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Microbial Genomics Jul 2021species are increasingly being detected in cystic fibrosis (CF) patients, where they can establish chronic infections by adapting to the lower airway environment. To...
species are increasingly being detected in cystic fibrosis (CF) patients, where they can establish chronic infections by adapting to the lower airway environment. To better understand the mechanisms contributing to a successful colonization by species, we sequenced the whole genome of 54 isolates from 26 patients with occasional and early/late chronic lung infection. We performed a phylogenetic analysis and compared virulence and resistance genes, genetic variants and mutations, and hypermutability mechanisms between chronic and occasional isolates. We identified five species as well as two non-affiliated genogroups (NGs). Among them were the frequently isolated and four other species whose clinical importance is not yet clear: and . While and were isolated only from chronically infected patients and only from occasionally infected patients, the other species were found in both groups. Most of the occasional isolates lacked functional genes involved in invasiveness, chemotaxis, type 3 secretion system and anaerobic growth, whereas the great majority (>60%) of chronic isolates had these genomic features. Interestingly, almost all (=22/23) late chronic isolates lacked functional genes involved in lipopolysaccharide production. Regarding antibiotic resistance, we observed a species-specific distribution of genes, confirming what has been reported in the literature and additionally identifying in some isolates and observing no genes in or NGs. No significant difference in resistance genes was found between chronic and occasional isolates. The results of the mutator genes analysis showed that no occasional isolate had hypermutator characteristics, while 60% of early chronic (<1 year from first colonization) and 78% of late chronic (>1 year from first colonization) isolates were classified as hypermutators. Although all and NG isolates presented two different genes, these seem to have a complementary rather than compensatory function. In conclusion, our results show that species can exhibit different adaptive mechanisms and some of these mechanisms might be more useful than others in establishing a chronic infection in CF patients, highlighting their importance for the clinical setting and the need for further studies on the less clinically characterized species.
Topics: Achromobacter; Cystic Fibrosis; Drug Resistance, Bacterial; Genome, Bacterial; Gram-Negative Bacterial Infections; Humans; Lung; MutS Proteins; Persistent Infection; Virulence Factors; Whole Genome Sequencing; beta-Lactamases
PubMed: 34292148
DOI: 10.1099/mgen.0.000606 -
Revista Argentina de Microbiologia 2020Different phenotype-based techniques and molecular tools were used to describe the distribution of different Achromobacter species in patients with cystic fibrosis (CF)...
Different phenotype-based techniques and molecular tools were used to describe the distribution of different Achromobacter species in patients with cystic fibrosis (CF) in Argentina, and to evaluate their antibiotic resistance profile. Phenotypic identification was performed by conventional biochemical tests, commercial galleries and MALDI-TOF MS. Genetic approaches included the detection of A. xylosoxidans specific marker bla, the amplification and sequencing of the 16S rRNA gene, nrdA and bla complete sequence, and MLST analysis. Phenotypic approaches, even MALDI-TOF, rendered inconclusive or misleading results. On the contrary, concordant results were achieved with the nrdA sequencing or sequence type (ST) analysis, and the complete bla sequencing, allowing a reliable discrimination of different Achromobacter species. A. xylosoxidans accounted for 63% of Achromobacter infections and A. ruhlandii accounted for 17%. The remaining species corresponded to A. insuavis, A. dolens, A. marplatensis and A. pulmonis. Antimicrobial susceptibilities were determined by the agar dilution method according to CLSI guidelines. Piperacillin, piperacillin/tazobactam and carbapenems were the most active antibiotics. However, the emergence of carbapenem-resistant isolates was detected. In conclusion, prompt and accurate identification tools were necessary to determine that different Achromobacter species may colonize/infect the airways of patients with CF. Moreover, antimicrobial therapy should be administered based on the susceptibility profile of individual Achromobacter sp. isolates.
Topics: Achromobacter; Anti-Bacterial Agents; Argentina; Cystic Fibrosis; Drug Resistance, Bacterial; Humans; Phenotype
PubMed: 31253503
DOI: 10.1016/j.ram.2019.03.004 -
Infection and Immunity Jul 2023Achromobacter xylosoxidans (Ax) is an opportunistic pathogen and causative agent of numerous infections particularly in immunocompromised individuals with increasing...
Achromobacter xylosoxidans (Ax) is an opportunistic pathogen and causative agent of numerous infections particularly in immunocompromised individuals with increasing prevalence in cystic fibrosis (CF). To date, investigations have focused on the clinical epidemiology and genomic comparisons of Ax isolates, yet little is known about disease pathology or the role that specific virulence factors play in tissue invasion or damage. Here, we model an acute Ax lung infection in immunocompetent C57BL/6 mice and immunocompromised CF mice, revealing a link between cytotoxicity and disease in an intact host. Mice were intratracheally challenged with sublethal doses of a cytotoxic (GN050) or invasive (GN008) strain of Ax. Bacterial burden, immune cell populations, and inflammatory markers in bronchoalveolar lavage fluid and lung homogenates were measured at different time points to assess disease severity. CF mice had a similar but delayed immune response toward both Ax strains compared to C57BL/6J mice. GN050 caused more severe disease and higher mortality which correlated with greater bacterial burden and increased proinflammatory responses in both mouse models. In agreement with the cytotoxicity of GN050 toward macrophages , mice challenged with GN050 had fewer macrophages. Mutants with transposon insertions in predicted virulence factors of GN050 showed that disease severity depended on the type III secretion system, Vi capsule, antisigma-E factor, and partially on the ArtA adhesin. The development of an acute infection model provides an essential tool to better understand the infectivity of diverse Ax isolates and enable improved identification of virulence factors important to bacterial persistence and disease.
Topics: Animals; Mice; Achromobacter denitrificans; Virulence Factors; Disease Models, Animal; Gram-Negative Bacterial Infections; Mice, Inbred C57BL; Cystic Fibrosis
PubMed: 37255468
DOI: 10.1128/iai.00037-23 -
Genes Apr 2021In patients with cystic fibrosis (CF), the lung is a remarkable ecological niche in which the microbiome is subjected to important selective pressures. An inexorable... (Review)
Review
In patients with cystic fibrosis (CF), the lung is a remarkable ecological niche in which the microbiome is subjected to important selective pressures. An inexorable colonization by bacteria of both endogenous and environmental origin is observed in most patients, leading to a vicious cycle of infection-inflammation. In this context, long-term colonization together with competitive interactions among bacteria can lead to over-inflammation. While and , the two pathogens most frequently identified in CF, have been largely studied for adaptation to the CF lung, in the last few years, there has been a growing interest in emerging pathogens of environmental origin, namely and . The aim of this review is to gather all the current knowledge on the major pathophysiological traits, their supporting mechanisms, regulation and evolutionary modifications involved in colonization, virulence, and competitive interactions with other members of the lung microbiota for these emerging pathogens, with all these mechanisms being major drivers of persistence in the CF lung. Currently available research on complex and shows that these emerging pathogens share important pathophysiological features with well-known CF pathogens, making them important members of the complex bacterial community living in the CF lung.
Topics: Achromobacter denitrificans; Adaptation, Physiological; Cystic Fibrosis; Gram-Negative Bacterial Infections; Humans; Lung; Mutation Rate; Stenotrophomonas maltophilia
PubMed: 33919046
DOI: 10.3390/genes12050610 -
Frontiers in Bioscience (Scholar... Mar 2022The role of species in lung disease remains unclear. The aim of this study was to characterize isolated from persons with cystic fibrosis and from other clinical...
The role of species in lung disease remains unclear. The aim of this study was to characterize isolated from persons with cystic fibrosis and from other clinical samples. Whole genome sequences from 101 isolates were determined (81 from patients with cystic fibrosis and 20 from other patients) and analysed. Taxonomic analysis showed nine species including two putative novel species. Thirty-five novel sequence types were present. The most active agent was co-trimoxazole followed by imipenem, but Minimal Inhibitory Concentrations (MICs) were high. Acquired antibiotic resistance genes were rare. Their presence did not correlate with minimal inhibitory concentrations suggesting that other mechanisms are involved. Genes for proposed virulence factors were present in only some isolates. Two putative novel species were identified. The putative virulence properties of involved in infections are variable. Despite the high MICs, acquired resistance genes are uncommon.
Topics: Achromobacter; Anti-Bacterial Agents; Cystic Fibrosis; Drug Resistance, Microbial; Gram-Negative Bacterial Infections; Humans; Virulence Factors
PubMed: 35730434
DOI: 10.31083/j.fbs1402009 -
International Journal of Microbiology 2022Hydrocarbon-derived pollutants are becoming one of the most concerning ecological issues. Thus, there is a need to investigate and develop innovative, low-cost,...
Hydrocarbon-derived pollutants are becoming one of the most concerning ecological issues. Thus, there is a need to investigate and develop innovative, low-cost, eco-friendly, and fast techniques to reduce and/or eliminate pollutants using biological agents. The study was conducted to isolate, characterize, and identify potential diesel-degrading bacteria. Samples were collected from flower farms, lakeshores, old aged garages, asphalt, and bitumen soils and spread on selective medium (Bushnell Haas mineral salt agar) containing diesel as the growth substrate. The isolates were characterized based on their growth patterns using optical density measurement, biochemical tests, and gravimetric analysis and identified using the Biolog database and 16S rRNA gene sequencing techniques. Subsequently, six diesel degraders were identified and belong to , , , , , and . Among these, based on gravimetric analysis, the three potent isolates AAUW23, AAUG11, and AAUG36 achieved 84%, 83.4%, and 83% diesel degradation efficiency, respectively, in 15 days. Consequently, the partial 16S rRNA gene sequences revealed that the two most potent bacterial strains (AAUW23 and AAUG11) were , while AAUG36 was . This study demonstrated that bacterial species isolated from hydrocarbon-contaminated and/or uncontaminated environments could be optimized to be used as potential bioremediation agents for diesel removal.
PubMed: 35096070
DOI: 10.1155/2022/5655767 -
Sexual Medicine Apr 2021Vulvodynia, vulvar pain syndrome, is defined as vulvar pain of at least a 3-month duration without a clear identifiable cause, which may have associated factor and the...
INTRODUCTION
Vulvodynia, vulvar pain syndrome, is defined as vulvar pain of at least a 3-month duration without a clear identifiable cause, which may have associated factor and the etiology and treatment of this challenging disease is still unclear. Dyspareunia is a relevant symptom of patients with vulvodynia. Vaginal microbiome has known an important role in local immune-inflammatory responses and it may be important pathogenic mechanism in vulvodynia.
AIM
The objective of this study was to investigate the association of vaginal microbiome and vulvodynia.
METHODS
We analyzed the microbial compositions of the vestibule and vagina among women with clinically diagnosed vulvodynia (n = 22) and age-matched healthy controls (n = 22) without vulvodynia. The compositions of bacterial microbiomes were compared by pyrosequencing of the 16S rRNA.
MAIN OUTCOME MEASURE
Vaginal microbiome alpha and beta diversity were assessed using the Shannon diversity index and Heat map. Linear discriminant analysis effect size was used to find out marker for vulvodynia.
RESULTS
There were no significant differences in the age, duration of marriage, history of gynecologic surgery, parity, and menopause status between cases and controls. A total of 1,661,934 high-quality pyrosequencing reads was obtained to evaluate bacterial diversity, and 50,246 unique sequences represented all phylotypes. The type and mean number of the genera were not different between cases and controls. However, the most predominant phyla of bacteria were significantly different between cases and controls. 3 phyla (Firmicutes, Actinobacteria, and Tenericutes) and 11 genera including Gardnerella, Ureaplasma, Achromobacter, Mycoplasma, and Bifidobacteria were significantly more prevalent in cases than in controls (P < .05). Linear discriminant analysis effect size analysis suggest the Bifidobacterium, Mycoplasma, and Fenollaria species can be potential markers for vulvodynia.
CONCLUSION
Our results suggest the differences in vaginal microbiome can be associated with the vulvodynia. Park SY, Lee ES, Lee SR, et al. Vaginal Microbiome Is Associated With Vulvodynia, Vulvar Pain Syndrome: A Case-Control Study. Sex Med 2021;9:100314.
PubMed: 33652201
DOI: 10.1016/j.esxm.2020.100314 -
Antimicrobial Agents and Chemotherapy Oct 2020spp. are recognized as emerging pathogens in patients with cystic fibrosis (CF). Though recent works have established species-level identification using sequencing,...
spp. are recognized as emerging pathogens in patients with cystic fibrosis (CF). Though recent works have established species-level identification using sequencing, there is a dearth in knowledge relating to species-level antimicrobial susceptibility patterns and antimicrobial combinations, which hampers the use of optimal antimicrobial combinations for the treatment of chronic infections. The aims of this study were to (i) identify at species-level referred isolates, (ii) describe species-level antimicrobial susceptibility profiles, and (iii) determine the most promising antimicrobial combination for chronic infections. A total of 112 multidrug-resistant (MDR) species isolates from 39 patients were identified using sequencing. Antimicrobial susceptibility and combination testing were carried out using the Etest method. We detected six species of and found that was the most prevalent species. Interestingly, sequence analysis showed it was responsible for persistent infection (18/28 patients), followed by (2/3 patients). Piperacillin-tazobactam (70.27%) and co-trimoxazole (69.72%) were the most active antimicrobials. Differences were observed in species-level susceptibility to ceftazidime, carbapenems, ticarcillin-clavulanate, and tetracycline. Antimicrobial combinations with co-trimoxazole or tobramycin demonstrate the best synergy, while co-trimoxazole gave the best susceptibility breakpoint index values. This study enriches the understanding of MDR spp. epidemiology and confirms prevalence and chronic colonization of in CF lungs. It presents data to support the efficacy of new combinations for use in the treatment of chronic infections.
Topics: Achromobacter; Achromobacter denitrificans; Anti-Bacterial Agents; Cystic Fibrosis; Gram-Negative Bacterial Infections; Humans; Microbial Sensitivity Tests
PubMed: 32816722
DOI: 10.1128/AAC.01467-20 -
European Review For Medical and... Sep 2022Achromobacter spp. are aerobic, non-fermentative Gram-negative bacilli that can be widely found in aquatic environments. Nosocomial outbreaks and pseudo-outbreaks of...
OBJECTIVE
Achromobacter spp. are aerobic, non-fermentative Gram-negative bacilli that can be widely found in aquatic environments. Nosocomial outbreaks and pseudo-outbreaks of Achromobacter spp. bacteremia have been recognized for decades. Notably, commonly used germicides in hospital settings constitute important sources for these outbreaks. This review aims at summarizing the latest studies and presents the characteristics of nosocomial outbreaks of Achromobacter spp. bacteremia caused by germicide contamination.
MATERIALS AND METHODS
A systematic search of the PubMed and EMBASE databases was conducted for articles published in English between January 1, 2000, and June 10, 2022.
RESULTS
Overall, 170 articles were retrieved, and 7 studies were finally included in the systematic review. Whether true or pseudo-bacteremia, positive blood culture results were most commonly reported in immunosuppressed patients or those with indwelling catheters. The most commonly reported contaminated germicide was chlorhexidine solution used as both an antiseptic and disinfectant. Atomizers, dispensers, and various product containers were identified as reservoirs. The prognoses of the affected patients were generally favorable.
CONCLUSIONS
Awareness about the high survival ability of Achromobacter spp. in germicides and the possible hospital reservoirs of these microbes will help to improve infection control and prevent nosocomial outbreaks or pseudo-outbreaks caused by Achromobacter spp.
Topics: Achromobacter; Anti-Infective Agents; Anti-Infective Agents, Local; Bacteremia; Chlorhexidine; Cross Infection; Disease Outbreaks; Disinfectants; Hospitals; Humans
PubMed: 36111940
DOI: 10.26355/eurrev_202209_29664 -
The Canadian Journal of Infectious... 2022Cystic fibrosis (CF) is an inherited recessive disorder characterized by recurrent and persistent pulmonary infections, resulting in lung function deterioration and...
BACKGROUND
Cystic fibrosis (CF) is an inherited recessive disorder characterized by recurrent and persistent pulmonary infections, resulting in lung function deterioration and early mortality.
METHODS
A cross-sectional study was conducted on the bacterial profile and antibiotic resistance pattern of 103 respiratory specimens from CF patients with signs of pulmonary exacerbation. Antibiotic susceptibility testing and biofilm formation of and isolates were performed by the Kirby-Bauer disc diffusion method and microtiter plate assay, respectively. Molecular typing of and isolates was carried out by spa typing and repetitive extragenic palindromic element PCR.
RESULTS
In a total of 129 isolates, the most prevalent organisms were (55.3%) and (41.7%). Other less prevalent bacterial isolates include coagulase-negative staphylococci, , , , and . The highest rate of resistance for was observed to azithromycin and erythromycin (80%), ciprofloxacin (52.3%), clindamycin (44.6%) and tetracycline (43%). Twenty percent of isolates were methicillin-resistant (MRSA) and 47.6% were MDR . For isolates the highest resistance was to cefepime (38.3%) and levofloxacin (33.3%) and 20% showed MDR phenotype.
CONCLUSION
Our study demonstrated a significant decline in the prevalence of infections in comparison to previous studies. We found to be more prevalent in younger patients, whereas mucoid showed a shift in prevalence toward older ages. Molecular typing methods showed great diversity between isolates.
PubMed: 36593975
DOI: 10.1155/2022/5831139