Cultivation of cilia-associated respiratory bacillus in artificial medium and determination of the 16S rRNA gene sequence

A novel Filobacterium sp can cause chronic bronchitis in cats

Background

Cilia-associated respiratory bacillus (CARB; now known as Filobacterium rodentium gen. nov., sp. nov.) is a primary pathogen of rodents. A CARB-like organism was reported in post-mortem lung samples of cats using light and electron microscopy. Here we explore by molecular procedures if a Filobacterium sp. is a part of the normal feline lower respiratory microbiome and whether it could in some cats contribute to the development of chronic bronchial disease.

Methodology

A Filobacterium sp. was identified in three Czech cats clinically diagnosed as having chronic neutrophilic bronchitis. Bronchoalveolar lavage fluid (BALF) specimens obtained from these cats were subjected to panbacterial 16S rDNA PCR followed by Sanger sequencing of the V5 to V8 region. After these cats were treated with specific antimicrobials, their clinical signs resolved promptly, without recurrence. Next, BALF specimens from 13 Australian and 11 Italian cats with lower respiratory disease and an additional 16 lung samples of Italian cats who died of various causes were examined using next generation sequencing (NGS). Subsequently, a Filobacterium-specific qPCR assay was developed and used to re-test BALF specimens from the 11 Italian cats and lung tissue homogenates from the additional 16 deceased cats.

Principal findings

An amplicon of 548 bp with 91.24% sequence agreement with Filobacterium rodentium was obtained from all three patients, suggesting the novel Filobacterium sp. was the cause of their lower respiratory disease. The novel Filobacterium sp., which we propose to call F. felis, was detected in 3/3 Czech cats with chronic neutrophilic bronchitis, 13/13 Australian cats and 6/11 Italian cats with chronic lower respiratory disease, and 14/16 necropsy lung specimens from Italian cats. NGS and qPCR results all showed identical sequences. The Filobacterium sp. was sometimes the preponderant bacterial species in BALF specimens from cats with lower airway disease. There was an association between the presence of large numbers (greater than 10⁵ organisms/mL) of Filobacterium and the presence of neutrophilic and/or histiocytic inflammation, although only a subset of inflammatory BALF specimens had F. felis as the preponderant organism.

Conclusion

The novel Filobacterium sp. comprises a finite part of the normal feline lower respiratory microbiome. Under certain circumstances it can increase in absolute and relative abundance and give rise to neutrophilic and/or histiocytic bronchitis, bronchiolitis and bronchopneumonia. These findings strongly suggest that F. felis could be an underdiagnosed cause of feline bronchial disease.

Filobacterium rodentium gen. nov., sp. nov., a member of Filobacteriaceae fam. nov. within the phylum Bacteroidetes; includes a microaerobic filamentous bacterium isolated from specimens from diseased rodent respiratory tracts

Strain SMR-CT, which was originally isolated from rats as the SMR strain, had been named 'cilia-associated respiratory bacillus' ('CAR bacillus'). 'CAR bacillus' was a Gram-stain-negative, filamentous argentophilic bacterium without flagella. SMR-CT grew at 37 °C under microaerobic conditions, showed gliding activity, hydrolysed urea and induced chronic respiratory diseases in rodents. The dominant cellular fatty acids detected were iso-C15 : 0 and anteiso-C15 : 0. The DNA G+C content was 47.7 mol%. 16S rRNA gene sequence analysis revealed SMR-CT and other strains of 'CAR bacillus' isolated from rodents all belonged to the phylum Bacteroidetes. The nearest known type strain, with 86 % 16S rRNA gene sequence similarity, was Chitinophaga pinensis DSM 2588T in the family Chitinophagaceae. Strain SMR-CT and closely related strains of 'CAR bacillus' rodent-isolates formed a novel family-level clade in the phylum Bacteroidetes with high bootstrap support (98-100 %). Based on these results, we propose a novel family, Filobacteriaceae fam. nov., in the order Sphingobacteriales as well as a novel genus and species, Filobacterium rodentium gen. nov., sp. nov., for strain SMR-CT. The type strain is SMR-CT ( = JCM 19453T = DSM 100392T).

Cilia-associated respiratory bacillus infection in rats in New Zealand

AIMS

To demonstrate cilia-associated respiratory (CAR) bacillus associated with chronic pneumonia in wild and pet rats in New Zealand.

METHODS

A range of tissues from 4 rats were examined grossly and by light microscopy and affected lungs were examined by transmission electron microscopy.

RESULTS

All 4 rats had moderate to severe cranioventral bronchopneumonia with bronchiectasis and large numbers of argentophilic bacteria resembling CAR bacillus, intimately associated with the bronchial epithelium.

CONCLUSIONS

CAR bacillus infection should be considered as a differential diagnosis for pneumonia in rats in New Zealand.

Differential interleukin-10 and gamma interferon mRNA expression in lungs of cilium-associated respiratory bacillus-infected mice

The cilium-associated respiratory (CAR) bacillus is a gram-negative, extracellular bacterium that causes persistent respiratory tract infections in rodents. We have previously demonstrated that BALB/c mice are more susceptible to CAR bacillus-induced disease than resistant C57BL/6 mice, with elevations in pulmonary gamma interferon (IFN-gamma) and interleukin (IL)-4. IL-10 is a type 2 cytokine that can increase host susceptibility to bacterial diseases through its anti-inflammatory effects, including suppression of macrophage function. The purpose of this study was to further describe the cytokine profiles associated with histologic lesions in CAR bacillus-infected mice and to assess the effects of cytokine depletion on the pathogenesis of disease. Six-week-old female BALB/c and C57BL/6 mice and mice with targeted mutations in IFN-gamma and IL-4 were inoculated intratracheally with 10(5) CAR bacillus organisms, and samples were collected at 6 to 7 weeks postinoculation. Lung samples were collected for histopathologic examination and analysis of cytokine mRNA. IFN-gamma, IL-10, and IL-4 mRNA levels in the lungs of infected mice were semiquantitatively measured using a reverse transcriptase-mediated PCR assay and compared to those in uninfected control animals of each strain. BALB/c mice infected with CAR bacillus had a median lung lesion score of 6 and IL-10 and IL-4 mRNA levels were significantly elevated. The majority of C57BL/6 mice were resistant to disease characterized by lung lesions scores of 2 or less and a dominant IFN-gamma mRNA cytokine profile. A few C57BL/6 mice with lesions scores of 5 or greater had elevations in all three cytokines and were susceptible to disease. C57BL/6 IFN-gamma knockout mice had increased disease with elevations in IL-10 and IL-4 mRNA, while BALB/c IL-4 knockout mice infected with CAR bacillus had a mild decrease in lesion severity and an attenuated IL-10 mRNA expression compared to wild-type BALB/c mice. These data indicate that IL-10 and IL-4 predominate in CAR bacillus-induced histologic lesions in mice, while IFN-gamma may play a role in resistance to disease.

Antibody and cytokine responses to the cilium-associated respiratory bacillus in BALB/c and C57BL/6 mice

The cilium-associated respiratory (CAR) bacillus is a gram-negative, gliding bacterium that causes persistent respiratory tract infections in rodents despite histologic and serologic evidence of a marked immune response. To assess humoral immunity and cytokine responses in CAR bacillus disease, 6-week-old female BALB/c and C57BL/6 mice were inoculated intratracheally with 10(5) CAR bacillus organisms. CAR bacillus-specific serum immunoglobulins (immunoglobulin M [IgM], IgG1, IgG2a, IgG2b, IgG3, and IgA) and local pulmonary cytokines (tumor necrosis factor alpha [TNF-alpha], gamma interferon [IFN-gamma], and interleukin-4 [IL-4]) were evaluated by enzyme-linked immunosorbent assay every 7 days for 49 days. BALB/c mice developed CAR bacillus-induced lesions early in the course of disease that became more severe with time. Correlating with increasing disease severity, BALB/c mice had elevations in all antibody isotypes tested, and elevations in pulmonary TNF-alpha, IFN-gamma, and IL-4. C57BL/6 mice developed mild lesions with mild increases in serum IgM, IgG1, IgG2b, and IgG3 levels and minimally detectable IgG2a and IgA. Cytokine perturbations were not detected in C57BL/6 mice. The persistence of infection in BALB/c mice with vigorous serum antibody responses and increased IFN-gamma and IL-4 responses suggests that humoral immunity and T-cell responses are ineffective at preventing CAR bacillus disease. Furthermore, the lackluster antibody responses and undetectable cytokine responses in C57BL/6 mice suggest that humoral immunity and T-cell responses are not critical in resistance to CAR bacillus-induced disease.

Sequence of 16S rRNA gene of rat-origin cilia-associated respiratory (CAR) bacillus SMR strain

The 16S rRNA gene of the SMR strain of cilia-associated respiratory (CAR) bacillus, which was isolated from a spontaneously infected rat at our institute, was sequenced. Its 1,521 nucleotides were determined. On the basis of the results of the sequence analysis, the SMR strain was found to be most closely related to members of the Flavobacter/Flexibacter group. This sequence was compared with the previously determined 16S rRNA gene sequences (rat-origin: three; mouse-origin: one; rabbit-origin: one) of CAR bacillus isolates. The SMR strain showed the highest sequence similarity (99.9%) to the rat-origin CARB-NIH strain (Schoeb et al., 1993), and it was concluded that the strains are identical.

Isolation of cilia-associated respiratory (CAR) bacillus from pigs and calves and experimental infection of gnotobiotic pigs and rodents

Filamentous, gram-negative bacteria morphologically similar to cilia-associated respiratory (CAR) bacillus of rodents and rabbits were isolated from the tracheas of 5 pigs and 4 calves. All pigs but none of the calves had histologic lesions of chronic tracheitis. In silver-stained histologic sections, CAR bacilli were adhered to the tracheal epithelium of each pig but were not found in the calves. Like CAR bacillus of rats, the bacteria displayed gliding motility and grew only in cell culture or cell culture medium supplemented with fetal serum. Initially, all isolates were contaminated by Mycoplasma spp. This contamination was eliminated from 4 pig isolates by limiting dilutions, and mycoplasma-free isolates were used to intranasally inoculate gnotobiotic pigs and CAR bacillus-free mice and rats and to immunize guinea pigs. The gnotobiotic pigs remained healthy, and when they were necropsied 4 and 7 weeks after infection no macroscopic or microscopic lesions were found in the respiratory tract. However, CAR bacillus was isolated at both times from the nasal cavities and tracheas of inoculated pigs, and the ciliated tracheal epithelium of infected pigs necropsied 7 weeks after infection was colonized by low numbers of CAR bacillus-like bacteria. The rats and mice remained healthy through week 12 postinoculation, and evidence of short- or long-term colonization was not detected by histologic examination or culture. When used as primary antibody for immunohistochemical staining, sera from guinea pigs immunized with pig CAR bacillus specifically stained CAR bacilli colonizing the respiratory epithelium of naturally infected pigs, whereas sera collected prior to immunization failed to react with the bacteria. These results indicate that CAR bacilli are unlikely to be primary pathogens of pigs or cattle and that rodents do not act as reservoirs.

Cilia-associated respiratory (CAR) bacillus infection in conventionally reared rabbits

This study was designed to investigate the prevalence of Cilia-associated respiratory (CAR) bacillus infection in rabbits reared for meat production in Italy and to correlate the presence of CAR bacillus with inflammatory lesions of the respiratory tract. Seventy health, 3-month-old, New Zealand White rabbits, raised in 10 different rabbitries in Northern Italy were randomly selected at slaughter. No gross lesions were found at necropsy in any rabbit. In each animal, the trachea and lungs were sampled, fixed in 10% formalin, embedded in paraffin and stained with the Warthin-Starry method to evaluate the presence of CAR bacillus, and with haematoxylin and eosin to evaluate the presence of inflammatory lesions. CAR bacillus was present in 50 out of 70 rabbits (71.4%) with a prevalence of the infection that varied from 30% to 100% in the seven rabbitries. CAR bacillus was present both in the trachea and bronchi in 23 cases (32.8%), only in the trachea in 24 cases (34.3%) and only in the bronchi in three cases (4.3%). Inflammatory lesions were found in the trachea (22 cases, 31.4%) and the bronchi (58 cases, 82.8). There was a strong, statically significant correlation between the presence of CAR bacillus in the bronchi and bronchial inflammatory lesions (P < 0.0001). This study indicates that CAR bacillus infection is widespread in conventionally reared rabbits in Italy and that a possible correlation exists between the presence of CAR bacillus and bronchial inflammatory lesions.

Association of cilia-associated respiratory (CAR) bacillus with natural chronic tracheitis in goats

A histological, histochemical and immunohistological study of the respiratory tract of 83 slaughtered goats (50 adults and 33 kids) is described. Cilia-associated respiratory (CAR) bacillus was detected by means of the Warthin Starry method in the tracheal epithelium of seven (21.2%) of the kids and 16 (32%) of the adult goats. A chronic diffuse tracheitis characterized by mixed lymphocyte and plasma-cell infiltration was found in all seven kids and in 17 adults, including the 16 infected with the CAR bacillus. Although not proved, it is possible that the CAR bacillus caused the chronic tracheitis. Immunohistochemical results suggested that the caprine CAR bacillus was closely related to the rabbit CAR bacillus.

Natural cilia-associated respiratory bacillus infection in rabbits used for elaboration of hyperimmune serum against Mycoplasma sp

Cilia-associated respiratory (CAR) bacillus was identified in lung lesions of rabbits used for elaboration of hyperimmune serum against Mycoplasma mycoides ssp. capri (Mmc). Numerous Warthin Starry (WS) positive filamentous bacteria aligned perpendicularly to the surface of bronchial epithelial lining were observed. Immunoperoxidase staining of these bacteria was detected using a serum anti-rabbit CAR bacillus. Ultrastructural morphology corresponds to that of CAR bacilli previously reported in rabbits. The desirability of monitoring laboratory rabbits for CAR bacillus infection as part of the health programme is reinforced, especially in rabbits used for raising sera against respiratory pathogens of animal species in which CAR bacillus infection has been described. This is the first report of natural CAR bacillus infection in rabbits in Europe.

Pathogenicity of cilia-associated respiratory (CAR) bacillus isolates for F344, LEW, and SD rats

We conducted experiments to test whether rats of F344, LEW, and SD strains differ in susceptibility to mycoplasma-free isolates of cilia-associated respiratory (CAR) bacillus, whether Mycoplasma pulmonis can affect expression of CAR bacillus disease, and whether isolates of CAR bacillus differ in virulence for rats. In the first experiment, 24 rats of each strain were inoculated intranasally with 10(7) bacilli of CAR bacillus X1428D/AS, and 24 rats of each strain were inoculated with sterile medium (controls). Eight weeks later, eight inoculated rats and eight control rats of each strain were euthanatized, eight inoculated and eight control rats were given 10(6.5) colony-forming units of M. pulmonis X1428D, and eight inoculated rats and eight control rats were sham inoculated. Four rats of each group were euthanatized 4 or 8 weeks after the second inoculation. Severity of lesions in nasal passages, middle ear, trachea, and lungs was assessed by scoring. Rats of all three strains given CAR bacillus had typical lesions of similar severity; M. pulmonis X1428D was avirulent and did not exacerbate CAR bacillus disease. In the second experiment, groups of eight rats of F344 and SD strains were given 10(5) or 10(7) CAR bacillus X1328E, X1428D/AS, or X2450D and euthanatized 8 or 16 weeks later. Isolates X1428D/AS and X2450D caused similar lesions in rats of both strains and at both doses, but CAR bacillus X1328E was avirulent. Rats of the tested strains are similarly susceptible to CAR bacillus disease, but CAR bacillus isolates differ in virulence.

Detection of Mycoplasma pulmonis in cilia-associated respiratory bacillus isolates and in respiratory tracts of rats by nested PCR

To improve the detection of Mycoplasma pulmonis contamination of isolates of cilia-associated respiratory (CAR) bacillus, we developed a nested PCR method using primers for 16S rRNA gene sequences. Of 140 samples of 16 different CAR bacillus isolates, 73 (52%) were inhibitory in the first PCR, as indicated by the absence of amplicons of the internal control, but only 11 of 140 (7.9%) were inhibitory in the second PCR. Of 27 samples known to contain M. pulmonis, only 12 (44%) were positive in the first PCR, but 25 of 27 (93%) were positive in the second PCR. Nested PCR also detected M. pulmonis in 21 of 61 (34%) CAR bacillus samples from which M. pulmonis could not be cultured and identified 2 additional M. pulmonis-contaminated CAR bacillus isolates. Of 359 respiratory and reproductive tract lavage samples from rats and mice, 35 (9.8%) were inhibitory in the first PCR, but only 15 (4.2%) were inhibitory in the second PCR. Of 72 lavage specimens from rats inoculated with an avirulent, poorly infective M. pulmonis strain, 14 (19%) were positive by nested PCR, but only 2 of 72 (2.8%) were positive by culture. Nested PCR also detected M. pulmonis in 14 of 20 (70%) paraffin sections of lung and trachea from rats and mice inoculated with CAR bacillus isolates known to contain M. pulmonis, whereas single PCR gave no positive results. We conclude that nested PCR is superior to single PCR or culture for detecting M. pulmonis, and that M. pulmonis is present in all but four CAR bacillus isolates in our collection that were from naturally infected rats; the four isolates that were exceptions were obtained from rats from a single colony.

Development of techniques to genetically manipulate members of the genera Cytophaga, Flavobacterium, Flexibacter, and Sporocytophaga

The Bacteroides-Cytophaga-Flavobacterium branch of the eubacterial phylogenetic tree contains a diverse group of bacterial species. Techniques for the genetic manipulation of Bacteroides spp. are well developed (A. A. Salyers, N. B. Shoemaker, and E. P. Guthrie, Crit. Rev. Microbiol. 14:49-71, 1987). Recently we developed techniques to genetically manipulate the gliding bacterium Cytophaga johnsonae (M. J. McBride and M. J. Kempf, J. Bacteriol. 178:583-590, 1996). We now demonstrate that some of these techniques allow genetic manipulation of a number of environmentally or medically significant bacteria in this group. The Bacteroides transposon Tn4351 was introduced into Cytophaga hutchinsonii, Cytophaga succinicans, Flavobacterium meningosepticum, Flexibacter canadensis, Flexibacter sp. strain FS1, and Sporocytophaga myxococcoides by conjugation. Tn4351 integrated itself into the host chromosomes and conferred erythromycin resistance. We isolated several auxotrophic mutants of Flavobacterium meningosepticum following Tn4351 mutagenesis. The C. johnsonae-Escherichia coli shuttle vector pCP11 functioned in C. succinicans but not in the other bacteria. pLYL03 did not replicate in any of these bacteria and should function as a convenient suicide vector. The identification of a system of gene transfer, a selectable marker, a suicide vector, and a transposon that functions in these diverse bacteria allows genetic manipulations to be performed.

Morphological evidence of a filamentous cilia-associated respiratory (CAR) bacillus in goats

A filamentous cilia-associated respiratory (CAR) bacillus was discovered in 12 3-4 month-old goats experimentally infected with two different strains of mycoplasmas belonging to the Mycoplasma mycoides type. The CAR bacilli were always arranged parallel to the cilia, and the morphology of these bacilli is very similar to that of other bacilli described previously in other species from various parts of the world.

Development of techniques for the genetic manipulation of the gliding bacterium Cytophaga johnsonae

Cytophaga johnsonae displays many features that make it an excellent model of bacterial gliding motility. Unfortunately, genetic analyses of C. johnsonae, or any related gliding bacteria, were not possible because of a complete lack of selectable markers, cloning vectors, transposons, and convenient methods of gene transfer. As a first step toward a molecular analysis of gliding motility of C. johnsonae, we developed these genetic techniques and tools. Common broad-host-range plasmids and transposons did not function in C. johnsonae. We identified one Bacteroides transposon, Tn4351, that could be introduced into C. johnsonae on plasmid R751 by conjugation from Escherichia coli. Tn4351 inserted in the C. johnsonae genome and conferred erythromycin resistance. Tn-4351 insertions resulted in auxotrophic mutations and motility mutations. We constructed novel plasmids and cosmids for genetic analyses of C. johnsonae. These cloning vectors are derived from a small cryptic plasmid (pCP1) that we identified in the fish pathogen Cytophaga psychrophila D12. These plasmids contain the ermF (erythromycin resistance) gene from Tn4351 and a variety of features that facilitate propagation and selection in E. coli and conjugative transfer from E. coli to C. johnsonae.

Detection of cilia-associated respiratory bacillus in experimentally and naturally infected mice and rats by the polymerase chain reaction

Cilia-associated respiratory (CAR) bacillus was detected by means of the reverse transcription (RT)-polymerase chain reaction (PCR), and the results were compared with those of indirect immunofluorescence test (IFAT) for the detection of the organism. In the experimental infections, 15 mice were in contact with mice previously inoculated with CAR bacillus. Three mice each were tested at days 3, 5, 7, 12 and 20 postexposure. On day 3 postexposure, CAR bacillus was detected in oral swab samples from all 3 mice by RT-PCR, but was not detected in any sampling sites from the mice by IFAT. Total numbers of positive samples from nasal, oral and tracheal swabs obtained through the test were 6/15, 14/15 and 8/15, respectively, by RT-PCR, and 2/15, 6/15 and 3/15, respectively by IFAT. For the detection of CAR bacillus in samples from 52 rats, 34 serum antibody negative rats by enzyme-linked immunosorbent assay were also negative by RT-PCR and IFAT except for one sample from the oral cavity, and all serum antibody positive rats were positive for the organism by RT-PCR but it could not be detected in five of them by IFAT. By means of RT-PCR, no differences in the positive rates depending on sampling sites were observed except in one rat. The RT-PCR was found to be a specific, highly sensitive and reliable procedure for detecting CAR bacillus in mice and rats. The oral cavity was the most suitable site for the diagnosis of the early stage of this infection by RT-PCR.

Colonization of the tracheal epithelium of pigs by filamentous bacteria resembling cilia-associated respiratory bacillus

Warthin Starry staining revealed filamentous bacteria colonizing the tracheal epithelium of 41 of 88 (46.6%) pigs submitted for necropsy at 2 midwestern veterinary diagnostic laboratories. The bacteria were interspersed between and oriented parallel to the cilia. In 4 of 4 colonized pig tracheas, filamentous bacteria were demonstrated by transmission electron microscopy. The bacteria were approximately the same length and diameter as cilia, and in areas of heavy colonization the bacteria outnumbered cilia. The filamentous bacteria were similar in location and morphologic characteristics to cilia-associated respiratory (CAR) bacilli of rats, mice, rabbits, and cattle. Results of immunoperoxidase staining and polymerase chain reaction analysis indicated that the pig CAR bacillus is a different bacterium than the rat CAR bacillus. Rat CAR bacillus causes chronic respiratory disease in rats and mice. The association, if any, between pig CAR bacillus and swine respiratory disease is unknown.

Detection of cilia-associated respiratory bacillus by PCR

The cilia-associated respiratory (CAR) bacillus is an unclassified, gram-negative, motile bacterium that has been implicated as an etiologic agent of respiratory disease in laboratory rodents. In the present study, approximately 1,200 bases of the 16S rRNA gene from three CAR bacillus isolates were sequenced. CAR bacillus-specific primers were designed on the basis of the 16S rRNA gene sequence and used in a PCR assay. The PCR assay detected as little as 500 fg of purified CAR bacillus DNA. The expected 267-bp DNA fragment was amplified from respiratory tissue of frozen, formalin-fixed, and paraffin-embedded samples from experimentally and naturally infected rats and mice. In contrast, no product was amplified from respiratory tissues of sham-infected experimental animals or animals that were serologically or histopathologically negative for the CAR bacillus. Our findings indicate that this PCR assay is a rapid, specific, and sensitive detection method for the diagnosis of CAR bacillus infection in rats and mice.