Phenotypic and Transcriptomic Analyses of Seven Clinical Stenotrophomonas maltophilia Isolates Identify a Small Set of Shared and Commonly Regulated Genes Involved in the Biofilm Lifestyle

ABSTRACT Stenotrophomonas maltophilia is one of the most frequently isolated multidrug-resistant nosocomial opportunistic pathogens. It contributes to disease progression in cystic fibrosis (CF) patients and is frequently isolated from wounds, infected tissues, and catheter surfaces. On these diverse surfaces S. maltophilia lives in single-species or multispecies biofilms. Since very little is known about common processes in biofilms of different S. maltophilia isolates, we analyzed the biofilm profiles of 300 clinical and environmental isolates from Europe of the recently identified main lineages Sgn3, Sgn4, and Sm2 to Sm18. The analysis of the biofilm architecture of 40 clinical isolates revealed the presence of multicellular structures and high phenotypic variability at a strain-specific level. Further, transcriptome analyses of biofilm cells of seven clinical isolates identified a set of 106 shared strongly expressed genes and 33 strain-specifically expressed genes. Surprisingly, the transcriptome profiles of biofilm versus planktonic cells revealed that just 9.43% ± 1.36% of all genes were differentially regulated. This implies that just a small set of shared and commonly regulated genes is involved in the biofilm lifestyle. Strikingly, iron uptake appears to be a key factor involved in this metabolic shift. Further, metabolic analyses implied that S. maltophilia employs a mostly fermentative growth mode under biofilm conditions. The transcriptome data of this study together with the phenotypic and metabolic analyses represent so far the largest data set on S. maltophilia biofilm versus planktonic cells. This study will lay the foundation for the identification of strategies for fighting S. maltophilia biofilms in clinical and industrial settings. IMPORTANCE Microorganisms living in a biofilm are much more tolerant to antibiotics and antimicrobial substances than planktonic cells are. Thus, the treatment of infections caused by microorganisms living in biofilms is extremely difficult. Nosocomial infections (among others) caused by S. maltophilia, particularly lung infection among CF patients, have increased in prevalence in recent years. The intrinsic multidrug resistance of S. maltophilia and the increased tolerance to antimicrobial agents of its biofilm cells make the treatment of S. maltophilia infection difficult. The significance of our research is based on understanding the common mechanisms involved in biofilm formation of different S. maltophilia isolates, understanding the diversity of biofilm architectures among strains of this species, and identifying the differently regulated processes in biofilm versus planktonic cells. These results will lay the foundation for the treatment of S. maltophilia biofilms.

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Global analyses imply that Stenotrophomonas maltophilia biofilms are phenotypically highly diverse despite a common transcriptome profile

10.5194/biofilms9-73 ◽

2020 ◽

Author(s):

Ifey Alio ◽

Mirja Gudzuhn ◽

Marie Schölmerich ◽

Pablo Pérez García ◽

Christel Vollstedt ◽

...

Keyword(s):

Biofilm Formation ◽

Stenotrophomonas Maltophilia ◽

Phenotypic Variability ◽

Multidrug Resistant ◽

Clinical Isolates ◽

Clinical Settings ◽

Data Set ◽

Specific Level ◽

Key Factor ◽

Fermentative Growth

Stenotrophomonas maltophilia is one of the most frequently isolated multidrug resistant opportunistic pathogens. It contributes to disease progression in cystic fibrosis patients and is found in wounds, other infected tissues and on catheter surfaces. Only little is known on key processes linked to biofilm formation of S. maltophilia on a broader basis. Thus the aim of this study was the identification of key processes involved in biofilm formation of S. maltophilia on a global level. Therefore, we analyzed biofilm profiles of 300 globally collected clinical and environmental isolates of the main and recently identified lineages Sgn3, Sgn4 and Sm2 - Sm18 (Groeschel et al., 2020). These data together with the 3D structural analysis of a subset of clinical 40 clinical isolates revealed an unexpectedly high phenotypic variability on a strain specific level. Further transcriptome analysis of seven clinical isolates using biofilm grown cells identified a set of 106 shared and coexpressed genes and roughly 30-35 strain-specific genes. Based on these findings S. maltophilia employs a mostly fermentative growth modus under the biofilm conditions and uptake of iron, phosphorous and other metals appears to be of high relevance. Surprisingly, the transcriptome profiles of biofilm versus planktonic cells revealed that only 8.6% of all genes were differentially regulated when both conditions were compared.&#160; This implies that only relatively few genes contribute to the change from planktonic to biofilm life style. Thereby iron uptake appears to be a key factor involved in this metabolic shift. The transcriptome data generated in this study together with the phenotypic and metabolic analysis represent so far the largest data set on S. maltophilia biofilm versus planktonic grown cells. This study now lays the foundation for the identification of new strategies in fighting S. maltophilia infections in clinical settings. Ref: &#160;Gr&#246;schel et al., 2020 ,The phylogenetic landscape and nosocomial spread of the multidrug-resistant opportunist Stenotrophomonas maltophilia. Nature Commun. 2020 Apr 27;11(1):2044. doi: 10.1038/s41467-020-15123-0.

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Prevalence of Antimicrobial Resistance among Clinical Isolates of Bacteroides fragilis Group in Canada in 2010-2011: CANWARD Surveillance Study

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.05823-11 ◽

2011 ◽

Vol 56 (3) ◽

pp. 1247-1252 ◽

Cited By ~ 58

Author(s):

James A. Karlowsky ◽

Andrew J. Walkty ◽

Heather J. Adam ◽

Melanie R. Baxter ◽

Daryl J. Hoban ◽

...

Keyword(s):

Antimicrobial Agents ◽

Bacteroides Fragilis ◽

Clinical Isolates ◽

Surveillance Study ◽

Content Type ◽

Microdilution Method ◽

Broth Microdilution Method ◽

Amoxicillin Clavulanate ◽

Bacteroides Fragilis Group ◽

Bacteroides Ovatus

ABSTRACTClinical isolates of theBacteroides fragilisgroup (n= 387) were collected from patients attending nine Canadian hospitals in 2010-2011 and tested for susceptibility to 10 antimicrobial agents using the Clinical and Laboratory Standards Institute (CLSI) broth microdilution method.B. fragilis(59.9%),Bacteroides ovatus(16.3%), andBacteroides thetaiotaomicron(12.7%) accounted for ∼90% of isolates collected. Overall rates of percent susceptibility were as follows: 99.7%, metronidazole; 99.5%, piperacillin-tazobactam; 99.2%, imipenem; 97.7%, ertapenem; 92.0%, doripenem; 87.3%, amoxicillin-clavulanate; 80.9%, tigecycline; 65.9%, cefoxitin; 55.6%, moxifloxacin; and 52.2%, clindamycin. Percent susceptibility to cefoxitin, clindamycin, and moxifloxacin was lowest forB. thetaiotaomicron(n= 49, 24.5%),Parabacteroides distasonis/P. merdae(n= 11, 9.1%), andB. ovatus(n= 63, 31.8%), respectively. One isolate (B. thetaiotaomicron) was resistant to metronidazole, and two isolates (bothB. fragilis) were resistant to both piperacillin-tazobactam and imipenem. Since the last published surveillance study describing Canadian isolates ofB. fragilisgroup almost 20 years ago (A.-M. Bourgault et al., Antimicrob. Agents Chemother. 36:343–347, 1992), rates of resistance have increased for amoxicillin-clavulanate, from 0.8% (1992) to 6.2% (2010-2011), and for clindamycin, from 9% (1992) to 34.1% (2010-2011).

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Epidemiology and Outcomes of Nontyphoidal Salmonella Bacteremias from England, 2004 to 2015

Journal of Clinical Microbiology ◽

10.1128/jcm.01189-18 ◽

2018 ◽

Vol 57 (1) ◽

Cited By ~ 1

Author(s):

Shannon Katiyo ◽

Berit Muller-Pebody ◽

Mehdi Minaji ◽

David Powell ◽

Alan P. Johnson ◽

...

Keyword(s):

Antimicrobial Agents ◽

High Morbidity ◽

First Line ◽

Data Set ◽

Content Type ◽

Increased Risk ◽

Resistance Patterns ◽

Prolonged Hospital ◽

Antibiotic Resistance Patterns ◽

Emergence Of Resistance

ABSTRACT Nontyphoidal Salmonella (NTS) bacteremia causes hospitalization and high morbidity and mortality. We linked Gastrointestinal Bacteria Reference Unit (GBRU) data to the Hospital Episode Statistics (HES) data set to study the trends and outcomes of NTS bacteremias in England between 2004 and 2015. All confirmed NTS isolates from blood from England submitted to GBRU between 1 January 2004 and 31 December 2015 were deterministically linked to HES records. Adjusted odds ratios (AOR), proportions, and confidence intervals (CI) were calculated to describe differences in age, sex, antibiotic resistance patterns, and serotypes over time. Males, neonates, and adults above 65 years were more likely to have NTS bacteremia (AOR, 1.54 [95% CI, 1.46 to 1.67]; 2.57 [95% CI, 1.43 to 4.60]; and 3.56 [95% CI, 3.25 to 3.90], respectively). Proportions of bacteremia increased from 1.41% in 2004 to 2.67% in 2015. Thirty-four percent of all blood isolates were resistant to a first-line antibiotic, and 1,397 (56%) blood isolates were linked to an HES record. Of the patients with NTS bacteremia, 969 (69%) had a cardiovascular condition and 155 (12%) patients died, out of which 120 (77%) patients were age 65 years and above. NTS bacteremia mainly affects older people with comorbidities placing them at increased risk of prolonged hospital stay and death. Resistance of invasive NTS to first-line antimicrobial agents appeared to be stable in England, but the emergence of resistance to last-resort antibiotics, such as colistin, requires careful monitoring.

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In Vitro Activity of Eravacycline against Gram-Positive Bacteria Isolated in Clinical Laboratories Worldwide from 2013 to 2017

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01715-19 ◽

2019 ◽

Vol 64 (3) ◽

Cited By ~ 1

Author(s):

Ian Morrissey ◽

Stephen Hawser ◽

Sibylle H. Lob ◽

James A. Karlowsky ◽

Matteo Bassetti ◽

...

Keyword(s):

Antimicrobial Agents ◽

Clinical Isolates ◽

Gram Positive ◽

Content Type ◽

Gram Positive Bacteria ◽

Microdilution Method ◽

Clinical Laboratories ◽

Broth Microdilution Method ◽

Doubling Dilution

ABSTRACT Eravacycline is a novel, fully synthetic fluorocycline antibiotic being developed for the treatment of serious infections, including those caused by resistant Gram-positive pathogens. Here, we evaluated the in vitro activities of eravacycline and comparator antimicrobial agents against a recent global collection of frequently encountered clinical isolates of Gram-positive bacteria. The CLSI broth microdilution method was used to determine in vitro MIC data for isolates of Enterococcus spp. (n = 2,807), Staphylococcus spp. (n = 4,331), and Streptococcus spp. (n = 3,373) isolated primarily from respiratory, intra-abdominal, urinary, and skin specimens by clinical laboratories in 37 countries on three continents from 2013 to 2017. Susceptibilities were interpreted using both CLSI and EUCAST breakpoints. There were no substantive differences (a >1-doubling-dilution increase or decrease) in eravacycline MIC90 values for different species/organism groups over time or by region. Eravacycline showed MIC50 and MIC90 results of 0.06 and 0.12 μg/ml, respectively, when tested against Staphylococcus aureus, regardless of methicillin susceptibility. The MIC90 values of eravacycline for Staphylococcus epidermidis and Staphylococcus haemolyticus were equal (0.5 μg/ml). The eravacycline MIC90s for Enterococcus faecalis and Enterococcus faecium were 0.06 μg/ml and were within 1 doubling dilution regardless of the vancomycin susceptibility profile. Eravacycline exhibited MIC90 results of ≤0.06 μg/ml when tested against Streptococcus pneumoniae and beta-hemolytic and viridans group streptococcal isolates. In this surveillance study, eravacycline demonstrated potent in vitro activity against frequently isolated clinical isolates of Gram-positive bacteria (Enterococcus, Staphylococcus, and Streptococcus spp.), including isolates collected over a 5-year period (2013 to 2017), underscoring its potential benefit in the treatment of infections caused by common Gram-positive pathogens.

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In VitroActivities of Retapamulin and 16 Other Antimicrobial Agents against Recently Obtained Streptococcus pyogenes Isolates

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01665-10 ◽

2011 ◽

Vol 55 (5) ◽

pp. 2406-2408 ◽

Cited By ~ 4

Author(s):

Emilio Pérez-Trallero ◽

Esther Tamayo ◽

Milagrosa Montes ◽

José M. García-Arenzana ◽

Victor Iriarte

Keyword(s):

Streptococcus Pyogenes ◽

Antimicrobial Agents ◽

Clinical Isolates ◽

Intrinsic Activity ◽

Antimicrobial Drugs ◽

Blood Samples ◽

Content Type ◽

Topical Antimicrobial

ABSTRACTRetapamulinin vitroactivity against 400Streptococcus pyogenesclinical isolates obtained from skin, pharynx, ear fluid, and blood samples recovered from 2007 to 2009 was studied. The isolates belonged to 26 differentemmtypes, including isolates nonsusceptible to erythromycin (n= 187), tetracycline (n= 99), ciprofloxacin (n= 59), and bacitracin (n= 43). Results were compared to the activities of 16 other antibiotics for topical and systemic use. Retapamulin MICs ranged from ≤0.015 to 0.12 μg/ml, showing the highest intrinsic activity among the topical antimicrobial drugs studied.

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Susceptibility of 186 Nocardia sp. Isolates to 20 Antimicrobial Agents

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01279-10 ◽

2011 ◽

Vol 55 (6) ◽

pp. 2995-2998 ◽

Cited By ~ 72

Author(s):

Julián Larruskain ◽

Pedro Idigoras ◽

José M. Marimón ◽

Emilio Pérez-Trallero

Keyword(s):

Antimicrobial Agents ◽

Clinical Isolates ◽

Northern Spain ◽

Content Type ◽

Antimicrobial Susceptibilities ◽

Nocardia Sp

ABSTRACTThis study determined the antimicrobial susceptibilities of 186 clinical isolates ofNocardiaspp. isolated in Gipuzkoa, northern Spain, between 1998 and 2009. Most isolates were recovered from respiratory samples,Nocardia nova,N. farcinica,N. cyriacigeorgica,N. abscessus, andN. carneabeing the species most frequently isolated. Linezolid and amikacin were the only two antimicrobials to which all isolates were susceptible. The majority ofN. flavorosea,N. carnea, andN. farcinicaisolates were trimethoprim-sulfamethoxazole resistant.

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Involvement of Mutation inampDI,mrcA, and at Least One Additional Gene in β-Lactamase Hyperproduction in Stenotrophomonas maltophilia

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01446-13 ◽

2013 ◽

Vol 57 (11) ◽

pp. 5486-5491 ◽

Cited By ~ 16

Author(s):

Asmaa Talfan ◽

Oliver Mounsey ◽

Matthew Charman ◽

Eleanor Townsend ◽

Matthew B. Avison

Keyword(s):

Escherichia Coli ◽

Degradation Product ◽

Stenotrophomonas Maltophilia ◽

Enteric Bacteria ◽

Clinical Isolates ◽

Wild Type ◽

Targeted Disruption ◽

Content Type ◽

Additional Gene ◽

Multiple Loci

ABSTRACTIt has been reported that targeted disruption ofampDI ormrcAcauses β-lactamase hyperproduction inStenotrophomonas maltophilia. We show here that β-lactamase-hyperproducing laboratory selected mutants and clinical isolates can have wild-typeampDI andmrcAgenes, implicating mutation of at least one additional gene in this phenotype. The involvement of mutations at multiple loci in the activation of β-lactamase production inS. maltophiliareveals that there are significant deviations from the enterobacterial paradigm of AmpR-mediated control of β-lactamase induction. We do show, however, thatS. maltophiliaampDI can complement a mutation inEscherichia coliampD. This suggests that an anhydromuropeptide degradation product of peptidoglycan is used to activate AmpR inS. maltophilia, as is also the case in enteric bacteria.

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Mutations in Ribosomal Protein RplA or Treatment with Ribosomal Acting Antibiotics Activates Production of Aminoglycoside Efflux Pump SmeYZ in Stenotrophomonas maltophilia

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01524-19 ◽

2019 ◽

Vol 64 (2) ◽

Cited By ~ 1

Author(s):

Karina Calvopiña ◽

Punyawee Dulyayangkul ◽

Matthew B. Avison

Keyword(s):

Ribosomal Protein ◽

Stenotrophomonas Maltophilia ◽

Efflux Pump ◽

Clinical Isolates ◽

Efflux System ◽

Aminoglycoside Resistance ◽

Content Type ◽

Ribosomal Protein L1 ◽

Significant Mechanism

ABSTRACT Aminoglycoside resistance in Stenotrophomonas maltophilia is multifactorial, but the most significant mechanism is overproduction of the SmeYZ efflux system. By studying laboratory-selected mutants and clinical isolates, we show here that damage to the 50S ribosomal protein L1 (RplA) activates SmeYZ production. We also show that gentamicin and minocycline, which target the ribosome, induce expression of smeYZ. These findings explain the role of SmeYZ in both intrinsic and mutationally acquired aminoglycoside resistance.

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Candida albicansBiofilms Are Generally Devoid of Persister Cells

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01979-18 ◽

2019 ◽

Vol 63 (5) ◽

Cited By ~ 5

Author(s):

Iryna Denega ◽

Christophe d’Enfert ◽

Sophie Bachellier-Bassi

Keyword(s):

Extracellular Matrix ◽

Antimicrobial Agents ◽

Laboratory Strain ◽

Clinical Isolates ◽

Wild Type ◽

Persister Cells ◽

Content Type ◽

High Concentrations ◽

Ambiguous Data ◽

Very High

ABSTRACTCandida albicansis known for its ability to form biofilms, which are communities of microorganisms embedded in an extracellular matrix developing on different surfaces. Biofilms are highly tolerant to antifungal therapy. This phenomenon has been partially explained by the appearance of so-called persister cells, phenotypic variants of wild-type cells, capable of surviving very high concentrations of antimicrobial agents. Persister cells inC. albicanswere found exceptionally in biofilms, while none were detected in planktonic cultures of this fungus. Yet, this topic remains controversial, as others could not observe persister cells in biofilms formed by theC. albicansSC5314 laboratory strain. Due to ambiguous data in the literature, this work aimed to reevaluate the presence of persister cells inC. albicansbiofilms. We demonstrated that the isolation ofC. albicans“persister cells” as described previously was likely to be the result of the survival of biofilm cells that were not reached by the antifungal. We tested biofilms of SC5314 and its derivatives, as well as 95 clinical isolates, using an improved protocol, demonstrating that persister cells are not a characteristic trait ofC. albicansbiofilms. Although some clinical isolates are able to yield survivors upon the antifungal treatment of biofilms, this phenomenon is rather stochastic and inconsistent.

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In VitroInteractions between Aspirin and Amphotericin B against Planktonic Cells and Biofilm Cells of Candida albicans and C. parapsilosis

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.06082-11 ◽

2012 ◽

Vol 56 (6) ◽

pp. 3250-3260 ◽

Cited By ~ 43

Author(s):

Yabin Zhou ◽

Ganggang Wang ◽

Yutang Li ◽

Yang Liu ◽

Yu Song ◽

...

Keyword(s):

Candida Albicans ◽

Amphotericin B ◽

Antimicrobial Agents ◽

Positive Interactions ◽

Antibiofilm Activity ◽

Data Generation ◽

Planktonic Cells ◽

Content Type ◽

Time Kill

ABSTRACTThe increase in drug resistance and invasion caused by biofilm formation brings enormous challenges to the management ofCandidainfection. Aspirin's antibiofilm activityin vitrowas discovered recently. The spectrophotometric method and the XTT {2,3-bis(2-methoxy-4-nitro-5-sulfophenyl)-5-[(phenylamino)carbonyl]-2H-tetrazolium hydroxide} reduction assay used for data generation make it possible to evaluate fungal biofilm growth accurately. The combined use of the most commonly used methods, the fractional inhibitory concentration index (FICI) and a newly developed method, the ΔEmodel, which uses the concentration-effect relationship over the whole concentration range instead of using the MIC index alone, makes the interpretation of results more reliable. As an attractive tool for studying the pharmacodynamics of antimicrobial agents, time-kill curves can provide detailed information about antimicrobial efficacy as a function of both time and concentration. In the present study,in vitrointeractions between aspirin (acetylsalicylic acid [ASA]) and amphotericin B (AMB) against planktonic cells and biofilm cells ofCandida albicansandC. parapsilosiswere evaluated by the checkerboard microdilution method and the time-kill test. Synergistic and indifferent effects were found for the combination of ASA and AMB against planktonic cells, while strong synergy was found against biofilm cells analyzed by FICI. The ΔEmodel gave more consistent results with FICI. The positive interactions in concentration were also confirmed by the time-kill test. Moreover, this approach also revealed the pharmacodynamics changes of ASA and synergistic action on time. Our findings suggest a potential clinical use for combination therapy with ASA and AMB to augment activity against biofilm-associated infections.

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