Moraxella pluranimalium sp. nov., isolated from animal specimens

Moraxella haemolytica sp. nov., isolated from a goat with respiratory disease

An aerobic, haemolytic, Gram-negative and rod-shaped bacterial strain ZY171148T was isolated from the lung of a dead goat with respiratory disease in Southwest China. The strain grew at 24-39 °C, at pH 6.0-9.0 and in the presence of 0.5-2.0% (w/v) NaCl. Phylogenetic analysis of 16S rRNA gene sequences showed that the strain belongs to the genus Moraxella. The nucleotide sequence similarity analysis of the 16S rRNA gene showed that the strain has the highest similarity of 98.1% to Moraxella (M.) caprae ATCC 700019 T. Phylogenomic analysis of 800 single-copy protein sequences indicated that the strain is a member of the genus Moraxella and forms a separated branch on the Moraxella phylogenetic tree. The strain exhibited the highest orthologous average nucleotide identity (OrthoANI) and average amino acid identity (AAI) values of 77.0 and 77.9% to M. nasibovis CCUG 75921T and M. ovis CCUG 354T, respectively. The strain shared the highest digital DNA-DNA hybridization (dDDH) value of 26.2% to M. osloensis CCUG 350T. The genome G + C content of strain ZY171148T was 42.6 mol%. The strain had C18:1 ω9c (41.7%), C18:0 (11.2%), C16:0 (14.1%) and C12:0 3OH (9.7%) as the predominant fatty acids and CoQ-8 as the major respiratory quinone. The strain contained phosphatidylglycerol, phosphatidylethanolamine, cardiolipin, dilysocardiolipin, monolysocardiolipin and phosphatidic acid as the major polar lipids. β-haemolysis was observed on Columbia blood agar. All results confirmed that strain ZY171148T represents a novel species of the genus Moraxella, for which the name Moraxella haemolytica sp. nov. is proposed, with strain ZY171148T = CCTCC AB 2021471T = CCUG 75920T as the type strain.

Moraxella nasibovis sp. nov., Isolated from a Cow with Respiratory Disease

Strain ZY190618T, isolated from the nasal cavity of a cow with respiratory disease, was subjected to taxonomic characterization. Cells of the strain were Gram-stain-negative, aerobic and coccus-shaped. Phylogenetic analysis based on 16 S rRNA gene sequences indicated that the strain belonged to the genus Moraxella with the highest similarity of 98.1% to Moraxella nasovis CCUG 75922T. Phylogenomic analysis based on 810 single-copy genes revealed that the strain was a member of the genus Moraxella and formed a deep and separated clade within the genus. The strain showed the highest orthologous average nucleotide identity (OrthoANI) value of 77.1% with Moraxella ovis CCUG 354T and digital DNA-DNA hybridization (dDDH) value of 24.7% with Moraxella equi NCTC 11012T, respectively. The DNA G + C content was 46.5 mol%. The strain optimally grew at 37 °C (temperature range, 24-42 °C), at pH 8.0 (pH range, 6.0-9.0) and with 1.5% (w/v) NaCl (NaCl range, 0.5-3.0%). The strain contained C18:1 ω9c as the sole predominant fatty acid (> 5 %) and CoQ-8 as the major respiratory quinone. The major polar lipids included phosphatidylglycerol, phosphatidylethanolamine, cardiolipin, monolysocardiolipin and hemibismonoacylglycerophosphate. Based on these data, strain ZY190618T clearly represents a novel species in the genus Moraxella, for which the name Moraxella nasibovis sp. nov. (The type strain ZY190618T = CCUG 75921T = CCTCC AB 2021472T) is proposed.

Evidence for wastewaters as environments where mobile antibiotic resistance genes emerge

The emergence and spread of mobile antibiotic resistance genes (ARGs) in pathogens have become a serious threat to global health. Still little is known about where ARGs gain mobility in the first place. Here, we aimed to collect evidence indicating where such initial mobilization events of clinically relevant ARGs may have occurred. We found that the majority of previously identified origin species did not carry the mobilizing elements that likely enabled intracellular mobility of the ARGs, suggesting a necessary interplay between different bacteria. Analyses of a broad range of metagenomes revealed that wastewaters and wastewater-impacted environments had by far the highest abundance of both origin species and corresponding mobilizing elements. Most origin species were only occasionally detected in other environments. Co-occurrence of origin species and corresponding mobilizing elements were rare in human microbiota. Our results identify wastewaters and wastewater-impacted environments as plausible arenas for the initial mobilization of resistance genes.

Moraxella nasicaprae sp. nov., Isolated from a Goat with Respiratory Disease

A novel Gram-stain-negative, aerobic, irregular coccus designated as ZY201224^T, was isolated from the nasal cavity of a goat with respiratory disease in a goat farm, located at Jianshui, Yunnan Province, PR China and its taxonomic position was clarified using a polyphasic approach. The strain grew optimally at 37 °C, at pH 8.0 and in the presence of 1% NaCl. Phylogenetic analysis based on 16S rRNA gene sequence and phylogenomic analysis based on 808 single-copy genes revealed that the strain is affiliated to the genus Moraxella and is distinct from the recognized species of the genus. The 16S rRNA gene sequence similarity analysis indicated that the strain is most closely related to Moraxella caviae CCUG 355^T with sequence similarity of 98.1%. The genomic OrthoANI and digital DNA-DNA hybridization (dDDH) values between the strain and the type strains of Moraxella species were no higher than 74.7% (Moraxella pluranimalium CCUG 54913^T) and 26.0% (Moraxella oblonga NBRC 102422^T), respectively. The G + C content of the complete genome sequence was 43.6 mol%. The strain contained CoQ-8 as the major respiratory quinone, and C_18:1ω9c, C17:1ω8c, C16:0 and summed feature 3 (C_16:1 ω7c and/ or C_16:1ω6c) as the predominant fatty acids (> 5%). The major polar lipids comprised phosphatidylglycerol (PG), cardiolipin (CL), monolysocardiolipin (MLCL), phosphatidylethanolamine (PE) and lysophosphatidylglycerol (LPG). Based on these taxonomic characterizations, strain ZY201224^T represents a novel species of the genus Moraxella, for which the name Moraxella nasicaprae sp. nov. is proposed. The type strain is ZY201224^T (= CCTCC AB 2021474^T = NBRC 115473^T).

Moraxella nasovis sp. nov., isolated from a sheep with respiratory disease

A novel Gram-stain-negative, aerobic, coccus-shaped bacteria, designated ZY201115T, was isolated from the nasal cavity of a sheep with respiratory disease in Yunnan Province, south-west China, and its taxonomic affiliation was studied by applying a polyphasic approach. The strain grew at 18–41 °C (optimum, 37 °C), at pH 6.0–9.0 (optimum, pH 8.0) and in 0.5–3.0% (w/v) NaCl (optimum, 1.0 % NaCl). Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain is affiliated to the genus Moraxella with highest similarity to Moraxella bovis ATCC 10900T (96.6 %). Phylogenomic analysis based on 811 single-copy genes also indicated that the strain represents a novel species in the genus Moraxella and formed a deep and separated clade with Moraxella caviae NCTC 10293T. The highest genomic orthologous average nucleotide identity and digital DNA–DNA hybridization values between the strain and the type strains in the genus Moraxella were 73.7% ( M. caviae NCTC 10293T) and 25.3% ( Moraxella osloensis CCUG 350T), respectively. The G+C content of the complete genome sequence was 42.1 mol%. The predominant fatty acids (>5 %) were C18:1 ω9c, C17:1 ω8c, C12:03OH and summed feature 3 (C16:1 ω7c and/or C16:1 ω6c). The major polar lipids were phosphatidylglycerol, cardiolipin, monolysocardiolipin, phosphatidylethanolamine and hemibismonoacylglycerophosphate. The major respiratory quinone was CoQ-8. On the basis of the results of phylogenetic, phenotypic and chemotaxonomic characterizations, strain ZY201115T clearly represents a novel species of the genus Moraxella , for which the name Moraxella nasovis sp. nov. is proposed. The type strain is ZY201115T (=CCTCC AB 2021473T=CCUG 75922T).

Free-Living, Psychrotrophic Bacteria of the Genus Psychrobacter Are Descendants of Pathobionts

Host-adapted microorganisms are generally assumed to have evolved from free-living, environmental microorganisms, as examples of the reverse process are rare. In the phylum Gammaproteobacteria, family Moraxellaceae, the genus Psychrobacter includes strains from a broad ecological distribution including animal bodies as well as sea ice and other nonhost environments. To elucidate the relationship between these ecological niches and Psychrobacter's evolutionary history, we performed tandem genomic analyses with phenotyping of 85 Psychrobacter accessions. Phylogenomic analysis of the family Moraxellaceae reveals that basal members of the Psychrobacter clade are Moraxella spp., a group of often-pathogenic organisms. Psychrobacter exhibited two broad growth patterns in our phenotypic screen: one group that we called the "flexible ecotype" (FE) had the ability to grow between 4 and 37°C, and the other, which we called the "restricted ecotype" (RE), could grow between 4 and 25°C. The FE group includes phylogenetically basal strains, and FE strains exhibit increased transposon copy numbers, smaller genomes, and a higher likelihood to be bile salt resistant. The RE group contains only phylogenetically derived strains and has increased proportions of lipid metabolism and biofilm formation genes, functions that are adaptive to cold stress. In a 16S rRNA gene survey of polar bear fecal samples, we detect both FE and RE strains, but in in vivo colonizations of gnotobiotic mice, only FE strains persist. Our results indicate the ability to grow at 37°C, seemingly necessary for mammalian gut colonization, is an ancestral trait for Psychrobacter, which likely evolved from a pathobiont.IMPORTANCE Host-associated microbes are generally assumed to have evolved from free-living ones. The evolutionary transition of microbes in the opposite direction, from host associated toward free living, has been predicted based on phylogenetic data but not studied in depth. Here, we provide evidence that the genus Psychrobacter, particularly well known for inhabiting low-temperature, high-salt environments such as sea ice, permafrost soils, and frozen foodstuffs, has evolved from a mammalian-associated ancestor. We show that some Psychrobacter strains retain seemingly ancestral genomic and phenotypic traits that correspond with host association while others have diverged to psychrotrophic or psychrophilic lifestyles.

Heterogeneity of Moraxella isolates found in the nasal cavities of piglets

BACKGROUND

Previous studies have shown that the genus Moraxella is commonly present in the nasal microbiota of swine.

RESULTS

In this study, 51 isolates of Moraxella were obtained from nasal swabs from 3 to 4 week old piglets, which represented 26 different fingerprintings by enterobacterial repetitive intergenic consensus (ERIC)-PCR. Whole 16S rRNA gene sequencing allowed the identification at species level of the Moraxella spp. isolates. The majority of the field strains were identified as Moraxella pluranimalium, but Moraxella porci was also detected. In addition, a cluster of 7 strains did not group with any described Moraxella species, probably representing a new species. Subsequent phenotypic characterization indicated that strains of Moraxella pluranimalium were mainly sensitive to serum complement, while the cluster representing the putative new species was highly resistant. Biofilm formation capacity was very variable among the Moraxella spp. isolates, while adherence to epithelial cell lines was similar among selected strains. Additionally, variability was also observed in the association of selected strains to porcine alveolar macrophages. Antimicrobial tests evidenced the existence of multidrug-resistance in the strains.

CONCLUSIONS

In summary, phenotypic characterization revealed heterogeneity among Moraxella strains from the nasal cavity of piglets. Strains with pathogenic potential were detected as well as those that may be commensal members of the nasal microbiota. However, the role of Moraxella in porcine diseases and health should be further evaluated.

Comparative analysis of the fecal microbiota from different species of domesticated and wild suids

Most of the microorganisms living in a symbiotic relationship in different animal body sites (microbiota) reside in the gastrointestinal tract (GIT). Several studies have shown that the microbiota is involved in host susceptibilities to pathogens. The fecal microbiota of domestic and wild suids was analyzed. Bacterial communities were determined from feces obtained from domestic pigs (Sus scrofa) raised under different conditions: specific-pathogen-free (SPF) pigs and domestic pigs from the same bred, and indigenous domestic pigs from a backyard farm in Kenya. Secondly, the fecal microbiota composition of the African swine fever (ASF) resistant warthogs (Phacochoerus africanus) from Africa and a European zoo was determined. African swine fever (ASF) is a devastating disease for domestic pigs. African animals showed the highest microbial diversity while the SPF pigs the lowest. Analysis of the core microbiota from warthogs (resistant to ASF) and pigs (susceptible to ASF) showed 45 shared OTUs, while 6 OTUs were exclusively present in resistant animals. These six OTUs were members of the Moraxellaceae family, Pseudomonadales order and Paludibacter, Anaeroplasma, Petrimonas, and Moraxella genera. Further characterization of these microbial communities should be performed to determine the potential involvement in ASF resistance.

Antimicrobial removal on piglets promotes health and higher bacterial diversity in the nasal microbiota

The view on antimicrobials has dramatically changed due to the increased knowledge on the importance of microbiota composition in different body parts. Antimicrobials can no longer be considered only beneficial, but also potentially deleterious for favourable bacterial populations. Still, the use of metaphylactic antimicrobial treatment at early stages of life is a practice in use in porcine production. Many reports have shown that antibiotics can critically affect the gut microbiota, however the effect of perinatal antimicrobial treatment on the nasal microbiota has not been explored yet. To gain insights on the potential changes in nasal microbial composition due to antimicrobial treatments, piglets from two different farms were sampled at weaning. The nasal microbiota was analysed when antimicrobial treatment was used early in life, and later, when no antimicrobial treatment was used during the lactation period. Removal of perinatal antimicrobials resulted in an increased bacterial diversity in nasal microbiota at weaning. Concurrently, elimination of antimicrobials produced an increase in the relative abundance of Prevotella and Lactobacillus, and a decrease in Moraxella and Bergeyella. These changes in microbiota composition were accompanied by an improvement of the piglets' health and a higher productivity in the nursery phase.

mcr-1 and mcr-2 variant genes identified in Moraxella species isolated from pigs in Great Britain from 2014 to 2015

Objectives

To determine the occurrence of mcr-1 and mcr-2 genes in Gram-negative bacteria isolated from healthy pigs in Great Britain.

Methods

Gram-negative bacteria (n = 657) isolated from pigs between 2014 and 2015 were examined by WGS.

Results

Variants of mcr-1 and mcr-2 were identified in Moraxella spp. isolated from pooled caecal contents of healthy pigs at slaughter collected from six farms in Great Britain. Other bacteria, including Escherichia coli from the same farms, were not detected harbouring mcr-1 or mcr-2. A Moraxella porci-like isolate, MSG13-C03, harboured MCR-1.10 with 98.7% identity to MCR-1, and a Moraxella pluranimalium-like isolate, MSG47-C17, harboured an MCR-2.2 variant with 87.9% identity to MCR-2, from E. coli; the isolates had colistin MICs of 1-2 mg/L. No intact insertion elements were identified in either MSG13-C03 or MSG47-C17, although MSG13-C03 harboured the conserved nucleotides abutting the ISApl1 composite transposon found in E. coli plasmids and the intervening ∼2.6 kb fragment showed 97% identity. Six Moraxella osloensis isolates were positive for phosphoethanolamine transferase (EptA). They shared 62%-64.5% identity to MCR-1 and MCR-2, with colistin MICs from 2 to 4 mg/L. Phylogenetic analysis indicated that MCR and EptA have evolved from a common ancestor. In addition to mcr, the β-lactamase gene, blaBRO-1, was found in both isolates, whilst the tetracycline resistance gene, tetL, was found in MSG47-C17.

Conclusions

Our results add further evidence for the mobilization of the mcr-pap2 unit from Moraxella via composite transposons leading to its global dissemination. The presence of mcr-pap2 from recent Moraxella isolates indicates they may comprise a reservoir for mcr.

Defining ICR-Mo, an intrinsic colistin resistance determinant from Moraxella osloensis

Polymyxin is the last line of defense against severe infections caused by carbapenem-resistant gram-negative pathogens. The emergence of transferable MCR-1/2 polymyxin resistance greatly challenges the renewed interest in colistin (polymyxin E) for clinical treatments. Recent studies have suggested that Moraxella species are a putative reservoir for MCR-1/2 genetic determinants. Here, we report the functional definition of ICR-Mo from M. osloensis, a chromosomally encoded determinant of colistin resistance, in close relation to current MCR-1/2 family. ICR-Mo transmembrane protein was prepared and purified to homogeneity. Taken along with an in vitro enzymatic detection, MALDI-TOF mass spectrometry of bacterial lipid A pools determined that the ICR-Mo enzyme might exploit a possible "ping-pong" mechanism to accept the phosphoethanolamine (PEA) moiety from its donor phosphatidylethanolamine (PE) and then transfer it to the 1(or 4')-phosphate position of lipid A via an ICR-Mo-bound PEA adduct. Structural decoration of LPS-lipid A by ICR-Mo renders the recipient strain of E. coli resistant to polymyxin. Domain swapping assays indicate that the two domains of ICR-Mo cannot be functionally-exchanged with its counterparts in MCR-1/2 and EptA, validating its phylogenetic position in a distinct set of MCR-like genes. Structure-guided functional mapping of ICR-Mo reveals a PE lipid substrate recognizing cavity having a role in enzymatic catalysis and the resultant conference of antibiotic resistance. Expression of icr-Mo in E. coli significantly prevents the formation of reactive oxygen species (ROS) induced by colistin. Taken together, our results define a member of a group of intrinsic colistin resistance genes phylogenetically close to the MCR-1/2 family, highlighting the evolution of transferable colistin resistance.

Faucicola mancuniensis gen. nov., sp. nov., isolated from the human oropharynx

An aerobic, Gram-stain-negative, non-motile coccus, designated strain GVCNT2T, was isolated from the tonsils of a healthy adult female. Cells were oxidase- and catalase-positive, positive for the production of esterase (C4), esterase lipase (C8) and leucine arylamidase, and weakly positive for naphthol-AS-BI-phosphohydrolase and alkaline phosphatase. Cells were also capable of hydrolysing DNA. Growth was observed at 20–37 °C and in the presence of up to 1.5 % NaCl. Phylogenetic analysis of near full-length 16S rRNA gene sequences indicated that the strain exhibited closest sequence similarity to Moraxella boevrei ATCC 700022T (94.68 %) and an uncultured, unspeciated bacterial clone (strain S12-08; 99 %). The major fatty acids were C18 : 1ω9c, C18 : 0, C16 : 0 and C16 : 1ω6c/C16 : 1ω7c. The DNA G+C content of strain GVCNT2T was 40.7 mol%. The major respiratory quinone identified was Q-8. Strain GVCNT2T exhibited a comparable phenotypic profile to other members of the genus Moraxella but could be distinguished based on its ability to produce acid (weakly) from d-glucose, melibiose, l-arabinose and rhamnose and on its ability to hydrolyse DNA. On the basis of phenotypic and phylogenetic differences from other members of the family Moraxellaceae , strain GVCNT2T is considered to represent a novel species of a new genus, for which the name Faucicola mancuniensis gen. nov., sp. nov. is proposed. The type strain of Faucicola mancuniensis is GVCNT2T ( = DSM 28411T = NCIMB 14946T).

Genus Enhydrobacter Staley et al. 1987 should be recognized as a member of the family Rhodospirillaceae within the class Alphaproteobacteria

The genus Enhydrobacter, first reported as a member of the family Vibrionaceae, has been placed in the family Moraxellaceae, but as a genus incertae sedis in Bergey's Manual of Systematic Bacteriology 2nd edition. During our taxonomic investigation of Enhydrobacter-like organisms, we observed that the 16S rRNA sequences of E. aerosaccus-type strain versions NCIMB 12535(T) , ATCC 27094( T) and CCUG 58314(T) were very different from the accessible data (accession no. AJ550856). Phylogenetic analysis of our 16S rRNA sequence data revealed that these organisms were located within the family Rhodospirillaceae. The genera Inquilinus, Oceanibaculum, Skermanella and Nisaea were closely related (sequence similarities were 88.3~87.0%), but Enhydrobacter could be distinguished from these genera by growth characteristics, fatty acid profiles (C(19:0) cyclo ω8c; 38.4% C(18:1) ω7c; 32.2%, and C(16:0) ; 8.9% were major components), in being non-flagellated, and differing in enzymatic activities, including trypsin and β-glucosidase. From these data, we conclude that the genus Enhydrobacter should be recognized as an independent genus of the family Rhodospirillaceae within the class Alphaproteobacteria.

Moraxella porci sp. nov., isolated from pigs

Nine Gram-negative, catalase- and oxidase-positive, coccus-shaped bacteria were isolated from pigs affected by different pathological processes. Phenotypic and genotypic methods were adopted to determine the relationships of these new isolates to recognized species of the genus Moraxella. Analysis of the 16S rRNA gene sequences demonstrated that the clinical isolates represented a new lineage within the genus Moraxella. The isolates were closely related to Moraxella cuniculi and Moraxella pluranimalium with 16S rRNA gene sequence similarities of 98.1 % and 99.1 %, respectively. The isolates displayed DNA-DNA relative binding ratios of 74 % to each other, but distinctly lower levels of DNA-DNA hybridization were observed with phylogenetically closely related moraxellae (<32 %). The new isolates could be distinguished from all other recognized species of the genus Moraxella by physiological and biochemical tests. On the basis of the phenotypic and molecular data, the nine new isolates from pigs represent a novel species within the genus Moraxella, for which the name Moraxella porci sp. nov. is proposed. The type strain is SN9-4M(T) (=CECT 7294(T)=CCUG 54912(T)).