Enterobacter muelleri sp. nov., isolated from the rhizosphere of Zea mays

Model architectures for bacterial membranes

The complex composition of bacterial membranes has a significant impact on the understanding of pathogen function and their development towards antibiotic resistance. In addition to the inherent complexity and biosafety risks of studying biological pathogen membranes, the continual rise of antibiotic resistance and its significant economical and clinical consequences has motivated the development of numerous in vitro model membrane systems with tuneable compositions, geometries, and sizes. Approaches discussed in this review include liposomes, solid-supported bilayers, and computational simulations which have been used to explore various processes including drug-membrane interactions, lipid-protein interactions, host-pathogen interactions, and structure-induced bacterial pathogenesis. The advantages, limitations, and applicable analytical tools of all architectures are summarised with a perspective for future research efforts in architectural improvement and elucidation of resistance development strategies and membrane-targeting antibiotic mechanisms.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12551-021-00913-7.

The Changing Face of the Family Enterobacteriaceae (Order: "Enterobacterales"): New Members, Taxonomic Issues, Geographic Expansion, and New Diseases and Disease Syndromes

The family Enterobacteriaceae has undergone significant morphogenetic changes in its more than 85-year history, particularly during the past 2 decades (2000 to 2020). The development and introduction of new and novel molecular methods coupled with innovative laboratory techniques have led to many advances. We now know that the global range of enterobacteria is much more expansive than previously recognized, as they play important roles in the environment in vegetative processes and through widespread environmental distribution through insect vectors. In humans, many new species have been described, some associated with specific disease processes. Some established species are now observed in new infectious disease settings and syndromes. The results of molecular taxonomic and phylogenetics studies suggest that the current family Enterobacteriaceae should possibly be divided into seven or more separate families. The logarithmic explosion in the number of enterobacterial species described brings into question the relevancy, need, and mechanisms to potentially identify these taxa. This review covers the progression, transformation, and morphogenesis of the family from the seminal Centers for Disease Control and Prevention publication (J. J. Farmer III, B. R. Davis, F. W. Hickman-Brenner, A. McWhorter, et al., J Clin Microbiol 21:46-76, 1985, https://doi.org/10.1128/JCM.21.1.46-76.1985) to the present.

Summary of Novel Bacterial Isolates Derived from Human Clinical Specimens and Nomenclature Revisions Published in 2018 and 2019

Knowledge of novel prokaryotic taxon discovery and nomenclature revisions is of importance to clinical microbiology laboratory practice, infectious disease epidemiology, and studies of microbial pathogenesis. Relative to bacterial isolates derived from human clinical specimens, we present an in-depth summary of novel taxonomic designations and revisions to prokaryotic taxonomy that were published in 2018 and 2019. Included are several changes pertinent to former designations of or within Propionibacterium spp., Corynebacterium spp., Clostridium spp., Mycoplasma spp., Methylobacterium spp., and Enterobacteriaceae Future efforts to ascertain clinical relevance for many of these changes may be augmented by a document development committee that has been appointed by the Clinical and Laboratory Standards Institute.

Precise Species Identification for Enterobacter: a Genome Sequence-Based Study with Reporting of Two Novel Species, Enterobacter quasiroggenkampii sp. nov. and Enterobacter quasimori sp. nov

Enterobacter species are major human pathogens. Precise species identification lays a foundation for microbiology, but the taxonomy of Enterobacter is complicated and confusing. In this study, first, we significantly updated the taxonomy of Enterobacter by rigorous genome analyses and found that all subspecies assignments of Enterobacter were incorrect. Second, we characterized and reported two novel Enterobacter species with clinical significance. Third, we curated 1,997 Enterobacter genome sequences deposited in GenBank and found that the species identification of most Enterobacter strains needed to be corrected. Fourth, we found that the most common Enterobacter species seen in clinical samples is Enterobacter xiangfangensis rather than Enterobacter cloacae. Fifth, we identified 14 tentative novel Enterobacter and 18 tentative novel non-Enterobacter species. This study highlights that updated and curated taxonomic assignments are the premise of correct species identification. We recommend that future Enterobacter studies need to use the updated taxonomy to avoid misleading information.

The genus Enterobacter comprises common pathogens and has a complicated taxonomy. Precise taxonomic assignation lays a foundation for microbiology. In this study, we updated the Enterobacter taxonomy based on robust genome analyses. We found that all Enterobacter subspecies assignments were incorrect. Enterobacter cloacae subsp. dissolvens and Enterobacter hormaechei subsp. hoffmannii are species (Enterobacter dissolvens and Enterobacter hoffmannii, respectively) rather than subspecies. Enterobacter xiangfangensis, Enterobacter hormaechei subsp. oharae, and Enterobacter hormaechei subsp. steigerwaltii are not Enterobacter hormaechei subspecies but belong to the same species (Enterobacter xiangfangensis). Enterobacter timonensis should be removed to Pseudenterobacter, a novel genus. We then reported two novel species, Enterobacter quasiroggenkampii and Enterobacter quasimori, by genome- and phenotype-based characterization. We also applied the updated taxonomy to curate 1,997 Enterobacter genomes in GenBank. Species identification was changed following our updated taxonomy for the majority of publicly available strains (1,542, 77.2%). The most common Enterobacter species was E. xiangfangensis. We identified 14 novel tentative Enterobacter genomospecies. This study highlights that updated and curated taxonomic assignments are the premise of correct identification.

IMPORTANCEEnterobacter species are major human pathogens. Precise species identification lays a foundation for microbiology, but the taxonomy of Enterobacter is complicated and confusing. In this study, first, we significantly updated the taxonomy of Enterobacter by rigorous genome analyses and found that all subspecies assignments of Enterobacter were incorrect. Second, we characterized and reported two novel Enterobacter species with clinical significance. Third, we curated 1,997 Enterobacter genome sequences deposited in GenBank and found that the species identification of most Enterobacter strains needed to be corrected. Fourth, we found that the most common Enterobacter species seen in clinical samples is Enterobacter xiangfangensis rather than Enterobacter cloacae. Fifth, we identified 14 tentative novel Enterobacter and 18 tentative novel non-Enterobacter species. This study highlights that updated and curated taxonomic assignments are the premise of correct species identification. We recommend that future Enterobacter studies need to use the updated taxonomy to avoid misleading information.

Scandinavium goeteborgense gen. nov., sp. nov., a New Member of the Family Enterobacteriaceae Isolated From a Wound Infection, Carries a Novel Quinolone Resistance Gene Variant

The family Enterobacteriaceae is a taxonomically diverse and widely distributed family containing many human commensal and pathogenic species that are known to carry transferable antibiotic resistance determinants. Characterization of novel taxa within this family is of great importance in order to understand the associated health risk and provide better treatment options. The aim of the present study was to characterize a Gram-negative bacterial strain (CCUG 66741) belonging to the family Enterobacteriaceae, isolated from a wound infection of an adult patient, in Sweden. Initial phenotypic and genotypic analyses identified the strain as a member of the family Enterobacteriaceae but could not assign it to any previously described species. The complete 16S rRNA gene sequence showed highest similarity (98.8%) to four species. Whole genome sequencing followed by in silico DNA-DNA similarity analysis and average nucleotide identity (ANI) analysis confirmed that strain CCUG 66741 represents a novel taxon. Sequence comparisons of six house-keeping genes (16S rRNA, atpD, dnaJ, gyrB, infB, rpoB) with those of the type strains of the type species of related genera within the family Enterobacteriaceae indicated that the strain embodies a novel species within the family. Phylogenomic analyses (ANI-based and core genome-based phylogeny) showed that strain CCUG 66741 forms a distinct clade, representing a novel species of a distinct, new genus within the family Enterobacteriaceae, for which the name Scandinavium goeteborgense gen. nov., sp. nov. is proposed, with CCUG 66741^T as the type strain (= CECT 9823^T = NCTC 14286^T). S. goeteborgense CCUG 66741^T carries a novel variant of a chromosomally-encoded quinolone resistance gene (proposed qnrB96). When expressed in Escherichia coli, the qnrB96 gene conferred five-fold increase in minimum inhibitory concentration against ciprofloxacin. This study highlights the importance and the utility of whole genome sequencing for pathogen identification in clinical settings.

Enterobacter huaxiensis sp. nov. and Enterobacter chuandaensis sp. nov., recovered from human blood

Enterobacter strains 090008^T and 090028^T were recovered from the blood of two different patients at West China Hospital, Chengdu, PR China in 2017. Phylogenetic analysis based on the 16S rRNA gene and multi-locus sequence analysis of the rpoB, gyrB, infB and atpD housekeeping genes revealed that the two strains were distinct from any previously known species of the genus Enterobacter. Both average nucleotide identity (ANI) and in silico DNA-DNA hybridization (isDDH) values between strains 090008^T, 090028^T and type strains of all known Enterobacter species were lower than the cut-off (≥95-96 % for ANI and ≥70 % for isDDH) to define a bacterial species. The major cellular fatty acids of strains 090008^T and 090028^T are C16 : 0, C17 : 0cyclo and C18 : 1ω7c, which are similar to other Enterobacter species, and the genomic DNA G+C content was 55.73 and 55.68 mol%, respectively. Strain 090008^T can be differentiated from other Enterobacter species by its ability to ferment sucrose, melibiose and d-arabitol, but with a negative methyl α-d-mannopyranoside reaction. Strain 090028^T can ferment potassium gluconate, but is negative for l-fucose, mdecarboxylase, deaminase aelibiose and d-sorbitol, which distinguishes it from all other Enterobacter species. Genotypic and phenotypic characteristics indicate that strains 090008^T and 090028^T represent two novel species of the genus Enterobacter, for which the names Enterobacter huaxiensissp. nov. and Enterobacter chuandaensis sp. nov. are proposed, respectively. The type strain of Enterobacter huaxiensissp. nov. is 090008^T (=GDMCC1.1426^T=CCTCC AB 2018174^T=CNCTC 7648^T) and the type strain of Enterobacter chuandaensissp. nov. is 090028^T (=GDMCC1.1427^T=CCTCC AB 2018173^T=CNCTC 7649^T).

Superficieibacter electus gen. nov., sp. nov., an Extended-Spectrum β-Lactamase Possessing Member of the Enterobacteriaceae Family, Isolated From Intensive Care Unit Surfaces

Two Gram-negative bacilli strains, designated BP-1(T) and BP-2, were recovered from two different Intensive Care Unit surfaces during a longitudinal survey in Pakistan. Both strains were unidentified using the bioMerieux VITEK MS IVD v2.3.3 and Bruker BioTyper MALDI-TOF mass spectrometry platforms. To more precisely determine the taxonomic identity of BP-1(T) and BP-2, we employed a biochemical and phylogenomic approach. The 16S rRNA gene sequence of strain BP-1(T) had the highest identity to Citrobacter farmeri CDC 2991-81(T) (98.63%) Citrobacter amalonaticus CECT 863(T) (98.56%), Citrobacter sedlakii NBRC 105722(T) (97.74%) and Citrobacter rodentium NBRC 105723(T) (97.74%). The biochemical utilization scheme of BP-1(T) using the Analytic Profile Index for Enterobacteriaceae (API20E) indicated its enzymatic functions are unique within the Enterobacteriaceae but most closely resemble Kluyvera spp., Enterobacter cloacae and Citrobacter koseri/farmeri. Phylogenomic analysis of the shared genes between BP-1(T), BP-2 and type strains from Kluyvera, Citrobacter, Escherichia, Salmonella, Kosakonia, Siccibacter and Shigella indicate that BP-1(T) and BP-2 isolates form a distinct branch from these genera. Average Nucleotide Identity analysis indicates that BP-1(T) and BP-2 are the same species. The biochemical and phylogenomic analysis indicate strains BP-1(T) and BP-2 represent a novel species from a new genus within the Enterobacteriaceae family, for which the name Superficieibacter electus gen. nov., sp. nov., is proposed. The type strain is BP-1(T) (= ATCC BAA-2937, = NBRC 113412).

Enterobacterhormaechei subsp. hoffmannii subsp. nov., Enterobacter hormaechei subsp. xiangfangensis comb. nov., Enterobacter roggenkampii sp. nov., and Enterobacter muelleri is a later heterotypic synonym of Enterobacter asburiae based on computational analysis of sequenced Enterobacter genomes

Background: The predominant species in clinical Enterobacter isolates is E. hormaechei. Many articles, clinicians, and GenBank submissions misname these strains as E. cloacae. The lack of sequenced type strains or named species/subspecies for some clades in the E. cloacae complex complicate the issue. Methods: The genomes of the type strains for Enterobacter hormaechei subsp.  oharae, E.  hormaechei subsp.  steigerwaltii, and E. xiangfangensis, and two strains from Hoffmann clusters III and IV of the E. cloacae complex were sequenced. These genomes, the E.  hormaechei subsp.  hormaechei type strain, and other available Enterobacter type strains were analysed in conjunction with all extant Enterobacter genomes in NCBI's RefSeq using Average Nucleotide Identity (ANI). Results: There were five recognizable subspecies of E. hormaechei: E. hormaechei subsp. hoffmannii subsp. nov., E. hormaechei subsp. xiangfangensis comb. nov., and the three previously known subspecies. One of the strains sequenced from the E. cloacae complex was not a novel E. hormaechei subspecies but rather a member of a clade of a novel species: E. roggenkampii sp. nov.. E. muelleri was determined to be a later heterotypic synonym of E. asburiae which should take precedence. Conclusion: The phylogeny of the Enterobacter genus, particularly the cloacae complex, was re-evaluated based on the type strain genome sequences and all other available Enterobacter genomes in RefSeq.

Enterobacterhormaechei subsp. hoffmannii subsp. nov., Enterobacter hormaechei subsp. xiangfangensis comb. nov., Enterobacter roggenkampii sp. nov., and Enterobacter muelleri is a later heterotypic synonym of Enterobacter asburiae based on computational analysis of sequenced Enterobacter genomes

Background: The predominant species in clinical Enterobacter isolates is E. hormaechei. Many articles, clinicians, and GenBank submissions misname these strains as E. cloacae. The lack of sequenced type strains or named species/subspecies for some clades in the E. cloacae complex complicate the issue. Methods: The genomes of the type strains for Enterobacter hormaechei subsp.  oharae, E.  hormaechei subsp.  steigerwaltii, and E. xiangfangensis, and two strains from Hoffmann clusters III and IV of the E. cloacae complex were sequenced. These genomes, the E.  hormaechei subsp.  hormaechei type strain, and other available Enterobacter type strains were analysed in conjunction with all extant Enterobacter genomes in NCBI's RefSeq using Average Nucleotide Identity (ANI). Results: There were five recognizable subspecies of E. hormaechei: E. hormaechei subsp. hoffmannii subsp. nov., E. hormaechei subsp. xiangfangensis comb. nov., and the three previously known subspecies. One of the strains sequenced from the E. cloacae complex was not a novel E. hormaechei subspecies but rather a member of a clade of a novel species: E. roggenkampii sp. nov.. E. muelleri was determined to be a later heterotypic synonym of E. asburiae which should take precedence. Conclusion: The phylogeny of the Enterobacter genus, particularly the cloacae complex, was re-evaluated based on the type strain genome sequences and all other available Enterobacter genomes in RefSeq.

High-yield production of indole-3-acetic acid by Enterobacter sp. DMKU-RP206, a rice phyllosphere bacterium that possesses plant growth-promoting traits

Enterobacter sp. DMKU-RP206 was isolated from rice leaves in Thailand and identified by the 16S rRNA gene and multilocus sequence (gyrB, rpoB, atpD, and infB genes) analysis. The bacterium was assessed on plant growth-promoting traits including indole-3-acetic acid (IAA) production. Phosphate solubilization, ammonia production, and antagonism to fungal plant pathogens, as well as siderophore production, were shown by this bacterium. However, only IAA production was focused on. The production of IAA by Enterobacter sp. DMKU-RP206 was optimized by statistical methods. A Box-Behnken design was used for the investigation of interactions among the basic influencing factors and for the optimization of IAA production. The results showed that l-tryptophan had a significant importance in terms of IAA production. Enterobacter sp. DMKU-RP206 produced a higher amount of IAA than previously reported for the genus Enterobacter. 0.85% of lactose as a carbon source, 1.3% of yeast extract as a nitrogen source, 1.1% of l-tryptophan as a precursor, 0.4% of NaCl, an initial pH of 5.8, an incubation temperature at 30 °C, and a shaking speed of 200 rpm were found to be the optimum conditions for IAA production. In addition, IAA production was performed to scale up IAA production, and the highest amount, 5561.7 mg l^-1, was obtained. This study reported a 13.4-fold improvement in IAA production by Enterobacter sp. DMKU-RP206.