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Microbiology Spectrum Feb 2023The genus includes opportunistic pathogens that can cause chronic infections in immunocompromised patients, especially in people with cystic fibrosis (CF). Treatment of...
The genus includes opportunistic pathogens that can cause chronic infections in immunocompromised patients, especially in people with cystic fibrosis (CF). Treatment of infections is complicated by antimicrobial resistance. In this study, a collection of clinical isolates, from CF and non-CF sources, was investigated for polymyxin B (PmB) resistance. Additionally, the effect of PmB challenge in a subset of isolates was examined and the presence of PmB-resistant subpopulations within the isolates was described. Further, chemical and mass spectrometry analyses of the lipid A of clinical isolates enabled the determination of the most common structures and showed that PmB challenge was associated with lipid A modifications that included the addition of glucosamine and palmitoylation and the concomitant loss of the free phosphate at the C-1 position. This study demonstrates that lipid A modifications associated with PmB resistance are prevalent in and that subresistant populations displaying the addition of positively charged residues and additional acyl chains to lipid A can be selected for and isolated from PmB-sensitive clinical isolates. species can cause chronic and potentially severe infections in immunocompromised patients, especially in those with cystic fibrosis. Bacteria cannot be eradicated due to 's intrinsic multidrug resistance. We report that intrinsic resistance to polymyxin B (PmB), a last-resort antimicrobial peptide used to treat infections by multiresistant bacteria, is prevalent in clinical isolates; many isolates also display increased resistance upon PmB challenge. Analysis of the lipopolysaccharide lipid A moiety of several species reveals a penta-acylated lipid A, which in the PmB-resistant isolates was modified by the incorporation of glucosamine residues, an additional acyl chain, loss of phosphates, and hydroxylation of acyl chains, all of which can enhance PmB resistance in other bacteria. We conclude that PmB resistance, particularly in isolates from chronic respiratory infections, is a common phenomenon, and that lipid A displays modifications that may confer increased resistance to polymyxins and potentially other antimicrobial peptides.
Topics: Humans; Polymyxins; Achromobacter; Polymyxin B; Lipid A; Lipopolysaccharides; Cystic Fibrosis; Anti-Bacterial Agents; Microbial Sensitivity Tests
PubMed: 36519943
DOI: 10.1128/spectrum.03729-22 -
Pathogens (Basel, Switzerland) Jan 2022is an opportunistic pathogen that mainly causes chronic lung infections in cystic fibrosis (CF) patients and is associated with increased mortality. Little is known...
is an opportunistic pathogen that mainly causes chronic lung infections in cystic fibrosis (CF) patients and is associated with increased mortality. Little is known about spp. in the lung transplant recipient (LTXr) population. We aimed at describing rates of spp. infection in LTXr prior to, in relation to, and after transplantation, as well as all-cause mortality proportion in infected and uninfected LTXr. We included 288 adult LTXr who underwent lung transplantation (LTX) between 1 January 2010 and 31 December 2019 in Denmark. Bronchoalveolar lavage was performed at regular intervals starting two weeks after transplantation. Positive cultures of spp. were identified in nationwide microbiology registries, and infections were categorized as persistent or transient, according to the proportion of positive cultures. A total of 11 of the 288 LTXr had transient ( = 7) or persistent ( = 4) spp. infection after LTX; CF was the underlying disease in 9 out of 11 LTXr. Three out of the four patients, with persistent infection after LTX, also had persistent infection before LTX. The cumulative incidence of the first episode of infection one year after LTX was 3.8% (95% CI: 1.6-6.0). The incidence rates of transient and persistent infection in the first year after LTX were 27 (12-53) and 15 (5-37) per 1000 person-years of follow-up, respectively. The all-cause mortality proportion one year after LTX was 27% in the spp. infected patients and 12% in the uninfected patients ( = 0.114). spp. mainly affected LTXr with CF as the underlying disease and was rare in non-CF LTXr. Larger studies are needed to assess long-term outcomes of spp. in LTXr.
PubMed: 35215124
DOI: 10.3390/pathogens11020181 -
Applied and Environmental Microbiology Nov 2021In this study, comprehensive analyses were performed to determine the function of an atypical MarR homolog in sp. strain As-55. Genomic analyses of sp. As-55 showed...
In this study, comprehensive analyses were performed to determine the function of an atypical MarR homolog in sp. strain As-55. Genomic analyses of sp. As-55 showed that this is located adjacent to an gene. ArsV is a flavin-dependent monooxygenase that confers resistance to the antibiotic methylarsenite [MAs(III)], the organoarsenic compound roxarsone(III) [Rox(III)], and the inorganic antimonite [Sb(III)]. Similar genes are widely distributed in arsenic-resistant bacteria. Phylogenetic analyses showed that these MarRs are found in operons predicted to be involved in resistance to inorganic and organic arsenic species, so the subfamily was named MarR. MarR orthologs have three conserved cysteine residues, which are Cys36, Cys37, and Cys157 in sp. As-55, mutation of which compromises the response to MAs(III)/Sb(III). GFP-fluorescent biosensor assays show that AdMarR (MarR protein of Achromobacter deleyi As-55) responds to trivalent As(III) and Sb(III) but not to pentavalent As(V) or Sb(V). The results of RT-qPCR assays show that is expressed constitutively in a deletion mutant, indicating that represses transcription of . Moreover, electrophoretic mobility shift assays (EMSAs) demonstrate that AdMarR binds to the promoters of both and in the absence of ligands and that DNA binding is relieved upon binding of As(III) and Sb(III). Our results demonstrate that AdMarR is a novel As(III)/Sb(III)-responsive transcriptional repressor that controls expression of which confers resistance to MAs(III), Rox(III), and Sb(III). AdMarR and its orthologs form a subfamily of MarR proteins that regulate genes conferring resistance to arsenic-containing antibiotics. In this study, a MarR family member, AdMarR was shown to regulate the gene, which confers resistance to arsenic-containing antibiotics. It is a founding member of a distinct subfamily that we refer to as MarR, regulating genes conferring resistance to arsenic and antimony antibiotic compounds. AdMarR was shown to be a repressor containing conserved cysteine residues that are required to bind As(III) and Sb(III), leading to a conformational change and subsequent derepression. Here we show that members of the MarR family are involved in regulating arsenic-containing compounds.
Topics: Achromobacter; Anti-Bacterial Agents; Arsenic; Arsenicals; Cysteine; Drug Resistance, Bacterial; Genes, Bacterial; Multigene Family; Phylogeny; Roxarsone
PubMed: 34613763
DOI: 10.1128/AEM.01588-21 -
Microorganisms Jul 2022Case reports and small series indicate that species bloodstream infection (BSI) is most commonly a complication of hospitalization among patients with chronic lung...
BACKGROUND
Case reports and small series indicate that species bloodstream infection (BSI) is most commonly a complication of hospitalization among patients with chronic lung disease. The aim of the present study was to determine the incidence, risk factors, and outcomes of sp. BSI in an Australian population.
METHODS
Retrospective, laboratory-based surveillance was conducted in Queensland, Australia (population ≈ 5 million) during 2000-2019. Clinical and outcome data were obtained by linkage to state hospital admissions and vital statistics databases. BSI diagnosed within the community or within the first two calendar days of stay in hospital were classified as community-onset. Community-onset BSIs were grouped into community-associated and healthcare-associated.
RESULTS
During more than 86 million person-years of surveillance, 210 incidents of sp. BSI occurred among 195 individuals for an overall age-and sex-standardized annual incidence of 2.6 per million residents. Older individuals and males were at highest risk (2.9 vs. 2.0 per million, IRR for males 1.5; 95% CI, 1.1-1.9; = 0.008). Most (153; 73%) cases were of community-onset of which 100 (48%) and 53 (25%) were healthcare- and community-associated, respectively. An increasing proportion of community-onset cases were observed during twenty years of surveillance. Underlying medical illnesses were common with median (interquartile range) Charlson Comorbidity Index (CCI) scores of 3 (1-5). CCI scores of 0, 1, 2, and 3+ were observed in 37 (18%), 27 (13%), 40 (19%), and 105 (50%) of cases, respectively. All but one of the cases were admitted to hospital for a median (interquartile range) length of stay of 12 (5-34) days. All-cause case-fatality rates in hospital by day 30 and by day 90 were 30 (14%), 28 (13%), and 42 (20%), respectively. The 90-day case-fatality rate increased with increasing comorbidity and was 3% (1/37), 11% (3/27), 25% (10/40), and 27% (28/105) among those with Charlson Comorbidity Indices of 0, 1, 2, and 3+, respectively ( = 0.004).
CONCLUSIONS
Although comorbidity is an important determinant of risk, most sp. BSI are of community-onset and one-fifth of cases occur in patients without significant underlying chronic co-morbidities. This study highlights the value of population-based methodologies to define the epidemiology of an infectious disease.
PubMed: 35889168
DOI: 10.3390/microorganisms10071449 -
Frontiers in Microbiology 2022genus (including , the most prevalent species in patients with cystic fibrosis) is poorly susceptible to most conventional antibiotics. Contribution of efflux by...
genus (including , the most prevalent 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 and 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 to several drugs.
PubMed: 35418957
DOI: 10.3389/fmicb.2022.762307 -
Microbial Genomics Jul 2020Several members of the Gram-negative environmental bacterial genus are associated with serious infections, with being the most common. Despite their pathogenic...
Several members of the Gram-negative environmental bacterial genus are associated with serious infections, with 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 spp. genomes to robustly identify species boundaries, reassign several incorrectly speciated taxa and identify genetic sequences specific for the genus and for . Next, we developed a Black Hole Quencher probe-based duplex real-time PCR assay, Ac-Ax, for the rapid and simultaneous detection of spp. and from both purified colonies and polymicrobial clinical specimens. Ac-Ax was tested on 119 isolates identified as spp. using phenotypic or genotypic methods. In comparison to these routine diagnostic methods, the duplex assay showed superior identification of spp. and , with five isolates failing to amplify with Ac-Ax confirmed to be different genera according to 16S rRNA gene sequencing. Ac-Ax quantified both spp. and down to ~110 genome equivalents and detected down to ~12 and ~1 genome equivalent(s), respectively. Extensive analysis, and laboratory testing of 34 non- 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 spp. and and will facilitate the rapid and accurate diagnosis of this important group of pathogens.
Topics: Achromobacter; Achromobacter denitrificans; Cystic Fibrosis; Early Diagnosis; Genomics; Gram-Negative Bacterial Infections; Humans; Multilocus Sequence Typing; Phenotype; Phylogeny; RNA, Ribosomal, 16S; Real-Time Polymerase Chain Reaction; Sequence Analysis, DNA; Sputum
PubMed: 32667877
DOI: 10.1099/mgen.0.000406 -
Microbiology Spectrum Mar 2024spp. are opportunistic pathogens of environmental origin increasingly isolated in patients with underlying conditions like cystic fibrosis (CF). Despite recent...
UNLABELLED
spp. are opportunistic pathogens of environmental origin increasingly isolated in patients with underlying conditions like cystic fibrosis (CF). Despite recent advances, their virulence factors remain incompletely studied, and siderophore production has not yet been investigated in this genus. The aim of this study was to evaluate the production of siderophores in a large collection of spp. and evaluate the variability according to the origin of the strain and species. A total of 163 strains were studied, including 128 clinical strains (CF and non-CF patients) and 35 strains of environmental origin. Siderophores were quantified by the liquid chrome azurol-sulphonate assay. Species were identified by gene-based phylogeny. Strains were assigned to 20 species, with being the most represented (51.5% of strains). Siderophore production was observed in 72.4% of the strains, with amounts ranging from 10.1% to 90% siderophore units. A significantly higher prevalence of siderophore-producing strains and greater production of siderophores were observed for clinical strains compared with strains of environmental origin. Highly variable observations were made according to species: presented unique characteristics (one of the highest prevalence of producing strains and highest amounts produced, particularly by CF strains). Siderophores are important factors for bacterial growth commonly produced by members of the genus. The significance of the observations made during this study must be further investigated. Indeed, the differences observed according to species and the origin of strains suggest that siderophores may represent important determinants of the pathophysiology of spp. infections and also contribute to the particular epidemiological success of in human infections.
IMPORTANCE
spp. are recognized as emerging opportunistic pathogens in humans with various underlying diseases, including cystic fibrosis (CF). Although their pathophysiological traits are increasingly studied, their virulence factors remain incompletely described. Particularly, siderophores that represent important factors of bacterial growth have not yet been studied in this genus. A population-based study was performed to explore the ability of members of the genus to produce siderophores, both overall and in relevant subgroups ( species; strain origin, either clinical-from CF or non-CF patients-or environmental). This study provides original data showing that siderophore production is a common trait of strains, particularly observed among clinical strains. The major species, , encompassed both one of the highest prevalence of siderophore-producing strains and strains producing the largest amounts of siderophores, particularly observed for CF strains. These observations may represent additional advantages accounting for the epidemiological success of this species.
Topics: Humans; Achromobacter; Cystic Fibrosis; Prevalence; Gram-Negative Bacterial Infections; Achromobacter denitrificans; Virulence Factors; Siderophores
PubMed: 38315029
DOI: 10.1128/spectrum.02953-23 -
Ecotoxicology and Environmental Safety Dec 2021Neonicotinoids are among the most widely used insecticides worldwide, and as such, have garnered increasing attention from the scientific community in regards to their...
Neonicotinoids are among the most widely used insecticides worldwide, and as such, have garnered increasing attention from the scientific community in regards to their potentially negative environmental impacts. Recently, the degradability of neonicotinoid in soil has gained more attentions. However, what role soil microbes play in this degradation remains vastly underexplored. In this study, we compared the capacity of soil microbes sampled from different geographic regions and fields to degrade the neonicotinoid insecticide imidacloprid. Additionally, the composition of microbiota having low, middle, and high degradation activity was analyzed via high throughput sequencing. Correlations between microbiota composition and degradation activities were analyzed and reconfirmed. The results showed that the composition of soil microbiota and their degradation activity (ranged from zero to 96.25%) varied significantly between soil samples from different geographic locations. Correlation analysis showed that Paracoccus and Achromobacter bacteria were positively correlated with high degradation activity. Imidacloprid degradation experiments using these bacteria showed that Achromobacter sp. alone exhibited degradation activity reaching and sustaining 100% by day 20 while Paracoccus sp. did not. However, combining these bacteria resulted in increased degradation activity which reached 100% at day 15 relative to that achieved by Achromobacter sp. alone. This study demonstrated the capacity of soil microbes to degrade imidacloprid, and identified two promising bacterial candidates that could be potentially used in future to reduce imidacloprid accumulation in soils.
Topics: Achromobacter; Bacteria; Biodegradation, Environmental; Insecticides; Neonicotinoids; Nitro Compounds; Paracoccus; Soil; Soil Microbiology; Soil Pollutants
PubMed: 34544021
DOI: 10.1016/j.ecoenv.2021.112785 -
Microbiology Spectrum Apr 2022Achromobacter denitrificans is an environmental opportunistic pathogen that is infecting a large number of immunocompromised patients. A more recently identified strain...
Achromobacter denitrificans is an environmental opportunistic pathogen that is infecting a large number of immunocompromised patients. A more recently identified strain from the historical collection of strains of Achromobacter denitrificans is Achromobacter mucicolens. In hosts with a variety of underlying diseases, spp. can induce a wide spectrum of disorders. Because of the bacterium's intrinsic genetic constitution and resistance gained over time, antibiotics are challenged to handle Due to the fact that is rare and its taxonomy is not completely understood, it is difficult to define clinical symptoms, acquisition risk factors, and thus the best therapeutic course of action. To help comprehend this intrinsic and acquired resistance, we analyzed the entire genome of the strain and utilized bioinformatics methods to estimate the strain's probable drug resistance profile. In our study, we have isolated and cultured a clinically important strain and subjected it to antimicrobial susceptibility tests against antibiotics in the Vitek 2 testing system. The strain's genome sequence as well as an investigation of 27 of its phenotypic traits provides important information regarding this pathogen. The genome of this strain possesses a number of antibiotic resistance genes that code for efflux pump systems and other antibiotic-regulating as well as -modifying enzymes. Our research analysis predicted genes involved in drug resistance, including genes for efflux pump systems, antibiotic efflux, antibiotic inactivation, and antibiotic target alteration. studies validated the genomic evidence for its ability to exhibit resistance against a wide range of antibiotics. Our investigation paves the way for more research on understanding the functioning of the key discovered genes that contribute toward the pathogenicity of and hence gives new information and treatment options for this emerging pathogen. species are well-known opportunistic human pathogens that can be found in water and soil and most commonly in hospital settings. They thrive in immunocompromised individuals, producing sporadic cases of pneumonia, septicemia, peritonitis, urinary tract infections, and other illnesses. strains are inherently resistant to a wide spectrum of antibiotics, making them difficult to treat promptly. The strain under study, , was notably resistant to various antibiotics, and the infection could be controlled only after several rounds of prescription medications at different doses. This consumed a lot of time and put the already immunosuppressed leukemic patient through a great ordeal. The study aimed to raise awareness about the importance of the bacterium's lethality, and doctors should evaluate the bacterium's potential for resistance before prescribing antibiotics. Sanitation and other precautions should also be implemented in hospitals and other public places.
Topics: Achromobacter; Achromobacter denitrificans; Anti-Bacterial Agents; Drug Resistance, Microbial; Genomics; Humans; Microbial Sensitivity Tests
PubMed: 35377213
DOI: 10.1128/spectrum.01916-21 -
Microorganisms Nov 2021species are isolated from rare but severe healthcare-associated infections, including surgical site infections. They are considered to preferentially infect... (Review)
Review
species are isolated from rare but severe healthcare-associated infections, including surgical site infections. They are considered to preferentially infect immunocompromised patients but so far with limited evidence. We conducted a systematic review on spp. surgical site infections (SSIs) to determine if such infections were indeed more commonly associated with immunocompromised patients. The secondary objective was to describe the characteristics of infected patients. Eligible articles had to be published before 30 September 2020 and to report spp. SSIs across all surgical specialties excluding ophthalmology. Analyses were performed on individual data without meta-analysis. Cases were divided into 2 subgroups: one group which had either prosthesis or implant and the other group which did not. A first selection led to a review of 94 articles, of which 37 were analyzed. All were case reports or case series and corresponded to 49 infected patients. Most of the patients were under 65 years of age and had undergone a heart or digestive surgery followed by deep infection with no co-infecting pathogens. Nine out of the 49 cases were immunocompromised, with similar distribution between the two subgroups (16.6% and 20%, respectively). This review suggests that spp. SSIs do not preferentially target immunocompromised patients.
PubMed: 34946073
DOI: 10.3390/microorganisms9122471