was dismissed.

First definite case of aortic valve endocarditis due to Moraxella phenylpyruvica

Described here is the first definite case of endocarditis due to Moraxella phenylpyruvica, which occurred in a 50-year-old male with a bicuspid aortic valve. The diagnosis was delayed because of the confounding positivity of the Widal and Wright tests. The patient was cured with surgical valve replacement and antibiotic treatment.

Nomenclature of the subgenera Moraxella and Branhamella and of the nine species included in these subgenera and proposal to modify rule 34a of the Bacteriological Code (1990 Revision). Request for an opinion

The subgenera Moraxella and Branhamella and the nine species included in these subgenera were inadvertently omitted from the Approved Lists of Bacterial Names and have never been revived according to Rule 28a of the Bacteriological Code (1990 Revision). The author requests that these names be revived and considered to be validly published in the 'Index of the bacterial and yeast nomenclatural changes published in the International Journal of Systematic Bacteriology since the 1980 Approved Lists of Bacterial Names (1 January 1980 to 1 January 1985)', which appears in the July 1985 issue of the International Journal of Systematic Bacteriology. Another problem is the status of the species included in the subgenera Moraxella and Branhamella because the Bacteriological Code (1990 Revision) does not envisage the status of a species transferred into a subgenus. The same is true for a species transferred into a subspecies. The author requests that such species be considered as new combinations and, according to this, proposes to modify Rule 34a of the Bacteriological Code (1990 Revision).

[Bacteriologic evaluation of middle ear fluid during the course of secretory otitis media in children]

Fluid collected from tympanic cavity during operation from 43 children with O.M.S. was subjected to bacteriological examination. After the collection, each sample was immediately applied to Bactec Peds Plus/F liquid medium from Becton Dickinson. The number of samples, where each genus and species of bacteria were found, was determined, as well as the number of samples where every two genus coexisted; also the pH genes, in which each genus was found were calculated. Obtained results showed that 22 species of bacteria, belonging to 6 genus lived in the samples. The most commonly occurring genus were Staphylococcus, Streptococcus and Haemophilus; the most rare genus were Moraxella and Bacillus. The most common species were: Haemophilus influenzae (18.6% of samples), Staphylococcus aureus (14.0%), Staphylococcus epidermidis (11.6%), Staphylococcus warneri (9.3%) and Streptococcus oralis (7.0%). Streptococcus coexisted most frequently with Staphylococcus and Haemophilus; Staphylococcus--with Haemophilus and Bacillus; Haemophilus--with Streptococcus and Staphylococcus. The pH ranges for the three most often found genus were: for Staphylococcus--7.7-9, for Streptococcus--7.7-9.3 and for Haemophilus--8.2-8.8.

Diagnostics of neisseriaceae and moraxellaceae by ribosomal DNA sequencing: ribosomal differentiation of medical microorganisms

Fast and reliable identification of microbial isolates is a fundamental goal of clinical microbiology. However, in the case of some fastidious gram-negative bacterial species, classical phenotype identification based on either metabolic, enzymatic, or serological methods is difficult, time-consuming, and/or inadequate. 16S or 23S ribosomal DNA (rDNA) bacterial sequencing will most often result in accurate speciation of isolates. Therefore, the objective of this study was to find a hypervariable rDNA stretch, flanked by strongly conserved regions, which is suitable for molecular species identification of members of the Neisseriaceae and Moraxellaceae. The inter- and intrageneric relationships were investigated using comparative sequence analysis of PCR-amplified partial 16S and 23S rDNAs from a total of 94 strains. When compared to the type species of the genera Acinetobacter, Moraxella, and Neisseria, an average of 30 polymorphic positions was observed within the partial 16S rDNA investigated (corresponding to Escherichia coli positions 54 to 510) for each species and an average of 11 polymorphic positions was observed within the 202 nucleotides of the 23S rDNA gene (positions 1400 to 1600). Neisseria macacae and Neisseria mucosa subsp. mucosa (ATCC 19696) had identical 16S and 23S rDNA sequences. Species clusters were heterogeneous in both genes in the case of Acinetobacter lwoffii, Moraxella lacunata, and N. mucosa. Neisseria meningitidis isolates failed to cluster only in the 23S rDNA subset. Our data showed that the 16S rDNA region is more suitable than the partial 23S rDNA for the molecular diagnosis of Neisseriaceae and Moraxellaceae and that a reference database should include more than one strain of each species. All sequence chromatograms and taxonomic and disease-related information are available as part of our ribosomal differentiation of medical microorganisms (RIDOM) web-based service (http://www.ridom.hygiene.uni-wuerzburg.de/). Users can submit a sequence and conduct a similarity search against the RIDOM reference database for microbial identification purposes.

Analysis of the psychrotolerant property of hormone-sensitive lipase through site-directed mutagenesis

Mammalian hormone-sensitive lipase (HSL) has given its name to a family of primarily prokaryotic proteins which are structurally related to type B carboxylesterases. In many of these alpha/beta hydrolases, a conserved HG-dipeptide flanks the catalytic pocket. In HSL this dipeptide is followed by two additional glycine residues. Through site-directed mutagenesis, we have investigated the importance of this motif for enzyme activity. Since the presence of multiple glycine residues in a critical region could contribute to cold adaptation by providing local flexibility, we studied the effect of mutating these residues on the psychrotolerant property of HSL. Any double mutation rendered the enzyme completely inactive, without any major effect on the enzyme stability. The partially active single mutants retained the same proportion of activity at reduced temperatures as the wild-type enzyme. These results do not support a role for the HGGG motif in catalysis at low temperatures, but provide further validation of the current three-dimensional model of HSL. Rat HSL was found to be relatively more active than human HSL at low temperatures. This difference was, however, not due to the 12 amino acids which are present in the regulatory module of the rat enzyme but absent in human HSL.

Isolation of Moraxella canis from an ulcerated metastatic lymph node

Moraxella canis was isolated in large numbers from an ulcerated supraclavicular lymph node of a terminal patient, who died a few days later. Although the patient presented with septic symptoms and with a heavy growth of gram-negative diplococci in the lymph node, blood cultures remained negative. M. canis is an upper-airway commensal from dogs and cats and is considered nonpathogenic for humans, although this is the third reported human isolate of this species.

Bacteremia and possible endocarditis caused by Moraxella phenylpyruvica

Moraxella phenylpyruvica, a gram-negative coccobacillus, is usually considered a nonpathogenic bacterium. Only a few cases of invasive disease caused by this organism were reported in the 1970s. We report a well-documented case of bacteremia and possible endocarditis due to M phenylpyruvica in a previously healthy man.

Phylogenetic analysis of psychrophilic bacteria isolated from the Japan Trench, including a description of the deep-sea species Psychrobacter pacificensis sp. nov

Phylogenetic positions of psychrophilic bacteria isolated from the Japan Trench were determined by sequencing analysis of PCR-amplified bacterial small subunit (16S) rRNA genes. Between surface and deep-sea psychrophiles, distinct positions clearly differed within the gamma-Proteobacteria. In phylogenetic analysis using neighbour-joining, maximum-parsimony and maximum-likelihood, strains from surface seawater were inferred to be located in the Halomonas aquamarina-meridiana clade within the family Halomonadaceae. Strains from deep seawater (5000-6000 m), however, formed a novel monophyletic clade within the Moraxella-Psychrobacter branch in the family Moraxellaceae, showing separation from terrestrial and Antarctic relatives. These deep-sea strains were also discriminated from other known Psychrobacter species in phenotype, e.g. limited growth in the absence of NaCl (optimum at about 3% NaCl), positive urease activity, acid production from xylose and arabinose, and the presence of multiple fimbriae. DNA relatedness values among six deep-sea strains were > 85% in DNA-DNA hybridization experiments and > 98% in aligned 16S rDNA sequences. From this evidence, a new species, Psychrobacter pacificensis, is proposed for these deep-sea psychrophiles; the type strain of Psychrobacter pacificensis is strain NIBH P2K6T (= IFO 16270T). Occurrence of psychrobacters in cold Japan Trench deep seawater and at the Antarctic sea surface suggests that deep-sea bacterial habitation and evolution have been mediated by global deep-ocean circulation linked to the sinking of cooled seawater in polar regions.

The incidence of Weeksella- and Bergeyella-like bacteria in the food environment

Eighty-five catalase- and oxidase-positive Gram-negative rods and cocci susceptible to penicillin G were isolated from a variety of food sources. The phenotypic relationships of these isolates with reference cultures of Bergeyella-like, Chryseobacterium, Empedobacter, Myroides, Moraxella, Sphingobacterium and Weeksella-like strains were examined by numerical taxonomy. Seventy-three isolates were recovered in five groups; 80% of the isolates clustered in groups 1, 2 and 3 and produced indole, bearing a strong resemblance to Weeksella and Bergeyella. They could not, however, be regarded as belonging to the known species of W. virosa and B. zoohelcum. It is suggested that three species may be necessary to accommodate the environmental Weeksella- or Bergeyella-like bacteria. The isolates in groups 4 and 5 had white colonies and were unable to produce indole, in this way resembling the Moraxella genus.

Phylogenetic position of Riemerella anatipestifer based on 16S rRNA gene sequences

Riemerella anatipestifer, the causative agent of septicemia anserum exsudativa (also called new duckling disease), belongs to the family Flavobacteriaceae of gram-negative bacteria. We determined the DNA sequences of the rrs genes encoding the 16S rRNAs of four R. anatipestifer strains by directly sequencing PCR-amplified rrs genes. A sequence similarity analysis confirmed the phylogenetic position of R. anatipestifer in the family Flavobacteriaceae in rRNA superfamily V and allowed fine mapping of R. anatipestifer on a separate rRNA branch comprising the most closely related species, Bergeyella zoohelcum, as well as Chryseobacterium balustinum, Chryseobacterium indologenes, and Chryseobacterium gleum. The sequences of the rrs genes of the four R. anatipestifer strains varied between 0.5 and 1.0%, but all of the strains occupied the same position on the phylogenetic tree. In general, differences in rrs genes were observed among R. anatipestifer strains, even within a given serotype, as shown by restriction fragment length polymorphism of PCR-amplified rrs genes.

Moraxella boevrei sp. nov., a new Moraxella species found in goats

Six Moraxella-like strains that formed a phenotypically homogeneous group were isolated from the nasal flora of healthy goats. Total genomic DNA-DNA hybridization, rRNA gene restriction pattern, DNA base composition, and genetic transformation studies were performed to determine the relationships of these bacteria to species belonging to the genus Moraxella and other fastidious gram-negative species. The new group of isolates was very homogeneous, as shown by rRNA gene restriction fragment length patterns (ribotyping), and these organisms displayed high relative binding ratios (RBRs) to each other in DNA-DNA hybridization experiments (RBRs, > or = 58%) but distinctly lower levels of DNA homology with all other species investigated. However, the RBRs obtained with species of the genus Moraxella were higher than the RBRs obtained with all other gram-negative strains examined. Although the new strains had most of the Moraxella bovis phenotypic characteristics except nitrate reduction, quantitative and qualitative genetic transformation data led to the conclusion that they belong to a distinct new cluster in the genus Moraxella. The results of this study, combined with the general morphological and phenotypic profiles of the new strains, are consistent with the creation of a new Moraxella species, for which the name Moraxella boevrei is proposed. Strain 88365 (= ATCG 700022 = CCUG 35435 = NCTC 12925 = CIP 104716) is the type strain of M. boevrei.

Novel Psychrobacter species from Antarctic ornithogenic soils

Ornithogenic soil is derived from the deposition of the fecal matter of various species of birds and is a major source of nutrient input in the Antarctic marine ecosystem. A significant proportion of microbiota of ornithogenic soil collected from an Adélie penguin colony in eastern Antarctica (Vestfold Hills ice-free zone) consisted of gram-negative, coccoid bacteria identified on the basis of their phospholipid ester-linked fatty acid and lipid class profiles as Psychrobacter strains. Phenotypic, genotypic, and 16S ribosomal DNA phylogenetic analyses revealed that the Antarctic psychrobacters belonged to three distinct groups. Comparisons with Psychrobacter immobilis and Moraxella phenylpyruvica reference cultures isolated from fish, seawater, poultry, and human clinical specimens revealed the relationships of these groups within the genus Psychrobacter. Two of the groups represent the following two novel species: Psychrobacter urativorans sp. nov. (type strain, strain ACAM 534) and Psychrobacter frigidicola sp. nov. (type strain, strain ACAM 304). The third group of strains included members of the previously described species P. immobilis (Juni and Heym 1986). In addition, M. phenylpyruvica (Bøvre and Henriksen 1967) is renamed Psychrobacter phenylpyruvicus comb. nov. (type strain, strain ACAM 535) on the basis of 16S ribosomal DNA phylogenetic data. In general, the genus Psychrobacter could be differentiated from the related genera Moraxella and Acinetobacter by the fact that the members of the genus Psychrobacter are psychrotolerant or psychrophilic and halotolerant, which reflects the ubiquitous distribution of the genus in both marine and terrestrial environments. On the basis of the results of this and previous studies, the genus Psychrobacter is the predominant genus in ornithogenic soils in Antarctica and is diverse.

Moraxella caprae sp. nov., a new member of the classical Moraxellae with very close affinity to Moraxella bovis

Eight phenotypically homogeneous Moraxella-like strains were isolated from the nasal flora of healthy goats. Total genomic DNA-DNA hybridization, DNA base composition determination, and genetic transformation studies were performed to determine the relationships of these bacteria to the classical moraxellae. The eight new isolates exhibited very high levels of genetic affinity to Moraxella bovis, as shown by quantitative and qualitative genetic transformation data, and exhibited high DNA-DNA relative binding ratios to each other (63% or more) but lower levels of DNA homology with all of the other species investigated, including the closely related classical moraxellae. Our results, combined with the general morphologic and phenotypic profiles of these organisms, indicate that they should be classified with the classical moraxellae, and we propose the name Moraxella caprae for them. Strain 8897 (= CCUG 33296 [corrected] = NCTC 12877) is the type strain of M. caprae.

Phylogenetic relationships between some members of the genera Neisseria, Acinetobacter, Moraxella, and Kingella based on partial 16S ribosomal DNA sequence analysis

We obtained 16S ribosomal DNA (rDNA) sequence data for strains belonging to 11 species of Proteobacteria, including the type strains of Kingella kingae, Neisseria lactamica, Neisseria meningitidis, Moraxella lacunata subsp. lacunata, [Neisseria] ovis, Moraxella catarrhalis, Moraxella osloensis, [Moraxella] phenylpyruvica, and Acinetobacter lwoffii, as well as strains of Neisseria subflava and Acinetobacter calcoaceticus. The data in a distance matrix constructed by comparing the sequences supported the proposal that the genera Acinetobacter and Moraxella and [N.] ovis should be excluded from the family Neisseriaceae. Our results are consistent with hybridization data which suggest that these excluded taxa should be part of a new family, the Moraxellaceae. The strains that we studied can be divided into the following five groups: (i) M. lacunata subsp. lacunata, [N.] ovis, and M. catarrhalis; (ii) M. osloensis; (iii) [M.] phenylpyruvica; (iv) A. calcoaceticus and A. lwoffii; and (v) N. meningitidis, N. subflava, N. lactamica, and K. kingae. We agree with the previous proposal that [N.] ovis should be renamed Moraxella ovis, as this organism is closely related to Moraxella species and not to Neisseria species. The generically misnamed taxon [M.] phenylpyruvica belongs to the proposed family Moraxellaceae, but it is sufficiently different to warrant exclusion from the genus Moraxella. Further work needs to be done to investigate genetically similar species, such as Psychrobacter immobilis, before the true generic position of this organism can be determined. Automated 16S rDNA sequencing with the PCR allows workers to accurately determine phylogenetic relationships between groups of organisms.(ABSTRACT TRUNCATED AT 250 WORDS)

Comparison of three rapid methods, tributyrine, 4-methylumbelliferyl butyrate, and indoxyl acetate, for rapid identification of Moraxella catarrhalis

Moraxella catarrhalis can easily be differentiated from other oxidase-positive, gram-negative cocci with tributyrine, 4-methylumbelliferyl butyrate, or indoxyl acetate. All M. catarrhalis give positive reactions, and all Neisseria spp. give negative reactions. The 4-methylumbelliferyl butyrate tube test and indoxyl acetate strip test provide same-day identification of M. catarrhalis isolates.

Moraxella lincolnii sp. nov., isolated from the human respiratory tract, and reevaluation of the taxonomic position of Moraxella osloensis

A polyphasic taxonomic study was performed to determine the relationships of 10 Moraxella-like strains isolated mainly from the human respiratory tract in Sweden. Two of the strains formed a separate subgroup on the basis of both their protein contents and their fatty acid contents. However, the overall protein and fatty acid profiles revealed that all 10 strains were highly related. Representative strains of the two subgroups exhibited high DNA binding values (98%) with each other and had an identical DNA base ratio (44 mol% G+C). DNA-rRNA hybridizations revealed that this taxon can be included in the genus Moraxella, which is only distantly related to phenotypically similar genera, such as the genera Neisseria and Kingella. The results of an extensive phenotypic analysis indicated that the general biochemical profile of the 10 strains conforms with the description of the genus Moraxella given in Bergey's Manual of Systematic Bacteriology. We therefore consider these organisms members of a new Moraxella species, for which the name Moraxella lincolnii is proposed. Furthermore, we also conclude that Moraxella osloensis belongs, genotypically as well as phenotypically, to the genus Moraxella.

Polyphasic taxonomy leading to the proposal of Moraxella canis sp. nov. for Moraxella catarrhalis-like strains

The taxonomic position of a group of 16 Moraxella catarrhalis-like strains, isolated mainly from dogs, was examined by using morphological tests, biochemical tests, serology, ribotyping with oligonucleotide probes, polymerase chain reaction typing of the 16S rRNA gene and the 16S-23S rRNA gene spacer region, polyacrylamide gel electrophoresis of total proteins, fatty acid profiles, moles percent G+C, dot spot and in-solution DNA-DNA hybridizations, and DNA-rRNA hybridizations. It was found that these organisms constitute a distinct cluster within the genus Moraxella. Since they differ genotypically as well as phenotypically from previously described Moraxella species, a new species, Moraxella canis, is proposed to accommodate these isolates. The type strain is LMG 11194 (= N7 = CCUG 8415A).

Differentiation of Moraxella nonliquefaciens, M. lacunata, and M. bovis by using multilocus enzyme electrophoresis and hybridization with pilin-specific DNA probes

Genetic relationships among strains of Moraxella nonliquefaciens, M. lacunata, and M. bovis were studied by using multilocus enzyme electrophoresis and DNA-DNA hybridization. The 74 isolates analyzed for electrophoretic variation at 12 enzyme loci were assigned to 59 multilocus genotypes. The multilocus genotypes were grouped in four major clusters, one representing strains of M. nonliquefaciens, two representing strains of M. lacunata, and one comprising strains of M. bovis and the single strain of M. equi analyzed. DNA-DNA hybridization with total genomic probes also revealed four major distinctive entities that corresponded to those identified by multilocus enzyme electrophoresis. The two distinct clusters recognized among the M. lacunata strains apparently corresponded to the species previously designated M. lacunata and M. liquefaciens. Distinction of the four entities was improved by hybridization with polymerase chain reaction products of nonconserved parts of pilin genes as DNA probes. With these polymerase chain reaction probes, new isolates of M. nonliquefaciens, M. lacunata, M. liquefaciens, and M. bovis can be identified easily by hybridization.

Preliminary study on relationships among strains forming a bacterial community selected on naphthalene from a marine sediment

Two bacterial strains were isolated from a bacterial community formed of nine strains, selected from a marine sediment on a seawater medium with naphthalene as sole carbon source. The two strains studied in the present work were the only strains of this community able to grow in pure culture on naphthalene; therefore, they were called "primary" strains. The seven other strains were maintained in the community by using metabolic intermediates of the two primary strains; they were called "auxiliary" strains. Regulation of naphthalene metabolism was studied for the two primary strains. They oxidized naphthalene into catechol, which was degraded only by the meta pathway. For Pseudomonas Lav. 4, naphthalene oxygenase and salicylate hydroxylase were inducible; catechol 2,3-dioxygenase was constitutive. For Moraxella Lav. 7, naphthalene oxygenase was constitutive; salicylate hydroxylase and catechol 2,3-oxygenase were inducible. The Moraxella strain carries two cryptic plasmids, about 63- and 85-kb in molecular size. In the bacterial community culture medium, Moraxella Lav. 7 prevented accumulation of 2-hydroxymuconate semialdehyde formed by Pseudomonas Lav. 4. The auxiliary strains take up formic, acetic, pyruvic, propionic, and succinic acids released by the two primary strains.

Infectious bovine keratoconjunctivitis epizootic associated with area-wide emergence of a new Moraxella bovis pilus type

Pilus-mediated adherence is a virulence attribute of Moraxella bovis. Several pilus types have been shown to exist among strains of this bacterium, but correlation between pilus type and specific field cases of the disease has not been done. During the summer of 1987, an epizootic of infectious bovine keratoconjunctivitis was reported in 7 Iowa counties. Eight isolates of M bovis were secured from 12 episodes studied. All 8 of the isolates were nearly homogeneous in biochemical properties and had the same plasmid biotype. Pilus typing performed by immunofluorescence and immunogold electron microscopy identified a single new pilus type among 5 of the 8 isolates. This pilus type was identified in field cases that developed within a narrow time frame and over large distances. The implication of these findings is that infectious bovine keratoconjunctivitis epizootics may be associated with emergence of a novel pilus type, and that rapid dissemination over wide distances can occur, presumably by transportation of carrier cattle.

Clinical manifestations of Kingella kingae infections: case report and review

A patient with antecedent coccidioidal pulmonary cavitary disease who developed an empyema due to Kingella kingae prompted our analysis of the literature regarding this unusual bacterial pathogen. Formerly classified among other genera and considered a nonpathogen, K. kingae has been increasingly recognized as a cause of human infection. While the most commonly diagnosed infections due to this organism are endocarditis and septic arthritis, there have also been isolated reports of bacteremia, diskitis, abscesses, meningitis, and oropharyngeal infections. The treatment of choice is penicillin, to which K. kingae strains are uniformly susceptible. Recognition of the potential pathogenicity of this microorganism in appropriate clinical settings will probably result in more prompt and specific therapy.

Application of gas-liquid chromatography to the routine identification of nonfermenting gram-negative bacteria in clinical specimens

A total of 430 strains of glucose-nonfermenting gram-negative bacteria representing 35 species were analyzed for their cellular fatty acid composition by gas-liquid chromatography (GLC). On the basis of qualitative differences in their cellular fatty acid composition, these bacteria could be divided into 19 distinct chromatographic groups. Eight Pseudomonas species, Achromobacter xylosoxidans, group Vd, and Agrobacterium radiobacter were identified from their fatty acid compositions alone. The other glucose-nonfermenting gram-negative bacterial species studied here, classified within nine distinct GLC groups, were easily recognized by using the GLC fatty acid analysis supplemented with a limited number of conventional biochemical tests. The results support the hypothesis that bacterial fatty acid composition is rather specific and that qualitative GLC fatty acid analysis can be adapted in the clinical laboratory either to provide additional criteria for differentiation of closely related groups or to serve as a rapid and highly reproducible method for their routine identification.

Infectivity and virulence of Australian strains of Moraxella bovis for the murine and bovine eye in relation to pilus serogroup sub-unit size and degree of piliation

The degree of piliation of 29 haemolytic and 4 non-haemolytic Australian strains of Moraxella bovis representing 7 different pilus antigen groups was determined. The infectivity and virulence for the eye was measured in steroid-treated mice and in cattle. Non-piliated strains failed to infect the murine eye. Most moderately or heavily piliated strains reproducibly produced the highest infectivity and virulence scores in mice when compared with lightly or very lightly piliated strains (p less than 0.05). Non-haemolytic, piliated strains were infective and in one instance virulent for mice. Almost similar levels of infectivity and virulence were observed for 7 representative haemolytic strains tested in both cattle and mice. The relative molecular weight of pilin sub-units was compared using sodium dodecyl-sulphate polyacrylamide gel electrophoresis. Three classes of pili, alpha, beta and gamma of ascending sub-unit size were identified among the 7 pilus antigen serogroups. Pilin sub-unit size bore no relationship to the degree of piliation but most strains that were highly virulent in mice and cattle expressed alpha and gamma sub-units. Some strains appeared capable of switching from alpha to beta or form beta to gamma sub-unit production.

[Species-forming involution of pathogenic bacteria as a biological pattern (exemplified by bacteria of the genus Moraxella)]

The author advances a hypothesis stating that a species disappearing as a result of new conditions evolving in a colonized animal or human body, unfavorable for the existence of this species, does not become extinct, but reverts into newly developing species due to the loss of its properties and acquiring new properties corresponding to new conditions. Thus the genus is preserved through the loss of species characteristics by individual organisms. The advanced hypothesis is substantiated by the analysis of the relevant processes observed in cases of infectious keratoconjunctivitis in humans and cattle, caused by bacteria of the genus Moraxella. The data indicating the possibility of such reversion in the genera Neisseria and Bordetella are presented.

Differentiation of some gram-negative glucose nonfermenting bacteria using miniaturized carbon sources assimilation tests

In water and soil the gram-negative nonfermenting bacteria play an important role in the biological mineralization process. To improve the methods for species differentiation of these heterogenous bacterial group, a total of 481 reference strains of gram-negative glucose nonfermenting bacteria belonging to the genera Pseudomonas, Alcaligenes, Bordetella, Agrobacterium, Moraxella, Acinetobacter, Flavobacterium and some CDC groups have been investigated for their ability to utilize 42 different carbon substrates with the help of a standardized and automated micromethod. Most species showed a typical pattern of carbon utilization and hence could be differentiated from each other within their genera. As already has been demonstrated by more clinical significant Pseudomonas species, this method proves to be a useful alternative to existing methods of differentiation, especially with representatives of the families Pseudomonadaceae and Alcaligenaceae.

Cultural and chemical characterization of CDC groups EO-2, M-5, and M-6, Moraxella (Moraxella) species, Oligella urethralis, Acinetobacter species, and Psychrobacter immobilis

We determined phenotypic characteristics, cellular fatty acid composition, and isoprenoid quinone content of representative strains of CDC groups EO-2, M-5, and M-6, Moraxella (Moraxella) species, Oligella urethralis, Acinetobacter species, and Psychrobacter immobilis. All organisms contained ubiquinone with eight isoprene units as the major isoprenolog, but distinct differences were observed in fatty acid composition. Twenty-eight of the original collection of CDC group EO-2 strains were further identified as P. immobilis, EO-2, or EO-3 by distinctive cellular fatty acid profiles, cellular morphology, and pigment production. The cellular fatty acid compositions of M-5 and M-6 were similar but were clearly different from those of other organisms. The genus Acinetobacter was differentiated from other organisms in the study by small amounts of 2-hydroxydodecanoic acid (2-OH-12:0), and P. immobilis was differentiated by small amounts of decanoic acid (10:0) and a branched-chain 17-carbon acid (i-17:0). All Moraxella species were distinguished by small amounts of decanoic acid (10:0) and the absence of i-17:0. M. bovis, M. nonliquefaciens, and some strains of M. lacunata formed a single fatty acid group, while M. osloensis, M. phenylpyruvica, M. atlantae, and other strains of M. lacunata (M. lacunata II) had species-specific fatty acid profiles. O. urethralis differed from Moraxella species by the presence of large amounts (49%) of cis-vaccenic acid (18:1 omega 7c), small amounts (1%) of 3-hydroxyhexadecanoate (3-OH-16:0), and the absence of 10:0 and 3-hydroxydodecanoate (3-OH-12:0). The combined use of chemical data and a small number of conventional tests permitted rapid identification and differentiation of these organisms from each other and from related organisms.

Combined genetic transformation and nutritional assay for identification of Moraxella nonliquefaciens

A combined genetic transformation and nutritional assay is described that permits definitive identification of clinically isolated strains of Moraxella nonliquefaciens. Crude DNA preparations of strains of various Moraxella species were used to transform nutritional mutants of a stably competent strain of M. nonliquefaciens for ability to grow on a defined medium (Mn-B). DNA samples from 24 independently isolated strains of M. nonliquefaciens all resulted in massive (4+) transformation of each of two mutant assay strains. DNA samples from strains of M. bovis and M. lacunata frequently gave weak (1+) transformation of one of the mutant assay strains (Mn64) but almost always failed to transform another assay strain (Mn136). DNA samples from eight other Moraxella species failed completely to transform either of the mutant assay strains. When streaked on the defined medium used for the transformation assay (Mn-B), 23 of the 24 strains of M. nonliquefaciens grew well, but all strains of M. bovis and M. lacunata failed to grow on this medium.

Taxonomy of pasteurella anatipestifer. 1. DNA base composition and DNA-DNA hybridization analysis

DNA was isolated from 15 strains of Pasteurella anatipestifer and from one strain each of Moraxella nonliquefaciens, M. bovis, Pasteurella multocida, P. haemolytica, P. gallinarum, P. pneumotropica, and P. ureae. The guanine-plus-cytosine contents of P. anatipestifer ranged from 32 to 35 mole %, whereas those of Moraxella and Pasteurella spp. were much higher, ranging from 40 to 45 mole %. DNA-DNA hybridization analysis revealed that homology of nine P. anatipestifer strains to strains ATCC 11845 and PA 15 was 52 to 100%, whereas homology of Moraxella and Pasteurella strains to these strains was only 3 to 17%. Similarly, homology of P. anatipestifer strains, Moraxella, and Pasteurella species other than P. multocida to P. multocida reference strain P-2192 was low. These results strongly suggest that P. anatipestifer is genetically unrelated to either Pasteurella or Moraxella.