Achromobacter xylosoxidans in cystic fibrosis: prevalence and clinical relevance

Practical Guidance for Clinical Microbiology Laboratories: Updated guidance for processing respiratory tract samples from people with cystic fibrosis

SUMMARYThis guidance presents recommendations for clinical microbiology laboratories for processing respiratory samples from people with cystic fibrosis (pwCF). Appropriate processing of respiratory samples is crucial to detect bacterial and fungal pathogens, guide treatment, monitor the epidemiology of cystic fibrosis (CF) pathogens, and assess therapeutic interventions. Thanks to CF transmembrane conductance regulator modulator therapy, the health of pwCF has improved, but as a result, fewer pwCF spontaneously expectorate sputum. Thus, the collection of sputum samples has decreased, while the collection of other types of respiratory samples such as oropharyngeal and bronchoalveolar lavage samples has increased. To optimize the detection of microorganisms, including Pseudomonas aeruginosa, Staphylococcus aureus, Haemophilus influenzae, and Burkholderia cepacia complex; other less common non-lactose fermenting Gram-negative bacilli, e.g., Stenotrophomonas maltophilia, Inquilinus, Achromobacter, Ralstonia, and Pandoraea species; and yeasts and filamentous fungi, non-selective and selective culture media are recommended for all types of respiratory samples, including samples obtained from pwCF after lung transplantation. There are no consensus recommendations for laboratory practices to detect, characterize, and report small colony variants (SCVs) of S. aureus, although studies are ongoing to address the potential clinical impact of SCVs. Accurate identification of less common Gram-negative bacilli, e.g., S. maltophilia, Inquilinus, Achromobacter, Ralstonia, and Pandoraea species, as well as yeasts and filamentous fungi, is recommended to understand their epidemiology and clinical importance in pwCF. However, conventional biochemical tests and automated platforms may not accurately identify CF pathogens. MALDI-TOF MS provides excellent genus-level identification, but databases may lack representation of CF pathogens to the species-level. Thus, DNA sequence analysis should be routinely available to laboratories for selected clinical circumstances. Antimicrobial susceptibility testing (AST) is not recommended for every routine surveillance culture obtained from pwCF, although selective AST may be helpful, e.g., for unusual pathogens or exacerbations unresponsive to initial therapy. While this guidance reflects current care paradigms for pwCF, recommendations will continue to evolve as CF research expands the evidence base for laboratory practices.

Pneumonia due to Achromobacter xylosoxidans with a chronic course resembling non-tuberculous mycobacterial infection

Achromobacter xylosoxidans is a common bacterium that rarely causes pneumonia. Determining whether A. xylosoxidans is the cause of lung infection in patients suspected of having chronic infectious lung disease is challenging because it can present with colonization. We report a case of a 56-year-old immunocompetent woman suspected of having non-tuberculous mycobacteria (NTM) infection on imaging examination and monitored for 3 years. Sputum examinations revealed A. xylosoxidans several times, and it was determined to be a colonization. A. xylosoxidans was isolated from bronchial lavage fluid and aspirated sputum, but no evidence of NTM was observed. She was diagnosed with A. xylosoxidans infection and given ceftazidime for 2 weeks. Her symptoms and imaging findings improved rapidly after treatment, without recurrences. A. xylosoxidans rarely causes chronic lower respiratory tract infections similar to NTM in immunocompetent patients. A. xylosoxidans may be a target for treatment when detected in lower respiratory tract specimens.

Genetic and Biochemical Characterization of AXC-2 from Achromobacter ruhlandii

Achromobacter spp. are intrinsically resistant to multiple antibiotics and can also acquire resistance to those commonly used for the treatment of respiratory infections, especially in patients with cystic fibrosis. The aim of this study was to perform the genetic and biochemical characterization of AXC-2 from A. ruhlandii and to analyze all available AXC variants. Steady-state kinetic parameters were determined on a purified AXC-2 enzyme. It exhibited higher catalytic efficiencies towards amino-penicillins and older cephalosporins, while carbapenems behaved as poor substrates. Phylogenetic analysis of all blaAXC variants available in the NCBI was conducted. AXC was encoded in almost all A. ruhlandii genomes, whereas it was only found in 30% of A. xylosoxidans. AXC-1 was prevalent among A. xylosoxidans. AXC variants were clustered in two main groups, correlating with the Achromobacter species. No association could be established between the presence of blaAXC variants and a specific lineage of A. xylosoxidans; however, a proportion of AXC-1-producing isolates corresponded to ST 182 and ST 447. In conclusion, this study provides valuable insights into the genetic context and kinetic properties of AXC-2, identified in A. ruhlandii. It also provides a thorough description of all AXC variants and their association with Achromobacter species and various lineages.

Achromobacter pneumonia in a patient with advanced COPD, a diagnostic challenge

Bacterial pneumonia causes significant morbidity and mortality especially in elderly and immunocompromised hosts. Achromobacter xylosoxidans denitrificans pneumonia is very rarely reported. However, the reported cases have been in patients who are either immunocompromised or have bronchiectasis. We hereby present a unique case of Achromobacter xylosoxidans denitrificans pneumonia in an immunocompetent patient with advanced chronic obstructive pulmonary disease (COPD). Our patient is a Caucasian male admitted with shortness of breath, fever and cough. Chest X-ray demonstrated right-sided infiltrates and he was treated with intravenous ceftriaxone and azithromycin. He was discharged home on oral amoxicillin-clavulanate 875-125 mg two times per day for a total of 7 days. Patient returned to emergency room after 5 weeks with persistent symptoms and chest X-ray revealed persistent right-sided infiltrate and sputum culture showed Achromobacter xylosoxidans denitrificans. The patient was started on oral levofloxacin 750 mg one time per day for 2 weeks with resolution of symptoms.

Comparative in vitro activities of eravacycline in combination with colistin, meropenem, or ceftazidime against various Achromobacter spp. strains isolated from patients with cystic fibrosis

The Achromobacter species is an emerging pathogen causing chronic bacterial infections in patients with certain conditions, such as cystic fibrosis (CF), hematologic and solid organ malignancies, renal failure, and certain immune deficiencies. In the present study, we assessed the in vitro bactericidal activities of eravacycline, either alone or in combination with colistin, meropenem, or ceftazidime, using 50 Achromobacter spp. strains isolated from CF patients. We also investigated the synergistic interactions of these combinations using microbroth dilutions against 50 strains of Achromobacter spp. Bactericidal, and we assessed the synergistic effects of the tested antibiotic combinations using the time-kill curve (TKC) technique. Our studies show that meropenem alone is the most effective antibiotic of those tested. Based on the TKCs, we found that eravacycline-colistin combinations display both bactericidal and synergistic activities for 24 h against 5 of the 6 Achromobacter spp. strains, including colistin-resistant ones, at 4xMIC of colistin. Although we did not observe synergistic interactions with eravacycline-meropenem or eravacycline-ceftazidime combinations, we did not observe antagonism with any combination tested.This study's findings could have important implications for antimicrobial therapy with tested antibiotics.

Exoproducts of the Most Common Achromobacter Species in Cystic Fibrosis Evoke Similar Inflammatory Responses In Vitro

Achromobacter is a genus of Gram-negative rods, which can cause persistent airway infections in people with cystic fibrosis (CF). The knowledge about virulence and clinical implications of Achromobacter is still limited, and it is not fully established whether Achromobacter infections contribute to disease progression or if it is a marker of poor lung function. The most commonly reported Achromobacter species in CF is A. xylosoxidans. While other Achromobacter spp. are also identified in CF airways, the currently used Matrix-Assisted Laser Desorption/Ionization Time Of Flight Mass Spectrometry (MALDI-TOF MS) method in routine diagnostics cannot distinguish between species. Differences in virulence between Achromobacter species have consequently not been well studied. In this study, we compare phenotypes and proinflammatory properties of A. xylosoxidans, A. dolens, A. insuavis, and A. ruhlandii using in vitro models. Bacterial supernatants were used to stimulate CF bronchial epithelial cells and whole blood from healthy individuals. Supernatants from the well-characterized CF-pathogen Pseudomonas aeruginosa were included for comparison. Inflammatory mediators were analyzed with ELISA and leukocyte activation was assessed using flow cytometry. The four Achromobacter species differed in morphology seen in scanning electron microscopy (SEM), but there were no observed differences in swimming motility or biofilm formation. Exoproducts from all Achromobacter species except A. insuavis caused significant IL-6 and IL-8 secretion from CF lung epithelium. The cytokine release was equivalent or stronger than the response induced by P. aeruginosa. All Achromobacter species activated neutrophils and monocytes ex vivo in a lipopolysaccharide (LPS)-independent manner. Our results indicate that exoproducts of the four included Achromobacter species do not differ consistently in causing inflammatory responses, but they are equally or even more capable of inducing inflammation compared with the classical CF pathogen P. aeruginosa. IMPORTANCE Achromobacter xylosoxidans is an emerging pathogen among people with cystic fibrosis (CF). Current routine diagnostic methods are often unable to distinguish A. xylosoxidans from other Achromobacter species, and the clinical relevance of different species is still unknown. In this work, we show that four different Achromobacter species relevant to CF evoke similar inflammatory responses from airway epithelium and leukocytes in vitro, but they are all equally or even more proinflammatory compared to the classic CF-pathogen Pseudomonas aeruginosa. The results suggest that Achromobacter species are important airway pathogens in CF, and that all Achromobacter species are relevant to treat.

Antimicrobial Strategies for Cystic Fibrosis

Lung infection is the leading cause of death in cystic fibrosis (CF), and antimicrobial therapies are the backbone of infection management. While many different strategies may be applied, rigorous microbiological surveillance, intensive eradication therapy, and long-term maintenance therapy based on inhaled antibiotics may be considered the main strategy for infection control in individuals with CF. While most of the existing evidence is based on infection with Pseudomonas aeruginosa, other important pathogens causing lung inflammation and deterioration exist and should be treated despite the evidence gap. In this chapter, we describe the approaches to the antimicrobial treatment of the most important pathogens in CF and the evidence behind.

Microbial Epidemiology of the Cystic Fibrosis Airways: Past, Present, and Future

Progressive obstructive lung disease secondary to chronic airway infection, coupled with impaired host immunity, is the leading cause of morbidity and mortality in cystic fibrosis (CF). Classical pathogens found in the airways of persons with CF (pwCF) include Pseudomonas aeruginosa, Staphylococcus aureus, the Burkholderia cepacia complex, Achromobacter species, and Haemophilus influenzae. While traditional respiratory-tract surveillance culturing has focused on this limited range of pathogens, the use of both comprehensive culture and culture-independent molecular approaches have demonstrated complex highly personalized microbial communities. Loss of bacterial community diversity and richness, counteracted with relative increases in dominant taxa by traditional CF pathogens such as Burkholderia or Pseudomonas, have long been considered the hallmark of disease progression. Acquisition of these classic pathogens is viewed as a harbinger of advanced disease and postulated to be driven in part by recurrent and frequent antibiotic exposure driven by frequent acute pulmonary exacerbations. Recently, CF transmembrane conductance regulator (CFTR) modulators, small molecules designed to potentiate or restore diminished protein levels/function, have been successfully developed and have profoundly influenced disease course. Despite the multitude of clinical benefits, structural lung damage and consequent chronic airway infection persist in pwCF. In this article, we review the microbial epidemiology of pwCF, focus on our evolving understanding of these infections in the era of modulators, and identify future challenges in infection surveillance and clinical management.

Myxinidin-Derived Peptide against Biofilms Caused by Cystic Fibrosis Emerging Pathogens

Chronic lung infections in cystic fibrosis (CF) patients are triggered by multidrug-resistant bacteria such as Pseudomonas aeruginosa, Achromobacter xylosoxidans, and Stenotrophomonas maltophilia. The CF airways are considered ideal sites for the colonization and growth of bacteria and fungi that favor the formation of mixed biofilms that are difficult to treat. The inefficacy of traditional antibiotics reinforces the need to find novel molecules able to fight these chronic infections. Antimicrobial peptides (AMPs) represent a promising alternative for their antimicrobial, anti-inflammatory, and immunomodulatory activities. We developed a more serum-stable version of the peptide WMR (WMR-4) and investigated its ability to inhibit and eradicate C. albicans, S. maltophilia, and A. xylosoxidans biofilms in both in vitro and in vivo studies. Our results suggest that the peptide is able better to inhibit than to eradicate both mono and dual-species biofilms, which is further confirmed by the downregulation of some genes involved in biofilm formation or in quorum-sensing signaling. Biophysical data help to elucidate its mode of action, showing a strong interaction of WMR-4 with lipopolysaccharide (LPS) and its insertion in liposomes mimicking Gram-negative and Candida membranes. Our results support the promising therapeutic application of AMPs in the treatment of mono- and dual-species biofilms during chronic infections in CF patients.

Deciphering Microbiota of Acute Upper Respiratory Infections: A Comparative Analysis of PCR and mNGS Methods for Lower Respiratory Trafficking Potential

Although it is clinically important for acute respiratory tract (co)infections to have a rapid and accurate diagnosis, it is critical that respiratory medicine understands the advantages of current laboratory methods. In this study, we tested nasopharyngeal samples (n = 29) with a commercially available PCR assay and compared the results with those of a hybridization-capture-based mNGS workflow. Detection criteria for positive PCR samples was Ct < 35 and for mNGS samples it was >40% target coverage, median depth of 1X and RPKM > 10. A high degree of concordance (98.33% PPA and 100% NPA) was recorded. However, mNGS yielded positively 29 additional microorganisms (23 bacteria, 4 viruses, and 2 fungi) beyond PCR. We then characterized the microorganisms of each method into three phenotypic categories using the IDbyDNA Explify^® Platform (Illumina^® Inc, San Diego, CA, USA) for consideration of infectivity and trafficking potential to the lower respiratory region. The findings are significant for providing a comprehensive yet clinically relevant microbiology profile of acute upper respiratory infection, especially important in immunocompromised or immunocompetent with comorbidity respiratory cases or where traditional syndromic approaches fail to identify pathogenicity. Accordingly, this technology can be used to supplement current syndrome-based tests, and data can quickly and effectively be phenotypically characterized for trafficking potential, clinical (co)infection, and comorbid consideration-with promise to reduce morbidity and mortality.

The Efficacy of an N-Acetylcysteine-Antibiotic Combination Therapy on Achromobacter xylosoxidans in a Cystic Fibrosis Sputum/Lung Cell Model

Cystic fibrosis (CF) is a disorder causing dysfunctional ion transport resulting in the accumulation of viscous mucus. This environment fosters a chronic bacterial biofilm-associated infection in the airways. Achromobacter xylosoxidans, a gram-negative aerobic bacillus, has been increasingly associated with antibiotic resistance and chronic colonisation in CF. In this study, we aimed to create a reproducible model of CF infection using an artificial sputum medium (ASMDM-1) with bronchial (BEAS-2B) and macrophage (THP-1) cells to test A. xylosoxidans infection and treatment toxicity. This study was conducted in three distinct stages. First, the tolerance of BEAS-2B cell lines and two A. xylosoxidans strains against ASMDM-1 was optimised. Secondly, the cytotoxicity of combined therapy (CT) comprising N-acetylcysteine (NAC) and the antibiotics colistin or ciprofloxacin was tested on cells alone in the sputum model in both BEAS-2B and THP-1 cells. Third, the efficacy of CT was assessed in the context of a bacterial infection within the live cell/sputum model. We found that a model using 20% ASMDM-1 in both cell populations tolerated a colistin-NAC-based CT and could significantly reduce bacterial loads in vitro (~2 log10 CFU/mL compared to untreated controls). This pilot study provides the foundation to study other bacterial opportunists that infect the CF lung to observe infection and CT kinetics. This model also acts as a springboard for more complex co-culture models.

Clinical outcomes associated with Achromobacter species infection in people with cystic fibrosis

BACKGROUND

Achromobacter species are emerging pathogens isolated from respiratory samples of Patients with cystic fibrosis (pwCF) causing growing concerns in the CF community. The epidemiology and the clinical impact of Achromobacter in CF is unclear since data are restricted to small case control studies or selected populations.

AIM

To characterize the effect of Achromobacter respiratory infection on CF lung disease.

METHODS

European CF Society Patient Registry data was analysed for association between Achromobacter infection and demographic/clinical characteristics and outcomes of pwCF.

RESULTS

Of eligible 38,795 patients, Achromobacter infection was reported in 2,093 (prevalence (95% CI) of 5.40% (5.17 - 5.62). The prevalence varied significantly between the countries and increased with age peaking at the age 20-30. Achromobacter infection was more prevalent in pwCF carrying class minimal function mutations, having worse nutrition or lower pulmonary function, and more patients inhaled antibiotics against P. aeruginosa. Patient infected with Achromobacter had similar pulmonary function and BMI to patients infected with P. aeruginosa at all age groups. Being infected with both bacteria was associated with significantly lower pulmonary function and BMI at all age groups.

CONCLUSIONS

Achromobacter infection was associated with disease severity similar to infection with P. aeruginosa. Being infected with both bacteria is associated with even more severe disease. This suggests to study if eradication will improve the outcome of pwCF.

Antibacterial contact-dependent proteins secreted by Gram-negative cystic fibrosis respiratory pathogens

Cystic fibrosis (CF) is a genetic disease that affects almost 100 000 people worldwide. CF patients suffer from chronic bacterial airway infections that are often polymicrobial and are the leading cause of mortality. Interactions between pathogens modulate expression of genes responsible for virulence and antibiotic resistance. One of the ways bacteria can interact is through contact-dependent systems, which secrete antibacterial proteins (effectors) that confer advantages to cells that harbor them. Here, we highlight recent work that describes effectors used by Gram-negative CF pathogens to eliminate competitor bacteria. Understanding the mechanisms of secreted effectors may lead to novel insights into the ecology of bacteria that colonize respiratory tracts and could also pave the way for the design of new therapeutics.

Opportunistic Pathogens in Cystic Fibrosis: Epidemiology and Pathogenesis of Lung Infection

Cystic fibrosis (CF) is one of the most common life-shortening genetic diseases in Caucasians. Due to abnormal accumulation of mucus, respiratory failure caused by chronic infections is the leading cause of mortality in this patient population. The microbiology of these respiratory infections includes a distinct set of opportunistic pathogens, including Pseudomonas aeruginosa, Burkholderia spp., Achromobacter spp., Stenotrophomonas maltophilia, anaerobes, nontuberculous mycobacteria, and fungi. In recent years, culture-independent methods have shown the polymicrobial nature of lung infections, and the dynamics of microbial communities. The unique environment of the CF airway predisposes to infections caused by opportunistic pathogens. In this review, we will highlight how the epidemiology and role in disease of these pathogens in CF differ from that in individuals with other medical conditions. Infectious diseases (ID) physicians should be aware of these differences and the specific characteristics of infections associated with CF.

Multidrug-Resistant Bacteria in Children and Adolescents with Cystic Fibrosis

In patients with cystic fibrosis (CF), multidrug-resistant (MDR) bacteria can predispose to exacerbations, limit the effectiveness of antibiotic treatments and promote the progression of lung disease. The aim of this retrospective study was to compare pulmonary exacerbations (Pex), hospitalizations, lung function and nutritional status in a group of children and adolescents with CF colonized by MDR bacteria and in a noncolonized control group. Overall, 7/54 pediatric patients (12.9%) were colonized by MDR bacteria and enrolled (3 with Achromobacter xyloxidans, 3 with Stenotrophomonas maltophilia and 1 with Burkholderia cepacia). The control group included 14 sex- and age-matched CF patients (8/14 colonized by Staphylococcus aureus, 2/14 by Pseudomonas aeruginosa, 2/14 by both microorganisms and 2/14 germ free). At the time of enrollment and 12 months before the first detection of the MDR microorganism, children colonized by MDR bacteria showed lower body mass index (BMI) and lower FEV₁/FVC compared to the control group. Over the previous year before the first detection, children colonized with MDR had more Pex compared to control group; those colonized by S. maltophilia experienced the highest number of Pex. In the 12 months following the first detection of MDR bacteria, all seven patients colonized by MDR had at least one Pex and patients colonized by S. maltophilia had the highest number (mean ± SD: 6 ± 2.6 vs. 1.7 ± 2.3). Our study suggests that CF pediatric patients infected by MDR bacteria have lower BMI, more obstructive disease and experience more exacerbations than patients without MDR bacteria. These differences are present even before being infected, suggesting that children and adolescents with more severe disease are predisposed to be colonized by MDR bacteria. S. maltophilia appeared to be the most aggressive pathogen. Further studies and the implementation of antimicrobial stewardship programs are necessary to clarify when and how to treat patients with CF and MDR bacteria in order to avoid the improper use of antibiotics and the development of antibiotic resistance.

Antibiotherapy in Children with Cystic Fibrosis—An Extensive Review

In cystic fibrosis (CF), the respiratory disease is the main factor that influences the outcome and the prognosis of patients, bacterial infections being responsible for severe exacerbations. The etiology is often multi-microbial and with resistant strains. The aim of this paper is to present current existing antibiotherapy solutions for CF-associated infections in order to offer a reliable support for individual, targeted, and specific treatment. The inclusion criteria were studies about antibiotherapy in CF pediatric patients. Studies involving adult patients or those with only in vitro results were excluded. The information sources were all articles published until December 2021, in PubMed and ScienceDirect. A total of 74 studies were included, with a total number of 26,979 patients aged between 0–18 years. We approached each pathogen individual, with their specific treatment, comparing treatment solutions proposed by different studies. Preservation of lung function is the main goal of therapy in CF, because once parenchyma is lost, it cannot be recovered. Early personalized intervention and prevention of infection with reputable germs is of paramount importance, even if is an asymmetrical challenge. This research received no external funding.

Managing Pulmonary Infection in Adults With Cystic Fibrosis: Adult Cystic Fibrosis Series

Cystic fibrosis (CF) is characterized by chronic airway infection and progressive respiratory decline. Historically, a narrow spectrum of bacterial pathogens was believed to comprise the bulk of respiratory infections in CF, with Haemophilus influenzae and Staphylococcus aureus dominating childhood infections, and Pseudomonas aeruginosa or, less commonly, a member of the Burkholderia cepacia complex becoming the dominant infecting organism in adulthood. Today, the landscape is changing for airway infection in CF. The prevalence of "less typical" gram-negative bacterial infections are rising due to a number of factors: the CF population is aging; new therapies are being introduced; antibiotic usage is increasing; diagnostic tests are evolving; and taxonomic changes are being made as new bacterial species are being discovered. Less is known about the clinical relevance and evidence for treatment strategies for many of the other lower prevalence organisms that are encountered in CF. The aim of this article was to discuss the current evidence and recommended strategies for treating airway infection in CF, focusing on bacterial infections.

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.

Impact of Achromobacter spp. isolation on clinical outcomes in children with cystic fibrosis

BACKGROUND

The prevalence of Achromobacter spp. in cystic fibrosis (CF) has increased while its significance remains controversial. Our aim was to investigate the impact of Achromobacter spp. isolation on clinical outcomes in children with CF.

METHODS

Children with Achromobacter spp. isolation were retrospectively included from the CF database of our center. Control groups of children with CF, who had never been infected by Achromobacter spp., were individually case-matched by age, sex, and Pseudomonas aeruginosa isolation status. Pulmonary function and exacerbation frequency were compared between groups during follow-up.

RESULTS

Thirty-seven children had at least one respiratory specimen positive for Achromobacter spp. Achromobacter spp. were chronically isolated from 15 (40.5%) and intermittently from 22 (59.5%) of these 37 children. Although the baseline forced expiratory volume in 1 s (FEV1) z-score was similar between the Achromobacter spp.-infected and -uninfected groups (-0.65 ± 2.22 vs. -0.15 ± 1.30, respectively; p = 0.318), children infected by Achromobacter spp. had a lower FEV1 z-score compared to the control group by the end of the first year (-1.37 ± 2.17 vs. -0.14 ± 1.65, respectively; p = 0.025). In addition, the FEV1 decline in 1 year was significantly greater in the group infected by Achromobacter spp. compared to the uninfected group (-1.18%/year vs. -9.07%/year, respectively; p = 0.043). Furthermore, the cumulative numbers of exacerbations observed in the Achromobacter spp.-infected group were higher compared to the control group by the end of the second year (4 [0-17] versus 3 [0-9], respectively; p = 0.001).

CONCLUSIONS

Achromobacter spp. isolation is associated with more accelerated decline in lung function parameters and frequent exacerbations in children with CF.

An 18-Year Dataset on the Clinical Incidence and MICs to Antibiotics of Achromobacter spp. (Labeled Biochemically or by MAL-DI-TOF MS as A. xylosoxidans), Largely in Patient Groups Other than Those with CF

Achromobacter spp. are intrinsically multidrug-resistant environmental microorganisms which are known to cause opportunistic, nosocomial, and sometimes chronic infections. The existing literature yields scarcely any larger datasets, especially with regard to the incidence in patient groups other than those with cystic fibrosis. The aim of this study was to fill this gap. We present a retrospective analysis of 314 clinical and 130 screening isolates detected in our diagnostic unit between 2004 and 2021, combined with patients’ demographic and clinical information (ward type and length of hospitalization), and the results of routine diagnostic antibiotic MIC determination. We found the apparent increase in prevalence in our diagnostic unit, in which cystic fibrosis patients are an underrepresented group, in large part to be attributable to an overall increase in the number of samples and, more importantly, changes in the diagnostic setting, such as the introduction of rigorous screening for Gram-negative multidrug-resistant pathogens. We found these Achromobacter spp. to be most commonly detected in urine, stool, wounds and airway samples, and found the resistance rates to vary strongly between different sample types. Intestinal carriage is frequently not investigated, and its frequency is likely underestimated. Isolates resistant to meropenem can hardly be treated.

In Vitro Activity of 22 Antibiotics against Achromobacter Isolates from People with Cystic Fibrosis. Are There New Therapeutic Options?

Bacteria belonging to the genus Achromobacter are increasingly isolated from respiratory samples of people with cystic fibrosis (PWCF). The management of this multidrug-resistant genus is challenging and characterised by a lack of international recommendations, therapeutic guidelines and data concerning antibiotic susceptibility, especially concerning the newer antibiotics. The objective of this study was to describe the antibiotic susceptibility of Achromobacter isolates from PWCF, including susceptibility to new antibiotics. The minimum inhibitory concentrations (MICs) of 22 antibiotics were determined for a panel of 23 Achromobacter isolates from 19 respiratory samples of PWCF. Two microdilution MIC plates were used: EUMDROXF^® plate (Sensititre) and Micronaut-S Pseudomonas MIC^® plate (Merlin) and completed by a third method if necessary (E-test^® or UMIC^®). Among usual antimicrobial agents, the most active was imipenem (70% susceptibility). Trimethoprim-sulfamethoxazole, piperacillin and tigecycline (65%, 56% and 52% susceptibility, respectively) were still useful for the treatment of Achromobacter infections. Among new therapeutic options, β-lactams combined with a β-lactamase-inhibitor did not bring benefits compared to β-lactam alone. On the other hand, cefiderocol appeared as a promising therapeutic alternative for managing Achromobacter infections in PWCF. This study provides the first results on the susceptibility of clinical Achromobacter isolates concerning new antibiotics. More microbiological and clinical data are required to establish the optimal treatment of Achromobacter infections.

Adaptive Interactions of Achromobacter spp. with Pseudomonas aeruginosa in Cystic Fibrosis Chronic Lung Co-Infection

In the lungs of patients with cystic fibrosis (CF), the main pathogen Pseudomonas aeruginosa is often co-isolated with other microbes, likely engaging in inter-species interactions. In the case of chronic co-infections, this cohabitation can last for a long time and evolve over time, potentially contributing to the clinical outcome. Interactions involving the emerging pathogens Achromobacter spp. have only rarely been studied, reporting inhibition of P. aeruginosa biofilm formation. To evaluate the possible evolution of such interplay, we assessed the ability of Achromobacter spp. isolates to affect the biofilm formation of co-isolated P. aeruginosa strains during long-term chronic co-infections. We observed both competition and cohabitation. An Achromobacter sp. isolate secreted exoproducts interfering with the adhesion ability of a co-isolated P. aeruginosa strain and affected its biofilm formation. Conversely, a clonal Achromobacter sp. strain later isolated from the same patient, as well as two longitudinal strains from another patient, did not show similar competitive behavior against its P. aeruginosa co-isolates. Genetic variants supporting the higher virulence of the competitive Achromobacter sp. isolate were found in its genome. Our results confirm that both inter-species competition and cohabitation are represented during chronic co-infections in CF airways, and evolution of these interplays can happen even at the late stages of chronic infection.

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.

Achromobacter xylosoxidans airway infection is associated with lung disease severity in children with cystic fibrosis

Background

Despite the increasing prevalence of Achromobacter xylosoxidans lung infection in patients with cystic fibrosis (CF), its clinical pathogenicity remains controversial. The objective of this study was to evaluate the effects of this emerging bacterium on lung disease severity in CF children.

Methods

This case-control retrospective study took place in two French paediatric CF centres. 45 cases infected by A. xylosoxidans were matched for age, sex, CFTR genotypes and pancreatic status to 45 never-infected controls. Clinical data were retrieved from clinical records over the 2 years before and after A. xylosoxidans initial infection.

Results

At infection onset, lung function was lower in cases compared with controls (p=0.006). Over the 2 years prior to A. xylosoxidans acquisition, compared with controls, cases had more frequent pulmonary exacerbations (p=0.02), hospitalisations (p=0.05), and intravenous (p=0.03) and oral (p=0.001) antibiotic courses. In the 2 years following A. xylosoxidans infection, cases remained more severe with more frequent pulmonary exacerbations (p=0.0001), hospitalisations (p=0.0001), and intravenous (p=0.0001) and oral antibiotic courses (p=0.0001). Lung function decline tended to be faster in cases (-5.5% per year) compared with controls (-0.5% per year).

Conclusions

This case-control study demonstrates that A. xylosoxidans occurs more frequently in the patients with the worse lung disease. Further studies assessing the pathogenicity of this emerging pathogen and international treatment recommendations are warranted.

Inflammation in children with cystic fibrosis: contribution of bacterial production of long-chain fatty acids

BACKGROUND

Cystic fibrosis (CF) affects >70,000 people worldwide, yet the microbiologic trigger for pulmonary exacerbations (PExs) remains unknown. The objective of this study was to identify changes in bacterial metabolic pathways associated with clinical status.

METHODS

Respiratory samples were collected at hospital admission for PEx, end of intravenous (IV) antibiotic treatment, and follow-up from 27 hospitalized children with CF. Bacterial DNA was extracted and shotgun DNA sequencing was performed. MetaPhlAn2 and HUMAnN2 were used to evaluate bacterial taxonomic and pathway relative abundance, while DESeq2 was used to evaluate differential abundance based on clinical status.

RESULTS

The mean age of study participants was 10 years; 85% received combination IV antibiotic therapy (beta-lactam plus a second agent). Long-chain fatty acid (LCFA) biosynthesis pathways were upregulated in follow-up samples compared to end of treatment: gondoate (p = 0.012), oleate (p = 0.048), palmitoleate (p = 0.043), and pathways of fatty acid elongation (p = 0.012). Achromobacter xylosoxidans and Escherichia sp. were also more prevalent in follow-up compared to PEx (p < 0.001).

CONCLUSIONS

LCFAs may be associated with persistent infection of opportunistic pathogens. Future studies should more closely investigate the role of LCFA production by lung bacteria in the transition from baseline wellness to PEx in persons with CF.

IMPACT

Increased levels of LCFAs are found after IV antibiotic treatment in persons with CF. LCFAs have previously been associated with increased lung inflammation in asthma. This is the first report of LCFAs in the airway of persons with CF. This research provides support that bacterial production of LCFAs may be a contributor to inflammation in persons with CF. Future studies should evaluate LCFAs as predictors of future PExs.

Antibacterial and antibiofilm activities of ceragenins against Achromobacter species isolated from cystic fibrosis patients

Achromobacter species, which are recognized as emerging pathogens isolated from patients with cystic fibrosis, are capable of forming biofilm in the respiratory tract in patients and innate multidrug resistance to antimicrobials. CSAs are cationic salt derivatives that mimic the activity of antimicrobial peptides and exhibit antimicrobial activity against bacteria. In this study, the in vitro activities of various ceragenins against Achromobacter-species biofilms were investigated comparatively with a conventional antibiotic (meropenem). Biofilm-formation inhibition and biofilm-adhesion inhibition were investigated on five strong biofilm-producing strains. The lowest MIC₅₀ result was obtained with CSA-13. All of the tested CSAs showed significant biofilm inhibitory activity in the manner of a time- and concentration-dependent effect. To the best of our knowledge, this is the first article to evaluate the antibacterial and antibiofilm activities of tested CSAs against Achromobacter species.

Chronic, Recurrent Bacterial Endophthalmitis Caused by Achromobacter xylosoxidans: Clinical Features and Management

A 79-year-old man presented to a tertiary referral center from the Dominican Republic with an opaque corneal graft and a diagnosis of chronic, recurrent culture-positive Achromobacter xylosoxidans endophthalmitis of the left eye. The patient had a history of penetrating keratoplasty for Fuchs' dystrophy and had undergone multiple intraocular surgeries including pars plana vitrectomy and anterior chamber wash out for the diagnosis and management of chronic endophthalmitis. After being referred, the patient underwent a third PKP, removal of his intraocular lens (IOL), capsulectomy, and injection of intravitreal antibiotics. All surgical specimens demonstrated the growth of A. xylosoxidans. Five months after surgery, the graft remained clear without evidence of infection and best-corrected visual acuity was 20/350.

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.

Comparative in vitro activities of meropenem in combination with colistin, levofloxacin, or chloramphenicol against Achromobacter xylosoxidans strains isolated from patients with cystic fibrosis

OBJECTIVES

Achromobacter xylosoxidans is an emerging pathogen in cystic fibrosis (CF). Relatively little is known about its clinical impact and optimal management. In the present study, the in vitro bactericidal activities of meropenem, either alone or in combination with colistin, levofloxacin, or chloramphenicol, were assessed using A. xylosoxidans strains isolated from CF patients. The synergistic interactions of these combinations were also investigated.

METHODS

Minimal inhibitory concentrations (MICs) were determined by microbroth dilution. Bactericidal and synergistic effects of the tested antibiotic combinations were assessed by using the time-kill curve technique.

RESULTS

Based on the time-kill curves, we found that meropenem-colistin combinations have bactericidal and synergistic activities for 24 h against A. xylosoxidans strains, both at 1 × MIC and 4 × MIC. Although synergistic interactions were seen with meropenem-levofloxacin combinations, no bactericidal interactions were observed. Additionally, the meropenem-chloramphenicol combinations were found to be neither bactericidal nor synergistic. No antagonism was observed with any combination tested.

CONCLUSIONS

This study's findings could have important implications for empirical or combination antimicrobial therapy with tested antibiotics.

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.

Bacterial Infections and the Respiratory Microbiome

Cystic fibrosis (CF) is a genetic, multisystem disease due to defects in the cystic fibrosis transmembrane conductance regulator (CFTR) protein, an anion channel responsible for chloride and bicarbonate trafficking. Although this channel is expressed in many tissues, its impaired function in airway epithelial cells leads to hyperviscous mucous secretions impeding effective mucociliary clearance. Impaired clearance of inhaled microorganisms results in the establishment of chronic infection, triggering an overexaggerated inflammatory response. The resulting release of inflammatory cytokines and enzymes causes pulmonary damage in the form of bronchiectasis, further impairing mucociliary action, forming a vicious cycle. Subsequent respiratory failure remains the leading cause of death in individuals with CF.

Acute and Chronic Infection Management in CF

CFTR protein malfunction results in thick, copious mucus, causes poor mucociliary clearance and, ultimately, structural lung damage such as bronchiectasis. All of these manifestations of cystic fibrosis contribute to a rich milieu for lower respiratory pathogens in patients affected by the disease. CF patients are, therefore, highly susceptible to chronic colonization with many pathogens such as Staphylococcus aureus and Pseudomonas aeruginosa. They are also uniquely prone to acute infections with respiratory pathogens, which tend to persist longer and cause more impairment in lung function than in patients without CF. Tailored strategies for managing infectious complications of CF patients include chronic prophylactic antibiotics, use of systemic as well as inhaled antibiotics, mechanical assistance with mucus clearance, and scrupulous infection control measures.

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

Microbiology of Cystic Fibrosis Airway Disease

Although survival of individuals with cystic fibrosis (CF) has been continuously improving for the past 40 years, respiratory failure secondary to recurrent pulmonary infections remains the leading cause of mortality in this patient population. Certain pathogens such as Pseudomonas aeruginosa, methicillin-resistant Staphylococcus aureus, and species of the Burkholderia cepacia complex continue to be associated with poorer clinical outcomes including accelerated lung function decline and increased mortality. In addition, other organisms such as anaerobes, viruses, and fungi are increasingly recognized as potential contributors to disease progression. Culture-independent molecular methods are also being used for diagnostic purposes and to examine the interaction of microorganisms in the CF airway. Given the importance of CF airway infections, ongoing initiatives to promote understanding of the epidemiology, clinical course, and treatment options for these infections are needed.

Upper versus lower airway microbiome and metagenome in children with cystic fibrosis and their correlation with lung inflammation

Objective

Airways of children with cystic fibrosis (CF) harbor complex polymicrobial communities which correlates with pulmonary disease progression and use of antibiotics. Throat swabs are widely used in young CF children as a surrogate to detect potentially pathogenic microorganisms in lower airways. However, the relationship between upper and lower airway microbial communities remains poorly understood. This study aims to determine (1) to what extent oropharyngeal microbiome resembles the lung microbiome in CF children and (2) if lung microbiome composition correlates with airway inflammation.

Method

Throat swabs and bronchoalveolar lavage (BAL) were obtained concurrently from 21 CF children and 26 disease controls. Oropharyngeal and lung microbiota were analyzed using 16S rRNA deep sequencing and correlated with neutrophil counts in BAL and antibiotic exposure.

Results

Oropharyngeal microbial communities clustered separately from lung communities and had higher microbial diversity (p < 0.001). CF microbiome differed significantly from non-CF controls, with a higher abundance of Proteobacteria in both upper and lower CF airways. Neutrophil count in the BAL correlated negatively with the diversity but not richness of the lung microbiome. In CF children, microbial genes involved in bacterial motility proteins, two-component system, flagella assembly, and secretion system were enriched in both oropharyngeal and lung microbiome, whereas genes associated with synthesis and metabolism of nucleic acids and protein dominated the non-CF controls.

Conclusions

This study identified a unique microbial profile with altered microbial diversity and metabolic functions in CF airways which is significantly affected by airway inflammation. These results highlight the limitations of using throat swabs as a surrogate to study lower airway microbiome and metagenome in CF children.

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.

A putative enoyl-CoA hydratase contributes to biofilm formation and the antibiotic tolerance of Achromobacter xylosoxidans

Achromobacter xylosoxidans has attracted increasing attention as an emerging pathogen in patients with cystic fibrosis. Intrinsic resistance to several classes of antimicrobials and the ability to form robust biofilms in vivo contribute to the clinical manifestations of persistent A. xylosoxidans infection. Still, much of A. xylosoxidans biofilm formation remains uncharacterized due to the scarcity of existing genetic tools. Here we demonstrate a promising genetic system for use in A. xylosoxidans; generating a transposon mutant library which was then used to identify genes involved in biofilm development in vitro. We further described the effects of one of the genes found in the mutagenesis screen, encoding a putative enoyl-CoA hydratase, on biofilm structure and tolerance to antimicrobials. Through additional analysis, we find that a fatty acid signaling compound is essential to A. xylosoxidans biofilm ultrastructure and maintenance. This work describes methods for the genetic manipulation of A. xylosoxidans and demonstrated their use to improve our understanding of A. xylosoxidans pathophysiology.

Motility, Biofilm Formation and Antimicrobial Efflux of Sessile and Planktonic Cells of Achromobacter xylosoxidans

Achromobacter xylosoxidans is an innately multidrug-resistant bacterium capable of forming biofilms in the respiratory tract of cystic fibrosis (CF) patients. During the transition from the planktonic stage to biofilm growth, bacteria undergo a transcriptionally regulated differentiation. An isolate of A. xylosoxidans cultured from the sputum of a CF patient was separated into sessile and planktonic stages in vitro, and the transcriptomes were compared. The selected genes of interest were subsequently inactivated, and flagellar motility was found to be decisive for biofilm formation in vitro. The spectrum of a new resistance-nodulation-cell division (RND)-type multidrug efflux pump (AxyEF-OprN) was characterized by inactivation of the membrane fusion protein. AxyEF-OprN is capable of extruding some fluoroquinolones (levofloxacin and ciprofloxacin), tetracyclines (doxycycline and tigecycline) and carpabenems (ertapenem and imipenem), which are classes of antimicrobials that are widely used for treatment of CF pulmonary infections.

Microbiological Progress in Patients with Bronchial Infection with <b><i>Pseudomonas aeruginosa</i></b> Treated with Nebulised Colistin

<b><i>Background:</i></b> Inhaled antibiotics allow the delivery of higher drug concentrations at the site of infection without the systemic adverse effects observed with the use of parenteral or oral antibiotics. These antibiotics have shown to decrease the number of exacerbations, reduce bacterial load or improve pulmonary function in several chronic respiratory conditions. <b><i>Objectives:</i></b> The aim of this study was to describe changes in the bacteriology of sputum in patients with chronic bronchial infection with <i>Pseudomonas aeruginosa</i> treated with nebulised colistin. <b><i>Material and Methods:</i></b> All patients with chronical infection with <i>P. aeruginosa</i> treated with nebulised colistin attending a day care unit during a 5-year (January 2010 to December 2014) period were included. Repeated-measures <i>t</i> tests were used to assess whether the introduction of colistin was associated with changes in the number of exacerbations or the length of the hospitalisations. <b><i>Results:</i></b> Treatment with colistin was associated with a decrease in the number of ambulatory exacerbations (1.87–1.1, <i>p</i> = 0.007), of hospital exacerbations (1.3–0.7, <i>p</i> = 0.010) and of length of stay (15.7–8.6 days, <i>p</i> = 0.005). There was no linear trend in the proportion of isolate Enterobacteriaceae, gram-positive cocci, <i>Haemophilus influenzae</i> or fungi. Isolation of Enterobacteriaceae within 1 year after the beginning of the treatment with nebulised colistin was associated with an increase in the number of ambulatory exacerbations (incidence rate ratio 1.99, 95% CI 1.05–3.79). <b><i>Conclusions:</i></b> Nebulised colistin was effective in the treatment of chronic infection with <i>P. aeruginosa,</i> and no significant changes in the microbiological evolution were observed. Isolation of Enterobacteriaceae within 1 year after the beginning of the treatment with nebulised colistin was associated with an increase in the number of exacerbations.

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.

Antibiotic multidrug resistance in the cystic fibrosis airway microbiome is associated with decreased diversity

Background

Cystic fibrosis (CF) is associated with significant morbidity and early mortality due to recurrent acute and chronic lung infections. The chronic use of multiple antibiotics increases the possibility of multidrug resistance (MDR). Antibiotic susceptibility determined by culture-based techniques may not fully represent the resistance profile. The study objective was to detect additional antibiotic resistance using molecular methods and relate the presence of MDR to airway microbiome diversity and pulmonary function.

Methods

Bacterial DNA was extracted from sputum samples and amplified for the V4 region of the 16S rRNA gene. An qPCR array was used to detect antibiotic resistance genes. Clinical culture results and pulmonary function were also noted for each encounter.

Results

Six study participants contributed samples from 19 encounters. Those samples with MDR (n = 7) had significantly lower diversity measured by inverse Simpson's index than those without (n = 12) (2.193 ± 0.427 vs 6.023 ± 1.564, p = 0.035). Differential abundance showed that samples with MDR had more Streptococcus (p = 0.002) and Alcaligenaceae_unclassified (p = 0.002). Pulmonary function was also decreased when MDR was present (FEV₁, 51 ± 22.9 vs 77 ± 26.7, p = 0.054; FVC, 64.5 ± 22.7 vs 91.6 ± 27.7, p = 0.047).

Conclusions

The presence of MDR within the CF airway microbiome was associated with decreased microbial diversity, the presence of Alcaligenes, and decreased pulmonary function.

Proteomic identification of Axc, a novel beta-lactamase with carbapenemase activity in a meropenem-resistant clinical isolate of Achromobacter xylosoxidans

The development of antibiotic resistance during treatment is a threat to patients and their environment. Insight in the mechanisms of resistance development is important for appropriate therapy and infection control. Here, we describe how through the application of mass spectrometry-based proteomics, a novel beta-lactamase Axc was identified as an indicator of acquired carbapenem resistance in a clinical isolate of Achromobacter xylosoxidans. Comparative proteomic analysis of consecutively collected susceptible and resistant isolates from the same patient revealed that high Axc protein levels were only observed in the resistant isolate. Heterologous expression of Axc in Escherichia coli significantly increased the resistance towards carbapenems. Importantly, direct Axc mediated hydrolysis of imipenem was demonstrated using pH shift assays and ¹H-NMR, confirming Axc as a legitimate carbapenemase. Whole genome sequencing revealed that the susceptible and resistant isolates were remarkably similar. Together these findings provide a molecular context for the fast development of meropenem resistance in A. xylosoxidans during treatment and demonstrate the use of mass spectrometric techniques in identifying novel resistance determinants.

Clinical Outcomes Associated with Achromobacter Species Infection in Patients with Cystic Fibrosis

RATIONALE

Achromobacter species are increasingly identified in individuals with cystic fibrosis (CF), but the clinical outcomes in these patients remain poorly understood.

OBJECTIVES

We aimed to determine the association of Achromobacter infection on clinical outcomes in pediatric and adult patients with CF.

METHODS

A cohort study of pediatric and adult patients with CF was conducted from 1997 to 2014 in Toronto, Ontario, Canada. Achromobacter spp. infection was categorized as no history of infection, intermittent infection, and chronic infection (two or more positive cultures in the preceding 12 months). Cox models were used to estimate risk of death or transplantation. Mixed-effects models were used to assess odds of pulmonary exacerbations and effect on lung function (FEV₁%) by Achromobacter spp.

RESULTS

A total of 1,103 patients were followed-up over the course of 18 years; 88 patients (7.3%) had one or more culture for Achromobacter species. Chronic Achromobacter infection was associated with a greater risk of death or transplantation compared with in patients with no history of infection (adjusted hazard ratio, 2.03; 95% confidence interval, 1.05-3.95; P = 0.036). Pulmonary exacerbations were more common in patients with chronic infection, but after adjusting for confounding factors, the effect was no longer significant. The chronic group had lower FEV₁%, but it did not worsen after developing chronic infection.

CONCLUSIONS

Patients with CF and chronic Achromobacter infection are at increased risk of death or transplantation.

Achromobacter Infection Is Rare in Japanese Patients with Pulmonary B-cell Lymphoma

Objective Achromobacter xylosoxidans (A. xylosoxidans) has been recently reported to have an association with the development of pulmonary mucosa-associated lymphoid tissue (MALT) lymphoma in patients from European countries. However, the prevalence rates for A. xylosoxidans may vary significantly from country to country. To assess this association, the prevalence of A. xylosoxidans was analyzed in Japanese patients with pulmonary B-cell lymphoma. Methods DNA samples were obtained from formalin-fixed, paraffin-embedded sections of pulmonary MALT lymphomas (n=52), diffuse large B-cell lymphomas (DLBCLs, n=18), and benign pulmonary lesions (n=19). All samples were histopathologically reviewed by experienced hematopathologists, and the clonality of all MALT lymphoma cases was confirmed by a polymerase chain reaction (PCR)-based IGH rearrangement clonality assay. They were also tested for the API2-MALT1 fusion transcript. The presence of bacterial DNA was assessed with a nested PCR, and DNA sequencing was performed to confirm the PCR specificity. Results A. xylosoxidans DNA was detected in 1/52 cases of pulmonary MALT lymphoma, 2/18 cases of DLBCL, and 0/19 cases of benign pulmonary lesions. The prevalence of A. xylosoxidans in pulmonary lymphoma was not significantly higher than in benign lesions. Conclusion The present study shows that A. xylosoxidans infection may not be associated with pulmonary B-cell lymphoma in a Japanese case series. Large-scale international studies are needed to clarify the role of A. xylosoxidans in pulmonary lymphoma.

An orphan cbb3-type cytochrome oxidase subunit supports Pseudomonas aeruginosa biofilm growth and virulence

Hypoxia is a common challenge faced by bacteria during associations with hosts due in part to the formation of densely packed communities (biofilms). cbb3-type cytochrome c oxidases, which catalyze the terminal step in respiration and have a high affinity for oxygen, have been linked to bacterial pathogenesis. The pseudomonads are unusual in that they often contain multiple full and partial (i.e. 'orphan') operons for cbb3-type oxidases and oxidase subunits. Here, we describe a unique role for the orphan catalytic subunit CcoN4 in colony biofilm development and respiration in the opportunistic pathogen Pseudomonas aeruginosa PA14. We also show that CcoN4 contributes to the reduction of phenazines, antibiotics that support redox balancing for cells in biofilms, and to virulence in a Caenorhabditis elegans model of infection. These results highlight the relevance of the colony biofilm model to pathogenicity and underscore the potential of cbb3-type oxidases as therapeutic targets.