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Sapula SA, Hart BJ, Siderius NL, Amsalu A, Blaikie JM, Venter H. Multidrug-resistant Stenotrophomonas maltophilia in residential aged care facilities: An emerging threat. Microbiologyopen 2024; 13:e1409. [PMID: 38682784 PMCID: PMC11057060 DOI: 10.1002/mbo3.1409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 03/20/2024] [Accepted: 04/16/2024] [Indexed: 05/01/2024] Open
Abstract
Stenotrophomonas maltophilia is a multidrug-resistant (MDR), Gram-negative bacterium intrinsically resistant to beta-lactams, including last-resort carbapenems. As an opportunistic pathogen, it can cause serious healthcare-related infections. This study assesses the prevalence, resistance profiles, and genetic diversity of S. maltophilia isolated from residential aged care facilities (RACFs). RACFs are known for their overuse and often inappropriate use of antibiotics, creating a strong selective environment that favors the development of bacterial resistance. The study was conducted on 73 S. maltophilia isolates recovered from wastewater and facility swab samples obtained from three RACFs and a retirement village. Phenotypic and genotypic assessments of the isolates revealed high carbapenem resistance, exemplifying their intrinsic beta-lactam resistance. Alarmingly, 49.3% (36/73) of the isolates were non-wild type for colistin, with minimum inhibitory concentration values of > 4 mg/L, and 11.0% (8/73) were resistant to trimethoprim-sulfamethoxazole. No resistance mechanisms were detected for either antimicrobial. Genotypic assessment of known lineages revealed isolates clustering with Sm17 and Sm18, lineages not previously reported in Australia, suggesting the potential ongoing spread of MDR S. maltophilia. Lastly, although only a few isolates were biocide tolerant (2.7%, 2/73), their ability to grow in high concentrations (64 mg/L) of triclosan is concerning, as it may be selecting for their survival and continued dissemination.
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Affiliation(s)
- Sylvia A. Sapula
- Health and Biomedical Innovation, UniSA Clinical and Health SciencesUniversity of South AustraliaAdelaideSouth AustraliaAustralia
| | - Bradley J. Hart
- Health and Biomedical Innovation, UniSA Clinical and Health SciencesUniversity of South AustraliaAdelaideSouth AustraliaAustralia
| | - Naomi L. Siderius
- Health and Biomedical Innovation, UniSA Clinical and Health SciencesUniversity of South AustraliaAdelaideSouth AustraliaAustralia
| | - Anteneh Amsalu
- Health and Biomedical Innovation, UniSA Clinical and Health SciencesUniversity of South AustraliaAdelaideSouth AustraliaAustralia
- Department of Medical MicrobiologyUniversity of GondarGondarEthiopia
| | - Jack M. Blaikie
- Health and Biomedical Innovation, UniSA Clinical and Health SciencesUniversity of South AustraliaAdelaideSouth AustraliaAustralia
| | - Henrietta Venter
- Health and Biomedical Innovation, UniSA Clinical and Health SciencesUniversity of South AustraliaAdelaideSouth AustraliaAustralia
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2
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Bourdin T, Benoit MÈ, Bédard E, Prévost M, Quach C, Déziel E, Constant P. High-Throughput Short Sequence Typing Schemes for Pseudomonas aeruginosa and Stenotrophomonas maltophilia Pure Culture and Environmental DNA. Microorganisms 2023; 12:48. [PMID: 38257875 PMCID: PMC10819370 DOI: 10.3390/microorganisms12010048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 12/22/2023] [Accepted: 12/25/2023] [Indexed: 01/24/2024] Open
Abstract
Molecular typing techniques are utilized to determine genetic similarities between bacterial isolates. However, the use of environmental DNA profiling to assess epidemiologic links between patients and their environment has not been fully explored. This work reports the development and validation of two high-throughput short sequence typing (HiSST) schemes targeting the opportunistic pathogens Pseudomonas aeruginosa and Stenotrophomonas maltophilia, along with a modified SM2I selective medium for the specific isolation of S. maltophilia. These HiSST schemes are based on four discriminative loci for each species and demonstrate high discriminating power, comparable to pairwise whole-genome comparisons. Each scheme includes species-specific PCR primers for precise differentiation from closely related taxa, without the need for upstream culture-dependent methods. For example, the primers targeting the bvgS locus make it possible to distinguish P. aeruginosa from the very closely related Pseudomonas paraeruginosa sp. nov. The selected loci included in the schemes are adapted to massive parallel amplicon sequencing technology. An R-based script implemented in the DADA2 pipeline was assembled to facilitate HiSST analyses for efficient and accurate genotyping of P. aeruginosa and S. maltophilia. We demonstrate the performance of both schemes through in silico validations, assessments against reference culture collections, and a case study involving environmental samples.
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Affiliation(s)
- Thibault Bourdin
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, 531 Boulevard des Prairies, Laval, QC H7V 1B7, Canada;
| | - Marie-Ève Benoit
- CHU Sainte-Justine Research Center, Montréal, QC H3T 1C5, Canada; (M.-È.B.); (C.Q.)
| | - Emilie Bédard
- Department of Civil Engineering, Polytechnique Montréal, Montréal, QC H3T 1J4, Canada; (E.B.); (M.P.)
| | - Michèle Prévost
- Department of Civil Engineering, Polytechnique Montréal, Montréal, QC H3T 1J4, Canada; (E.B.); (M.P.)
| | - Caroline Quach
- CHU Sainte-Justine Research Center, Montréal, QC H3T 1C5, Canada; (M.-È.B.); (C.Q.)
| | - Eric Déziel
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, 531 Boulevard des Prairies, Laval, QC H7V 1B7, Canada;
| | - Philippe Constant
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, 531 Boulevard des Prairies, Laval, QC H7V 1B7, Canada;
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Guillén-Navarro D, González-Vázquez R, León-Ávila G, Giono-Cerezo S. Quorum Quenching with a Diffusible Signal Factor Analog in Stenotrophomonas maltophilia. Pathogens 2023; 12:1448. [PMID: 38133331 PMCID: PMC10746098 DOI: 10.3390/pathogens12121448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/04/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023] Open
Abstract
Stenotrophomonas maltophilia is a multidrug-resistant Gram-negative bacillus associated with nosocomial infections in intensive care units, and nowadays, its acquired resistance to trimethoprim-sulfamethoxazole (SXT) by sul genes within class 1 integrons is a worldwide health problem. Biofilm and motility are two of the major virulence factors in this bacterium and are auto-induced by the diffusible signal factor (DSF). In recent studies, retinoids have been used to inhibit (Quorum Quenching) these virulence factors and for their antimicrobial effect. The aim was to reduce biofilm formation and motility with retinoic acid (RA) in S. maltophilia SXT-resistant strains. Eleven SXT-resistant strains and two SXT-susceptible strains were tested for biofilm formation/reduction and planktonic/sessile cell viability with RA and SXT-MIC50/RA; motility (twitching, swimming, swarming) was measured with/without RA; and MLST typing was determined. The biofilm formation of the strains was classified as follows: 15.38% (2/13) as low, 61.54% (8/13) as moderate, and 23.08% (3/13) as high. It was significantly reduced with RA and SXT-MIC50/RA (p < 0.05); cell viability was not significantly reduced with RA (p > 0.05), but it was with SXT-MIC50/RA (p < 0.05); and swimming (p < 0.05) and swarming (p < 0.05) decreased significantly. MLST typing showed the first and novel strains of Mexican S. maltophilia registered in PubMLST (ST479-485, ST497, ST23, ST122, ST175, ST212, and ST300). In conclusion, RA reduced biofilm formation and motility without affecting cell viability; furthermore, antimicrobial synergism with SXT-MIC50/RA in different and novel STs of S. maltophilia was observed.
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Affiliation(s)
- Dafne Guillén-Navarro
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Departamento de Microbiología, Prolongación de Carpio y Plan de Ayala S/N, Col. Casco de Santo Tomás, Alcaldía Miguel Hidalgo, Mexico City 11340, Mexico
- Posgrado en Ciencias Quimicobiológicas, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Col. Casco de Santo Tomás, Alcaldía Miguel Hidalgo, Mexico City 11340, Mexico
| | - Rosa González-Vázquez
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Departamento de Microbiología, Prolongación de Carpio y Plan de Ayala S/N, Col. Casco de Santo Tomás, Alcaldía Miguel Hidalgo, Mexico City 11340, Mexico
- Instituto Mexicano del Seguro Social, Unidad Médica de Alta Especialidad, Hospital de Especialidades “Dr. Antonio Fraga Mouret”, Centro Médico Nacional La Raza. Seris y Zaachila S/N, Col. La Raza, Alcaldía Azcapotzalco, Mexico City 04960, Mexico
| | - Gloria León-Ávila
- Posgrado en Ciencias Quimicobiológicas, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Col. Casco de Santo Tomás, Alcaldía Miguel Hidalgo, Mexico City 11340, Mexico
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Departamento de Zoología, Prolongación de Carpio y Plan de Ayala S/N, Col. Casco de Santo Tomás, Alcaldía Miguel Hidalgo, Mexico City 11340, Mexico
| | - Silvia Giono-Cerezo
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Departamento de Microbiología, Prolongación de Carpio y Plan de Ayala S/N, Col. Casco de Santo Tomás, Alcaldía Miguel Hidalgo, Mexico City 11340, Mexico
- Posgrado en Ciencias Quimicobiológicas, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Col. Casco de Santo Tomás, Alcaldía Miguel Hidalgo, Mexico City 11340, Mexico
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Singh A, Kumar S, Bansal K, Patil PB. Taxonomic and Phylogenomic Assessment Identifies Phytopathogenicity Potential of Stenotrophomonas maltophilia Complex. PHYTOPATHOLOGY 2023; 113:1833-1838. [PMID: 37202377 DOI: 10.1094/phyto-11-22-0434-sc] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Stenotrophomonas maltophilia is a versatile bacterium found in plants, water, air, and even hospital settings. Deep taxono phylogenomics studies have revealed that S. maltophilia is a complex of several hidden species that are not differentiated using conventional approaches. In the last two decades, there have been increasing reports of S. maltophilia as a pathogen of diverse plants. Hence, proper taxonogenomic assessment of plant-pathogenic strains and species within the S. maltophilia complex (Smc) is required. In the present study, we formally propose a taxonomic amendment of Pseudomonas hibiscicola and P. beteli, reported as pathogens of Hibiscus rosa-sinensis and Betelvine (Piper betle) plants, respectively, as a misclassified member species of the Smc. Recently, a novel species of the genus, S. cyclobalanopsidis, was reported as a leaf spot pathogen of the oak tree genus Cyclobalanopsis. Interestingly, our investigation also revealed S. cyclobalanopsidis as another plant-pathogenic member species of the Smc lineage. In addition, we provide deep phylo-taxonogenomic evidence that S. maltophilia strain JZL8, reported as a plant pathogen, is a misclassified strain of S. geniculata, making it the fourth member species of the Smc harboring plant-pathogenic strains. Therefore, a proper taxonomic assessment of plant-pathogenic strains and species from the Smc is required for further systematic studies and management.
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Affiliation(s)
- Anu Singh
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Sanjeet Kumar
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Kanika Bansal
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Prabhu B Patil
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
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Petrzik K, Brázdová S. Jojan: a novel virus that lyses Stenotrophomonas maltophilia from dog. Virus Genes 2023; 59:775-780. [PMID: 37458918 DOI: 10.1007/s11262-023-02021-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 07/09/2023] [Indexed: 09/14/2023]
Abstract
Stenotrophomonas maltophilia is a Gram-negative bacterium widely distributed in the environment and associated with nosocomial infections, pneumonia, and bacteremia in humans and other mammals. We have isolated and sequenced a new virus that lyses the S. maltophilia strain from a dog skin. The virus has a siphovirus-like morphology and a linear dsDNA genome 60,804 pb in length with terminal repeats, four tRNA genes, and 111 putative proteins. The annotated genes resemble the corresponding genes of some siphoviruses, but the unique genome arrangement and limited similarity of the encoded proteins suggest that this virus does not belong to any known genus. The virus uses zinc metallopeptidase for lysis of its host. This enzyme is active in the presence of Zn2+ or Mg2+ ions and maintains its bactericidal activity up to 50 °C. Both the virus itself and the endolysin specifically degrade only the host bacterial strain.
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Affiliation(s)
- Karel Petrzik
- Institute of Plant Molecular Biology, Department of Plant Virology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 370 05, České Budějovice, Czech Republic.
| | - Sára Brázdová
- Institute of Plant Molecular Biology, Department of Plant Virology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 370 05, České Budějovice, Czech Republic
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Li Y, Zhao A, Yu Q, Yu N, Cui Y, Ma X, Liu H, Wang R. Effect of Stenotrophomonas maltophilia on Tuberculosis. Microbiol Spectr 2023; 11:e0094423. [PMID: 37306591 PMCID: PMC10433947 DOI: 10.1128/spectrum.00944-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 05/22/2023] [Indexed: 06/13/2023] Open
Abstract
Tuberculosis (TB) is an important infectious disease suffered by many countries, including China. In this stage, accurate diagnosis and treatment are key measures for the prevention and control of TB. Stenotrophomonas maltophilia is a global emerging Gram-negative, multidrug-resistant (MDR) organism characterized by its high contribution to the increase in crude mortality rates. By single cell preparation and strain identification, we isolated S. maltophilia from stored cultures of Mycobacterium tuberculosis (Mtb). We found that S. maltophilia could not be removed from sputum by alkali treatment or inhibited by antibiotic mixture added to MGIT 960 indicator tubes. When co-cultured with Mtb on a Löwenstein-Jensen (L-J) slant, it could inhibit the growth of Mtb and liquefy the medium. More seriously, it was resistant to 10 of the 12 anti-TB drugs, including isoniazid and rifampin, and made the mixed samples display multidrug-resistant Mtb (MDR-TB) results in the drug sensitivity test, which might change a treatment regimen and increase disease burden. Following, we conducted a small-scale surveillance which showed that the isolation rate of S. maltophilia in TB patients was 6.74%, but these patients had no special characteristics and the presence of S. maltophilia was hidden. The effect of S. maltophilus on TB and its mechanism are unclear and require more attention. IMPORTANCE China is a high-burden country for tuberculosis (TB), multidrug-resistant/rifampicin-resistant tuberculosis (MDR/RR-TB), and HIV-associated TB. Increasing the positive rate of culture and the accuracy of antibiotic susceptibility testing (AST) are important for diagnosis, treatment, and control of TB. In our study, we found that the isolation rate of Stenotrophomonas maltophilia in TB patients was not neglectable and that this bacterium affects the isolation and AST results of TB. Due to a lack of relevant research, the impact of S. maltophilia on the course and outcome of TB is unclear. However, the characteristics of S. maltophilia that increase disease mortality require attention. Therefore, in the clinical testing of TB, in addition to mycobacteria, it is recommended to increase the detection of co-infected bacteria and improve the awareness of TB clinicians of these bacteria.
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Affiliation(s)
- Yue Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Centre for Disease Control and Prevention, Beijing, China
| | - Ailan Zhao
- Tuberculosis Clinic, Chaoyang District Centre for Disease Control and Prevention, Beijing, China
| | - Qin Yu
- Tuberculosis Clinic, Chaoyang District Centre for Disease Control and Prevention, Beijing, China
| | - Nan Yu
- Tuberculosis Clinic, Chaoyang District Centre for Disease Control and Prevention, Beijing, China
| | - Yao Cui
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Centre for Disease Control and Prevention, Beijing, China
| | - Xiaohan Ma
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Centre for Disease Control and Prevention, Beijing, China
| | - Haican Liu
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Centre for Disease Control and Prevention, Beijing, China
| | - Ruibai Wang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Centre for Disease Control and Prevention, Beijing, China
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Genotypic Diversity, Antibiotic Resistance, and Virulence Phenotypes of Stenotrophomonas maltophilia Clinical Isolates from a Thai University Hospital Setting. Antibiotics (Basel) 2023; 12:antibiotics12020410. [PMID: 36830320 PMCID: PMC9951947 DOI: 10.3390/antibiotics12020410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 02/16/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
Stenotrophomonas maltophilia is a multidrug-resistant organism that is emerging as an important opportunistic pathogen. Despite this, information on the epidemiology and characteristics of this bacterium, especially in Thailand, is rarely found. This study aimed to determine the demographic, genotypic, and phenotypic characteristics of S. maltophilia isolates from Maharaj Nakorn Chiang Mai Hospital, Thailand. A total of 200 S. maltophilia isolates were collected from four types of clinical specimens from 2015 to 2016 and most of the isolates were from sputum. In terms of clinical characteristics, male and aged patients were more susceptible to an S. maltophilia infection. The majority of included patients had underlying diseases and were hospitalized with associated invasive procedures. The antimicrobial resistance profiles of S. maltophilia isolates showed the highest frequency of resistance to ceftazidime and the lower frequency of resistance to chloramphenicol, levofloxacin, trimethoprim/sulfamethoxazole (TMP/SMX), and no resistance to minocycline. The predominant antibiotic resistance genes among the 200 isolates were the smeF gene (91.5%), followed by blaL1 and blaL2 genes (43% and 10%), respectively. Other antibiotic resistance genes detected were floR (8.5%), intI1 (7%), sul1 (6%), mfsA (4%) and sul2 (2%). Most S. maltophilia isolates could produce biofilm and could swim in a semisolid medium, however, none of the isolates could swarm. All isolates were positive for hemolysin production, whereas 91.5% and 22.5% of isolates could release protease and lipase enzymes, respectively. In MLST analysis, a high degree of genetic diversity was observed among the 200 S. maltophilia isolates. One hundred and forty-one sequence types (STs), including 130 novel STs, were identified and categorized into six different clonal complex groups. The differences in drug resistance patterns and genetic profiles exhibited various phenotypes of biofilm formation, motility, toxin, and enzymes production which support this bacterium in its virulence and pathogenicity. This study reviewed the characteristics of genotypes and phenotypes of S. maltophilia from Thailand which is necessary for the control and prevention of S. maltophilia local spreading.
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Efficacy in Galleria mellonella Larvae and Application Potential Assessment of a New Bacteriophage BUCT700 Extensively Lyse Stenotrophomonas maltophilia. Microbiol Spectr 2023; 11:e0403022. [PMID: 36700630 PMCID: PMC9927281 DOI: 10.1128/spectrum.04030-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
In recent years, Stenotrophomonas maltophilia (S. maltophilia) has become an important pathogen of clinically acquired infections accompanied by high pathogenicity and high mortality. Moreover, infections caused by multidrug-resistant S. maltophilia have emerged as a serious challenge in clinical practice. Bacteriophages are considered a promising alternative for the treatment of S. maltophilia infections due to their unique antibacterial mechanism and superior bactericidal ability compared with traditional antibiotic agents. Here, we reported a new phage BUCT700 that has a double-stranded DNA genome of 43,214 bp with 70% GC content. A total of 55 ORFs and no virulence or antimicrobial resistance genes were annotated in the genome of phage BUCT700. Phage BUCT700 has a broad host range (28/43) and can lyse multiple ST types of clinical S. maltophilia (21/33). Furthermore, bacteriophage BUCT700 used the Type IV fimbrial biogenesis protein PilX as an adsorption receptor. In the stability test, phage BUCT700 showed excellent thermal stability (4 to 60°C) and pH tolerance (pH = 4 to 12). Moreover, phage BUCT700 was able to maintain a high titer during long-term storage. The adsorption curve and one-step growth curve showed that phage BUCT700 could rapidly adsorb to the surface of S. maltophilia and produce a significant number of phage virions. In vivo, BUCT700 significantly increased the survival rate of S. maltophilia-infected Galleria mellonella (G. mellonella) larvae from 0% to 100% within 72 h, especially in the prophylactic model. In conclusion, these findings indicate that phage BUCT700 has promising potential for clinical application either as a prophylactic or therapeutic agent. IMPORTANCE The risk of Stenotrophomonas maltophilia infections mediated by the medical devices is exacerbated with an increase in the number of ICU patients during the Corona Virus Disease 2019 (COVID-19) epidemic. Complications caused by S. maltophilia infections could complicate the state of an illness, greatly extending the length of hospitalization and increasing the financial burden. Phage therapy might be a potential and promising alternative for clinical treatment of multidrug-resistant bacterial infections. Here, we investigated the protective effects of phage BUCT700 as prophylactic and therapeutic agents in Galleria mellonella models of infection, respectively. This study demonstrates that phage therapy can provide protection in targeting S. maltophilia-related infection, especially as prophylaxis.
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Mojica MF, Humphries R, Lipuma JJ, Mathers AJ, Rao GG, Shelburne SA, Fouts DE, Van Duin D, Bonomo RA. Clinical challenges treating Stenotrophomonas maltophilia infections: an update. JAC Antimicrob Resist 2022; 4:dlac040. [PMID: 35529051 PMCID: PMC9071536 DOI: 10.1093/jacamr/dlac040] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2023] Open
Abstract
Stenotrophomonas maltophilia is a non-fermenting, Gram-negative bacillus that has emerged as an opportunistic nosocomial pathogen. Its intrinsic multidrug resistance makes treating infections caused by S. maltophilia a great clinical challenge. Clinical management is further complicated by its molecular heterogeneity that is reflected in the uneven distribution of antibiotic resistance and virulence determinants among different strains, the shortcomings of available antimicrobial susceptibility tests and the lack of standardized breakpoints for the handful of antibiotics with in vitro activity against this microorganism. Herein, we provide an update on the most recent literature concerning these issues, emphasizing the impact they have on clinical management of S. maltophilia infections.
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Affiliation(s)
- Maria F. Mojica
- Department of Molecular Biology and Microbiology, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
- Case Western Reserve University-Cleveland VA Medical Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, OH, USA
- Research Service, VA Northeast Ohio Healthcare System, Cleveland, OH, USA
- Grupo de Resistencia Antimicrobiana y Epidemiología Hospitalaria, Universidad El Bosque, Bogotá, Colombia
| | - Romney Humphries
- Department of Pathology, Immunology and Microbiology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - John J. Lipuma
- University of Michigan Medical School, Pediatric Infectious Disease, Ann Arbor, MI, USA
| | - Amy J. Mathers
- Division of Infectious Disease and International Health, Department of Medicine, University of Virginia Health System, Charlottesville, VA, USA
- Clinical Microbiology Laboratory, Department of Pathology, University of Virginia Health System, Charlottesville, VA, USA
| | - Gauri G. Rao
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Samuel A. Shelburne
- Department of Infectious Diseases Infection Control and Employee Health, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Center for Antimicrobial Resistance and Microbial Genomics, University of Texas Health Science Center McGovern Medical School, Houston, TX, USA
| | - Derrick E. Fouts
- Genomic Medicine, The J. Craig Venter Institute, Rockville, MD, USA
| | - David Van Duin
- Department of Medicine, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Robert A. Bonomo
- Case Western Reserve University-Cleveland VA Medical Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, OH, USA
- Research Service, VA Northeast Ohio Healthcare System, Cleveland, OH, USA
- Senior Clinician Scientist Investigator, Veterans Affairs Northeast Ohio Healthcare System, Cleveland, OH, USA
- Medical Service and Geriatric Research, Education, and Clinical Center (GRECC), Veterans Affairs Northeast Ohio Healthcare System, Cleveland, OH, USA
- Departments of Medicine, Biochemistry, Pharmacology, Molecular Biology and Microbiology, and Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
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Li F, Li L, Zhang Y, Bai S, Sun L, Guan J, Zhang W, Cui X, Feng J, Tong Y. Isolation and characterization of the novel bacteriophage vB_SmaS_BUCT626 against Stenotrophomonas maltophilia. Virus Genes 2022; 58:458-466. [PMID: 35633495 DOI: 10.1007/s11262-022-01917-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/17/2022] [Indexed: 11/28/2022]
Abstract
Stenotrophomonas maltophilia has been recognized as an emerging global opportunistic pathogen, and it is intrinsically resistant to most antibiotics, which makes the limited choice for treating S. maltophilia infections. Bacteriophage with the proper characterization is considered as a promising alternative treatment option to control S. maltophilia infections. In this study, we isolated a novel Siphoviridae bacteriophage vB_SmaS_BUCT626 with lytic activity against S. maltophilia. Phage vB_SmaS_BUCT626 can lysis 10 of 20 S. maltophilia and was relatively stable at a wide range of temperatures (4-70 °C) and pH values (3.0-13.0) and exhibited good tolerance to chloroform. The genome of phage vB_SmaS_BUCT626 was a 61,662-bp linear double-stranded DNA molecule with a GC content of 56.2%, and contained 100 open-reading frames. It carried no antibiotic resistance, toxin, virulence-related genes, or lysogen-formation gene clusters. Together, these characteristics make phage vB_SmaS_BUCT626, a viable candidate as a biocontrol agent against S. maltophilia infection.
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Affiliation(s)
- Fei Li
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.,Taian City Central Hospital, Taian, 271000, China
| | - Lingxing Li
- Taian City Central Hospital, Taian, 271000, China
| | - Yong Zhang
- Taian City Central Hospital, Taian, 271000, China
| | - Shiyu Bai
- Taian City Central Hospital, Taian, 271000, China
| | - Li Sun
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan, 030006, China
| | - Jingli Guan
- Taian City Central Hospital, Taian, 271000, China
| | | | - Xiaogang Cui
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan, 030006, China.
| | - Jiao Feng
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan, 030006, China.
| | - Yigang Tong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
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Fluit AC, Bayjanov JR, Aguilar MD, Cantón R, Elborn S, Tunney MM, Scharringa J, Benaissa-Trouw BJ, Ekkelenkamp MB. Taxonomic position, antibiotic resistance and virulence factor production by Stenotrophomonas isolates from patients with cystic fibrosis and other chronic respiratory infections. BMC Microbiol 2022; 22:129. [PMID: 35549675 PMCID: PMC9097388 DOI: 10.1186/s12866-022-02466-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 02/07/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The potential pathogenic role of Stenotrophomonas maltophilia in lung disease and in particular in cystic fibrosis is unclear. To develop further understanding of the biology of this taxa, the taxonomic position, antibiotic resistance and virulence factors of S. maltophilia isolates from patients with chronic lung disease were studied. RESULTS A total of 111 isolates recovered between 2003 and 2016 from respiratory samples from patients in five different countries were included. Based on a cut-off of 95%, analysis of average nucleotide identity by BLAST (ANIb) showed that the 111 isolates identified as S. maltophilia by Matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF/MS) belonged to S. maltophilia (n = 65), S. pavanii (n = 6) and 13 putative novel species (n = 40), which each included 1-5 isolates; these groupings coincided with the results of the 16S rDNA analysis, and the L1 and L2 ß-lactamase Neighbor-Joining phylogeny. Chromosomally encoded aminoglycoside resistance was identified in all S. maltophilia and S. pavani isolates, while acquired antibiotic resistance genes were present in only a few isolates. Nevertheless, phenotypic resistance levels against commonly used antibiotics, determined by standard broth microbroth dilution, were high. Although putative virulence genes were present in all isolates, the percentage of positive isolates varied. The Xps II secretion system responsible for the secretion of the StmPr1-3 proteases was mainly limited to isolates identified as S. maltophilia based on ANIb, but no correlation with phenotypic expression of protease activity was found. The RPF two-component quorum sensing system involved in virulence and antibiotic resistance expression has two main variants with one variant lacking 190 amino acids in the sensing region. CONCLUSIONS The putative novel Stenotrophomonas species recovered from patient samples and identified by MALDI-TOF/MS as S. maltophilia, differed from S. maltophilia in resistance and virulence genes, and therefore possibly in pathogenicity. Revision of the Stenotrophomonas taxonomy is needed in order to reliably identify strains within the genus and elucidate the role of the different species in disease.
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Affiliation(s)
- Ad C Fluit
- Department of Medical Microbiology, University Medical Center Utrecht, PO Box 85500, 3508, GA, Utrecht, the Netherlands.
| | - Jumamurat R Bayjanov
- Department of Medical Microbiology, University Medical Center Utrecht, PO Box 85500, 3508, GA, Utrecht, the Netherlands
| | - María Díez Aguilar
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain.,Red Española de Investigación en Patología Infecciosa (REIPI), Madrid, Spain.,Present Address: Servicio de Microbiología, Hospital Universitario La Princesa, Madrid, Spain
| | - Rafael Cantón
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain.,Red Española de Investigación en Patología Infecciosa (REIPI), Madrid, Spain
| | - Stuart Elborn
- Queen's University Belfast, School of Pharmacy, Belfast, UK
| | | | - Jelle Scharringa
- Department of Medical Microbiology, University Medical Center Utrecht, PO Box 85500, 3508, GA, Utrecht, the Netherlands
| | - Barry J Benaissa-Trouw
- Department of Medical Microbiology, University Medical Center Utrecht, PO Box 85500, 3508, GA, Utrecht, the Netherlands
| | - Miquel B Ekkelenkamp
- Department of Medical Microbiology, University Medical Center Utrecht, PO Box 85500, 3508, GA, Utrecht, the Netherlands
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Jean SS, Harnod D, Hsueh PR. Global Threat of Carbapenem-Resistant Gram-Negative Bacteria. Front Cell Infect Microbiol 2022; 12:823684. [PMID: 35372099 PMCID: PMC8965008 DOI: 10.3389/fcimb.2022.823684] [Citation(s) in RCA: 85] [Impact Index Per Article: 42.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 02/15/2022] [Indexed: 01/08/2023] Open
Abstract
Infections caused by multidrug-resistant (MDR) and extensively drug-resistant (XDR) Gram-negative bacteria (GNB), including carbapenem-resistant (CR) Enterobacterales (CRE; harboring mainly blaKPC, blaNDM, and blaOXA-48-like genes), CR- or MDR/XDR-Pseudomonas aeruginosa (production of VIM, IMP, or NDM carbapenemases combined with porin alteration), and Acinetobacter baumannii complex (producing mainly OXA-23, OXA-58-like carbapenemases), have gradually worsened and become a major challenge to public health because of limited antibiotic choice and high case-fatality rates. Diverse MDR/XDR-GNB isolates have been predominantly cultured from inpatients and hospital equipment/settings, but CRE has also been identified in community settings and long-term care facilities. Several CRE outbreaks cost hospitals and healthcare institutions huge economic burdens for disinfection and containment of their disseminations. Parenteral polymyxin B/E has been observed to have a poor pharmacokinetic profile for the treatment of CR- and XDR-GNB. It has been determined that tigecycline is suitable for the treatment of bloodstream infections owing to GNB, with a minimum inhibitory concentration of ≤ 0.5 mg/L. Ceftazidime-avibactam is a last-resort antibiotic against GNB of Ambler class A/C/D enzyme-producers and a majority of CR-P. aeruginosa isolates. Furthermore, ceftolozane-tazobactam is shown to exhibit excellent in vitro activity against CR- and XDR-P. aeruginosa isolates. Several pharmaceuticals have devoted to exploring novel antibiotics to combat these troublesome XDR-GNBs. Nevertheless, only few antibiotics are shown to be effective in vitro against CR/XDR-A. baumannii complex isolates. In this era of antibiotic pipelines, strict implementation of antibiotic stewardship is as important as in-time isolation cohorts in limiting the spread of CR/XDR-GNB and alleviating the worsening trends of resistance.
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Affiliation(s)
- Shio-Shin Jean
- Department of Emergency and Critical Care Medicine, Min-Sheng General Hospital, Taoyuan, Taiwan
- Department of Pharmacy, College of Pharmacy and Health care, Tajen University, Pingtung, Taiwan
| | - Dorji Harnod
- Division of Critical Care Medicine, Department of Emergency and Critical Care Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan
- Department of Emergency, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Po-Ren Hsueh
- Departments of Laboratory Medicine and Internal Medicine, China Medical University Hospital, School of Medicine, China Medical University, Taichung, Taiwan
- School of Medicine, China Medical University, Taichung, Taiwan
- Ph.D Program for Aging, School of Medicine, China Medical University, Taichung, Taiwan
- Departments of Laboratory Medicine and Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
- *Correspondence: Po-Ren Hsueh,
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13
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Multilocus Sequence Typing for Molecular Epidemiology of Stenotrophomonas maltophilia Clinical and Environmental Isolates from a Tertiary Hospital in West of Iran. IRANIAN BIOMEDICAL JOURNAL 2022; 26:142-52. [PMID: 35032967 PMCID: PMC8987417 DOI: 10.52547/ibj.26.2.142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Background Stenotrophomonas maltophilia is an opportunistic bacterium, contributing to different hospital-acquired infections and can be acquired from different hospital setting sources. Epidemiological study of S. maltophilia in the hospital also demonstrates the intrahospital distribution of certain strains of bacteria in healthcare facilities. The aim of the current study was to identify the molecular epidemiology of S. maltophilia isolates from clinical and environmental sources within a hospital. Methods A total of 400 samples (clinical and environmental) were collected from the different settings of hospital. Following the standard biochemical testing and 23S rRNA genotyping, the molecular typing of S. maltophilia isolates was determined using the multilocus sequence typing (MLST) technique. Also, the frequencies of zot and entF virulence genes among S. maltophilia isolates were examined by PCR technique. Results Based on the biochemical testes and PCRs targeting 23S rRNA gene, 22 S. maltophilia isolates were identified. The MLST analysis demonstrated that these isolates were assigned to 14 ST, and 6 out of 14 STs were common among clinical and environmental samples. All 22 isolates were identified in the PubMLST database. The PCR screening demonstrated that none of 22 S. maltophilia isolates had zot virulence gene, while the entF gene with the 59% frequency was observed in 13 out of 22 isolates. Among these 13 isolates, 6 STs were common in clinical and environmental isolates. Conclusion Our study showed the clonal relatedness between clinical and environmental sources of the S. maltophilia isolates in a hospital. Further studies are required to understand the epidemic situation of this pathogen in the clinic and the environment.
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14
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Zając OM, Tyski S, Laudy AE. Phenotypic and Molecular Characteristics of the MDR Efflux Pump Gene-Carrying Stenotrophomonas maltophilia Strains Isolated in Warsaw, Poland. BIOLOGY 2022; 11:biology11010105. [PMID: 35053103 PMCID: PMC8772754 DOI: 10.3390/biology11010105] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 12/30/2021] [Accepted: 01/05/2022] [Indexed: 02/05/2023]
Abstract
Simple Summary Nosocomial infections caused by Stenotrophomonas maltophilia have been increasing worldwide. These bacteria are intrinsically resistant to most antibiotics. The underestimated resistance mechanism of Gram-negative rods is an overexpression of multidrug-resistant (MDR) efflux pumps. The aim of this study was to analyze the genetic diversity of isolates derived from various clinical materials, including blood, and the prevalence of MDR efflux pump genes and susceptibility profiles to the anti-S. maltophilia drugs. The research was conducted on 94 S. maltophilia isolates derived from hospitalized patients and outpatients in Warsaw, Poland. All isolates were susceptible to trimethoprim-sulfamethoxazole and minocycline, while 44/94 isolates demonstrated reduction in susceptibility to levofloxacin. A large genetic variation was observed among these isolates. However, a clonal relationship was revealed among two groups of bloodstream isolates from one hospital ward: (1) nine isolates, (2) six isolates. Moreover, the presence of genes encoding ten different efflux pumps from the resistance-nodulation-division family and the ATP-binding cassette family was shown in the majority of the 94 isolates. The obtained knowledge about the prevalence of efflux pump genes in clinical S. maltophilia strains makes it possible to predict the scale of the risk of resistance emergence in strains as a result of gene overexpression. Abstract An increase of nosocomial infections caused by Stenotrophomonas maltophilia strains has recently been observed all over the world. The isolation of these bacteria from the blood is of particular concern. In this study we performed the phenotypic and genotypic characterization of 94 S. maltophilia isolates, including isolates from patients hospitalized in a tertiary Warsaw hospital (n = 79) and from outpatients (n = 15). All isolates were found to be susceptible to trimethoprim-sulfamethoxazole and minocycline, while 44/94 isolates demonstrated a reduction in susceptibility to levofloxacin. A large genetic variation was observed among the isolates tested by pulsed-field gel electrophoresis. A clonal relationship with 100% similarity was observed between isolates within two sub-pulsotypes: the first included nine bloodstream isolates and the second involved six. Multilocus sequence typing showed two new sequence types (ST498 and ST499) deposited in public databases for molecular typing. Moreover, the presence of genes encoding ten different efflux pumps from the resistance-nodulation-division family and the ATP-binding cassette family was shown in the majority of the 94 isolates. The obtained knowledge about the prevalence of efflux pump genes in clinical S. maltophilia strains makes it possible to predict the scale of the risk of resistance emergence in strains as a result of gene overexpression.
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Affiliation(s)
- Olga M. Zając
- Department of Pharmaceutical Microbiology, Medical University of Warsaw, 02091 Warsaw, Poland; (O.M.Z.); (S.T.)
| | - Stefan Tyski
- Department of Pharmaceutical Microbiology, Medical University of Warsaw, 02091 Warsaw, Poland; (O.M.Z.); (S.T.)
- Department of Antibiotics and Microbiology, National Medicines Institute, 02091 Warsaw, Poland
| | - Agnieszka E. Laudy
- Department of Pharmaceutical Microbiology, Medical University of Warsaw, 02091 Warsaw, Poland; (O.M.Z.); (S.T.)
- Correspondence:
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15
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Gautam V, Patil PP, Bansal K, Kumar S, Kaur A, Singh A, Korpole S, Singhal L, Patil PB. Description of Stenotrophomonas sepilia sp. nov., isolated from blood culture of a hospitalized patient as a new member of Stenotrophomonas maltophilia complex. New Microbes New Infect 2021; 43:100920. [PMID: 34457314 PMCID: PMC8379335 DOI: 10.1016/j.nmni.2021.100920] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 06/15/2021] [Accepted: 07/07/2021] [Indexed: 11/27/2022] Open
Abstract
Stenotrophomonas sepilia strain SM16975 (= JCM 32102; = KCTC 62052) is a new species isolated from the blood culture of a hospitalized patient. The biochemical characterization, phenotypic criteria, phylogenomic reconstruction, and genomic analysis were carried out to differentiate it from its phylogenetic neighbours, establishing novel species status in the genus Stenotrophomonas and within Stenotrophomonas maltophilia complex (Smc).
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Affiliation(s)
- V Gautam
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - P P Patil
- CSIR- Institute of Microbial Technology, Chandigarh, India
| | - K Bansal
- CSIR- Institute of Microbial Technology, Chandigarh, India
| | - S Kumar
- CSIR- Institute of Microbial Technology, Chandigarh, India
| | - A Kaur
- CSIR- Institute of Microbial Technology, Chandigarh, India
| | - A Singh
- CSIR- Institute of Microbial Technology, Chandigarh, India
| | - S Korpole
- CSIR- Institute of Microbial Technology, Chandigarh, India
| | - L Singhal
- Department of Microbiology, Government Medical College & Hospital, Chandigarh, India
| | - P B Patil
- CSIR- Institute of Microbial Technology, Chandigarh, India
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16
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Abstract
Stenotrophomonas maltophilia is an opportunistic pathogen of significant concern to susceptible patient populations. This pathogen can cause nosocomial and community-acquired respiratory and bloodstream infections and various other infections in humans. Sources include water, plant rhizospheres, animals, and foods. Studies of the genetic heterogeneity of S. maltophilia strains have identified several new genogroups and suggested adaptation of this pathogen to its habitats. The mechanisms used by S. maltophilia during pathogenesis continue to be uncovered and explored. S. maltophilia virulence factors include use of motility, biofilm formation, iron acquisition mechanisms, outer membrane components, protein secretion systems, extracellular enzymes, and antimicrobial resistance mechanisms. S. maltophilia is intrinsically drug resistant to an array of different antibiotics and uses a broad arsenal to protect itself against antimicrobials. Surveillance studies have recorded increases in drug resistance for S. maltophilia, prompting new strategies to be developed against this opportunist. The interactions of this environmental bacterium with other microorganisms are being elucidated. S. maltophilia and its products have applications in biotechnology, including agriculture, biocontrol, and bioremediation.
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17
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Shimizu T, Tsuyuki Y, Shimoike K, Iyori K, Miyamoto T, Harada K. Antimicrobial resistance and multilocus sequence types of Stenotrophomonas maltophilia isolated from dogs and cats in Japan. J Med Microbiol 2021; 70. [PMID: 33826489 DOI: 10.1099/jmm.0.001344] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
As the representative multidrug-resistant pathogen, Stenotrophomonas maltophilia has multiple intrinsic and acquired resistances, including carbapenem resistance. In companion animals, the antimicrobial susceptibility and sequence types (STs) of S. maltophilia are not well understood due to its limited isolation rate. We investigated the antimicrobial susceptibilities and multilocus sequence types (MLSTs) of 38 S. maltophilia strains isolated from dogs and cats in Japan. Prevalence of resistance was detected for imipenem (100 %), aztreonam (94.7 %), piperacillin (65.8 %), trimethoprim-sulfamethoxazole (65.8 %), and ceftazidime (60.5 %). Rates of resistances to chloramphenicol, minocycline, and levofloxacin were low (2.6-5.3 %). MLST analysis revealed that all 38 strains were assigned to 34 STs, including 11 previously reported STs and 23 newly identified STs. Phylogenetic analysis of MLSTs enabled categorization of 13 isolates (34.2 %) into genogroup 6, which is a major genogroup of human isolates. Multinational surveillance would be needed to clarify the significance of antimicrobial-resistant S. maltophilia isolates from companion animals.
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Affiliation(s)
- Takae Shimizu
- Department of Veterinary Internal Medicine, Tottori University, Minami 4-101, Koyama, Tottori-shi, Tottori 680-8553, Japan
| | - Yuzo Tsuyuki
- Sanritsu Zelkova Veterinary Laboratory Inc., 2-5-8 Kuji, Takatsu, Kawasaki-shi, Kanagawa 213-0032, Japan
| | - Kenta Shimoike
- Vet Derm Tokyo Inc., 910 Shobuzawa, Fujisawa-shi, Kanagawa 252-0823, Japan
| | - Keita Iyori
- Vet Derm Tokyo Inc., 910 Shobuzawa, Fujisawa-shi, Kanagawa 252-0823, Japan
| | - Tadashi Miyamoto
- Miyamoto Animal Hospital, 2265-8 Kurokawa, Yamaguchi-shi, Yamaguchi 753-0851, Japan
| | - Kazuki Harada
- Department of Veterinary Internal Medicine, Tottori University, Minami 4-101, Koyama, Tottori-shi, Tottori 680-8553, Japan
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18
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Zhang W, Zhang R, Hu Y, Liu Y, Wang L, An X, Song L, Shi T, Fan H, Tong Y, Liu H. Biological characteristics and genomic analysis of a Stenotrophomonas maltophilia phage vB_SmaS_BUCT548. Virus Genes 2021; 57:205-216. [PMID: 33471272 DOI: 10.1007/s11262-020-01818-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 12/04/2020] [Indexed: 12/12/2022]
Abstract
Stenotrophomonas maltophilia (hereinafter referred to as S. maltophilia) has developed into an important opportunistic pathogenic bacterium, which is prevalent in nosocomial and community infections, and has adverse effects on patients with a compromised immune system. Phage vB_SmaS_BUCT548 was isolated from sewage of Beijing 307 Hospital with S. maltophilia (strain No.824) as a host. Phage morphology was observed by transmission electron microscopy and its biological and genomic characteristics were determined. The electron microscope shows that the bacteriophage belonged to the Siphoviridae and MOI is 0.001. One-step growth curve shows that the incubation period is 30 min and the burst size is 134 PFU/Cell. The host range is relatively wide and it can lysis 11of 13 S. maltophilia strains. Next-Generation Sequencing (NGS) results show that the genome sequence is a dsDNA with 62354 bp length, and the GC content is 56.3% (GenBank: MN937349). One hundred and two online reading frames (ORFs) are obtained after RAST online annotation and the BlastN nucleic acid comparison shows that the phage had low homology with other phages in NCBI database. This study reports a novel S. maltophilia phage named vB_SmaS_BUCT548, which has a short incubation period, strong lytic ability, and a wide host range. The main characteristic of this bacteriophage is the novelty of the genomic sequence and the analysis of the other characteristics provides basic data for further exploring the interaction mechanism between the phage and the host.
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Affiliation(s)
- Wenjing Zhang
- School of Public Health, Lanzhou University, Lanzhou, 730000, China.,Beijing Advanced Innovation Center for Soft Matter Science and Engineering (BAIC-SM), College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Rongrong Zhang
- School of Public Health, Lanzhou University, Lanzhou, 730000, China.,Beijing Advanced Innovation Center for Soft Matter Science and Engineering (BAIC-SM), College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Yunjia Hu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering (BAIC-SM), College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Yujie Liu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering (BAIC-SM), College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Liqin Wang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering (BAIC-SM), College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.,Medical College Qingdao University, Qingdao, 266071, China
| | - Xiaoping An
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering (BAIC-SM), College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Lihua Song
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering (BAIC-SM), College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Taoxing Shi
- Academy of Military Medical Sciences, Beijing, 100085, China.
| | - Huahao Fan
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering (BAIC-SM), College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
| | - Yigang Tong
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering (BAIC-SM), College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
| | - Hui Liu
- School of Public Health, Lanzhou University, Lanzhou, 730000, China.
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Cluster of S. maltophilia among patients with respiratory tract infections at an intensive care unit. Infect Prev Pract 2020; 2:100097. [PMID: 34368727 PMCID: PMC8336028 DOI: 10.1016/j.infpip.2020.100097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 09/21/2020] [Indexed: 12/03/2022] Open
Abstract
Background Stenotrophomonas maltophilia is associated with respiratory tract infections in immunocompromised patients, and it has emerged as an important nosocomial pathogen, with admission to intensive care units (ICUs) and ventilators as recognized risk factors. Aim To describe the investigation of a sudden increase in patients with pneumonia caused by S. maltophilia at a Swedish ICU and the control measures taken. Methods Lower respiratory tract cultures from patients admitted to the ICU were obtained, and environmental cultures were collected from sink drains and medical equipment. Isolates identified as S. maltophilia were subjected to antibiotic susceptibility testing and whole genome sequencing (WGS). Findings A total of 17 S. maltophilia isolates were found (four from patients and 13 from the environment). The WGS identified two outbreak clones, sequence type (ST) 361 and ST138, and seven unique ones. Most likely, the outbreak clones originated from two sinks, and transmission was enhanced by a calorimeter. After changing the sink and calorimeter routines, no more cases were registered. Conclusion Acquisition of S. maltophilia from the hospital environment appears to be easy, especially if water is involved. To control this bacterium, better knowledge of its transmission routes in hospital environments is required.
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20
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Duan Z, Qin J, Liu Y, Li C, Ying C. Molecular epidemiology and risk factors of Stenotrophomonas maltophilia infections in a Chinese teaching hospital. BMC Microbiol 2020; 20:294. [PMID: 32993493 PMCID: PMC7526397 DOI: 10.1186/s12866-020-01985-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 09/23/2020] [Indexed: 12/13/2022] Open
Abstract
Background Stenotrophomonas maltophilia (S. maltophilia) is an important opportunistic pathogen that can be isolated in hospitals. With the abuse of broad spectrum antibiotics and invasive surgical devices, the rate of S. maltophilia infection is increasing every year. This study was an epidemiological analysis of the clinical and molecular characteristics of S. maltophilia infection in a Chinese teaching hospital. The goal was to obtain a comprehensive understanding of the status of S. maltophilia infection to provide strong epidemiological data for the prevention and treatment of S. maltophilia infection. Results A total of 93 isolates from Renji Hospital affiliated with the Shanghai Jiaotong University School of Medicine were included, in which 62 isolates were from male patients. In addition, 81 isolates were isolated from sputum samples. A total of 86 patients had underlying diseases. All patients received antibiotics. Multilocus sequence typing (MLST) analysis indicated that 61 different sequence types (STs) were found (including 45 novel STs), and MLST did not show significantly dominant STs. Pulsed field gel electrophoresis (PFGE) results showed that 93 isolates could be divided into 73 clusters, and they also showed weak genetic linkages between isolates. The resistant rates to trimethoprim/sulfamethoxazole (TMP/SMX) and levofloxacin were 9.7 and 4.3%, respectively, and all isolates were susceptible to minocycline. Four virulence gene’s loci Stmpr1, Stmpr2, Smf-1, and Smlt3773 were positive in 79.6, 91.4, 94.6, and 52.7% of the isolates, respectively. Three biofilm genes rmlA, spgM, and rpfF were positive in 82.8, 92.5, and 64.5% of the isolates, respectively. Mean biofilm forming level of OD492 was 0.54 ± 0.49. We did not find any significant difference between different genders and different age-groups. We retrospectively analyzed data from patients in the intensive care unit (ICU) and the control group. The independent risk factors of those who were infected in the ICU included immunosuppression and the increased antibiotic usage. Conclusions Most of the patients had prior medical usage histories and baseline diseases. The positive rate of virulence genes was high, the drug resistance rate of S. maltophilia was low, and the biofilm formation ability was strong. The increased use of antibiotics was an independent risk factor for S. maltophilia infection, which should receive more attention. No obvious clonal transmissions were found in the same departments.
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Affiliation(s)
- Zhongliang Duan
- Department of Clinical Laboratory, Obstetrics and Gynecology Hospital of Fudan University, 419 Fangxie Road, Shanghai, 200011, China
| | - Juanxiu Qin
- Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200001, China
| | - Yao Liu
- Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200001, China
| | - Cui Li
- Department of Clinical Laboratory, Obstetrics and Gynecology Hospital of Fudan University, 419 Fangxie Road, Shanghai, 200011, China
| | - Chunmei Ying
- Department of Clinical Laboratory, Obstetrics and Gynecology Hospital of Fudan University, 419 Fangxie Road, Shanghai, 200011, China.
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Menetrey Q, Dupont C, Chiron R, Jumas-Bilak E, Marchandin H. High Occurrence of Bacterial Competition Among Clinically Documented Opportunistic Pathogens Including Achromobacter xylosoxidans in Cystic Fibrosis. Front Microbiol 2020; 11:558160. [PMID: 33013789 PMCID: PMC7513574 DOI: 10.3389/fmicb.2020.558160] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 08/14/2020] [Indexed: 12/12/2022] Open
Abstract
Cystic Fibrosis (CF) airways favor abnormal microbial development. Infections are considered as polymicrobial and competition can be observed between microorganisms. The current literature on bacterial competition in CF mostly consists of studies with limited numbers of strains, mainly focused on the major pathogens Pseudomonas aeruginosa (Pa) and Staphylococcus aureus (Sa) and does not give a comprehensive overview of the overall importance of bacterial interactions or the behavior of less often encountered emerging bacteria such as Achromobacter. In this context, we screened a panel of 39 strains from six CF patients, of either clinical or domestic environmental origin, distinguished according to genotype and belonging to four opportunistic pathogens, Pa (n = 15), Sa (n = 3), Stenotrophomonas maltophilia (Sm, n = 10) and Achromobacter xylosoxidans (Ax, n = 11). We investigated their capacity to compete in terms of growth, motility, and pigment production on agar media through 203 crossing experiments. Eleven strains selected via the initial screening results were further studied for competitive growth in liquid medium and biofilm formation. Competition was noted for 33% (67/203) of the pairs of strains with 85 modifications observed between monocultures and co-cultures, impacting growth (23.6%), motility (13.8%), and/or pigment production (6.1%). Under all conditions of the study (clinical, environmental strains; intra-, inter-patients; intra-, inter-species levels), competition was significantly more frequent among pairs of strains with at least one clinical strain. While Pa mainly outcompeted other species, in one patient with chronic colonization by Ax and sporadic colonization by Pa, we showed that some Ax inhibited the growth and pigmentation of Pa whereas biofilm formation was drastically reduced. Enlarging the panel of strains tested in competition assays gave new perspectives on the complex interactions taking place among the CF airway community. Indeed, the frequent occurrence of varied, strain-dependent interactions is revealed here. We report the first results of competition assays for Ax with the ability of certain strains to outcompete Pa. Our results are linked to the patient’s colonization history and question the importance of bacterial competitiveness in the colonization pattern of CF airways.
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Affiliation(s)
- Quentin Menetrey
- HydroSciences Montpellier, Univ Montpellier, CNRS, IRD, Montpellier, France
| | - Chloé Dupont
- HydroSciences Montpellier, Univ Montpellier, CNRS, IRD, Montpellier, France.,HydroSciences Montpellier, Univ Montpellier, CNRS, IRD, Laboratoire d'Ecologie Microbienne Hospitalière, CHU Montpellier, Montpellier, France
| | - Raphaël Chiron
- HydroSciences Montpellier, Univ Montpellier, CNRS, IRD, Montpellier, France.,HydroSciences Montpellier, Univ Montpellier, CNRS, IRD, Centre de Ressources et de Compétences de la Mucoviscidose, CHU Montpellier, Montpellier, France
| | - Estelle Jumas-Bilak
- HydroSciences Montpellier, Univ Montpellier, CNRS, IRD, Montpellier, France.,HydroSciences Montpellier, Univ Montpellier, CNRS, IRD, Laboratoire d'Ecologie Microbienne Hospitalière, CHU Montpellier, Montpellier, France
| | - Hélène Marchandin
- HydroSciences Montpellier, Univ Montpellier, CNRS, IRD, Montpellier, France.,HydroSciences Montpellier, Univ Montpellier, CNRS, IRD, Département de Microbiologie, CHU Nîmes, Nîmes, France
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22
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Radeke LJ, Herman MA. Identification and characterization of differentially expressed genes in Caenorhabditis elegans in response to pathogenic and nonpathogenic Stenotrophomonas maltophilia. BMC Microbiol 2020; 20:170. [PMID: 32560629 PMCID: PMC7304212 DOI: 10.1186/s12866-020-01771-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 03/29/2020] [Indexed: 12/27/2022] Open
Abstract
Background Stenotrophomonas maltophilia is an emerging nosocomial pathogen that causes infection in immunocompromised patients. S. maltophilia isolates are genetically diverse, contain diverse virulence factors, and are variably pathogenic within several host species. Members of the Stenotrophomonas genus are part of the native microbiome of C. elegans, being found in greater relative abundance within the worm than its environment, suggesting that these bacteria accumulate within C. elegans. Thus, study of the C. elegans-Stenotrophomonas interaction is of both medical and ecological significance. To identify host defense mechanisms, we analyzed the C. elegans transcriptomic response to S. maltophilia strains of varying pathogenicity: K279a, an avirulent clinical isolate, JCMS, a virulent strain isolated in association with soil nematodes near Manhattan, KS, and JV3, an even more virulent environmental isolate. Results Overall, we found 145 genes that are commonly differentially expressed in response to pathogenic S. maltophilia strains, 89% of which are upregulated, with many even further upregulated in response to JV3 as compared to JCMS. There are many more JV3-specific differentially expressed genes (225, 11% upregulated) than JCMS-specific differentially expressed genes (14, 86% upregulated), suggesting JV3 has unique pathogenic mechanisms that could explain its increased virulence. We used connectivity within a gene network model to choose pathogen-specific and strain-specific differentially expressed candidate genes for functional analysis. Mutations in 13 of 22 candidate genes caused significant differences in C. elegans survival in response to at least one S. maltophilia strain, although not always the strain that induced differential expression, suggesting a dynamic response to varying levels of pathogenicity. Conclusions Variation in observed pathogenicity and differences in host transcriptional responses to S. maltophilia strains reveal that strain-specific mechanisms play important roles in S. maltophilia pathogenesis. Furthermore, utilizing bacteria closely related to strains found in C. elegans natural environment provides a more realistic interaction for understanding host-pathogen response.
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Affiliation(s)
- Leah J Radeke
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Michael A Herman
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA.
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23
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Yero D, Huedo P, Conchillo-Solé O, Martínez-Servat S, Mamat U, Coves X, Llanas F, Roca I, Vila J, Schaible UE, Daura X, Gibert I. Genetic Variants of the DSF Quorum Sensing System in Stenotrophomonas maltophilia Influence Virulence and Resistance Phenotypes Among Genotypically Diverse Clinical Isolates. Front Microbiol 2020; 11:1160. [PMID: 32582100 PMCID: PMC7283896 DOI: 10.3389/fmicb.2020.01160] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 05/06/2020] [Indexed: 12/16/2022] Open
Abstract
The pathogenicity of Stenotrophomonas maltophilia is regulated in part by its quorum sensing (QS) system. The main QS signaling molecule in S. maltophilia is known as diffusible signal factor (DSF), and the rpf gene cluster is responsible for its synthesis and perception. Two cluster variants have been previously described, rpf-1 and rpf-2, which differ basically in the conditions under which DSF is produced. Here, correlations between the rpf variant and antibiotic susceptibility, LPS electrophoretic profiles and virulence-related phenotypes were evaluated for a collection of 78 geographically and genetically diverse clinical strains of S. maltophilia. In general there were associations between previously established genogroups and the genetic variant of the rpf cluster. However, only few genotype-phenotype correlations could be observed. Resistance to the β-lactam antibiotics ceftazidime and ticarcillin was associated with strains carrying the rpf-1 variant, whereas strains of variant rpf-2, particularly those of genogroup C, showed higher resistance levels to colistin. Strains of variant rpf-2 were also significantly more virulent to Galleria mellonella larvae than those of rpf-1, most likely due to an increased ability of rpf-2 strains to form biofilms. A comparative genomic analysis revealed the presence of proteins unique to individual genogroups. In particular, the strains of genogroup C share an operon that encodes for a new virulence determinant in S. maltophilia related to the synthesis of an alternative Flp/Tad pilus. Overall, this study establishes a link between the DSF-based QS system and the virulence and resistance phenotypes in this species, and identifies potential high-risk clones circulating in European hospitals.
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Affiliation(s)
- Daniel Yero
- Institut de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain.,Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Pol Huedo
- Institut de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain.,Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Oscar Conchillo-Solé
- Institut de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain.,Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Sònia Martínez-Servat
- Institut de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain.,Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Uwe Mamat
- Cellular Microbiology, Priority Research Area Infections, Research Center Borstel - Leibniz Lung Center, Borstel, Germany
| | - Xavier Coves
- Institut de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain.,Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Ferran Llanas
- Institut de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Ignasi Roca
- Department of Clinical Microbiology-ISGlobal, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - Jordi Vila
- Department of Clinical Microbiology-ISGlobal, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - Ulrich E Schaible
- Cellular Microbiology, Priority Research Area Infections, Research Center Borstel - Leibniz Lung Center, Borstel, Germany
| | - Xavier Daura
- Institut de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Isidre Gibert
- Institut de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain.,Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
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24
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Vitale GA, Sciarretta M, Palma Esposito F, January GG, Giaccio M, Bunk B, Spröer C, Bajerski F, Power D, Festa C, Monti MC, D'Auria MV, de Pascale D. Genomics-Metabolomics Profiling Disclosed Marine Vibrio spartinae 3.6 as a Producer of a New Branched Side Chain Prodigiosin. JOURNAL OF NATURAL PRODUCTS 2020; 83:1495-1504. [PMID: 32275146 DOI: 10.1021/acs.jnatprod.9b01159] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
A wide range of prescreening tests for antimicrobial activity of 59 bacterial isolates from sediments of Ria Formosa Lagoon (Algarve, Portugal) disclosed Vibrio spartinae 3.6 as the most active antibacterial producing strain. This bacterial strain, which has not previously been submitted for chemical profiling, was subjected to de novo whole genome sequencing, which aided in the discovery and elucidation of a prodigiosin biosynthetic gene cluster that was predicted by the bioinformatic tool KEGG BlastKoala. Comparative genomics led to the identification of a new membrane di-iron oxygenase-like enzyme, annotated as Vspart_02107, which is likely to be involved in the biosynthesis of cycloprodigiosin and analogues. The combined genomics-metabolomics profiling of the strain led to the isolation and identification of one new branched-chain prodigiosin (5) and to the detection of two new cyclic forms. Furthermore, the evaluation of the minimum inhibitory concentrations disclosed the major prodigiosin as very effective against multi-drug-resistant pathogens including Stenotrophomonas maltophilia, a clinical isolate of Listeria monocytogenes, as well as some human pathogens reported by the World Health Organization as prioritized targets.
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Affiliation(s)
- Giovanni Andrea Vitale
- Institute of Biochemistry and Cellular Biology, National Research Council (IBBC-CNR), Via Pietro Castellino 111, I-80131 Naples, Italy
| | - Martina Sciarretta
- Department of Pharmacy, University of Naples "Federico II" (UNINA), Via Domenico Montesanto, 49, I-80131 Naples, Italy
| | - Fortunato Palma Esposito
- Institute of Biochemistry and Cellular Biology, National Research Council (IBBC-CNR), Via Pietro Castellino 111, I-80131 Naples, Italy
- Stazione Zoologica Anton Dohrn (SZN), Villa Comunale di Napoli, I-80121 Naples, Italy
| | - Grant Garren January
- Institute of Biochemistry and Cellular Biology, National Research Council (IBBC-CNR), Via Pietro Castellino 111, I-80131 Naples, Italy
| | - Marianna Giaccio
- Institute of Biochemistry and Cellular Biology, National Research Council (IBBC-CNR), Via Pietro Castellino 111, I-80131 Naples, Italy
| | - Boyke Bunk
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstraße 7B, 38124 Braunschweig, German
| | - Cathrin Spröer
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstraße 7B, 38124 Braunschweig, German
| | - Felizitas Bajerski
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstraße 7B, 38124 Braunschweig, German
| | - Deborah Power
- Centro de Ciencias do Mar (CCMAR), Universidade do Algarve Campus de Gambelas, 8005-139 Faro, Portugal
| | - Carmen Festa
- Department of Pharmacy, University of Naples "Federico II" (UNINA), Via Domenico Montesanto, 49, I-80131 Naples, Italy
| | - Maria Chiara Monti
- Department of Pharmacy, University of Salerno (UNISA), I-84084 Fisciano, SA, Italy
| | - Maria Valeria D'Auria
- Department of Pharmacy, University of Naples "Federico II" (UNINA), Via Domenico Montesanto, 49, I-80131 Naples, Italy
| | - Donatella de Pascale
- Institute of Biochemistry and Cellular Biology, National Research Council (IBBC-CNR), Via Pietro Castellino 111, I-80131 Naples, Italy
- Stazione Zoologica Anton Dohrn (SZN), Villa Comunale di Napoli, I-80121 Naples, Italy
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25
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Characterization of a New Mixture of Mono-Rhamnolipids Produced by Pseudomonas gessardii Isolated from Edmonson Point (Antarctica). Mar Drugs 2020; 18:md18050269. [PMID: 32443698 PMCID: PMC7281774 DOI: 10.3390/md18050269] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 05/14/2020] [Accepted: 05/18/2020] [Indexed: 12/16/2022] Open
Abstract
Rhamnolipids (RLs) are surface-active molecules mainly produced by Pseudomonas spp. Antarctica is one of the less explored places on Earth and bioprospecting for novel RL producer strains represents a promising strategy for the discovery of novel structures. In the present study, 34 cultivable bacteria isolated from Edmonson Point Lake, Ross Sea, Antarctica were subjected to preliminary screening for the biosurfactant activity. The positive strains were identified by 16S rRNA gene sequencing and the produced RLs were characterized by liquid chromatography coupled to high resolution mass spectrometry (LC-HRESIMS) and liquid chromatography coupled with tandem spectrometry (LC-MS/MS), resulting in a new mixture of 17 different RL congeners, with six previously undescribed RLs. We explored the influence of the carbon source on the RL composition using 12 different raw materials, such as monosaccharides, polysaccharides and petroleum industry derivatives, reporting for the first time the production of RLs using, as sole carbon source, anthracene and benzene. Moreover, we investigated the antimicrobial potential of the RL mixture, towards a panel of both Gram-positive and Gram-negative pathogens, reporting very interesting results towards Listeria monocytogenes with a minimum inhibitory concentration (MIC) value of 3.13 µg/mL. Finally, we report for the first time the antimicrobial activity of RLs towards three strains of the emerging multidrug resistant Stenotrophomonas maltophilia with MIC values of 12.5 µg/mL.
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26
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Comparative Whole-Genome Phylogeny of Animal, Environmental, and Human Strains Confirms the Genogroup Organization and Diversity of the Stenotrophomonas maltophilia Complex. Appl Environ Microbiol 2020; 86:AEM.02919-19. [PMID: 32198168 DOI: 10.1128/aem.02919-19] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 03/02/2020] [Indexed: 01/17/2023] Open
Abstract
The Stenotrophomonas maltophilia complex (Smc) comprises opportunistic environmental Gram-negative bacilli responsible for a variety of infections in both humans and animals. Beyond its large genetic diversity, its genetic organization in genogroups was recently confirmed through the whole-genome sequencing of human and environmental strains. As they are poorly represented in these analyses, we sequenced the whole genomes of 93 animal strains to determine their genetic background and characteristics. Combining these data with 81 newly sequenced human strains and the genomes available from RefSeq, we performed a genomic analysis that included 375 nonduplicated genomes with various origins (animal, 104; human, 226; environment, 30; unknown, 15). Phylogenetic analysis and clustering based on genome-wide average nucleotide identity confirmed and specified the genetic organization of Smc in at least 20 genogroups. Two new genogroups were identified, and two previously described groups were further divided into two subgroups each. Comparing the strains isolated from different host types and their genogroup affiliation, we observed a clear disequilibrium in certain groups. Surprisingly, some antimicrobial resistance genes, integrons, and/or clusters of attC sites lacking integron-integrase (CALIN) sequences targeting antimicrobial compounds extensively used in animals were mainly identified in animal strains. We also identified genes commonly found in animal strains coding for efflux systems. The result of a large whole-genome analysis performed by us supports the hypothesis of the putative contribution of animals as a reservoir of Stenotrophomonas maltophilia complex strains and/or resistance genes for strains in humans.IMPORTANCE Given its naturally large antimicrobial resistance profile, the Stenotrophomonas maltophilia complex (Smc) is a set of emerging pathogens of immunosuppressed and cystic fibrosis patients. As it is group of environmental microorganisms, this adaptation to humans is an opportunity to understand the genetic and metabolic selective mechanisms involved in this process. The previously reported genomic organization was incomplete, as data from animal strains were underrepresented. We added the missing piece of the puzzle with whole-genome sequencing of 93 strains of animal origin. Beyond describing the phylogenetic organization, we confirmed the genetic diversity of the Smc, which could not be estimated through routine phenotype- or matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF)-based laboratory tests. Animals strains seem to play a key role in the diversity of Smc and could act as a reservoir for mobile resistance genes. Some genogroups seem to be associated with particular hosts; the genetic support of this association and the role of the determinants/corresponding genes need to be explored.
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27
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Gröschel MI, Meehan CJ, Barilar I, Diricks M, Gonzaga A, Steglich M, Conchillo-Solé O, Scherer IC, Mamat U, Luz CF, De Bruyne K, Utpatel C, Yero D, Gibert I, Daura X, Kampmeier S, Rahman NA, Kresken M, van der Werf TS, Alio I, Streit WR, Zhou K, Schwartz T, Rossen JWA, Farhat MR, Schaible UE, Nübel U, Rupp J, Steinmann J, Niemann S, Kohl TA. The phylogenetic landscape and nosocomial spread of the multidrug-resistant opportunist Stenotrophomonas maltophilia. Nat Commun 2020; 11:2044. [PMID: 32341346 PMCID: PMC7184733 DOI: 10.1038/s41467-020-15123-0] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 02/15/2020] [Indexed: 02/06/2023] Open
Abstract
Recent studies portend a rising global spread and adaptation of human- or healthcare-associated pathogens. Here, we analyse an international collection of the emerging, multidrug-resistant, opportunistic pathogen Stenotrophomonas maltophilia from 22 countries to infer population structure and clonality at a global level. We show that the S. maltophilia complex is divided into 23 monophyletic lineages, most of which harbour strains of all degrees of human virulence. Lineage Sm6 comprises the highest rate of human-associated strains, linked to key virulence and resistance genes. Transmission analysis identifies potential outbreak events of genetically closely related strains isolated within days or weeks in the same hospitals. Multidrug resistance of the opportunistic pathogen Stenotrophomonas maltophilia is an increasing problem. Here, analyzing strains from 22 countries, the authors show that the S. maltophilia complex is divided into 23 monophyletic lineages and find evidence for intra-hospital transmission.
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Affiliation(s)
- Matthias I Gröschel
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany.,Department of Pulmonary Diseases & Tuberculosis, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Conor J Meehan
- School of Chemistry and Bioscience, University of Bradford, Bradford, United Kingdom
| | - Ivan Barilar
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Margo Diricks
- bioMérieux, Applied Maths NV, Keistraat 120, 9830, St-Martens-Latem, Belgium
| | - Aitor Gonzaga
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Matthias Steglich
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Oscar Conchillo-Solé
- Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Barcelona, Spain.,Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Isabell-Christin Scherer
- Department of Infectious Diseases and Microbiology, University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Uwe Mamat
- Cellular Microbiology, Research Center Borstel, Borstel, Germany
| | - Christian F Luz
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Katrien De Bruyne
- bioMérieux, Applied Maths NV, Keistraat 120, 9830, St-Martens-Latem, Belgium
| | - Christian Utpatel
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Daniel Yero
- Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Barcelona, Spain.,Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Isidre Gibert
- Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Barcelona, Spain.,Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Xavier Daura
- Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Barcelona, Spain.,Catalan Institution for Research and Advanced Studies, Barcelona, Spain
| | | | | | - Michael Kresken
- Antiinfectives Intelligence GmbH, Rheinbach, Germany.,Rheinische Fachhochschule Köln gGmbH, Cologne, Germany
| | - Tjip S van der Werf
- Department of Pulmonary Diseases & Tuberculosis, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Ifey Alio
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Wolfgang R Streit
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Kai Zhou
- Shenzhen Institute of Respiratory Diseases, the First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen, China.,Second Clinical Medical College, Jinan University, Shenzhen, China
| | - Thomas Schwartz
- Karlsruhe Institute of Technology, Institute of Functional Interfaces, Eggenstein- Leopoldshafen, Germany
| | - John W A Rossen
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Maha R Farhat
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.,Division of Pulmonary and Critical Care, Massachusetts General Hospital, Boston, MA, USA
| | - Ulrich E Schaible
- Cellular Microbiology, Research Center Borstel, Borstel, Germany.,German Center for Infection Research (DZIF), partner site Hamburg - Lübeck - Borstel - Riems, Cologne, Germany.,Leibniz Research Alliance INFECTIONS'21, Cologne, Germany
| | - Ulrich Nübel
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.,Leibniz Research Alliance INFECTIONS'21, Cologne, Germany.,Germany Center for Infection Research (DZIF), partner site Hannover - Braunschweig, Cologne, Germany.,Braunschweig Integrated Center of Systems Biology (BRICS), Technical University, Braunschweig, Germany
| | - Jan Rupp
- Department of Infectious Diseases and Microbiology, University Hospital Schleswig-Holstein, Lübeck, Germany.,German Center for Infection Research (DZIF), partner site Hamburg - Lübeck - Borstel - Riems, Cologne, Germany
| | - Joerg Steinmann
- Institute of Medical Microbiology, University Medical Center Essen, Essen, Germany.,Medical Microbiology and Infection Prevention, Institute of Clinical Hygiene, Paracelsus Medical Private University, Klinikum Nürnberg, Nuremberg, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany. .,German Center for Infection Research (DZIF), partner site Hamburg - Lübeck - Borstel - Riems, Cologne, Germany. .,Leibniz Research Alliance INFECTIONS'21, Cologne, Germany.
| | - Thomas A Kohl
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany.,German Center for Infection Research (DZIF), partner site Hamburg - Lübeck - Borstel - Riems, Cologne, Germany
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28
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Cruz-Córdova A, Mancilla-Rojano J, Luna-Pineda VM, Escalona-Venegas G, Cázares-Domínguez V, Ormsby C, Franco-Hernández I, Zavala-Vega S, Hernández MA, Medina-Pelcastre M, Parra-Ortega I, la Rosa-Zamboni DD, Ochoa SA, Xicohtencatl-Cortes J. Molecular Epidemiology, Antibiotic Resistance, and Virulence Traits of Stenotrophomonas maltophilia Strains Associated With an Outbreak in a Mexican Tertiary Care Hospital. Front Cell Infect Microbiol 2020; 10:50. [PMID: 32133303 PMCID: PMC7040173 DOI: 10.3389/fcimb.2020.00050] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 01/27/2020] [Indexed: 01/19/2023] Open
Abstract
Stenotrophomonas maltophilia, an emerging opportunistic pathogen, is widely distributed in the environment the resistance mechanisms, and virulence factors of this bacterium facilitate its dissemination in hospitals. This study aimed to characterize the molecular epidemiology of S. maltophilia strains associated with an outbreak in the Children's Hospital of México Federico Gómez (HIMFG). Twenty-one clinical S. maltophilia strains were recovered from cultures of blood and urine samples from 10 pediatric patients at the emergency department, and nine environmental S. maltophilia strains recovered from faucets in the same area were also included. Two of the 10 patients were related with health care-associated infections (HCAIs), and the other eight patients (8/10) were infected with environmental S. maltophilia strains. The outbreak was controlled by monthly disinfection of the faucets in the emergency department. Typing using pulsed-field gel electrophoresis (PFGE) showed a 52% genetic diversity with seven pulsotypes denoted P1–P7 among all S. maltophilia strains. Three pulsotypes (P2, P3, and P7) were identified among both the clinical and environmental S. maltophilia strains and associated with two type sequences (STs), namely, ST304 and ST24. Moreover, 80% (24/30) of the strains exhibited resistance mainly to tetracycline, 76.66% (23/30) to trimethoprim-sulfamethoxazole, and 23.33% (7/30) to the extended-spectrum β-lactamase (ESBL) phenotype. The main resistance genes identified by multiplex PCR were sul1 in 100% (30/30), qnr in 86.66% (26/30), and intl1 in 80% (24/30) of the samples, respectively. Furthermore, the pilU, hlylII, and rmlA genes were identified in 96.6% (29/30), 90% (27/30), and 83.33% (25/30) of the samples, respectively. Additionally, 76.66% (23/30) of the S. maltophilia strains exhibited high swimming motility, 46.66% (14/30) showed moderate biofilm formation capacity, 43.33% (13/30) displayed moderate twitching motility, and 20% (6/30) exhibited high adherence. The clinical S. maltophilia strains isolated from blood most strongly adhered to HTB-9 cells. In conclusion, the molecular epidemiology and some of the features such as resistance, and virulence genes associated with colonization patterns are pathogenic attributes that can promote S. maltophilia dissemination, persistence, and facilitate the outbreak that occurred in the HIMFG. This study supports the need for faucet disinfection as a control strategy for clinical outbreaks.
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Affiliation(s)
- Ariadnna Cruz-Córdova
- Laboratorio de Investigación en Bacteriología Intestinal, Hospital Infantil de México "Federico Gómez", Ciudad de México, Mexico
| | - Jetsi Mancilla-Rojano
- Laboratorio de Investigación en Bacteriología Intestinal, Hospital Infantil de México "Federico Gómez", Ciudad de México, Mexico
| | - Víctor M Luna-Pineda
- Laboratorio de Investigación en Bacteriología Intestinal, Hospital Infantil de México "Federico Gómez", Ciudad de México, Mexico
| | - Gerardo Escalona-Venegas
- Laboratorio de Investigación en Bacteriología Intestinal, Hospital Infantil de México "Federico Gómez", Ciudad de México, Mexico
| | - Vicenta Cázares-Domínguez
- Laboratorio de Investigación en Bacteriología Intestinal, Hospital Infantil de México "Federico Gómez", Ciudad de México, Mexico
| | - Christopher Ormsby
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias, Ciudad de México, Mexico
| | - Isabel Franco-Hernández
- Laboratorio Central de Bacteriología, Hospital Infantil de México "Federico Gómez", Ciudad de México, Mexico
| | - Sergio Zavala-Vega
- Laboratorio de Neuropatología, Instituto Nacional de Neurología y Neurocirugía "Manuel Velasco Suárez", Ciudad de México, Mexico
| | | | - Marisol Medina-Pelcastre
- Departamento de Epidemiología, Hospital Infantil de México "Federico Gómez", Ciudad de México, Mexico
| | - Israel Parra-Ortega
- Laboratorio Central de Bacteriología, Hospital Infantil de México "Federico Gómez", Ciudad de México, Mexico
| | | | - Sara A Ochoa
- Laboratorio de Investigación en Bacteriología Intestinal, Hospital Infantil de México "Federico Gómez", Ciudad de México, Mexico
| | - Juan Xicohtencatl-Cortes
- Laboratorio de Investigación en Bacteriología Intestinal, Hospital Infantil de México "Federico Gómez", Ciudad de México, Mexico
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Sant' Anna D, Sampaio JLM, Sommaggio LRD, Mazzeo DEC, Marin-Morales MA, Marson FAL, Levy CE. The applicability of gene sequencing and MALDI-TOF to identify less common gram-negative rods (Advenella, Castellaniella, Kaistia, Pusillimonas and Sphingobacterium) from environmental isolates. Antonie van Leeuwenhoek 2019; 113:233-252. [PMID: 31560092 DOI: 10.1007/s10482-019-01333-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 09/13/2019] [Indexed: 11/26/2022]
Abstract
Our aim was to identify less common non-fermenting gram-negative rods during the bioremediation process. Five genera were found: Advenella, Castellaniella, Kaistia, Pusillimonas and Sphingobacterium, for a total of 15 isolates. Therefore, we evaluated the applicability of four methods currently available for bacteria identification: (1) conventional biochemical methods, (2) the VITEK®-2 system, (3) MALDI-TOF mass spectrometry and (4) 16S rRNA gene sequencing. The biochemical methods and the VITEK®-2 system were reliable only for the Sphingobacterium isolate and solely at the genus level. Both MALDI-TOF mass spectrometry platforms (Bruker and VITEK® MS) did not achieve reliable identification results for any of these genera. 16S rRNA gene sequencing identified eight isolates to the species level but not to the subspecies level, when applicable. The remaining seven isolates were reliably identified through 16S rRNA gene sequencing to the genus level only. Our findings suggest that the detection and identification of less common genera (and species) that appeared at certain moments during the bioremediation process can be a challenge to microbiologists considering the most used techniques. In addition, more studies are required to confirm our results.
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Affiliation(s)
- Débora Sant' Anna
- Microbiology Laboratory, Department of Clinical Pathology, Faculty of Medical Sciences, University of Campinas, Rua Tessália Vieira de Camargo, 126, Cidade Universitária, Campinas, São Paulo, 13083-887, Brazil.
- Molecular Oncology Research Center, Barretos Cancer Hospital, Rua Antenor Duarte Villela, 1331, Barretos, São Paulo, Brazil.
| | - Jorge Luiz Mello Sampaio
- Microbiology Section, Fleury-Centers for Diagnostic Medicine, Av. General Waldomiro de Lima 508, São Paulo, 04344-070, Brazil
- Clinical Analysis and Toxicology Department, School of Pharmacy, University of São Paulo, Av. Professor Lineu Prestes, 580, Butantã, São Paulo, 05508-000, Brazil
| | - Lais Roberta Deroldo Sommaggio
- Department of Biology, Institute of Biosciences, São Paulo State University - Rio Claro, Av. 24 A, 1515, Bela Vista, Rio Claro, São Paulo, 13506-900, Brazil
| | - Dânia Elisa Christofoletti Mazzeo
- Department of Analytical Chemistry, Institute of Chemistry, São Paulo State University - Araraquara, Rua Professor Francisco Degni, 55, Araraquara, São Paulo, 14800-060, Brazil
| | - Maria Aparecida Marin-Morales
- Department of Biology, Institute of Biosciences, São Paulo State University - Rio Claro, Av. 24 A, 1515, Bela Vista, Rio Claro, São Paulo, 13506-900, Brazil
| | - Fernando Augusto Lima Marson
- Department of Pediatrics, Faculty of Medical Sciences, University of Campinas, Rua Tessália Vieira de Camargo, 126, Cidade Universitária, Campinas, São Paulo, 13083-887, Brazil.
- Laboratory of Pulmonary Physiology, Center for Pediatrics Investigation, Faculty of Medical Sciences, University of Campinas, Rua Tessália Vieira de Camargo, 126, Cidade Universitária, Campinas, São Paulo, 13083-887, Brazil.
- Department of Medical Genetics and Genomic Medicine, Faculty of Medical Sciences, University of Campinas, Rua Tessália Vieira de Camargo, 126, Cidade Universitária, Campinas, São Paulo, 13083-887, Brazil.
- Post-Graduate Program in Health Science, São Francisco University, Avenida São Francisco de Assis, 218, Cidade Universitária, Bragança Paulista, São Paulo, 12916-400, Brazil.
| | - Carlos Emílio Levy
- Microbiology Laboratory, Department of Clinical Pathology, Faculty of Medical Sciences, University of Campinas, Rua Tessália Vieira de Camargo, 126, Cidade Universitária, Campinas, São Paulo, 13083-887, Brazil.
- Department of Pediatrics, Faculty of Medical Sciences, University of Campinas, Rua Tessália Vieira de Camargo, 126, Cidade Universitária, Campinas, São Paulo, 13083-887, Brazil.
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30
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Mojica MF, Rutter JD, Taracila M, Abriata LA, Fouts DE, Papp-Wallace KM, Walsh TJ, LiPuma JJ, Vila AJ, Bonomo RA. Population Structure, Molecular Epidemiology, and β-Lactamase Diversity among Stenotrophomonas maltophilia Isolates in the United States. mBio 2019; 10:e00405-19. [PMID: 31266860 PMCID: PMC6606795 DOI: 10.1128/mbio.00405-19] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 06/03/2019] [Indexed: 01/06/2023] Open
Abstract
Stenotrophomonas maltophilia is a Gram-negative, nonfermenting, environmental bacillus that is an important cause of nosocomial infections, primarily associated with the respiratory tract in the immunocompromised population. Aiming to understand the population structure, microbiological characteristics and impact of allelic variation on β-lactamase structure and function, we collected 130 clinical isolates from across the United States. Identification of 90 different sequence types (STs), of which 63 are new allelic combinations, demonstrates the high diversity of this species. The majority of the isolates (45%) belong to genomic group 6. We also report excellent activity of the ceftazidime-avibactam and aztreonam combination, especially against strains recovered from blood and respiratory infections for which the susceptibility is higher than the susceptibility to trimethoprim-sulfamethoxazole, considered the "first-line" antibiotic to treat S. maltophilia Analysis of 73 blaL1 and 116 blaL2 genes identified 35 and 43 novel variants of L1 and L2 β-lactamases, respectively. Investigation of the derived amino acid sequences showed that substitutions are mostly conservative and scattered throughout the protein, preferentially affecting positions that do not compromise enzyme function but that may have an impact on substrate and inhibitor binding. Interestingly, we detected a probable association between a specific type of L1 and L2 and genomic group 6. Taken together, our results provide an overview of the molecular epidemiology of S. maltophilia clinical strains from the United States. In particular, the discovery of new L1 and L2 variants warrants further study to fully understand the relationship between them and the β-lactam resistance phenotype in this pathogen.IMPORTANCE Multiple antibiotic resistance mechanisms, including two β-lactamases, L1, a metallo-β-lactamase, and L2, a class A cephalosporinase, make S. maltophilia naturally multidrug resistant. Thus, infections caused by S. maltophilia pose a big therapeutic challenge. Our study aims to understand the microbiological and molecular characteristics of S. maltophilia isolates recovered from human sources. A highlight of the resistance profile of this collection is the excellent activity of the ceftazidime-avibactam and aztreonam combination. We hope this result prompts controlled and observational studies to add clinical data on the utility and safety of this therapy. We also identify 35 and 43 novel variants of L1 and L2, respectively, some of which harbor novel substitutions that could potentially affect substrate and/or inhibitor binding. We believe our results provide valuable knowledge to understand the epidemiology of this species and to advance mechanism-based inhibitor design to add to the limited arsenal of antibiotics active against this pathogen.
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Affiliation(s)
- Maria F Mojica
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Research Service, Louis Stokes Veterans Affairs Medical Center, Cleveland, Ohio, USA
| | - Joseph D Rutter
- Research Service, Louis Stokes Veterans Affairs Medical Center, Cleveland, Ohio, USA
| | - Magdalena Taracila
- Research Service, Louis Stokes Veterans Affairs Medical Center, Cleveland, Ohio, USA
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Luciano A Abriata
- Laboratory for Biomolecular Modeling, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | | - Krisztina M Papp-Wallace
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Research Service, Louis Stokes Veterans Affairs Medical Center, Cleveland, Ohio, USA
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Thomas J Walsh
- Transplantation Oncology Infectious Diseases Program, Weill Cornell Medical Center, New York, New York, USA
| | - John J LiPuma
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Alejandro J Vila
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Rosario, Argentina
| | - Robert A Bonomo
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Center for Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Medical Service, Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, Ohio, USA
- GRECC, Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, Ohio, USA
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, Ohio, USA
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31
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Bostanghadiri N, Ghalavand Z, Fallah F, Yadegar A, Ardebili A, Tarashi S, Pournajaf A, Mardaneh J, Shams S, Hashemi A. Characterization of Phenotypic and Genotypic Diversity of Stenotrophomonas maltophilia Strains Isolated From Selected Hospitals in Iran. Front Microbiol 2019; 10:1191. [PMID: 31191502 PMCID: PMC6548850 DOI: 10.3389/fmicb.2019.01191] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Accepted: 05/10/2019] [Indexed: 12/25/2022] Open
Abstract
Stenotrophomonas maltophilia is an environmental Gram-negative bacterium that has rapidly emerged as an important nosocomial pathogen in hospitalized patients. Treatment of S. maltophilia infections is difficult due to increasing resistance to multiple antibacterial agents. The purpose of this study was to determine the phenotypic and genotypic characterization of S. maltophilia isolates recovered from patients referred to several hospitals. A total of 164 clinical isolates of S. maltophilia were collected from hospitals in various regions in Iran between 2016 and 2017. Antibiotic susceptibility testing was performed by disc diffusion method and E-test assay according to the Clinical and Laboratory Standards Institute (CLSI) guideline. The ability of biofilm formation was assessed with crystal violet staining and then, biofilm-associated genes were investigated by PCR-sequencing method. The presence of L1 (a metallo-β-lactamase), L2 (a clavulanic acid-sensitive cephalosporinase), sul1 and sul2 (resistance to Trimethoprim/Sulfamethoxazole), Smqnr (intrinsic resistance to quinolones), and dfrA genes (dihydrofolate reductase enzyme that contributes to trimethoprim resistance) was also examined by PCR-sequencing. Relative gene expression of smeDEF efflux pump was assessed by real-time PCR. Genotyping was performed using the multi-locus sequencing typing (MLST) and repetitive extragenic palindromic-PCR (Rep-PCR). Isolates were resistant to imipenem (100%), meropenem (96%), doripenem (96%), and ceftazidime (36.58%). Notably, 5 (3.04%) isolates showed resistant to trimethoprim-sulfamethoxazole (TMP-SMX), an alarming trend of decreased susceptibility to TMP-SMX in Iran. Minocycline and levofloxacin exhibited the highest susceptibility of 91.46 and 99.39%, respectively. Using the crystal violet staining, 157 (95.73%) isolates had biofilm phenotype: 49 (29.87%), 63 (38.41%), and 45 (27.43%) isolates were categorized as strong-, moderate- and weak-biofilm producer while 7 isolates (4.26%) were identified a non-biofilm producer. Biofilm genes had an overall prevalence of 145 (88.41%), 137 (83.53%), and 164 (100%) of rmlA, rpfF, and spgM, respectively. L1, L2, Smqnr, sul1, and sul2 resistance genes were detected in 145 (88.41%), 156 (96.12%), 103 (62.80%), 89 (54.26%), and 92 (56.09%) isolates, respectively. None of the S. maltophilia isolates were positive for dfrA12, dfrA17, and dfrA27 genes. Gene expression analysis showed that smeD efflux system was overexpressed in two out of the five clinical isolates (40%) that showed resistance to TMP-SMX. Most of the isolates were genetically unrelated. Two new sequence types (ST139 and ST259) were determined. Our results showed that TMP-SMX was still an effective antibiotic against S. maltophilia. The findings of the current study revealed an increasing prevalence of antibiotic resistance and biofilm genes in clinical S. maltophilia isolates in Iran.
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Affiliation(s)
- Narjess Bostanghadiri
- Infectious Diseases and Tropical Medicine Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zohreh Ghalavand
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Fatemeh Fallah
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Abbas Yadegar
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Abdollah Ardebili
- Infectious Diseases Research Center, Golestan University of Medical Sciences, Gorgan, Iran.,Department of Microbiology, Faculty of Medicine, Golestan University of Medical Sciences, Gorgan, Iran
| | - Samira Tarashi
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Abazar Pournajaf
- Department of Microbiology, School of Medicine, Babol University of Medical Sciences, Babol, Iran
| | - Jalal Mardaneh
- Microbiology Department, School of Medicine, Gonabad University of Medical Sciences, Gonabad, Iran
| | - Saeed Shams
- Cellular and Molecular Research Center, Qom University of Medical Sciences, Qom, Iran
| | - Ali Hashemi
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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32
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Pathogenic significance of hemorrhagic pneumonia in hematologic malignancy patients with Stenotrophomonas maltophilia bacteremia: clinical and microbiological analysis. Eur J Clin Microbiol Infect Dis 2018; 38:285-295. [PMID: 30421302 DOI: 10.1007/s10096-018-3425-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 11/06/2018] [Indexed: 10/27/2022]
Abstract
Hemorrhagic pneumonia (HP) is known as the clinical manifestation of Stenotrophomonas maltophilia infection, while catheter-related blood stream infection (CRBSI) is the common clinical presentation of S. maltophilia bacteremia (SMB). The purpose of this study is to evaluate the risk factors for mortality in hematologic malignancy patients with SMB and to analyze clinical and microbiological characteristics of HP associated with SMB and CRBSI. SMB cases of patients with a hematologic malignancy were collected from 2006 through 2016. The overall 30-day mortality rate and mortality risk factors were assessed. The expression of major virulence-associated genes from S. maltophilia isolates, which included genes encoding type-1 fimbriae (smf-1), proteases (StmPr1 and StmPr2), and esterase (Smlt3773), from the blood of patients with HP and CRBSI was investigated. The phenotypic and genotypic traits were also compared. A total of 118 cases of SMB were included. The overall 30-day mortality rate was 61.0%. A multivariable analysis showed that HP was the most important risk factor for mortality (adjusted OR = 106.41; 95% CI = 5.18-2184.55). Although no statistical significance was observed in microbiological analysis, isolates from HP have a trend toward a higher protease activity (93.8% vs. 73.3%, P = 0.172). Clinical analysis showed that thrombocytopenia (P = 0.037) and prolonged neutropenia (P = 0.043) were significant factors associated with HP. Our data, which includes hematologic malignancy patients with SMB, suggest that HP is the significant risk factor for mortality and that the unique characteristics of patients and microbes contribute to the pathogenesis.
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33
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Singhal L, Kaur P, Gautam V. Stenotrophomonas maltophilia: From trivial to grievous. Indian J Med Microbiol 2018; 35:469-479. [PMID: 29405136 DOI: 10.4103/ijmm.ijmm_16_430] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Stenotrophomonas maltophilia, once regarded as an organism of low virulence, has evolved as a significant opportunistic pathogen causing severe human infections in both hospital and community settings, especially amongst highly debilitated patients. Globally, S. maltophilia ranks third amongst the four most common pathogenic non-fermenting Gram-negative bacilli (NFGNBs), others being Pseudomonas aeruginosa, Acinetobacter baumannii and Burkholderia cepacia complex (Bcc). The worth of accurate identification of S. maltophilia comes to the forefront as it needs to be differentiated from other NFGNBs such as Acinetobacter, P. aeruginosa and Bcc due to its inherently contrasting antibiotic susceptibility pattern. Consequently, its correct identification is essential as no single drug is amply effective against all NFGNBs, which hinders initiation of appropriate empirical treatment resulting in increased morbidity and mortality.
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Affiliation(s)
- Lipika Singhal
- Department of Microbiology, Government Medical College and Hospital, Chandigarh, India
| | - Parvinder Kaur
- Department of Biotechnology, Amar Shaheed Baba Ajit Singh Jujhar Singh Memorial College, Bela, Ropar, Punjab, India
| | - Vikas Gautam
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
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34
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Patil PP, Kumar S, Midha S, Gautam V, Patil PB. Taxonogenomics reveal multiple novel genomospecies associated with clinical isolates of Stenotrophomonas maltophilia. Microb Genom 2018; 4:e000207. [PMID: 30084764 PMCID: PMC6159553 DOI: 10.1099/mgen.0.000207] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 07/11/2018] [Indexed: 01/25/2023] Open
Abstract
Stenotrophomonas maltophilia has evolved as one of the leading multidrug-resistant pathogens responsible for a variety of nosocomial infections especially in highly debilitated patients. As information on the genomic and intraspecies diversity of this clinically important pathogen is limited, we sequenced the whole genome of 27 clinical isolates from hospitalized patients. Phylogenomic analysis along with the genomes of type strains suggested that the clinical isolates are distributed over the Stenotrophomonas maltophilia complex (Smc) within the genus Stenotrophomonas. Further genome-based taxonomy coupled with the genomes of type strains of the genus Stenotrophomonas allowed us to identify five cryptic genomospecies, which are associated with the clinical isolates of S. maltophilia and are potentially novel species. These isolates share a very small core genome that implies a high level of genetic diversity within the isolates. Recombination analysis of core genomes revealed that the impact of recombination is more than mutation in the diversification of clinical S. maltophilia isolates. Distribution analysis of well-characterized antibiotic-resistance and efflux pump genes of S. maltophilia across multiple novel genomospecies provided insights into its antibiotic-resistant ability. This study supports the existence of multiple cryptic species within the Smc besides S. maltophilia, which are associated with human infections, and highlights the importance of genome-based approaches to delineate bacterial species. This data will aid in improving clinical diagnosis and for understanding species-specific clinical manifestations of infection due to Stenotrophomonas species.
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Affiliation(s)
- Prashant P. Patil
- Bacterial Genomics and Evolution Laboratory, CSIR–Institute of Microbial Technology (CSIR-IMTECH), Chandigarh, India
| | - Sanjeet Kumar
- Bacterial Genomics and Evolution Laboratory, CSIR–Institute of Microbial Technology (CSIR-IMTECH), Chandigarh, India
| | - Samriti Midha
- Bacterial Genomics and Evolution Laboratory, CSIR–Institute of Microbial Technology (CSIR-IMTECH), Chandigarh, India
- Present address: Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Vikas Gautam
- Department of Medical Microbiology, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | - Prabhu B. Patil
- Bacterial Genomics and Evolution Laboratory, CSIR–Institute of Microbial Technology (CSIR-IMTECH), Chandigarh, India
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35
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Huang YT, Chen JM, Ho BC, Wu ZY, Kuo RC, Liu PY. Genome Sequencing and Comparative Analysis of Stenotrophomonas acidaminiphila Reveal Evolutionary Insights Into Sulfamethoxazole Resistance. Front Microbiol 2018; 9:1013. [PMID: 29867899 PMCID: PMC5966563 DOI: 10.3389/fmicb.2018.01013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 04/30/2018] [Indexed: 11/23/2022] Open
Abstract
Stenotrophomonas acidaminiphila is an aerobic, glucose non-fermentative, Gram-negative bacterium that been isolated from various environmental sources, particularly aquatic ecosystems. Although resistance to multiple antimicrobial agents has been reported in S. acidaminiphila, the mechanisms are largely unknown. Here, for the first time, we report the complete genome and antimicrobial resistome analysis of a clinical isolate S. acidaminiphila SUNEO which is resistant to sulfamethoxazole. Comparative analysis among closely related strains identified common and strain-specific genes. In particular, comparison with a sulfamethoxazole-sensitive strain identified a mutation within the sulfonamide-binding site of folP in SUNEO, which may reduce the binding affinity of sulfamethoxazole. Selection pressure analysis indicated folP in SUNEO is under purifying selection, which may be owing to long-term administration of sulfonamide against Stenotrophomonas.
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Affiliation(s)
- Yao-Ting Huang
- Department of Computer Science and Information Engineering, National Chung Cheng University, Chiayi, Taiwan
| | - Jia-Min Chen
- Department of Computer Science and Information Engineering, National Chung Cheng University, Chiayi, Taiwan
| | - Bing-Ching Ho
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University Hospital, Taipei, Taiwan
| | - Zong-Yen Wu
- DOE Joint Genome Institute, Walnut Creek, CA, United States.,Department of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan
| | - Rita C Kuo
- DOE Joint Genome Institute, Walnut Creek, CA, United States
| | - Po-Yu Liu
- The Department of Nursing, Shu-Zen Junior College of Medicine and Management, Kaohsiung, Taiwan.,Rong Hsing Research Center for Translational Medicine, College of Life Sciences, National Chung Hsing University, Taichung, Taiwan.,Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
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36
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Vinuesa P, Ochoa-Sánchez LE, Contreras-Moreira B. GET_PHYLOMARKERS, a Software Package to Select Optimal Orthologous Clusters for Phylogenomics and Inferring Pan-Genome Phylogenies, Used for a Critical Geno-Taxonomic Revision of the Genus Stenotrophomonas. Front Microbiol 2018; 9:771. [PMID: 29765358 PMCID: PMC5938378 DOI: 10.3389/fmicb.2018.00771] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 04/05/2018] [Indexed: 12/17/2022] Open
Abstract
The massive accumulation of genome-sequences in public databases promoted the proliferation of genome-level phylogenetic analyses in many areas of biological research. However, due to diverse evolutionary and genetic processes, many loci have undesirable properties for phylogenetic reconstruction. These, if undetected, can result in erroneous or biased estimates, particularly when estimating species trees from concatenated datasets. To deal with these problems, we developed GET_PHYLOMARKERS, a pipeline designed to identify high-quality markers to estimate robust genome phylogenies from the orthologous clusters, or the pan-genome matrix (PGM), computed by GET_HOMOLOGUES. In the first context, a set of sequential filters are applied to exclude recombinant alignments and those producing anomalous or poorly resolved trees. Multiple sequence alignments and maximum likelihood (ML) phylogenies are computed in parallel on multi-core computers. A ML species tree is estimated from the concatenated set of top-ranking alignments at the DNA or protein levels, using either FastTree or IQ-TREE (IQT). The latter is used by default due to its superior performance revealed in an extensive benchmark analysis. In addition, parsimony and ML phylogenies can be estimated from the PGM. We demonstrate the practical utility of the software by analyzing 170 Stenotrophomonas genome sequences available in RefSeq and 10 new complete genomes of Mexican environmental S. maltophilia complex (Smc) isolates reported herein. A combination of core-genome and PGM analyses was used to revise the molecular systematics of the genus. An unsupervised learning approach that uses a goodness of clustering statistic identified 20 groups within the Smc at a core-genome average nucleotide identity (cgANIb) of 95.9% that are perfectly consistent with strongly supported clades on the core- and pan-genome trees. In addition, we identified 16 misclassified RefSeq genome sequences, 14 of them labeled as S. maltophilia, demonstrating the broad utility of the software for phylogenomics and geno-taxonomic studies. The code, a detailed manual and tutorials are freely available for Linux/UNIX servers under the GNU GPLv3 license at https://github.com/vinuesa/get_phylomarkers. A docker image bundling GET_PHYLOMARKERS with GET_HOMOLOGUES is available at https://hub.docker.com/r/csicunam/get_homologues/, which can be easily run on any platform.
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Affiliation(s)
- Pablo Vinuesa
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Luz E Ochoa-Sánchez
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Bruno Contreras-Moreira
- Estación Experimental de Aula Dei - Consejo Superior de Investigaciones Científicas, Zaragoza, Spain.,Fundación Agencia Aragonesa para la Investigacion y el Desarrollo (ARAID), Zaragoza, Spain
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37
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Steinmann J, Mamat U, Abda EM, Kirchhoff L, Streit WR, Schaible UE, Niemann S, Kohl TA. Analysis of Phylogenetic Variation of Stenotrophomonas maltophilia Reveals Human-Specific Branches. Front Microbiol 2018; 9:806. [PMID: 29755435 PMCID: PMC5932162 DOI: 10.3389/fmicb.2018.00806] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 04/10/2018] [Indexed: 11/16/2022] Open
Abstract
Stenotrophomonas maltophilia is a non-fermenting Gram-negative bacterium that is ubiquitous in the environment. In humans, this opportunistic multi-drug-resistant pathogen is responsible for a plethora of healthcare-associated infections. Here, we utilized a whole genome sequencing (WGS)-based phylogenomic core single nucleotide polymorphism (SNP) approach to characterize S. maltophilia subgroups, their potential association with human infection, and to detect any possible transmission events. In total, 89 isolates (67 clinical and 22 environmental) from Germany were sequenced. Fully finished genomes of five strains were included in the dataset for the core SNP phylogenomic analysis. WGS data were compared with conventional genotyping results as well as with underlying disease, biofilm formation, protease activity, lipopolysaccharide (LPS) SDS–PAGE profiles, and serological specificity of an antibody raised against the surface-exposed O-antigen of strain S. maltophilia K279a. The WGS-based phylogenies grouped the strains into 12 clades, out of which 6 contained exclusively human and 3 exclusively environmental isolates. Biofilm formation and proteolytic activity did correlate neither with the phylogenetic tree, nor with the origin of isolates. In contrast, the genomic classification correlated well with the reactivity of the strains against the K279a O-specific antibody, as well as in part with the LPS profiles. Three clusters of clinical strains had a maximum distance of 25 distinct SNP positions, pointing to possible transmission events or acquisition from the same source. In conclusion, these findings indicate the presence of specific subgroups of S. maltophilia strains adapted to the human host.
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Affiliation(s)
- Joerg Steinmann
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.,Institute of Clinical Hygiene, Medical Microbiology and Infectiology, Paracelsus Medical University, Nuremberg, Germany
| | - Uwe Mamat
- Cellular Microbiology, Priority Research Area Infections, Research Center Borstel, Borstel, Germany
| | - Ebrahim M Abda
- Department of Microbiology and Biotechnology, Biocenter Klein Flottbek - University of Hamburg, Hamburg, Germany
| | - Lisa Kirchhoff
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Wolfgang R Streit
- Department of Microbiology and Biotechnology, Biocenter Klein Flottbek - University of Hamburg, Hamburg, Germany
| | - Ulrich E Schaible
- Cellular Microbiology, Priority Research Area Infections, Research Center Borstel, Borstel, Germany.,TTU-TB, German Center for Infection Research, Borstel, Germany
| | - Stefan Niemann
- TTU-TB, German Center for Infection Research, Borstel, Germany.,Molecular and Experimental Mycobacteriology, Priority Research Area Infections, Research Center Borstel, Borstel, Germany
| | - Thomas A Kohl
- TTU-TB, German Center for Infection Research, Borstel, Germany.,Molecular and Experimental Mycobacteriology, Priority Research Area Infections, Research Center Borstel, Borstel, Germany
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Weber M, Schünemann W, Fuß J, Kämpfer P, Lipski A. Stenotrophomonas lactitubi sp. nov. and Stenotrophomonas indicatrix sp. nov., isolated from surfaces with food contact. Int J Syst Evol Microbiol 2018; 68:1830-1838. [PMID: 29638210 DOI: 10.1099/ijsem.0.002732] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Five Gram-stain-negative, rod-shaped, none-spore-forming isolates were obtained from biofilms on different sites of a milking machine in Germany. Another strain with similar morphological characteristics was isolated from dirty dishes. Based on phylogenetic analysis of the 16S rRNA and gyrB genes, all isolates were assigned to the genus Stenotrophomonas, but were divided into three different groups. Chemotaxonomic characterization of the isolates led to the detection of iso-C15 : 0 and anteiso-C15 : 0 as the predominant cellular fatty acids, as well as small amounts of the hydroxyl fatty acids iso-C11 : 0 3-OH, C12 : 0 3-OH and iso-C13 : 0 3-OH. One group could be assigned to the species Stenotrophomonas maltophilia, while the genome sequences of two groups displayed average nucleotide identity values of less than 94 % between each other and the genome sequences of the next related type strains Stenotrophomonas maltophilia ATCC 13637T and Stenotrophomonas rhizophila DSM 14405T. Further phylogenetic, phenotypic and chemotaxonomic analyses enabled the differentiation of these strains from these closely related species. They are therefore considered to represent two novel species, for which the names Stenotrophomonaslactitubi and Stenotrophomonasindicatrix are proposed, with strains M15T (=DSM 104152T=LMG29943T) and WS40T (=DSM28278T=LMG29942T) as type strains.
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Affiliation(s)
- Mareike Weber
- Rheinische Friedrich-Wilhelms-Universität Bonn, Institut für Ernährungs- und Lebensmittelwissenschaften, Abteilung Lebensmittelmikrobiologie und -hygiene, Meckenheimer Allee 168, 53115 Bonn, Germany
| | - Wiebke Schünemann
- Rheinische Friedrich-Wilhelms-Universität Bonn, Institut für Ernährungs- und Lebensmittelwissenschaften, Abteilung Lebensmittelmikrobiologie und -hygiene, Meckenheimer Allee 168, 53115 Bonn, Germany
| | - Janina Fuß
- Max Planck-Genome-Centre Cologne, Carl-von-Linné-Weg 10, 50829 Köln, Germany
| | - Peter Kämpfer
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, 35392 Giessen, Germany
| | - André Lipski
- Rheinische Friedrich-Wilhelms-Universität Bonn, Institut für Ernährungs- und Lebensmittelwissenschaften, Abteilung Lebensmittelmikrobiologie und -hygiene, Meckenheimer Allee 168, 53115 Bonn, Germany
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Jayol A, Corlouer C, Haenni M, Darty M, Maillard K, Desroches M, Lamy B, Jumas-Bilak E, Madec JY, Decousser JW. Are animals a source of Stenotrophomonas maltophilia in human infections? Contributions of a nationwide molecular study. Eur J Clin Microbiol Infect Dis 2018; 37:1039-1045. [PMID: 29488120 DOI: 10.1007/s10096-018-3203-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 01/26/2018] [Indexed: 01/25/2023]
Abstract
Stenotrophomonas maltophilia (Sm) is an archetypal environmental opportunistic bacterium responsible for health care-associated infections. The role of animals in human Sm infections is unknown. This study aims to reveal the genetic and phylogenetic relationships between pathogenic strains of Sm, both animal and human, and identify a putative role for animals as a reservoir in human infection. We phenotypically and genotypically characterized 61 Sm strains responsible for animal infections (mainly respiratory tract infections in horses) from a French nationwide veterinary laboratory network. We tested antimicrobial susceptibility and performed MLST and genogrouping using the concatenation of the seven housekeeping genes from the original MLST scheme. Excluding the eight untypeable strains owing to the lack of gene amplification, only 10 out of the 53 strains yielded a known ST (ST5, ST39, ST162, ST8, ST27, ST126, ST131). The genogroup distribution highlighted not only genogroups (genogroups 5 and 9) comprised exclusively of animal strains but also genogroups shared by human and animal strains. Interestingly, these shared genogroups were primarily groups 2 and 6, which have previously been identified as the two most frequent genogroups among human-pathogenic Sm strains, especially among respiratory pathogens. The antimicrobial susceptibility testing underlined the presence of acquired resistance: 18.8 and 7.5% of the tested isolates were resistant to the sulfonamide-trimethoprim combination and ciprofloxacin, respectively. Animal strains of Sm shared phylogenetic traits with some of the most successful human strains. The exact relationships between the human and animal strains, and the genetic support of these common traits, need to be determined.
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Affiliation(s)
- Aurélie Jayol
- Laboratory of Bacteriology and Infection Control, Department of Microbiology, Assistance Publique-Hôpitaux de Paris, University Hospital Henri Mondor, 94000, Créteil, France
- Emerging Antibiotic Resistance Unit, Medical and Molecular Microbiology, Department of Medicine, University of Fribourg, Fribourg, Switzerland
- INSERM European Unit (LEA-IAME Paris, France), University of Fribourg, Fribourg, Switzerland
| | - Camille Corlouer
- Laboratory of Bacteriology and Infection Control, Department of Microbiology, Assistance Publique-Hôpitaux de Paris, University Hospital Henri Mondor, 94000, Créteil, France
| | - Marisa Haenni
- Unité Antibiorésistance et Virulence Bactériennes, ANSES, Lyon, France
| | - Mélanie Darty
- Next Generation Sequencing Platform, University Hospital Henri Mondor, Assistance Publique-Hôpitaux de Paris, Créteil, France
| | | | - Marine Desroches
- Laboratory of Bacteriology and Infection Control, Department of Microbiology, Assistance Publique-Hôpitaux de Paris, University Hospital Henri Mondor, 94000, Créteil, France
| | - Brigitte Lamy
- Department of Bacteriology, Archet 2 Hospital, Nice Academic Hospital, Nice, France
- INSERM U1065, C3M, Team 6, Nice, France
| | - Estelle Jumas-Bilak
- Infection Control Department, Montpellier University Hospital, Montpellier, France
- UMR5569 HydroSciences Montpellier, Equipe «Pathogènes Hydriques Santé Environnements», Faculté de Pharmacie, 15 Avenue Charles Flahault BP 14491 34093 Montpellier UMR 5119 ECOSYM, Equipe Pathogènes et Environnements, U.F.R. des Sciences Pharmaceutiques et Biologiques, Université Montpellier 1, Montpellier, France
| | - Jean-Yves Madec
- Unité Antibiorésistance et Virulence Bactériennes, ANSES, Lyon, France
| | - Jean-Winoc Decousser
- Laboratory of Bacteriology and Infection Control, Department of Microbiology, Assistance Publique-Hôpitaux de Paris, University Hospital Henri Mondor, 94000, Créteil, France.
- EA 7380 Dynamyc Université Paris-Est Créteil (UPEC), Ecole nationale vétérinaire d'Alfort (EnvA), Faculté de Médecine de Créteil, 8 rue du Général Sarrail, 94010, Créteil, France.
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40
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Multi-locus sequence typing (MLST) of non-fermentative Gram-negative bacilli isolated from bloodstream infections in southern Poland. Folia Microbiol (Praha) 2017; 63:191-196. [PMID: 28940128 PMCID: PMC5805803 DOI: 10.1007/s12223-017-0550-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 09/15/2017] [Indexed: 12/20/2022]
Abstract
Non-fermentative Gram-negative bacilli are now one of the most important causes of severe infections in Polish hospitals. Acinetobacter species are serious concern because of the high prevalence of multi-drug resistance among strains. Resistance profiles for 53 Gram-negative non-fermentative blood isolates were done. MLST was carried out using 44 strains representing the most commonly isolated species: A. baumannii, P. aeruginosa, and S. maltophilia. MLST revealed that all 22 A. baumannii belonged to sequence type (ST) 2. The P. aeruginosa isolates belonged to 10 different STs. Four S. maltophilia isolates matched STs present in the database (ST4, ST15, ST116, ST142), seven isolates showing novel sequence types. Among P. aeruginosa and S. maltophilia PFGE confirmed the genetical variety of strains.
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Ochoa-Sánchez LE, Vinuesa P. Evolutionary Genetic Analysis Uncovers Multiple Species with Distinct Habitat Preferences and Antibiotic Resistance Phenotypes in the Stenotrophomonas maltophilia Complex. Front Microbiol 2017; 8:1548. [PMID: 28861062 PMCID: PMC5562727 DOI: 10.3389/fmicb.2017.01548] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Accepted: 07/31/2017] [Indexed: 12/20/2022] Open
Abstract
The genus Stenotrophomonas (Gammaproteobacteria) has a broad environmental distribution. Stenotrophomonas maltophilia is its best known species because it is a globally emerging, multidrug-resistant (MDR), opportunistic pathogen. Members of this species are known to display high genetic, ecological and phenotypic diversity, forming the so-called S. maltophilia complex (Smc). Heterogeneous resistance and virulence phenotypes have been reported for environmental Smc isolates of diverse ecological origin. We hypothesized that this heterogeneity could be in part due to the potential lumping of several cryptic species in the Smc. Here we used state-of-the-art phylogenetic and population genetics methods to test this hypothesis based on the multilocus dataset available for the genus at pubmlst.org. It was extended with sequences from complete and draft genome sequences to assemble a comprehensive set of reference sequences. This framework was used to analyze 108 environmental isolates obtained in this study from the sediment and water column of four rivers and streams in Central Mexico, affected by contrasting levels of anthropogenic pollution. The aim of the study was to identify species in this collection, defined as genetically cohesive sequence clusters, and to determine the extent of their genetic, ecological and phenotypic differentiation. The multispecies coalescent, coupled with Bayes factor analysis was used to delimit species borders, together with population genetic structure analyses, recombination and gene flow estimates between sequence clusters. These analyses consistently revealed that the Smc contains at least 5 significantly differentiated lineages: S. maltophilia and Smc1 to Smc4. Only S. maltophilia was found to be intrinsically MDR, all its members expressing metallo-β-lactamases (MBLs). The other Smc lineages were not MDR and did not express MBLs. We also obtained isolates related to S. acidaminiphila, S. humi and S. terrae. They were significantly more susceptible to antibiotics than S. maltophilia. We demonstrate that the sympatric lineages recovered display significantly differentiated habitat preferences, antibiotic resistance profiles and β-lactamase expression phenotypes, as shown by diverse multivariate analyses and robust univariate statistical tests. We discuss our data in light of current models of bacterial speciation, which fit these data well, stressing the implications of species delimitation in ecological, evolutionary and clinical research.
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Affiliation(s)
- Luz E Ochoa-Sánchez
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de MéxicoCuernavaca, Mexico
| | - Pablo Vinuesa
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de MéxicoCuernavaca, Mexico
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Imipenem-resistant Gram-negative bacterial isolates carried by persons upon medical examination in Korea. J Microbiol 2017; 55:612-618. [PMID: 28721477 DOI: 10.1007/s12275-017-6555-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 05/26/2017] [Accepted: 05/26/2017] [Indexed: 10/19/2022]
Abstract
Carbapenem-resistant Gram-negative bacteria (CR-GNB) have emerged and disseminated worldwide, become a great concern worldwide including Korea. The prevalence of fecal carriage of imipenem-resistant Gram-negative bacteria (IR-GNB) in persons in Korea was investigated. Stool samples were collected from 300 persons upon medical examination. Samples were screened for IR-GNB by using MacConkey agar with 2 μl/ml imipenem. Species were identified by 16S rRNA gene sequence analysis, and antimicrobial susceptibility was determined by the broth microdilution method. In total, 82 IR-GNB bacterial isolates were obtained from 79 (26.3%) out of 300 healthy persons. Multilocus sequence typing analysis showed very high diversity among IR P. aeruginosa, S. maltophilia, and E. cloacae isolates, and pulsed-field gel electrophoresis revealed five main pulsotypes of IR P. mirabilis. As for the presence of metallo-β-lactamases (MBLs), only one IMP-25-producing S. marcescens isolate was identified. Although only one carbapenemase-producing isolate was identified, the high colonization rates with IR-GNB isolates in this study is notable because carriers may be a reservoir for the dissemination of resistant pathogens within the community as well as in health care institutions.
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43
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Corlouer C, Lamy B, Desroches M, Ramos-Vivas J, Mehiri-Zghal E, Lemenand O, Delarbre JM, Decousser JW. Stenotrophomonas maltophilia healthcare-associated infections: identification of two main pathogenic genetic backgrounds. J Hosp Infect 2017; 96:183-188. [PMID: 28318778 DOI: 10.1016/j.jhin.2017.02.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 02/03/2017] [Indexed: 11/28/2022]
Abstract
BACKGROUND Stenotrophomonas maltophilia is an opportunistic multi-drug-resistant bacterium responsible for healthcare-associated infections. Strategies for in-hospital infection control and management of carriers and environmental reservoirs remain controversial. AIM To determine the population structure of S. maltophilia strains in hospitalized infected patients and to identify putative highly pathogenic subpopulations that require upgraded infection control measures. METHODS Eighty-three diverse human strains of various clinical origins from 18 geographically distant hospitals were characterized phenotypically and genotypically using a multi-locus sequence typing (MLST) approach. FINDINGS Neither a predominant nor emerging sequence type (ST) was identified. Among the 80 typeable strains, only 29% corresponded to described STs, especially ST5 (N=6) and ST4/26/31 (N=2). The ST distribution and the phylogenic tree based on the concatenated MLST genes did not account for geographical, clinical origin or antimicrobial susceptibility clustering. A phylogenic tree that included 173 ST profiles from the MLST database and the 80 typeable strains confirmed the high genetic diversity of S. maltophilia, the previously reported genogroup organization and the predominance of genogroup 6, as it represented 41% (33/80) of the strains. Unexpectedly, genogroup 2 was the second most prevalent genogroup and included 16% (13/80) of the strains. These genogroups represented 57% (20/35) of the strains in respiratory patients and 75% (9/12) of the strains in patients with cystic fibrosis. CONCLUSION Beyond MLST, the over-representation of some genogroups among strains responsible for healthcare-associated infections was confirmed. Genogrouping affiliation is recommended to implement infection control measures selectively for the most pathogenic strains isolated from patient or environmental reservoirs.
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Affiliation(s)
- C Corlouer
- Laboratory of Bacteriology, Department of Microbiology, University Hospital Henri Mondor, Créteil, France
| | - B Lamy
- Department of Bacteriology, Archet 2 Hospital, Nice Academic Hospital, Nice, France
| | - M Desroches
- Laboratory of Bacteriology, Department of Microbiology, University Hospital Henri Mondor, Créteil, France; University Paris East Créteil, Créteil, France
| | - J Ramos-Vivas
- Department of Microbiology, Marqués de Valdecilla University Hospital and IDIVAL Research Institute, Santander, Cantabria, Spain
| | - E Mehiri-Zghal
- Laboratory of Bacteriology, Abderahman MAMI Pneumo-Phthisiology Hospital, Tunis, Tunisia
| | - O Lemenand
- Laboratory of Bacteriology, Saint Nazaire Hospital, Saint Nazaire, France
| | - J-M Delarbre
- Laboratory of Bacteriology, Emile Muller Hospital, Mulhouse, France
| | - J-W Decousser
- Laboratory of Bacteriology, Department of Microbiology, University Hospital Henri Mondor, Créteil, France; University Paris East Créteil, Créteil, France.
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Madi H, Lukić J, Vasiljević Z, Biočanin M, Kojić M, Jovčić B, Lozo J. Genotypic and Phenotypic Characterization of Stenotrophomonas maltophilia Strains from a Pediatric Tertiary Care Hospital in Serbia. PLoS One 2016; 11:e0165660. [PMID: 27798695 PMCID: PMC5087882 DOI: 10.1371/journal.pone.0165660] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 10/14/2016] [Indexed: 01/15/2023] Open
Abstract
Background Stenotrophomonas maltophilia is an environmental bacterium and an opportunistic pathogen usually associated with healthcare-associated infections, which has recently been recognized as a globally multi-drug resistant organism. The aim of this study was genotyping and physiological characterization of Stenotrophomonas maltophilia isolated in a large, tertiary care pediatric hospital in Belgrade, Serbia, hosting the national reference cystic fibrosis (CF) center for pediatric and adult patients. Methods We characterized 42 strains of cystic fibrosis (CF) and 46 strains of non-cystic fibrosis (non-CF) origin isolated from 2013 to 2015 in order to investigate their genetic relatedness and phenotypic traits. Genotyping was performed using sequencing of 16S rRNA gene, Pulse Field Gel Electrophoresis (PFGE) and Multi locus sequencing typing (MLST) analysis. Sensitivity to five relevant antimicrobial agents was determined, namely trimethoprim/sulfamethoxazole (TMP/SMX), chloramphenicol, ciprofloxacin, levofloxacin and tetracycline. Surface characteristics, motility, biofilm formation and adhesion to mucin were tested in all strains. Statistical approach was used to determine correlations between obtained results. Results Most of the isolates were not genetically related. Six new sequence types were determined. Strains were uniformly sensitive to all tested antimicrobial agents. The majority of isolates (89.8%) were able to form biofilm with almost equal representation in both CF and non-CF strains. Swimming motility was observed in all strains, while none of them exhibited swarming motility. Among strains able to adhere to mucin, no differences between CF and non-CF isolates were observed. Conclusions High genetic diversity among isolates implies the absence of clonal spread within the hospital. Positive correlation between motility, biofilm formation and adhesion to mucin was demonstrated. Biofilm formation and motility were more pronounced among non-CF than CF isolates.
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Affiliation(s)
- Haowa Madi
- University of Belgrade, Institute of Molecular Genetics and Genetic Engineering, Belgrade, Serbia
| | - Jovanka Lukić
- University of Belgrade, Institute of Molecular Genetics and Genetic Engineering, Belgrade, Serbia
| | - Zorica Vasiljević
- Institute for Mother and Child Health Care of Serbia "Dr Vukan Čupić", Belgrade, Serbia
| | - Marjan Biočanin
- University of Belgrade, Institute of Molecular Genetics and Genetic Engineering, Belgrade, Serbia
| | - Milan Kojić
- University of Belgrade, Institute of Molecular Genetics and Genetic Engineering, Belgrade, Serbia
| | - Branko Jovčić
- University of Belgrade, Institute of Molecular Genetics and Genetic Engineering, Belgrade, Serbia
- University of Belgrade, Faculty of Biology, Belgrade, Serbia
| | - Jelena Lozo
- University of Belgrade, Institute of Molecular Genetics and Genetic Engineering, Belgrade, Serbia
- University of Belgrade, Faculty of Biology, Belgrade, Serbia
- * E-mail:
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Cha MK, Kang CI, Kim SH, Cho SY, Ha YE, Chung DR, Peck KR, Song JH. Emergence of fluoroquinolone-resistant Stenotrophomonas maltophilia in blood isolates causing bacteremia: molecular epidemiology and microbiologic characteristics. Diagn Microbiol Infect Dis 2016; 85:210-2. [PMID: 27117514 DOI: 10.1016/j.diagmicrobio.2016.02.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 02/23/2016] [Accepted: 02/23/2016] [Indexed: 10/22/2022]
Abstract
Among 127 Stenotrophomonas maltophilia isolates causing bacteremia, 41 (32.3%) were nonsusceptible to levofloxacin, in which four sequence types and 24 diverse allelic profiles were detected. The most prevalent ST was ST77 (n = 8, 19.5%), followed by ST28 (n = 3, 7.3%). Amino acid substitutions were found in the gyrB and parC genes of 10 and 1 isolates, respectively. No amino acid substitutions were identified in gyrA. Twenty-three (56.1%) isolates showed amino acid substitutions in the parE gene. These results suggest that quinolone resistance-determining regions of parE may not be the primary targets, but an important determining factor of high levels of fluoroquinolone resistance.
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Affiliation(s)
- Min Kyeong Cha
- Asia Pacific Foundation for Infectious Diseases (APFID), Seoul, South Korea
| | - Cheol-In Kang
- Division of Infectious Diseases, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea.
| | - So Hyun Kim
- Asia Pacific Foundation for Infectious Diseases (APFID), Seoul, South Korea; Division of Infectious Diseases, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Sun Young Cho
- Division of Infectious Diseases, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Young Eun Ha
- Division of Infectious Diseases, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Doo Ryeon Chung
- Asia Pacific Foundation for Infectious Diseases (APFID), Seoul, South Korea; Division of Infectious Diseases, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Kyong Ran Peck
- Division of Infectious Diseases, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Jae-Hoon Song
- Asia Pacific Foundation for Infectious Diseases (APFID), Seoul, South Korea; Division of Infectious Diseases, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
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Rhee JY, Song JH, Ko KS. Current Situation of Antimicrobial Resistance and Genetic Differences in Stenotrophomonas maltophilia Complex Isolates by Multilocus Variable Number of Tandem Repeat Analysis. Infect Chemother 2016; 48:285-293. [PMID: 28032486 PMCID: PMC5204007 DOI: 10.3947/ic.2016.48.4.285] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 11/23/2016] [Indexed: 11/24/2022] Open
Abstract
Background Stenotrophomonas maltophilia is one of several opportunistic pathogens of growing significance. Several studies on the molecular epidemiology of S. maltophilia have shown clinical isolates to be genetically diverse. Materials and Methods A total of 121 clinical isolates tentatively identified as S. malophilia from seven tertiary-care hospitals in Korea from 2007 to 2011 were included. Species and groups were identified using partial gyrB gene sequences and antimicrobial susceptibility testing was performed using a broth microdilution method. Multi locus variable number of tandem repeat analysis (MLVA) surveys are used for subtyping. Results Based on partial gyrB gene sequences, 118 isolates were identified as belonging to the S. maltophilia complex. For all S. maltophilia isolates, the resistance rates to trimethoprime-sulfamethoxazole (TMP/SMX) and levofloxacin were the highest (both, 30.5%). Resistance rate to ceftazidime was 28.0%. 11.0% and 11.9% of 118 S. maltophilia isolates displayed resistance to piperacillin/tazobactam and tigecycline, respectively. Clade 1 and Clade 2 were definitely distinguished from the data of MLVA with amplification of loci. All 118 isolates were classified into several clusters as its identification. Conclusion Because of high resistance rates to TMP/SMX and levofloxacin, the clinical laboratory department should consider providing the data about other antimicrobial agents and treatment of S. maltophilia infections with a combination of antimicrobials can be considered in the current practice. The MLVA evaluated in this study provides a fast, portable, relatively low cost genotyping method that can be employed in genotypic linkage or transmission networks comparing to analysis of the gyrB gene.
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Affiliation(s)
- Ji Young Rhee
- Division of Infectious Diseases, Department of Medicine, Dankook University, Cheonan, Korea
| | - Jae Hoon Song
- Division of Infectious Diseases, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.,Asia Pacific Foundation for Infectious Diseases, Seoul, Korea
| | - Kwan Soo Ko
- Asia Pacific Foundation for Infectious Diseases, Seoul, Korea.,Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, Korea.
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Complete Genome Sequencing of Stenotrophomonas acidaminiphila ZAC14D2_NAIMI4_2, a Multidrug-Resistant Strain Isolated from Sediments of a Polluted River in Mexico, Uncovers New Antibiotic Resistance Genes and a Novel Class-II Lasso Peptide Biosynthesis Gene Cluster. GENOME ANNOUNCEMENTS 2015; 3:3/6/e01433-15. [PMID: 26659678 PMCID: PMC4675943 DOI: 10.1128/genomea.01433-15] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Here, we report the first complete genome sequence of a Stenotrophomonas acidaminiphila strain, generated with PacBio RS II single-molecule real-time technology, consisting of a single circular chromosome of 4.13 Mb. We annotated mobile genetic elements and natural product biosynthesis clusters, including a novel class-II lasso peptide with a 7-residue macrolactam ring.
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48
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Roscetto E, Vitiello L, Muoio R, Soriano AA, Iula VD, Vollaro A, De Gregorio E, Catania MR. In vitro interaction of Stenotrophomonas maltophilia with human monocyte-derived dendritic cells. Front Microbiol 2015; 6:723. [PMID: 26236302 PMCID: PMC4504169 DOI: 10.3389/fmicb.2015.00723] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 07/02/2015] [Indexed: 11/20/2022] Open
Abstract
Stenotrophomonas maltophilia is increasingly identified as an opportunistic pathogen in immunocompromised, cancer and cystic fibrosis (CF) patients. Knowledge on innate immune responses to S. maltophilia and its potential modulation is poor. The present work investigated the ability of 12 clinical S. maltophilia strains (five from CF patients, seven from non-CF patients) and one environmental strain to survive inside human monocyte-derived dendritic cells (DCs). The effects of the bacteria on maturation of and cytokine secretion by DCs were also measured. S. maltophilia strains presented a high degree of heterogeneity in internalization and intracellular replication efficiencies as well as in the ability of S. maltophilia to interfere with normal DCs maturation. By contrast, all S. maltophilia strains were able to activate DCs, as measured by increase in the expression of surface maturation markers and proinflammatory cytokines secretion.
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Affiliation(s)
- Emanuela Roscetto
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II , Napoli, Italy
| | - Laura Vitiello
- Laboratorio di Immunologia Cellulare e Molecolare, Istituto di Ricovero e Cura a Carattere Scientifico , San Raffaele Pisana, Rome, Italy
| | - Rosa Muoio
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II , Napoli, Italy
| | - Amata A Soriano
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II , Napoli, Italy
| | - Vita D Iula
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II , Napoli, Italy
| | - Antonio Vollaro
- DAI Medicina di Laboratorio, Azienda Ospedaliera Universitaria Federico II , Napoli, Italy
| | - Eliana De Gregorio
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II , Napoli, Italy
| | - Maria R Catania
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II , Napoli, Italy
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Shestivska V, Dryahina K, Nunvář J, Sovová K, Elhottová D, Nemec A, Smith D, Španěl P. Quantitative analysis of volatile metabolites released
in vitro
by bacteria of the genus
Stenotrophomonas
for identification of breath biomarkers of respiratory infection in cystic fibrosis. J Breath Res 2015; 9:027104. [DOI: 10.1088/1752-7155/9/2/027104] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Berg G, Martinez JL. Friends or foes: can we make a distinction between beneficial and harmful strains of the Stenotrophomonas maltophilia complex? Front Microbiol 2015; 6:241. [PMID: 25873912 PMCID: PMC4379930 DOI: 10.3389/fmicb.2015.00241] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2014] [Accepted: 03/12/2015] [Indexed: 11/21/2022] Open
Abstract
Stenotrophomonas maltophilia is an emerging multi-drug-resistant global opportunistic pathogen of environmental, mainly plant-associated origin. It is also used as a biocontrol or stress protecting agent for crops in sustainable agricultural as well as in bioremediation strategies. In order to establish effective protocols to distinguish harmless from harmful strains, our discussion must take into consideration the current data available surrounding the ecology, evolution and pathogenicity of the species complex. The mutation rate was identified as one of several possible criteria for strain plasticity, but it is currently impossible to distinguish beneficial from harmful S. maltophilia strains. This may compromise the possibility of the release and application for environmental biotechnology of this bacterial species. The close relative S. rhizophila, which can be clearly differentiated from S. maltophilia, provides a harmless alternative for biotechnological applications without human health risks. This is mainly because it is unable to growth at the human body temperature, 37∘C due to the absence of heat shock genes and a potentially temperature-regulated suicide mechanism.
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Affiliation(s)
- Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz Austria
| | - Jose L Martinez
- Centro Nacional de Biotecnologia - Consejo Superior de Investigaciones Científicas, Madrid Spain
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