Kerstersia gyiorum gen. nov., sp. nov., a novel Alcaligenes faecalis-like organism isolated from human clinical samples, and reclassification of Alcaligenes denitrificans Rüger and Tan 1983 as Achromobacter denitrificans comb. nov

Analysis of twelve genomes of the bacterium Kerstersia gyiorum from brown-throated sloths (Bradypus variegatus), the first from a non-human host

Kerstersia gyiorum is a Gram-negative bacterium found in various animals, including humans, where it has been associated with various infections. Knowledge of the basic biology of K. gyiorum is essential to understand the evolutionary strategies of niche adaptation and how this organism contributes to infectious diseases; however, genomic data about K. gyiorum is very limited, especially from non-human hosts. In this work, we sequenced 12 K. gyiorum genomes isolated from healthy free-living brown-throated sloths (Bradypus variegatus) in the Parque Estadual das Fontes do Ipiranga (São Paulo, Brazil), and compared them with genomes from isolates of human origin, in order to gain insights into genomic diversity, phylogeny, and host specialization of this species. Phylogenetic analysis revealed that these K. gyiorum strains are structured according to host. Despite the fact that sloth isolates were sampled from a single geographic location, the intra-sloth K. gyiorum diversity was divided into three clusters, with differences of more than 1,000 single nucleotide polymorphisms between them, suggesting the circulation of various K. gyiorum lineages in sloths. Genes involved in mobilome and defense mechanisms against mobile genetic elements were the main source of gene content variation between isolates from different hosts. Sloth-specific K. gyiorum genome features include an IncN2 plasmid, a phage sequence, and a CRISPR-Cas system. The broad diversity of defense elements in K. gyiorum (14 systems) may prevent further mobile element flow and explain the low amount of mobile genetic elements in K. gyiorum genomes. Gene content variation may be important for the adaptation of K. gyiorum to different host niches. This study furthers our understanding of diversity, host adaptation, and evolution of K. gyiorum, by presenting and analyzing the first genomes of non-human isolates.

Kerstersia gyiorum isolated for the first time from two patients with neurodegenerative disease: report of two unusual cases and a review of the literature

With the development of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and 16S ribosomal RNA (rRNA) gene sequencing, increasing numbers of new microorganisms are being discovered. In this report, Kerstersia gyiorum was isolated for the first time from the sputum of two elderly patients with neurodegenerative disease, and integrated traditional Chinese and Western medicine was used for treatment. The bacteria's growth characteristics, biochemical reaction characteristics, sensitivity to antibiotics, and the patients' treatment are described, with a review of previous reports.

Polymyxin Resistance and Heteroresistance Are Common in Clinical Isolates of Achromobacter Species and Correlate with Modifications of the Lipid A Moiety of Lipopolysaccharide

The Achromobacter genus includes opportunistic pathogens that can cause chronic infections in immunocompromised patients, especially in people with cystic fibrosis (CF). Treatment of Achromobacter infections is complicated by antimicrobial resistance. In this study, a collection of Achromobacter clinical isolates, from CF and non-CF sources, was investigated for polymyxin B (PmB) resistance. Additionally, the effect of PmB challenge in a subset of isolates was examined and the presence of PmB-resistant subpopulations within the isolates was described. Further, chemical and mass spectrometry analyses of the lipid A of Achromobacter clinical isolates enabled the determination of the most common structures and showed that PmB challenge was associated with lipid A modifications that included the addition of glucosamine and palmitoylation and the concomitant loss of the free phosphate at the C-1 position. This study demonstrates that lipid A modifications associated with PmB resistance are prevalent in Achromobacter and that subresistant populations displaying the addition of positively charged residues and additional acyl chains to lipid A can be selected for and isolated from PmB-sensitive Achromobacter clinical isolates. IMPORTANCE Achromobacter species can cause chronic and potentially severe infections in immunocompromised patients, especially in those with cystic fibrosis. Bacteria cannot be eradicated due to Achromobacter's intrinsic multidrug resistance. We report that intrinsic resistance to polymyxin B (PmB), a last-resort antimicrobial peptide used to treat infections by multiresistant bacteria, is prevalent in Achromobacter clinical isolates; many isolates also display increased resistance upon PmB challenge. Analysis of the lipopolysaccharide lipid A moiety of several Achromobacter species reveals a penta-acylated lipid A, which in the PmB-resistant isolates was modified by the incorporation of glucosamine residues, an additional acyl chain, loss of phosphates, and hydroxylation of acyl chains, all of which can enhance PmB resistance in other bacteria. We conclude that PmB resistance, particularly in Achromobacter isolates from chronic respiratory infections, is a common phenomenon, and that Achromobacter lipid A displays modifications that may confer increased resistance to polymyxins and potentially other antimicrobial peptides.

Achromobacter denitrificans pneumonia in a kidney transplant recipient - dose-dependent decrease of phagocytic activity as a potential mechanism for everolimus pulmonary toxicity

Mammalian target of rapamycin (mTOR) inhibitors inclusive regimens are associated with increased risk of pulmonary toxicity, but the underlying mechanism has not been elucidated so far.

We present the case of a 68-year-old man, after deceased-donor kidney transplantation (KTx), maintained on de novo everolimus (EVR) based immunosuppression, who developed Achromobacter denitrificans pneumonia 3 months after KTx. There was clinical improvement with antibiotic treatment, but without a radiological resolution. An additional reduction of the EVR dose resulted only in partial resolution of radiological abnormalities. We performed a functional analysis of peripheral blood neutrophils and monocytes. The ability of phagocytosis and oxidative burst generation against A. denitrificans and Escherichia coli was significantly decreased on EVR treatment as compared to the control healthy person, and significantly improved after 3 weeks of EVR absence. Additionally, these processes were significantly affected by increasing doses of EVR in vitro in the control healthy donor in a dose-dependent manner. EVR discontinuation, with no additional antibiotic treatment, resulted in complete recovery and resolution of pulmonary infiltrates.

Our findings suggest that dose-dependent impairment of neutrophil/monocyte phagocytic activity and oxidative burst generation might be a potential mechanism for EVR pulmonary toxicity.

A case of Bordetella trematum and Kerstersia gyiorum infections in a patient with congestive dermatitis

Bordetella trematum and Kerstersia gyiorum are rare gram-negative bacilli that are not frequently detected in human infections. In this report, we describe a case of a 48-year-old man who presented to our hospital with an infected wound on his leg. Discharges from the cracks of the granulation were collected and evaluated in our microbiology laboratory. Gram staining of the specimen showed polymorphonuclear leukocytes and abundant gram-negative bacilli. Three types of colonies were isolated on blood agar and were identified as B. trematum and Alcaligenes faecalis using VITEK MS. Moreover, K. gyiorum and B. trematum were identified and confirmed via 16S ribosomal RNA (rRNA) gene sequencing. The patient successfully recovered following application of meropenem antibacterial therapy and surgical debridement. This is the first reported case of complex wound infection caused by both B. trematum and K. gyiorum. Identification of B. trematum has recently been made possible by routine bacterial identification using matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF MS). However, K. gyiorum isolation is still rare, and species identification requires 16S rRNA sequencing. Thus, this case highlighted the importance of using multiple methods, such as MALDI-TOF MS and 16S rRNA gene sequencing, for identification of rarely isolated species from clinical specimens.

Performance and Application of 16S rRNA Gene Cycle Sequencing for Routine Identification of Bacteria in the Clinical Microbiology Laboratory

This review provides a state-of-the-art description of the performance of Sanger cycle sequencing of the 16S rRNA gene for routine identification of bacteria in the clinical microbiology laboratory. A detailed description of the technology and current methodology is outlined with a major focus on proper data analyses and interpretation of sequences. The remainder of the article is focused on a comprehensive evaluation of the application of this method for identification of bacterial pathogens based on analyses of 16S multialignment sequences. In particular, the existing limitations of similarity within 16S for genus- and species-level differentiation of clinically relevant pathogens and the lack of sequence data currently available in public databases is highlighted. A multiyear experience is described of a large regional clinical microbiology service with direct 16S broad-range PCR followed by cycle sequencing for direct detection of pathogens in appropriate clinical samples. The ability of proteomics (matrix-assisted desorption ionization-time of flight) versus 16S sequencing for bacterial identification and genotyping is compared. Finally, the potential for whole-genome analysis by next-generation sequencing (NGS) to replace 16S sequencing for routine diagnostic use is presented for several applications, including the barriers that must be overcome to fully implement newer genomic methods in clinical microbiology. A future challenge for large clinical, reference, and research laboratories, as well as for industry, will be the translation of vast amounts of accrued NGS microbial data into convenient algorithm testing schemes for various applications (i.e., microbial identification, genotyping, and metagenomics and microbiome analyses) so that clinically relevant information can be reported to physicians in a format that is understood and actionable. These challenges will not be faced by clinical microbiologists alone but by every scientist involved in a domain where natural diversity of genes and gene sequences plays a critical role in disease, health, pathogenicity, epidemiology, and other aspects of life-forms. Overcoming these challenges will require global multidisciplinary efforts across fields that do not normally interact with the clinical arena to make vast amounts of sequencing data clinically interpretable and actionable at the bedside.

Development of a database for the rapid and accurate routine identification of Achromobacter species by matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS)

OBJECTIVES

Achromobacter spp. are emerging pathogens in respiratory samples from cystic fibrosis patients. The current reference methods (nrdA-sequencing or multilocus sequence typing) can identify 18 species which are often misidentified by conventional techniques as A. xylosoxidans. A few studies have suggested that matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF/MS) provides accurate identification of the genus but not of species. The aims of this study were (a) to generate a database for MALDI-TOF/MS Bruker including the 18 species, (b) to evaluate the suitability of the database for routine laboratory identification, and (c) to compare its performance with that of the currently available Bruker default database.

METHODS

A total of 205 isolates belonging to the 18 species identified by nrdA sequencing were used to build a local database. Main spectra profiles (MSPs) were created according to Bruker's recommendations for each isolate with the Biotyper software. Performance of the default Bruker database and ours for routine use were compared by testing 167 strains (including 38 isolates used from MSP creation) belonging to the 18 species identified by nrdA sequencing directly from colonies cultivated on various media.

RESULTS

Our new database accurately identified 99.4% (166/167) of the isolates from the 18 species (score ≥2.0) versus only 50.9% (85/167) with the Bruker database. In the Bruker database 17.3% of the isolates (29/167) were incorrectly identified as another species despite a score of ≥2.0.

CONCLUSIONS

The use of MALDI-TOF/MS in combination with a database developed with samples from 18 Achromobacter species provides rapid and accurate identification. This tool could be used to help future clinical studies.

Achromobacter veterisilvae sp. nov., from a mixed hydrogen-oxidizing bacteria enrichment reactor for microbial protein production

Strain LMG 30378^T was isolated from a hydrogen-oxidizing bacteria enrichment reactor inoculated with forest soil. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that this strain belonged to the genus Achromobacter. Multilocus sequence analysis combined with sequence analysis of a 765 bp nrd A gene fragment both showed Achromobacter agilis LMG 3411^T and Achromobacter denitrificans LMG 1231^T to be the closest-related neighbours to strain LMG 30378^T. Genome sequence analysis revealed a draft genome of 6.81 Mb with a G+C content of 67.2 mol%. In silico DNA-DNA hybridization with A. denitrificans LMG 1231^T and A. agilis LMG 3411^T showed 42.7 and 42.5% similarity, respectively, confirming that strain LMG 30378^T represented a novel Achromobacter species. Phenotypic and metabolic characterization revealed acid phosphatase activity and the absence of phosphoamidase activity as distinctive features. The draft genome composes all necessary metabolic components to fix carbon dioxide and to oxidize molecular hydrogen, suggesting that strain LMG 30378^T is a key organism in the enrichment reactor. Together, these data demonstrate that strain LMG 30378^T represents a novel species of the genus Achromobacter, for which the name Achromobacter veterisilvae sp. nov. is proposed. The type strain is LMG 30378^T (=CCUG 71558^T).

Corticimicrobacter populi gen. nov., sp. nov., a member of the family Alcaligenaceae, isolated from symptomatic bark of Populus × euramericana canker

One Gram-negative aerobic bacterial strain was isolated from the bark tissue of Populus × euramericana and investigated using a polyphasic approach including 16S rRNA gene sequencing and both phenotypic and chemotaxonomic assays. The 16S rRNA gene and housekeeping gene phylogenies suggest that the novel isolate is different from the other genera of the family Alcaligenaceae. The G+C content, major fatty acids, physiological and biochemical data supported the distinctiveness of the novel strain from reference species. The major fatty acids detected in the novel isolate were C_16 : 1ω7c and/or C_16 : 1ω6c, C_16 : 0, C_14 : 0 3OH and/or C_16 : 1isoI and C_18 : 1ω7c. The phospholipid profile of strain d3-2-2^T contained diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, aminolipid, aminophospholipid and an unidentified lipid. The quinone of the novel isolate was Q-8. Therefore, based on the data, the strain constitutes a novel species of a novel genus within the family Alcaligenaceae, for which the name Corticimicrobacter populi gen. nov., sp. nov. is proposed. The type strain is 3d-2-2^T (=CFCC 11891^T=KCTC 52807^T).

Algicoccus marinus gen. nov. sp. nov., a marine bacterium isolated from the surface of brown seaweed Laminaria japonica

A Gram-staining-negative, strictly aerobic, non-motile, ovoid- to rod-shaped bacterium, designated as HZ20T, was isolated from the surface of a brown seaweed (Laminaria japonica) sample collected from the East China Sea. Colonies are 1.0-2.0 mm in diameter, smooth, circular, convex and yellow after grown on MA at 28 °C for 72 h. The strain was found to grow at 4-50 °C (optimum, 37 °C), pH 5.0-9.5 (optimum, pH 7.0-7.5) and with 0-10% (w/v) NaCl (optimum, 1.0-1.5%). Chemotaxonomic analysis showed ubiquinone-8 as the only quinone, C17:0 cyclo, C16:0, summed feature 8 (C18:1ω7c and/or C18:1ω6c) and summed feature 2 (C12:0 aldehyde/unknown 10.9525/C16:1 iso I/C14:0 3OH) as the major fatty acids (> 5%), and diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, one unidentified amino phospholipid, two unidentified phospholipids, five unidentified glycolipid and two unidentified lipids as the polar lipids. The DNA G + C content was 55.5 mol %. 16S rRNA gene sequences of the isolate showed highest similarities to Bordetella flabilis AU10664T (97.1%), Parapusillimonas granuli Ch07T (97.1%), Paracandidimonas soli IMT-305T (97.1%), Kerstersia gyiorum LMG5906T (97.0%) and Bordetella sputigena LMG 28641T (97.0%). The phylogenetic trees using 16S rRNA gene and genome sequences both showed that the strain HZ20T formed a deep branch separated from other related genera, indicating that it represents a novel species of a novel genus. The calculated average nucleotide identity (ANI) and percent of conserved proteins (POCP) values using genome sequences of strain HZ20T and related strains also support this conclusion. Based on the phenotypic properties and phylogenetic distinctiveness, we propose strain HZ20T (= MCCC 1K03465T = KCTC 62330T) to represent a novel species of a novel genus with the name Algicoccus marinus gen. nov. sp. nov.

Genomic characterization of Kerstersia gyiorum SWMUKG01, an isolate from a patient with respiratory infection in China

BACKGROUND

The Gram-negative bacterium Kerstersia gyiorum, a potential etiological agent of clinical infections, was isolated from several human patients presenting clinical symptoms. Its significance as a possible pathogen has been previously overlooked as no disease has thus far been definitively associated with this bacterium. To better understand how the organism contributes to the infectious disease, we determined the complete genomic sequence of K. gyiorum SWMUKG01, the first clinical isolate from southwest China.

RESULTS

The genomic data obtained displayed a single circular chromosome of 3, 945, 801 base pairs in length, which contains 3, 441 protein-coding genes, 55 tRNA genes and 9 rRNA genes. Analysis on the full spectrum of protein coding genes for cellular structures, two-component regulatory systems and iron uptake pathways that may be important for the success of the bacterial survival, colonization and establishment in the host conferred new insights into the virulence characteristics of K. gyiorum. Phylogenomic comparisons with Alcaligenaceae species indicated that K. gyiorum SWMUKG01 had a close evolutionary relationships with Alcaligenes aquatilis and Alcaligenes faecalis.

CONCLUSIONS

The comprehensive analysis presented in this work determinates for the first time a complete genome sequence of K. gyiorum, which is expected to provide useful information for subsequent studies on pathogenesis of this species.

Endophthalmitis following Suture Removal - Clinical Outcomes and Microbiological Profile

AIMS

To review the clinical profile and report the microbiology and treatment outcomes of endophthalmitis following suture removal.

METHODS

In this multi-center, retrospective interventional case series, 11 eyes of 11 patients who developed endophthalmitis following suture removal from January 2006 to December 2017 were reviewed.

RESULTS

Nine of the 11 patients developed a culture-proven, acute onset endophthalmitis [5.3 ± 3.1 days (range 2-10 days)]. Mean age was 15.8 ± 21.2 years (median 7; range, 1-66 years). Presenting visual acuity was extremely low ranging from light perception (PL) to counting fingers close to face (CFCF) at the time of diagnosis of endophthalmitis. Out of the 11 patients, 8 belonged to the pediatric age group; four out of those eight had loose sutures secondary to cataract surgery, two patients had loose sutures secondary to penetrating keratoplasty and 1 case each had loose sutures secondary to corneal tear repair and secondary IOL implantation, respectively. Streptococcus pneumoniae was the most common organism and was identified in seven cases and was susceptible to vancomycin in all these cases. Other bacterial isolates were Haemophilus influenzae and Achromobacter denitrificans. Three out of the 11 eyes had visual outcome of 20/200 or better. Six eyes were phthisical and one eye was eviscerated. Mean follow-up was 26.3 ± 31.2 weeks (range 2-92 weeks). Visual outcomes ranged from 20/40 to no light perception at the last follow-up.

CONCLUSIONS

Endophthalmitis following suture removal though rare, is observed most commonly in the pediatric population and has an acute and a fulminant course. Streptococcus pneumoniae was the most commonly isolated microorganism. Visual acuity outcomes were poor despite prompt recognition of endophthalmitis and appropriate antibiotic therapy.

Molecular and eco-physiological characterization of arsenic (As)-transforming Achromobacter sp. KAs 3-5T from As-contaminated groundwater of West Bengal, India

Molecular and eco-physiological characterization of arsenic (As)-transforming and hydrocarbon-utilizing Achromobacter type strain KAs 3-5^T has been investigated in order to gain an insight into As-geomicrobiology in the contaminated groundwater. The bacterium is isolated from As-rich groundwater of West Bengal, India. Comparative 16S rRNA gene sequence phylogenetic analysis confirmed that the strain KAs 3-5^T is closely related to Achromobacter mucicolens LMG 26685^T (99.17%) and Achromobacter animicus LMG 26690^T (99.17%), thus affiliated to the genus Achromobacter. Strain KAs 3-5^T is nonflagellated, mesophilic, facultative anaerobe, having a broad metabolic repertoire of using various sugars, sugar-/fatty acids, hydrocarbons as principal carbon substrates, and O₂, NO₃^-, NO₂^-, and Fe³⁺ as terminal electron acceptors. Growth with hydrocarbons led to cellular aggregation and adherence of the cells to the hydrocarbon particles confirmed through electron microscopic observations. The strain KAs 3-5^T showed high As resistance (MIC of 5 mM for As³⁺, 25 mM for As⁵⁺) and reductive transformation of As⁵⁺ under aerobic conditions while utilizing both sugars and hydrocarbons. Molecular taxonomy specified a high genomic GC content (65.5 mol %), ubiquinone 8 (UQ-8) as respiratory quinone, spermidine as predominant polyamine in the bacterium. The differential presence of C_12:0, C_14:0 2-OH, C_18:1 ω7c, and C _14:0 iso 3-OH/ C_16:1 iso fatty acids, phosphatidylglycerol (PG), phosphatidylcholine (PC), two unknown phospholipid (PL1, PL2) as polar lipids, low DNA-DNA relatedness (33.0-41.0%) with the Achromobacter members, and unique metabolic capacities clearly indicated the distinct genomic and physiological properties of strain KAs 3-5^T among known species of the genus Achromobacter. These findings lead to improve our understanding on metabolic flexibility of bacteria residing in As-contaminated groundwater and As-bacteria interactions within oligotrophic aquifer system.

Proposal to emend Rules 50a and 50b of the International Code of Nomenclature of Prokaryotes

Rules 50a and 50b of the International Code of Nomenclature of Prokaryotes respectively regulate the elevation of a subspecies to the rank of a species and the lowering of a species to the rank of subspecies. The Code does not indicate that the resulting new names must be considered new combinations, as the cases described in Rules 50a and 50b are not covered by Rule 34a. Based on the rules of the Code, new combination events are applicable only at the identical rank, and therefore new combination events and new species/subspecies events are mutually exclusive. In spite of this there have been at least 44 cases in which the new names were described as comb. nov. during elevation in rank from subspecies to species and at least 30 such cases during lowering in rank from species to subspecies. To prevent confusion in the future we propose adding notes to Rules 50a and 50b to clarify the issue.

Chronic lower extremity wound infection due to Kerstersia gyiorum in a patient with Buerger's disease: a case report

Background

Kerstersia gyiorum is an extremely rare pathogen of human infection. It can cause chronic infection in patients with underlying conditions. It can easily be misdiagnosed if proper diagnostic methods are not used.

Case presentation

A 47-year-old male patient with a history of Buerger’s Disease for 28 years presented to our hospital with an infected chronic wound on foot. The wound was debrided, and the specimen was sent to Microbiology laboratory. Gram staining of the specimen showed abundant polymorphonuclear leukocytes and gram-negative bacilli. Four types of colonies were isolated on blood agar. These were identified as Kerstersia gyiorum, Proteus vulgaris, Enterobacter cloacae, Morganella morganii by Maldi Biotyper (Bruker Daltonics, Germany). The identification of K. gyiorum was confirmed by 16S ribosomal RNA gene sequencing. The patient was successfully recovered with antimicrobial therapy, surgical debridement, and skin grafting.

Conclusions

This is the first case of wound infection due to K. gyiorum in a patient with Buerger’s Disease. We made a brief review of K. gyiorum cases up to date. Also, this case is presented to draw attention to the use of new and advanced methods like MALDI-TOF MS and 16S rRNA gene sequencing for identification of rarely isolated species from clinical specimens of patients with chronic infections and with chronic underlying conditions.

Complete Genome Sequence of Achromobacter denitrificans PR1

Achromobacter denitrificans strain PR1 was isolated from an enrichment culture able to use sulfamethoxazole as an energy source. Here, we describe the complete genome of this strain sequenced by Illumina MiSeq and Oxford Nanopore MinION.

Role of AxyZ Transcriptional Regulator in Overproduction of AxyXY-OprZ Multidrug Efflux System in Achromobacter Species Mutants Selected by Tobramycin

AxyXY-OprZ is an RND-type efflux system that confers innate aminoglycoside resistance to Achromobacter spp. We investigated here a putative TetR family transcriptional regulator encoded by the axyZ gene located upstream of axyXY-oprZ An in-frame axyZ gene deletion assay led to increased MICs of antibiotic substrates of the efflux system, including aminoglycosides, cefepime, fluoroquinolones, tetracyclines, and erythromycin, indicating that the product of axyZ negatively regulates expression of axyXY-oprZ Moreover, we identified an amino acid substitution at position 29 of AxyZ (V29G) in a clinical Achromobacter strain that occurred during the course of chronic respiratory tract colonization in a cystic fibrosis (CF) patient. This substitution, also detected in three other strains exposed in vitro to tobramycin, led to an increase in the axyY transcription level (5- to 17-fold) together with an increase in antibiotic resistance level. This overproduction of AxyXY-OprZ is the first description of antibiotic resistance acquisition due to modification of a chromosomally encoded mechanism in Achromobacter and might have an impact on the management of infected CF patients. Indeed, tobramycin is widely used for aerosol therapy within this population, and we have demonstrated that it easily selects mutants with increased MICs of not only aminoglycosides but also fluoroquinolones, cefepime, and tetracyclines.

Achromobacter panacis sp. nov., isolated from rhizosphere of Panax ginseng

A novel strain DCY105^T was isolated from soil collected from the rhizosphere of ginseng (Panax ginseng), in Gochang, Republic of Korea. Strain DCY105^T is Gram-reaction-negative, white, non-motile, non-flagellate, rod-shaped and aerobic. The bacteria grow optimally at 30°C, pH 6.5-7.0 and in the absence of NaCl. Phylogenetically, strain DCY105^T is most closely related to Achromobacter marplatensis LMG 26219^T (96.81%). The DNA G+C content of strain DCY105^T was 64.4 mol%. Ubiquinone 8 was the major respiratory quinone, and phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol were amongst the major polar lipids. C_16:00, C_8:03OH and iso-C_17:03OH were identified as the major fatty acids present in DCY105^T. The results of physiological and biochemical tests allowed strain DCY105^T to be differentiated phenotypically from other recognized species belonging to the genus Achromobacter. Therefore, it is suggested that the newly isolated organism represents a novel species, for which the name Achromobacter panacis sp. nov. is proposed with the type strain designated as DCY105^T (=CCTCCAB 2015193^T =KCTC 42751^T).

Characterization of a novel biosurfactant produced by marine hydrocarbon-degrading bacterium Achromobacter sp. HZ01

AIMS

To purify and characterize the biosurfactants produced by Achromobacter sp. HZ01.

METHODS AND RESULTS

After fermentation, one biosurfactant was successfully purified from the fermentation broth of strain HZ01 by centrifugation, extraction using ethyl acetate, silica gel chromatography and reversed phase-high performance liquid chromatography. The critical micelle concentration (CMC) of the biosurfactant and the effects of temperatures, pH and salinities on its stability were determined. Fourier transform infrared spectroscopy, analysis of fatty acids and amino acids and mass spectrometry were used to characterize the biosurfactant. The maximum production yield of the crude biosurfactant reached to 6·84 g l(-1) after incubation for 96 h. Except the favourable adaptability to a wide range of temperatures, pH and salinities, the biosurfactant with a CMC value of 48 mg l(-1) could efficiently emulsify diverse hydrophobic compounds. The chemical formula of this biosurfactant was confirmed to be CH3 -(CH2 )17 -CHO-CH2 -CO-Gly-Gly-Leu-Met-Leu-Leu, in which the oxygen atom of group CHO linked to the last amino acid (Leu), a structure had never been reported before.

CONCLUSIONS

The purified biosurfactant is a novel cyclic lipopeptide.

SIGNIFICANCE AND IMPACT OF THE STUDY

One novel lipopeptide was purified and characterized. The novel biosurfactant exhibited good potential applications, such as bioremediation.

Distribution of innate efflux-mediated aminoglycoside resistance among different Achromobacter species

Achromobacter spp. are emerging respiratory pathogens in cystic fibrosis patients. Since 2013 the genus Achromobacter includes 15 species for which innate antibiotic resistance is unknown. Previously the AxyXY-OprZ efflux system has been described to confer aminoglycoside (AG) resistance in A. xylosoxidans. Nevertheless, some Achromobacter spp. strains are susceptible to AG. This study including 49 Achromobacter isolates reveals that AG resistance is correlated with different Achromobacter spp. It is noteworthy that the axyXY-oprZ operon is detected only in AG-resistant species, including the most frequently encountered in cystic fibrosis patients: A. xylosoxidans, A. ruhlandii, A. dolens and A. insuavis.

A first case of isolation of Kerstersia gyiorum from urinary tract

An 82-year-old man with percutaneous nephrostomy presented to our Hospital with dysuria for one day. The patient's percutaneous nephrostomy tube was exchanged, with about 20 mL of creamy purulent urine being collected. Direct smear of the urine specimen showed polymorphonuclear leukocytes and small Gram-negative bacilli, some of which had undergone phagocytosis. This organism was identified as Kerstersia gyiorum using 16S ribosomal RNA gene analysis. He was successfully recovered with exchange of his percutaneous nephrostomy tube and fluoroquinolone internal use treatment. This is the first case report of urinary tract infection due to K. gyiorum.

Draft Genome Sequence of Kerstersia gyiorum CG1, Isolated from a Leg Ulcer

We report the first draft genome sequence of Kerstersia gyiorum from a leg ulcer of a patient with diabetes and osteomyelitis. The 3.94-Mb genome assembly included 3,428 annotated coding sequences with an N₅₀ of 223,310 bp and a plasmid encoding a type IV secretion system gene and two antitoxin genes.

Bacteremia Caused by Kerstersia gyiorum

Kerstersia spp. are an unusual cause of human infections. We report the first known case of bacteremia and sepsis due to Kerstersia gyiorum, in a patient with chronic lower-extremity ulcers, and we review the literature on this uncommon pathogen.

Evaluation of matrix-assisted laser desorption ionization-time-of-flight mass spectrometry for species identification of nonfermenting Gram-negative bacilli

Matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) to identify 396 Nonfermenting Gram-Negative Bacilli clinical isolates was evaluated in comparison with conventional phenotypic tests and/or molecular methods. MALDI-TOF MS identified to species level 256 isolates and to genus or complex level 112 isolates. It identified 29 genera including uncommon species.

Genotypic and phenotypic applications for the differentiation and species-level identification of achromobacter for clinical diagnoses

The Achromobacter is a genus in the family Alcaligenaceae, comprising fifteen species isolated from different sources, including clinical samples. The ability to detect and correctly identify Achromobacter species, particularly A. xylosoxidans, and differentiate them from other phenotypically similar and genotypically related Gram-negative, aerobic, non-fermenting species is important for patients with cystic fibrosis (CF), as well as for nosocomial and other opportunistic infections. Traditional phenotypic profile-based analyses have been demonstrated to be inadequate for reliable identifications of isolates of Achromobacter species and genotypic-based assays, relying upon comparative 16S rRNA gene sequence analyses are not able to insure definitive identifications of Achromobacter species, due to the inherently conserved nature of the gene. The uses of alternative methodologies to enable high-resolution differentiation between the species in the genus are needed. A comparative multi-locus sequence analysis (MLSA) of four selected ‘house-keeping’ genes (atpD, gyrB, recA, and rpoB) assessed the individual gene sequences for their potential in developing a reliable, rapid and cost-effective diagnostic protocol for Achromobacter species identifications. The analysis of the type strains of the species of the genus and 46 strains of Achromobacter species showed congruence between the cluster analyses derived from the individual genes. The MLSA gene sequences exhibited different levels of resolution in delineating the validly published Achromobacter species and elucidated strains that represent new genotypes and probable new species of the genus. Our results also suggested that the recently described A. spritinus is a later heterotypic synonym of A. marplatensis. Strains were analyzed, using whole-cell Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight mass spectrometry (MALDI-TOF MS), as an alternative phenotypic profile-based method with the potential to support the identifications determined by the genotypic DNA sequence-based MLSA. The MALDI-TOF MS data showed good accordance in strain groupings and identifications by the MLSA data.

Achromobacter buckle infection diagnosed by a 16S rDNA clone library analysis: a case report

Background

In clinical settings, bacterial infections are usually diagnosed by isolation of colonies after laboratory cultivation followed by species identification with biochemical tests. However, biochemical tests result in misidentification due to similar phenotypes of closely related species. In such cases, 16S rDNA sequence analysis is useful. Herein, we report the first case of an Achromobacter-associated buckle infection that was diagnosed by 16S rDNA sequence analysis. This report highlights the significance of Achromobacter spp. in device-related ophthalmic infections.

Case presentation

A 56-year-old woman, who had received buckling surgery using a silicone solid tire for retinal detachment eighteen years prior to this study, presented purulent eye discharge and conjunctival hyperemia in her right eye. Buckle infection was suspected and the buckle material was removed. Isolates from cultures of preoperative discharge and from deposits on the operatively removed buckle material were initially identified as Alcaligenes and Corynebacterium species. However, sequence analysis of a 16S rDNA clone library using the DNA extracted from the deposits on the buckle material demonstrated that all of the 16S rDNA sequences most closely matched those of Achromobacter spp. We concluded that the initial misdiagnosis of this case as an Alcaligenes buckle infection was due to the unreliability of the biochemical test in discriminating Achromobacter and Alcaligenes species due to their close taxonomic positions and similar phenotypes. Corynebacterium species were found to be contaminants from the ocular surface.

Conclusions

Achromobacter spp. should be recognized as causative agents for device-related ophthalmic infections. Molecular species identification by 16S rDNA sequence analysis should be combined with conventional cultivation techniques to investigate the significance of Achromobacter spp. in ophthalmic infections.

Kerstersia gyiorum Isolated from a Bronchoalveolar Lavage in a Patient with a Chronic Tracheostomy

The use of the matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MS) generates rapid microbial identification. We are presenting a case of a 63-year-old woman with a medical history of chronic tracheostomy admitted for hypotension and fevers to illustrate the clinical implication of MALDI-TOF MS on bacterial identification. Kerstersia gyiorum was identified from the bronchoalveolar lavage isolate. Kerstersia gyiorum has been isolated from human sputum samples, and may be a previously unrecognized colonizer of the upper respiratory tract. Thus, patients with long-term tracheotomies or who are chronically aspirating may be at risk of lower respiratory infection with this organism. Increased use of MALDI-TOF MS in the clinical setting may increase reporting of this atypical isolate.

Achromobacter sediminum sp. nov., isolated from deep subseafloor sediment of South Pacific Gyre

A Gram-stain-negative, facultatively anaerobic, rod-shaped, motile bacterium with a subpolar or lateral flagellum, designated strain XH089T, was isolated from deep-sea sediment sample collected from the South Pacific Gyre (41°51′ S 153°06′ W) during the Integrated Ocean Drilling Program (IODP) Expedition 329. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain XH089T belonged to the genus Achromobacter and showed the highest 16S rRNA gene sequence similarities with Achromobacter ruhlandii ATCC 15749T (96.95 %), Achromobacter denitrificans DSM 30026T (96.70 %) and Achromobacter marplatensis B2T (96.66 %). The DNA G+C content of strain XH089T was 66.5 mol%. The major fatty acids were C16 : 0 and C17 : 0 cyclo. The major polar lipids were phosphatidylethanolamine, phosphatidylmonomethylethanolamine, diphosphatidylglycerol, three unknown phospholipids and four unknown polar lipids. On the basis of data from the polyphasic analysis, strain XH089T is considered to represent a novel species of the genus Achromobacter , for which the name Achromobacter sediminum sp. nov. is proposed. The type strain is XH089T ( = DSM 27279T = JCM 19223T).

Two cases of Kerstersia gyiorum isolated from sites of chronic infection

Kerstersia gyiorum is infrequently associated with human infection. We report the isolation of Kerstersia gyiorum from two patients: the first, a patient with chronic ear infections, and the second, a patient with a chronic leg wound. Both isolates were resistant to ciprofloxacin, which has not been previously reported.

Specific and sensitive detection of Alcaligenes species from an agricultural environment

A quantitative real-time PCR assay to specifically detect and quantify the genus Alcaligenes in samples from the agricultural environment, such as vegetables and farming soils, was developed. The minimum detection sensitivity was 106 fg of pure culture DNA, corresponding to DNA extracted from two cells of Alcaligenes faecalis. To evaluate the detection limit of A. faecalis, serially diluted genomic DNA from this organism was mixed with DNA extracted from soil and vegetables and then a standard curve was constructed. It was found that Alcaligenes species are present in the plant phytosphere at levels 10(2)-10(4) times lower than those in soil. The approach presented here will be useful for tracking or quantifying species of the genus Alcaligenes in the agricultural environment.

Metabolic characteristics of the species Variovorax paradoxus

This review outlines information about the Gram-negative, aerobic bacterium Variovorax paradoxus. The genomes of these species have G+C contents of 66.5-69.4 mol%, and the cells form yellow colonies. Some strains of V. paradoxus are facultative lithoautotrophic, others are chemoorganotrophic. Many of them are associated with important catabolic processes including the degradation of toxic and/or complex chemical compounds. The degradation pathways or other skills related to the following compounds, respectively, are described in this review: sulfolane, 3-sulfolene, 2-mercaptosuccinic acid, 3,3'-thiodipropionic acid, aromatic sulfonates, alkanesulfonates, amino acids and other sulfur sources, polychlorinated biphenyls, dimethyl terephthalate, linuron, 2,4-dinitrotoluene, homovanillate, veratraldehyde, 2,4-dichlorophenoxyacetic acid, anthracene, poly(3-hydroxybutyrate), chitin, cellulose, humic acids, metal-EDTA complexes, yttrium, rare earth elements, As(III), trichloroethylene, capsaicin, 3-nitrotyrosine, acyl-homoserine lactones, 1-aminocyclopropane-1-carboxylate, methyl tert-butyl ether, geosmin, and 2-methylisoborneol. Strains of V. paradoxus are also engaged in mutually beneficial interactions with other plant and bacterial species in various ecosystems. This species comprises probably promising strains for bioremediation and other biotechnical applications. Lately, the complete genomes of strains S110 and EPS have been sequenced for further investigations.

Identification and distribution of Achromobacter species in cystic fibrosis

BACKGROUND

We recently described a multilocus sequence typing scheme for Achromobacter that identified several novel species in this genus.

METHODS

We assessed the ability of nrdA sequence analysis to differentiate Achromobacter species, including the seven previously named species and 14 recently described genogroups. Confirmation of distinctness between groups was confirmed using the k parameter. Using this single locus sequence to differentiate species, we analyzed Achromobacter isolates obtained from 341 CF patients in the U.S.

RESULTS

We found that Achromobacter xylosoxidans accounts for 42% of Achromobacter infections, while Achromobacter ruhlandii accounted for 23.5% of infections. Isolates from 17% of patients were members of the novel genogroup 14. The remaining 17.5% of strains belonged to 11 other species/genogroups.

CONCLUSION

The use of nrdA sequence analysis allows differentiation of the several Achromobacter species that can infect persons with CF. Achromobacter species other than A. xylosoxidans account for the majority of Achromobacter infection in CF patients in the U.S.

Achromobacter piechaudii bloodstream infection in an immunocompetent host

Background:

Achromobacter piechaudii is a rare cause of clinical disease in humans. Previously, clinical disease has only been documented in immunocompromised patients. We present a case of Achromobacter piechaudii bacteremia in a patient with previous malignancy but no known immunosuppression.

Case Report:

A 67-year-old man with distant history of colon and prostate cancer presented with low grade fevers and malaise. Blood cultures initially identified Alcaligenes xylosoxidans ss. denitrificans. Based on susceptibility testing, antibiotics were narrowed to levofloxacin. After further evaluation, the isolate was identified as Achromobacter piechaudii, an organism rarely previously seen only in immunocompromised patients. The source was felt to be dental infection after transesophageal echocardiogram and CT abdomen/pelvis were unrevealing. He improved with oral levofloxacin and dental extraction

Conclusions:

This is the first case report of primary Achromobacter piechaudii bloodstream infection in an immunocompetent host and adds to the growing list of clinical syndromes caused by this organism.

Isolation of Kerstersia gyiorum from a patient with cholesteatomatous chronic otitis media

We describe the first case of a Kerstersia gyiorum strain isolated from a patient with cholesteatomatous chronic otitis media. We emphasize the isolation of members of the family Alcaligenaceae in serious infections and unusual sites and the importance of polyphasic identification addressing the definitive identification.

Kerstersia similis sp. nov., isolated from human clinical samples

Analysis of gyrB gene sequences, (GTG)5-primed PCR fingerprinting and biochemical characteristics determined in the Biolog GEN III microtest system were used to differentiate an unnamed Kerstersia species from Kerstersia gyiorum , the type and only named species in this genus. The inability to oxidize d-galacturonic and d-glucuronic acids and the ability to oxidize d-serine, along with gyrB gene sequence analysis and (GTG)5-PCR fingerprints, readily differentiated the unnamed taxon from the type species. Therefore, we propose to formally classify this unnamed taxon as Kerstersia similis sp. nov. with strain LMG 5890T ( = CCUG 46999T), isolated from a leg wound in the USA in 1983, as the type strain.