Achromobacter xylosoxidans n. sp. from human ear discharge

Acute cholangitis with Achromobacter xylosoxidans bacteremia after endoscopic retrograde cholangiopancreatography in hilar cholangiocarcinoma: A case report

BACKGROUND

Achromobacter xylosoxidans is a Gram-negative opportunistic aerobe, usually causing nosocomial infections in immunocompromised patients with manifestations including bacteremia, pneumonia, and catheter-related infections. However, A. xylosoxidans have not yet been reported to cause biliary system infections.

CASE SUMMARY

A 72-year-old woman presented to the outpatient department of our hospital with a chief complaint of jaundice. Computed tomography of her abdomen revealed the presence of a mass of approximately 2.4 cm in the hilar portion of the common hepatic duct, consistent with hilar cholangiocarcinoma. We performed endoscopic retrograde cholangiopancreatography (ERCP) to decompress the obstructed left and right intrahepatic ducts (IHDs) and placed 10 cm and 11 cm biliary stents in the left and right IHDs, respectively. However, the day after the procedure, the patient developed post-ERCP cholangitis as the length of the right IHD stent was insufficient for proper bile drainage. The blood culture of the patient tested positive for A. xylosoxidans. Management measures included the replacement of the right IHD stent (11 cm) with a longer one (12 cm) and administering culture-directed antibiotic therapy, solving the cholangitis-related complications. After the cholangitis had resolved, the patient underwent surgery for hilar cholangiocarcinoma and survived for 912 d without recurrence.

CONCLUSION

A. xylosoxidans-induced biliary system infections are extremely rare. Clinical awareness of physicians and endoscopists is required as this rare pathogen might cause infection after endoscopic procedures.

Cefiderocol susceptibility of Achromobacter spp.: study of an accurately identified collection of 230 strains

BACKGROUND

Achromobacter spp. are opportunistic pathogens, mostly infecting immunocompromised patients and patients with cystic fibrosis (CF) and considered as difficult-to-treat pathogens due to both intrinsic resistance and the possibility of acquired antimicrobial resistance. Species identification remains challenging leading to imprecise descriptions of resistance in each taxon. Cefiderocol is a broad-spectrum siderophore cephalosporin increasingly used in the management of Achromobacter infections for which susceptibility data remain scarce. We aimed to describe the susceptibility to cefiderocol of a collection of Achromobacter strains encompassing different species and isolation sources from CF or non-CF (NCF) patients.

METHODS

We studied 230 Achromobacter strains (67 from CF, 163 from NCF patients) identified by nrdA gene-based analysis, with available susceptibility data for piperacillin-tazobactam, meropenem and trimethoprim-sulfamethoxazole. Minimal inhibitory concentrations (MICs) of cefiderocol were determined using the broth microdilution reference method according to EUCAST guidelines.

RESULTS

Strains belonged to 15 species. A. xylosoxidans represented the main species (71.3%). MICs ranged from ≤ 0.015 to 16 mg/L with MIC50/90 of ≤ 0.015/0.5 mg/L overall and 0.125/2 mg/L against 27 (11.7%) meropenem-non-susceptible strains. Cefiderocol MICs were not related to CF/NCF origin or species although A. xylosoxidans MICs were statistically lower than those of other species considered as a whole. Considering the EUCAST non-species related breakpoint (2 mg/L), 228 strains (99.1%) were susceptible to cefiderocol. The two cefiderocol-resistant strains (A. xylosoxidans from CF patients) represented 3.7% of meropenem-non-susceptible strains and 12.5% of MDR strains.

CONCLUSIONS

Cefiderocol exhibited excellent in vitro activity against a large collection of accurately identified Achromobacter strains, irrespective of species and origin.

A case of community-acquired spondylodiscitis caused by Achromobacter xylosoxidans

Achromobacter xylosoxidans is a Gram-negative, aerobic, non-fermenting bacillus mainly responsible for nosocomial infections. We report the first case of community-acquired spondylodiscitis caused by Achromobacter xylosoxidans in a 61-year-old woman, immunocompromised with necrotizing dermohypodermitis of the right lower limb successfully treated with ertapenem and ciprofloxacin.

Chronic otorrhea and osteomyelitis of the external auditory canal by Achromobacter xylosoxidans: an uncommon diagnosis

PURPOSE

Achromobacter xylosoxidans is an emerging pathogen mainly associated with resistant nosocomial infections. This bacteria had been isolated in the ear together with other pathogens in cultures from patients with chronic otitis media, but it had never been reported as a cause of osteomyelitis of the external auditory canal.

CASE PRESENTATION

We present a unique case of a healthy 81-year-old woman who presented with left chronic otorrhea refractory to topical and oral antibiotic treatment. Otomicroscopy revealed an erythematous and exudative external auditory canal (EAC) with scant otorrhea. The tympanic membrane was intact, but an area of bone remodeling with a small cavity anterior and inferior to the bony tympanic frame was observed. Otic culture isolated multi-drug-resistant A. xylosoxidans, only sensitive to meropenem and cotrimoxazole. Temporal bone computed tomography showed an excavation of the floor of the EAC compatible with osteomyelitis. Targeted antibiotherapy for 12 weeks was conducted, with subsequent resolution of symptoms and no progression of the bone erosion.

CONCLUSIONS

Atypical pathogens such as A. xylosoxidans can be the cause of chronic otitis externa. Early diagnosis and specific antibiotherapy can prevent the development of further complications, such as osteomyelitis. In these cases, otic cultures play an essential role to identify the causal germ. This is the first case of EAC osteomyelitis due to A. xylosoxidans reported to date.

A Rare Case of Acute Post-cataract Surgery Endophthalmitis Associated With Achromobacter xylosoxidans

Achromobacter xylosoxidans is rarely reported as a causative agent of post-cataract surgery endophthalmitis. Here, we present a case where timely surgical intervention preserved the patient's vision. A 68-year-old man presented with clinical signs of endophthalmitis in his right eye three days after uneventful cataract surgery. He was initially treated with intravitreal, topical, and systemic antibiotics. After starting intravitreal, topical, and systemic antibiotics, his condition deteriorated on the second day of treatment. A prompt pars plana vitrectomy (PPV) with the removal of the posterior chamber intraocular lens (PCIOL) was performed. Culture from the intravitreal tapping yielded A. xylosoxidans, which was sensitive to ceftazidime and piperacillin. His condition was better post-PPV, and the infection was under control until day 10 post-first PPV. There was a recrudescence of infection with a recurrence of hypopyon and loculations detected on B-scan ultrasound. A second PPV with the complete removal of the lens capsule was performed. One month later, his right eye was quiet without inflammation, with a best-corrected vision of 20/30. A. xylosoxidans is a rare but serious pathogen of endophthalmitis that often necessitates multiple surgical interventions. Although it may not initially respond to intravitreal injections and vitrectomy, appropriate treatment, such as the removal of the intraocular lens and capsulectomy, can still result in favorable visual outcomes.

The Achromobacter type 3 secretion system drives pyroptosis and immunopathology via independent activation of NLRC4 and NLRP3 inflammasomes

How the opportunistic Gram-negative pathogens of the genus Achromobacter interact with the innate immune system is poorly understood. Using three Achromobacter clinical isolates from two species, we show that the type 3 secretion system (T3SS) is required to induce cell death in human macrophages by inflammasome-dependent pyroptosis. Macrophages deficient in the inflammasome sensors NLRC4 or NLRP3 undergo pyroptosis upon bacterial internalization, but those deficient in both NLRC4 and NLRP3 do not, suggesting either sensor mediates pyroptosis in a T3SS-dependent manner. Detailed analysis of the intracellular trafficking of one isolate indicates that the intracellular bacteria reside in a late phagolysosome. Using an intranasal mouse infection model, we observe that Achromobacter damages lung structure and causes severe illness, contingent on a functional T3SS. Together, we demonstrate that Achromobacter species can survive phagocytosis by promoting macrophage cell death and inflammation by redundant mechanisms of pyroptosis induction in a T3SS-dependent manner.

Atypical microbial keratitis

Atypical microbial keratitis refers to corneal infections caused by micro-organisms not commonly encountered in clinical practice. Unlike infections caused by common bacteria, cases of atypical microbial keratitis are often associated with worse clinical outcomes and visual prognosis. This is due to the challenges in the identification of causative organisms with standard diagnostic techniques, resulting in delays in the initiation of appropriate therapies. Furthermore, due to the comparatively lower incidence of atypical microbial keratitis, there is limited literature on effective management strategies for some of these difficult to manage corneal infections. This review highlights the current management and available evidence of atypical microbial keratitis, focusing on atypical mycobacteria keratitis, nocardia keratitis, achromobacter keratitis, and pythium keratitis. It will also describe the management of two uncommonly encountered conditions, infectious crystalline keratopathy and post-refractive infectious keratitis. This review can be used as a guide for clinicians managing patients with such challenging corneal infections.

Successful Treatment of Aortic Endocarditis by Achromobacter xylosoxidans with Cefiderocol Combination Therapy in a Non-Hodgkin Lymphoma Patient: Case Report and Literature Review

Achromobacter xylosoxidans is a Gram-negative aerobic opportunistic bacterium, belonging to the order of Burkholderiales, that can cause infections of virtually all body districts in patients with underlying diseases. However, A. xylosoxidans has rarely been associated with infective endocarditis. The treatment of A. xylosoxidans infections is complicated by both intrinsic and acquired resistance. Here we report on a case of aortic endocarditis by A. xylosoxidans in a Non-Hodgkin lymphoma patient treated with a combination of cefiderocol and other antibiotics, and summarize the available literature.

A Case of Pyometra Caused by Achromobacter xylosoxidans and γ-Streptococcus in an Elderly Frail Woman

Pyometra is an easily overlooked disease with nonspecific symptoms; however, a delayed diagnosis can lead to severe complications. An 80-year-old frail woman presented to our hospital with a chief complaint of persistent fever for 10 days. Her blood tests showed an elevated inflammatory response, and computed tomography showed a 10-cm cystic lesion in the pelvic floor compressing the bladder. A catheter was inserted from the vagina into the uterine cavity, resulting in pus drainage and pyometra diagnosis. A pus culture was subsequently performed, which detected Achromobacter xylosoxidans, a common cause of respiratory tract infections in cystic fibrosis and bloodstream infections, andγ-streptococcus. To the best of our knowledge, this is the first report of pyometra caused by Achromobacter xylosoxidans. The patient was treated with drainage and piperacillin-tazobactam administration. Pyometra is especially prevalent in older women with impaired activities of daily living and dementia. Although fever, lower abdominal pain, and increased discharge may occur, symptoms are often nonspecific, and half of such cases are asymptomatic. Furthermore, delayed diagnosis can lead to perforation of the uterus and consequent pan-peritonitis. Thus, the diagnosis of pyometra should be considered in older women presenting with unknown fever, and imaging studies and gynecological consultation should be requested promptly.

CD14 signaling mediates lung immunopathology and mice mortality induced by Achromobacter xylosoxidans

Objective and design

Our research aimed to investigate the role of CD14 in pulmonary infection by Achromobacter xylosoxidans in an experimental murine model.

Methods

C57Bl/6 or CD14-deficient mice were infected intratracheally with non-lethal inoculum of A. xylosoxidans. At times 1, 3 and 7 days after infection, lungs, bronchoalveolar lavage and blood were collected. CD14 gene expression was determined by RT-PCR. The bacterial load in the lungs was assessed by counting colony forming units (CFU). Cytokines, chemokines, lipocalin-2 and sCD14 were quantified by the ELISA method. Inflammatory infiltrate was observed on histological sections stained with HE, and leukocyte subtypes were assessed by flow cytometry. In another set of experiments, C57Bl/6 or CD14-deficient mice were inoculated with lethal inoculum and the survival rate determined.

Results

CD14-deficient mice are protected from A. xylosoxidans-induced death, which is unrelated to bacterial load. The lungs of CD14-deficient mice presented a smaller area of tissue damage, less neutrophil and macrophage infiltration, less pulmonary edema, and a lower concentration of IL-6, TNF-α, CXCL1, CCL2 and CCL3 when compared with lungs of C57Bl/6 mice. We also observed that A. xylosoxidans infection increases the number of leukocytes expressing mCD14 and the levels of sCD14 in BALF and serum of C57Bl/6-infected mice.

Conclusions

In summary, our data show that in A. xylosoxidans infection, the activation of CD14 induces intense pulmonary inflammatory response resulting in mice death.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00011-022-01641-8.

One-stage revision arthroplasty in a patient with ochronotic arthropathy accompanied by joint infection: A case report

BACKGROUND

Ochronotic arthropathy (OcA) is a rare disease, which is caused by the accumulation of homogentisic acid in the joint. Patients with OcA have obvious joint pain and the disease progresses rapidly, eventually resulting in disability. Arthroplasty is an efficacious treatment in patients with OcA. However, when OcA patients have joint infection, is joint replacement an option? In the present report, we performed total knee arthroplasty in a patient with OcA and knee infection under the guidance of one-stage revision theory.

CASE SUMMARY

A 64-year-old male was referred to our hospital due to severe left knee pain with limited mobility for 2 years. On physical examination, the patient was found to have dark brown pigmentation of the sclera and auricle. Laboratory test results showed elevations in C-reactive protein level (65.79 mg/L) and erythrocyte sedimentation rate (90.00 mm/h). The patient underwent debridement of the left knee joint, during which the cartilage surface of the knee joint was found to be black-brown in color. Bacterial culture of synovial fluid revealed Achromobacter xylosoxidans. We then carried out arthroplasty under the guidance of the theory of one-stage revision. After surgery, the patient's left knee joint pain disappeared and function recovered without joint infection.

CONCLUSION

OcA accompanied by joint infection is rare. One-stage revision arthroplasty may be a treatment option for this disease.

The In Vitro Replication Cycle of Achromobacter xylosoxidans and Identification of Virulence Genes Associated with Cytotoxicity in Macrophages

Achromobacter xylosoxidans is an opportunistic pathogen implicated in a wide variety of human infections including the ability to colonize the lungs of cystic fibrosis (CF) patients. The role of A. xylosoxidans in human pathology remains controversial due to the lack of optimized in vitro and in vivo model systems to identify and test bacterial gene products that promote a pathological response. We have previously identified macrophages as a target host cell for A. xylosoxidans-induced cytotoxicity. By optimizing our macrophage infection model, we determined that A. xylosoxidans enters macrophages and can reside within a membrane bound vacuole for extended periods of time. Intracellular replication appears limited with cellular lysis preceding an enhanced, mainly extracellular replication cycle. Using our optimized in vitro model system along with transposon mutagenesis, we identified 163 genes that contribute to macrophage cytotoxicity. From this list, we characterized a giant RTX adhesin encoded downstream of a type one secretion system (T1SS) that mediates bacterial binding and entry into host macrophages, an important first step toward cellular toxicity and inflammation. The RTX adhesin is encoded by other human isolates and is recognized by antibodies present in serum isolated from CF patients colonized by A. xylosoxidans, indicating this virulence factor is produced and deployed in vivo. This study represents the first characterization of A. xylosoxidans replication during infection and identifies a variety of genes that may be linked to virulence and human pathology. IMPORTANCE Patients affected by CF develop chronic bacterial infections characterized by inflammatory exacerbations and tissue damage. Advancements in sequencing technologies have broadened the list of opportunistic pathogens colonizing the CF lung. A. xylosoxidans is increasingly recognized as an opportunistic pathogen in CF, yet our understanding of the bacterium as a contributor to human disease is limited. Genomic studies have identified potential virulence determinants in A. xylosoxidans isolates, but few have been mechanistically studied. Using our optimized in vitro cell model, we identified and characterized a bacterial adhesin that mediates binding and uptake by host macrophages leading to cytotoxicity. A subset of serum samples from CF patients contains antibodies that recognize the RTX adhesion, suggesting, for the first time, that this virulence determinant is produced in vivo. This work furthers our understanding of A. xylosoxidans virulence factors at a mechanistic level.

Immunoinformatic Approach to Contrive a Next Generation Multi-Epitope Vaccine Against Achromobacter xylosoxidans Infections

Achromobacter xylosoxidans, previously identified as Alcaligenes xylosoxidans, is a rod-shaped, flagellated, non-fermenting Gram-negative bacterium that has the ability to cause diverse infections in humans. As a part of its intrinsic resistance to different antibiotics, Achromobacter spp. is also increasingly becoming resistant to Carbapenems. Lack of knowledge regarding the pathogen’s clinical features has led to limited efforts to develop countermeasures against infection. The current study utilized an immunoinformatic method to map antigenic epitopes (Helper T cells, B-cell and Cytotoxic-T cells) to design a vaccine construct. We found that 20 different epitopes contribute significantly to immune response instigation that was further supported by physicochemical analysis and experimental viability. The safety profile of our vaccine was tested for antigenicity, allergenicity, and toxicity against all the identified epitopes before they were used as vaccine candidates. The disulfide engineering was carried out in an area of high mobility to increase the stability of vaccine proteins. In order to determine if the constructed vaccine is compatible with toll-like receptor, the binding affinity of vaccine was investigated via molecular docking approach. With the in silico expression in host cells and subsequent immune simulations, we were able to detect the induction of both arms of the immune response, i.e., humoral response and cytokine induced response. To demonstrate its safety and efficacy, further experimental research is necessary.

JMM Profile: Achromobacter xylosoxidans: the cloak-and-dagger opportunist

Achromobacter xylosoxidans is associated with resilient nosocomial infections, with bacteraemia, pneumonia and chronic cystic fibrosis lung infection being the most common clinical presentations. Innate multi-drug resistance and a suite of virulence factors select for A. xylosoxidans infection during long-term antibiotic therapy, contributing to its persistence, treatment recalcitrance, association with poor clinical outcomes and emergence as a problematic pathogen. Horizontal gene transfer and maintenance of large genomes underpin the resilience and cosmopolitan lifestyle of A. xylosoxidans, and complicate its phylogenetic characterization.

Role of Efflux in Antibiotic Resistance of Achromobacter xylosoxidans and Achromobacter insuavis Isolates From Patients With Cystic Fibrosis

Achromobacter genus (including Achromobacter xylosoxidans, the most prevalent Achromobacter species in patients with cystic fibrosis) is poorly susceptible to most conventional antibiotics. Contribution of efflux by AxyABM, AxyXY-OprZ, and AxyEF-OprN and of target mutations were studied in clinical isolates of A. xylosoxidans and Achromobacter insuavis. Forty-one isolates longitudinally collected from 21 patients with CF were studied by whole-genome sequencing (WGS)-typing, determination of minimum inhibitory concentrations (MICs) of β-lactams, aminoglycosides, colistin, azithromycin, ciprofloxacin, chloramphenicol, and doxycycline, and expression (quantitative RT-PCR) and function (measure of the uptake of a fluorescent substrate) of efflux pumps. WGS-based typing resulted in 10 clusters comprising 2 or 3 isolates and 20 singletons. The efflux activity was high in strains with elevated MICs for amikacin or azithromycin. This work sheds a new light on the impact of efflux and target mutations in resistance of Achromobacter to several drugs.

A case of meningitis due to Achromobacter xylosoxidans in a child with a polymalformative syndrome: a case report

Achromobacter xylosoxidans (AX), also called alcaligenes xylosoxidans, is an aerobic, non-fermenting mobile, gram-negative bacillus which was first isolated in an otorrhea samples in 1971. Infections with these species are quite rare and have often been described in immunocompromised and in premature infants. However, very few cases of meningitis related to AX have been reported in the literature. The authors report a new case of meningitis due to AX in a 45-day-old female infant with polymarformative syndrome meningitis was confirmed by a cyto-biochemical analysis and culture of the cerebrospinal fluid and was treated by antibiotherapy. Hydrocephalus was managed initially with external ventricular drainage followed by a ventriculoperitoneal shunt after rigorous cerebrospinal fluid (CSF) sterilization, with good clinical and radiological outcomes. The prompt and adequate antibiotic adjustment following bacterial isolation has been shown to rapidly modify the clinical outcomes.

Genomic and Phenotypic Evolution of Achromobacter xylosoxidans during Chronic Airway Infections of Patients with Cystic Fibrosis

Bacterial pathogens evolve during chronic colonization of the human host by selection for pathoadaptive mutations. One of the emerging and understudied bacterial species causing chronic airway infections in patients with cystic fibrosis (CF) is Achromobacter xylosoxidans. It can establish chronic infections in patients with CF, but the genetic and phenotypic changes associated with adaptation during these infections are not completely understood. In this study, we analyzed the whole-genome sequences of 55 clinical A. xylosoxidans isolates longitudinally collected from the sputum of 6 patients with CF. Four genes encoding regulatory proteins and two intergenic regions showed convergent evolution, likely driven by positive selection for pathoadaptive mutations, across the different clones of A. xylosoxidans. Most of the evolved isolates had lower swimming motility and were resistant to multiple classes of antibiotics, while fewer of the evolved isolates had slower growth or higher biofilm production than the first isolates. Using a genome-wide association study method, we identified several putative genetic determinants of biofilm formation, motility and β-lactam resistance in this pathogen. With respect to antibiotic resistance, we discovered that a combination of mutations in pathoadaptive genes (phoQ and bigR) and two other genes encoding regulatory proteins (spoT and cpxA) were associated with increased resistance to meropenem and ceftazidime. Altogether, our results suggest that genetic changes within regulatory loci facilitate within-host adaptation of A. xylosoxidans and the emergence of adaptive phenotypes, such as antibiotic resistance or biofilm formation. IMPORTANCE A thorough understanding of bacterial pathogen adaptation is essential for the treatment of chronic bacterial infections. One unique challenge in the analysis and interpretation of genomics data is identifying the functional impact of mutations accumulated in the bacterial genome during colonization in the human host. Here, we investigated the genomic and phenotypic evolution of A. xylosoxidans in chronic airway infections of patients with CF and identified several mutations associated with the phenotypic evolution of this pathogen using genome-wide associations. Identification of phenotypes under positive selection and the associated mutations can enlighten the adaptive processes of this emerging pathogen in human infections and pave the way for novel therapeutic interventions.

Genomic and phylogenetic analysis of multidrug-resistant Achromobacter xylosoxidans ST273 strain MTYH1 co-carrying blaOXA-114g and blaCARB-2 recovered from a wound infection in China

OBJECTIVES

Achromobacter xylosoxidans is widely distributed in the environment and is increasingly recognised as a significant nosocomial pathogen in healthcare settings. However, the genomic and phylogenetic characteristics of this pathogen are not fully understood. Here we report the first genome sequence of a multidrug-resistant A. xylosoxidans ST273 strain (MTYH1) isolated from a wound infection in China.

METHODS

Whole-genome sequencing of the strain was performed using an Illumina NovaSeq 6000 platform. Generated short reads were de novo assembled into contigs using SPAdes v.3.13.0. Antimicrobial resistance genes (ARGs) were identified using ResFinder 4.0. Phylogenetic analysis was conducted using NJ/UPGMA phylogeny (MAFFT v.7) based on core genome single nucleotide polymorphism data.

RESULTS

The draft genome sequence of A. xylosoxidans ST273 strain MTYH1 consists of 45 contigs comprising 6 643 045 bp with a GC content of 67.5%. According to the Achromobacter spp. multilocus sequence typing (MLST) scheme, MTYH1 belongs to ST273. MTYH1 is resistant to aminoglycosides, ciprofloxacin, aztreonam and cephalosporins. Five ARGs belonging to three different classes were identified in the genome, namely aac(6')-IIa, ant(2'')-Ia, bla_CARB-2, bla_OXA-114g and sul1. Phylogenetic analysis showed that MTYH1 was not epidemiologically related to any of the strains retrieved from the NCBI GenBank database.

CONCLUSION

We unravelled the genome sequence of multidrug-resistant A. xylosoxidans ST273 clinical strain MTYH1 recovered from a wound infection in China. Our data may help to understand the antimicrobial resistance mechanisms, genomic features and phylogenetic characteristic of this bacterial pathogen.

SSNOMBACTER: A collection of scattering-type scanning near-field optical microscopy and atomic force microscopy images of bacterial cells

BACKGROUND

In recent years, a variety of imaging techniques operating at nanoscale resolution have been reported. These techniques have the potential to enrich our understanding of bacterial species relevant to human health, such as antibiotic-resistant pathogens. However, owing to the novelty of these techniques, their use is still confined to addressing very particular applications, and their availability is limited owing to associated costs and required expertise. Among these, scattering-type scanning near field optical microscopy (s-SNOM) has been demonstrated as a powerful tool for exploring important optical properties at nanoscale resolution, depending only on the size of a sharp tip. Despite its huge potential to resolve aspects that cannot be tackled otherwise, the penetration of s-SNOM into the life sciences is still proceeding at a slow pace for the aforementioned reasons.

RESULTS

In this work we introduce SSNOMBACTER, a set of s-SNOM images collected on 15 bacterial species. These come accompanied by registered Atomic Force Microscopy images, which are useful for placing nanoscale optical information in a relevant topographic context.

CONCLUSIONS

The proposed dataset aims to augment the popularity of s-SNOM and for accelerating its penetration in life sciences. Furthermore, we consider this dataset to be useful for the development and benchmarking of image analysis tools dedicated to s-SNOM imaging, which are scarce, despite the high need. In this latter context we discuss a series of image processing and analysis applications where SSNOMBACTER could be of help.

A Rare Case of Non-Prosthetic Aortic Valve Infectious Endocarditis Caused by Achromobacter xylosoxidans

Patient: Male, 19-year-old

Final Diagnosis: Endocarditis

Symptoms: Fever • weigh loss

Medication: —

Clinical Procedure: —

Specialty: Cardiology

Duplex real-time PCR assay for the simultaneous detection of Achromobacter xylosoxidans and Achromobacter spp

Several members of the Gram-negative environmental bacterial genus Achromobacter are associated with serious infections, with Achromobacter xylosoxidans being the most common. Despite their pathogenic potential, little is understood about these intrinsically drug-resistant bacteria and their role in disease, leading to suboptimal diagnosis and management. Here, we performed comparative genomics for 158 Achromobacter spp. genomes to robustly identify species boundaries, reassign several incorrectly speciated taxa and identify genetic sequences specific for the genus Achromobacter and for A. xylosoxidans. Next, we developed a Black Hole Quencher probe-based duplex real-time PCR assay, Ac-Ax, for the rapid and simultaneous detection of Achromobacter spp. and A. xylosoxidans from both purified colonies and polymicrobial clinical specimens. Ac-Ax was tested on 119 isolates identified as Achromobacter spp. using phenotypic or genotypic methods. In comparison to these routine diagnostic methods, the duplex assay showed superior identification of Achromobacter spp. and A. xylosoxidans, with five Achromobacter isolates failing to amplify with Ac-Ax confirmed to be different genera according to 16S rRNA gene sequencing. Ac-Ax quantified both Achromobacter spp. and A. xylosoxidans down to ~110 genome equivalents and detected down to ~12 and ~1 genome equivalent(s), respectively. Extensive in silico analysis, and laboratory testing of 34 non-Achromobacter isolates and 38 adult cystic fibrosis sputa, confirmed duplex assay specificity and sensitivity. We demonstrate that the Ac-Ax duplex assay provides a robust, sensitive and cost-effective method for the simultaneous detection of all Achromobacter spp. and A. xylosoxidans and will facilitate the rapid and accurate diagnosis of this important group of pathogens.

Achromobacter xylosoxidans Cellular Pathology Is Correlated with Activation of a Type III Secretion System

Achromobacter xylosoxidans is increasingly recognized as a colonizer of cystic fibrosis (CF) patients, but the role that A. xylosoxidans plays in pathology remains unknown. This knowledge gap is largely due to the lack of model systems available to study the toxic potential of this bacterium. Recently, a phospholipase A₂ (PLA₂) encoded by a majority of A. xylosoxidans genomes, termed AxoU, was identified. Here, we show that AxoU is a type III secretion system (T3SS) substrate that induces cytotoxicity to mammalian cells. A tissue culture model was developed showing that a subset of A. xylosoxidans isolates from CF patients induce cytotoxicity in macrophages, suggestive of a pathogenic or inflammatory role in the CF lung. In a toxic strain, cytotoxicity is correlated with transcriptional activation of axoU and T3SS genes, demonstrating that this model can be used as a tool to identify and track expression of virulence determinants produced by this poorly understood bacterium.

Bilateral Pneumonia in a Patient with Chronic Bronchiectasis Caused by Achromobacter xylosoxidans Subspecies denitrificans

Achromobacter xylosoxidans is a gram-negative bacillus that has a multitude of inherent and acquired antimicrobial resistance. It is a rare, isolated pathogen in patients without cystic fibrosis (CF). We report the case of a 76-year-old Caucasian male with a history of chronic obstructive pulmonary disease (COPD), previous Mycobacterium-avium intracellulare (MAI) infection, and chronic bronchiectasis who did not respond to three courses of outpatient antibiotics for a chronic cough. He also had a 21-lb weight loss. The diagnosis of Achromobacter xylosoxidans subspecies denitrificans was made through bronchoscopy with bronchoalveolar lavage (BAL). There are few case reports describing Achromobacter xylosoxidans subspecies denitrificans in non-CF patients. Achromobacter xylosoxidans colonization might be linked to predisposing lung damage such as in CF and bronchiectasis. The bacterium is frequently multidrug-resistant. More studies are needed to develop recommendations for clinical guidelines to address the increasing antibiotic resistance to Achromobacter xylosoxidans.

First Documented Case of Percutaneous Endoscopic Gastrostomy (PEG) Tube-Associated Bacterial Peritonitis due to Achromobacter Species with Literature Review

Introduction. Achromobacter species (spp.) peritonitis has seldom been identified in medical literature. Scarce cases of Achromobacter peritonitis described previously have been correlated with peritoneal dialysis and more sparingly with spontaneous bacterial peritonitis. Achromobacter exhibits intrinsic and acquired resistance, especially in chronic infections, to most antibiotics. This article conducts a literature review of all previously reported Achromobacter spp. peritonitis and describes the first reported case of Achromobacter peritonitis as a complication of percutaneous endoscopic gastrostomy (PEG) tube placement. Discussion. Achromobacter peritonitis as a complication of PEG-tube placement has not been previously reported. In our patients' case, the recently placed PEG-tube with ascitic fluid leakage was identified as the most plausible infection source. Although a rare bacterial peritonitis pathogen, Achromobacter may be associated with wide antimicrobial resistance and unfavorable outcomes. Conclusion. No current guidelines provide significant guidance on treatment of PEG-tube peritonitis regardless of microbial etiology. Infectious Disease Society of America identifies various broad-spectrum antibiotics targeting nosocomial intra-abdominal coverage; some of these antimicrobial selections (such as cefepime and metronidazole combination) may yet be inadequate for widely resistant Achromobacter spp. Recognizably, the common antibiotics utilized for spontaneous bacterial peritonitis, i.e., third generation cephalosporins and fluoroquinolones, to which Achromobacter is resistant and variably susceptible, respectively, would be extensively insufficient. Piperacillin/tazobactam (P/T) and carbapenem were identified to provide the most reliable coverage in vitro; clinically, 5 out of the 8 patients who received either P/T or a carbapenem, or both, eventually experienced clinical improvement.

Impact of Achromobacter xylosoxidans isolation on the respiratory function of adult patients with cystic fibrosis

Background

The prevalence of Achromobacter xylosoxidans lung isolation in cystic fibrosis (CF) patients has increased, but the impact on lung function is controversial. The aim of this study was to evaluate the long-term effects of A. xylosoxidans isolation on respiratory function of adult patients with CF in the first 3 years after identification of A. xylosoxidans isolation.

Methods

This was a case–control retrospective study performed at a single CF centre in Lille, France. Data for 36 patients with CF who had at least one sputum culture positive for A. xylosoxidans (Ax+) were evaluated and compared with control CF patients uninfected by A. xylosoxidans (Ax−). Respiratory function and exacerbation frequency were evaluated between 1 year prior to and 3 years after A. xylosoxidans isolation.

Results

Compared with the Ax− group, the Ax+ group had a lower forced expiratory volume in 1 s (FEV₁) at baseline (median (interquartile range): 55.2% (50.6–59.8%) versus 73.8% (67.2–80.4%); p=0.005), a greater decline in FEV₁ (±se) in the first year after A. xylosoxidans identification (−153.6±16.1 mL·year⁻¹versus −63.8±18.5 mL·year⁻¹; p=0.0003), and more exacerbations in the first 3 years after A. xylosoxidans identification (9 (7–12) versus 7 (5–10); p=0.03). Ax+ patients co-colonised with Pseudomonas aeruginosa (n=27, 75%) had a greater FEV₁ decline (p=0.003) and more exacerbations in the year after A. xylosoxidans identification (p=0.037) compared with patients colonised with A. xylosoxidans alone. Patients with chronic A. xylosoxidans isolation (n=23, 64%) had more exacerbations than intermittently colonised patients in the 3 years after A. xylosoxidans identification (p=0.012).

Conclusion

A. xylosoxidans isolation is associated with a decline in respiratory function in patients with CF. Chronic A. xylosoxidans isolation and P. aeruginosa co-isolation may be markers of more severe respiratory disease in Ax+ patients.

Respiratory isolation of Achromobacter xylosoxidans exacerbates the decline in respiratory function in CF. Chronic A. xylosoxidans isolation and Pseudomonas cocolonisation may be markers of more severe disease in A. xylosoxidans-positive patients.http://bit.ly/2yJbSOS

Altered Middle Ear Microbiome in Children With Chronic Otitis Media With Effusion and Respiratory Illnesses

Chronic otitis media with effusion (COME) is a common childhood disease characterized by an accumulation of fluid behind the eardrum. COME often requires surgical intervention and can also lead to significant hearing loss and subsequent learning disabilities. Recent characterization of the middle ear fluid (MEF) microbiome in pediatric patients has led to an improved understanding of the microbiota present in the middle ear during COME. However, it is not currently known how the MEF microbiome might vary due to other conditions, particularly respiratory disorders. Here, we apply an amplicon sequence variant (ASV) pipeline to MEF 16S rRNA high-throughput sequencing data from 50 children with COME (ages 3–176 months) undergoing tube placement. We achieve a more detailed taxonomic resolution than previously reported, including species and genus level resolution. Additionally, we provide the first report of the functional roles of the MEF microbiome and demonstrate that despite high taxonomic diversity, the functional capacity of the MEF microbiome remains uniform between patients. Furthermore, we analyze microbiome differences between children with COME with and without a history of lower airway disease (i.e., asthma or bronchiolitis). The MEF microbiome was less diverse in participants with lower airway disease than in patients without, and phylogenetic β-diversity (weighted UniFrac) was significantly different based on lower airway disease status. Differential abundance between patients with lower airway disease and those without was observed for the genera Haemophilus, Moraxella, Staphylococcus, Alloiococcus, and Turicella. These findings support previous suggestions of a link between COME and respiratory illnesses and emphasize the need for future study of the middle ear and respiratory tract microbiomes in diseases such as asthma and bronchiolitis.

Community-acquired Achromobacter xylosoxidans infection presenting as a cavitary lung disease in an immunocompetent patient

Achromobacter xylosoxidans is a gram-negative bacterium that can oxidize xylose. It is commonly found in contaminated soil and water but does not normally infect immunocompetent humans. We report a case of a cavitary lung lesion associated with community-acquired A. xylosoxidans infection, which mimicked pulmonary tuberculosis or lung cancer in an immunocompetent man. The patient was hospitalized due to hemoptysis, and chest computed tomography (CT) revealed a cavitary lesion in the superior segment of the left lower lobe. We performed bronchoscopy and bronchial washing, and subsequent bacterial cultures excluded pulmonary tuberculosis and identified A. xylosoxidans. We performed antibiotic sensitivity testing and treated the patient with a 6-week course of amoxicillin/clavulanate. After 2 months, follow-up chest CT revealed complete resolution of the cavitary lesion.

Achromobacter xylosoxidans resistance to antiseptics and disinfectants is far from obvious

BACKGROUND

Achromobacter xylosoxidans is described as being resistant to antiseptics and disinfectants. We studied in vitro the ability of five strains to survive and grow in such solutions, with and without starvation.

METHODS

Bacterial suspensions in rich media and in distilled water were inoculated into eight antiseptics or disinfectants under conditions of use.

RESULTS

All strains from cultures in distilled water survived in aqueous chlorhexidine and only environmental strains survived in a quaternary ammonium-based disinfectant. Survival did not exceed 30 min and no growth was observed.

CONCLUSIONS

This study highlights a relationship between starvation and survival in antiseptics and disinfectants.

Achromobacter xylosoxidans in idiopathic cystic bronchiectasis

This is the first case in the English language describing Achromobacter xylosoxidans in a patient with idiopathic bronchiectasis. A 66-year-old man with bronchiectasis presented with shortness of breath to the emergency department of our institution, a district hospital in the UK. His medications included long-term supplemental oxygen therapy and prophylactic azithromycin. Following 2 days admission to the respiratory unit, his saturations significantly deteriorated, and the patient was admitted to intensive care with type II respiratory failure. Following a week of intubation and ventilation, multidrug resistant A. xylosoxidans was isolated from the tracheal aspiration secretions. The patient recovered after receiving targeted intravenous antimicrobial therapy.

Keratitis Due to Achromobacter xylosoxidans in a Contact Lens User

OBJECTIVES

Ocular infections due to Achromobacter xylosoxidans are extremely uncommon; their diagnosis is a challenge and the optimal treatment remains controversial. We present a case of A. xylosoxidans in a contact lens user and a review of the literature to facilitate diagnostic suspicion and empirical therapeutic management.

METHODS

Review of the literature in PubMed and MEDLINE. We also document a case diagnosed in our department in January 2016.

SETTING

Hospital Clínico Universitario Lozano Blesa, Zaragoza, Spain.

RESULTS

According to the literature, clinical manifestations and antibiotic sensitivity of A. xylosoxidans varied greatly. Our patient with no history of keratopathy presented three risk factors that made the diagnosis suspicious. The infection was resolved with topical moxifloxacin and fluorometholone.

CONCLUSIONS

A. xylosoxidans is an uncommon cause of infection, but must be suspected in atypical keratitis, reported contact with warm or still waters, use of contact lenses, or previous corneal damage. In these cases, microbiological studies and antibiotic sensitivity testing are particularly important.

Achromobacter xylosoxidans Relapsing Peritonitis and Streptococcus suis Peritonitis in Peritoneal Dialysis Patients: A Report of Two Cases

Peritonitis is considered to be the most common complication of peritoneal dialysis (PD). It is usually caused by Gram positive Staphylococcus epidermidis. Achromobacter xylosoxidans (A. xylosoxidans) and Streptococcus suis (S. suis) are rare pathogens, but there is emerging evidence that they may be also responsible for PD related peritonitis. We described 2 cases of rare peritonitis treated in our center. In our opinion this is the first described case of PD related peritonitis caused by Streptococcus suis.

The successful treatment of a multidrug-resistant Achromobacter xylosoxidans corneal ulcer with topical meropenem

Microbial keratitis is a common corneal condition, with many known risk factors. We present a case of an 88-year-old female patient with a multidrug-resistant Achromobacter xylosoxidans corneal ulcer in a previously failed second penetrating keratoplasty, successfully managed with topical meropenem drops administered hourly around the clock, for five days preceding and then hourly day only, for five days following a repeat third penetrating keratoplasty. Topical meropenem 50 mg/mL was prepared by mixing a 500 mg vial of meropenem with 10 mL of sterile water with pharmacy advice that administration should be within an hour. To the best of our knowledge, this is the first report of the use of topical meropenem in the management of A.xylosoxidans keratitis. This case highlights the importance of the mean inhibitory concentrations for antibiotics when considering sensitivities. Topical meropenem may be a useful treatment option for multidrug-resistant bacterial corneal ulcers that are resistant to conventional therapy.

Severe Achromobacter xylosoxidans keratitis with deep corneal involvement

Purpose

To describe a case of Achromobacter xylosoxidans keratitis with deep involvement of the corneal stroma and discuss its management.

Observations

A 73 year-old monocular male with infectious keratitis of the right eye was referred to the Wilmer Eye Institute after a month of empiric treatment with besifloxacin. On presentation, slit lamp examination of the right eye demonstrated a diffusely edematous cornea with three areas of corneal infiltrates and an overlying epithelial defect and a 1.3 mm hypopyon in the anterior chamber. The corneal culture performed grew A. xylosoxidans. Empiric antibiotic regimen was adjusted once corneal culture susceptibility results were available. Seven days later, slit lamp examination demonstrated a resolving epithelial defect, stable infiltrates, and resolution of the hypopyon. After approximately two months of follow up with his primary ophthalmologist, he was noted to have recurrent hypopyon and infiltrates and was referred back to Wilmer. Slit lamp examination again demonstrated an epithelial defect, diffuse corneal haze, deep stromal infiltrates, and a 1 mm hypopyon. Corneal infiltrates were too deep to culture. Ultimately, the patient underwent a therapeutic penetrating keratoplasty with anterior chamber washout resulting in improvement of vision.

Conclusions and importance

The indolent progression of A. xylosoxidans keratitis may predispose patients to delayed presentation and treatment. This can result in deep stromal infection that complicates management due to poor antibiotic penetration. Deep stromal infections in A. xylosoxidans keratitis warrant the consideration of intrastromal antibiotic injection or early therapeutic penetrating keratoplasty.

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.

Native-valve endocarditis caused by Achromobacter xylosoxidans: a case report and review of literature

Achromobacter xylosoxidans is a Gram-negative aerobic bacterium first described by Yabuuchi and Ohyama in 1971. A. xylosoxidans is frequently found in aquatic environments. Abdominal, urinary tract, ocular, pneumonia, meningitis, and osteomyelitis are the most common infections. Infective endocarditis is rare. As far as we know, until now, only 19 cases have been described, including this current report. We report the case of community-acquired native valve endocarditis caused by A. xylosoxidans in an elderly patient without a concomitant diagnosis of a malignancy or any known immunodeficiency. The patient presented with a 2-month history of fever, weight loss, and progressive dyspnea. On physical examination, mitral and aortic murmurs were present, along with Janeway's lesions, and a positive blood culture for A. xylosoxidans. The transesophageal echocardiogram showed vegetation in the aortic valve, which was consistent with the diagnosis of infective endocarditis.

Characterization and genome comparisons of three Achromobacter phages of the family Siphoviridae

In this study, we present the characterization and genomic data of three Achromobacter phages belonging to the family Siphoviridae. Phages 83-24, JWX and JWF were isolated from sewage samples in Paris and Braunschweig, respectively, and infect Achromobacter xylosoxidans, an emerging nosocomial pathogen in cystic fibrosis patients. Analysis of morphology and growth parameters revealed that phages 83-24 and JWX have similar properties, both have nearly the same head and tail measurements, and both have a burst size between 85 and 100 pfu/cell. In regard to morphological properties, JWF had a much longer and more flexible tail compared to other phages. The linear double-stranded DNAs of all three phages are terminally redundant and not circularly permutated. The complete nucleotide sequences consist of 81,541 bp for JWF, 49,714 bp for JWX and 48,216 bp for 83-24. Analysis of the genome sequences showed again that phages JWX and 83-24 are quite similar. Comparison to the GenBank database via BLASTN revealed partial similarities to Roseobacter phage RDJL phi1 and Burkholderia phage BcepGomr. In contrast, BLASTN analysis of the genome sequence of phage JWF revealed only few similarities to non-annotated prophage regions in different strains of Burkholderia and Mesorhizobium.

A Case of Septic Shock caused by Achromobacter xylosoxidans in an Immunocompetent Female Patient after Extracorporeal Shock Wave Lithotripsy for a Ureteral Stone

Achromobacter xylosoxidans can cause various types of infections, but its infection in humans is rare. A. xylosoxidans has been reported as a rare etiological agent of infections including primary bacteremia, catheter-related bloodstream infection, endocarditis, otitis, and pneumonia, particularly in immunocompromised hosts. We encountered a case of septic shock caused by A. xylosoxidans in a 52-year-old, immunocompetent woman with no underlying disease, who received extracorporeal shock wave lithotripsy to remove a left upper ureteral stone. She was treated with antibiotics to which the organism was susceptible but died as a result of septic shock.

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.

Achromobacter respiratory infections

Achromobacteria are ubiquitous environmental organisms that may also become opportunistic pathogens in certain conditions, such as cystic fibrosis, hematologic and solid organ malignancies, renal failure, and certain immune deficiencies. Some members of this genus, such as xylosoxidans, cause primarily nosocomially acquired infections affecting multiple organ systems, including the respiratory tract, urinary tract, and, less commonly, the cardiovascular and central nervous systems. Despite an increasing number of published case reports and literature reviews suggesting a global increase in achromobacterial disease, most clinicians remain uncertain of the organism's significance when clinically isolated. Moreover, effective treatment can be challenging due to the organism's inherent and acquired multidrug resistance patterns. We reviewed all published cases to date of non-cystic fibrosis achromobacterial lung infections to better understand the organism's pathogenic potential and drug susceptibilities. We found that the majority of these cases were community acquired, typically presenting as pneumonias (88%), and were most frequent in individuals with hematologic and solid organ malignancies. Our findings also suggest that achromobacterial lung infections are difficult to treat, but respond well to extended-spectrum penicillins and cephalosporins, such as ticarcillin, piperacillin, and cefoperazone.

Recurrent Septic Arthritis Due to Achromobacter xylosoxidans in a Patient With Granulomatosis With Polyangiitis

We report a case of recurrent Achromobacter xylosoxidans infections including bacteremia, sepsis, septic joints and endocarditis in a 72 year old female with granulomatosis with polyangiitis. Achromobacter xylosoxidans is a gram negative bacteria increasingly identified in immunocompromised patients. Surgical and medical therapy may need to be combined.

Osteomyelitis caused by Achromobacter xylosoxidans

Achromobacter xylosoxidans is an aerobic, nonfermenting gram-negative rod and described as a waterborne bacterium since it habits aquatic environments ubiquitously. It has frequently been isolated from aquatic surroundings in the hospital and from various human body sites. Although occasionally considered a non-pathogen, A. xylosoxidans has been associated with outbreaks of nosocomial infection due to contaminated fluids. Moreover, a wide variety of infectious etiologies due to A. xylosoxidans has been reported primarily in immunocompromised individuals. Heightened awareness of this bacterium and associated clinical importance is warranted for clinicians since its broad disease spectrum in humans and frequent multi-drug resistance may result in an increased mortality rate. In this report, we describe a case of osteomyelitis caused by A. xylosoxidans in a patient with a history of diabetes mellitus.