1
|
Zhang K, Potter RF, Marino J, Muenks CE, Lammers MG, Dien Bard J, Dingle TC, Humphries R, Westblade LF, Burnham CAD, Dantas G. Comparative genomics reveals the correlations of stress response genes and bacteriophages in developing antibiotic resistance of Staphylococcus saprophyticus. mSystems 2023; 8:e0069723. [PMID: 38051037 PMCID: PMC10734486 DOI: 10.1128/msystems.00697-23] [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: 07/07/2023] [Accepted: 10/23/2023] [Indexed: 12/07/2023] Open
Abstract
IMPORTANCE Staphylococcus saprophyticus is the second most common bacteria associated with urinary tract infections (UTIs) in women. The antimicrobial treatment regimen for uncomplicated UTI is normally nitrofurantoin, trimethoprim-sulfamethoxazole (TMP-SMX), or a fluoroquinolone without routine susceptibility testing of S. saprophyticus recovered from urine specimens. However, TMP-SMX-resistant S. saprophyticus has been detected recently in UTI patients, as well as in our cohort. Herein, we investigated the understudied resistance patterns of this pathogenic species by linking genomic antibiotic resistance gene (ARG) content to susceptibility phenotypes. We describe ARG associations with known and novel SCCmec configurations as well as phage elements in S. saprophyticus, which may serve as intervention or diagnostic targets to limit resistance transmission. Our analyses yielded a comprehensive database of phenotypic data associated with the ARG sequence in clinical S. saprophyticus isolates, which will be crucial for resistance surveillance and prediction to enable precise diagnosis and effective treatment of S. saprophyticus UTIs.
Collapse
Affiliation(s)
- Kailun Zhang
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Robert F. Potter
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Jamie Marino
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, USA
| | - Carol E. Muenks
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Matthew G. Lammers
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Jennifer Dien Bard
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, California, USA
- Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Tanis C. Dingle
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Romney Humphries
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Lars F. Westblade
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, USA
| | - Carey-Ann D. Burnham
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
- Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
- Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Gautam Dantas
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
- Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
| |
Collapse
|
2
|
Chua KYL, Yang M, Wong L, Knox J, Lee LY. Antimicrobial resistance and its detection in Staphylococcus saprophyticus urinary isolates. Pathology 2023; 55:1013-1016. [PMID: 37793963 DOI: 10.1016/j.pathol.2023.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 06/29/2023] [Accepted: 07/11/2023] [Indexed: 10/06/2023]
Abstract
The aim of this study was to describe the antibiotic susceptibility of clinical Staphylococcus saprophyticus isolates collected prospectively from urine specimens over a 2-month period from September to October 2022 at a single centre in Melbourne, Australia. Species identification was performed by MALDI-TOF MS. All isolates underwent phenotypic antibiotic susceptibility testing by disc diffusion using European Committee on Antimicrobial Susceptibility Testing (EUCAST) and Clinical and Laboratory Standards Institute (CLSI) guidelines and VITEK2, and mecA polymerase chain reaction. A total of 302 S. saprophyticus isolates from 298 patients were included in this study. Most specimens (91.1%) were referred by community general practitioners from non-hospitalised patients. Antimicrobial resistance to non-β-lactam antibiotics was uncommon; trimethoprim susceptibility was 97%; trimethoprim/sulfamethoxazole, 98%; nitrofurantoin, 100%; and ciprofloxacin, 100% (100% ciprofloxacin susceptible, increased exposure by EUCAST breakpoints). Methicillin resistance (by mecA detection) was the most common form of urinary antibiotic resistance at 5.6%. VITEK2 susceptibility testing for methicillin resistance had a poor specificity of 61.8% (95% CI 55.8-67.4%) compared to mecA detection. These findings indicate that empiric antibiotic recommendations of trimethoprim, trimethoprim/sulfamethoxazole, and nitrofurantoin for treatment of urinary S. saprophyticus remain appropriate.
Collapse
Affiliation(s)
- Kyra Y L Chua
- Department of Microbiology, Dorevitch Pathology, Vic, Australia; Department of Infectious Diseases, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Vic, Australia; Department of Infectious Diseases, Austin Health, Vic, Australia.
| | - May Yang
- Department of Microbiology, Dorevitch Pathology, Vic, Australia
| | - Lillian Wong
- Department of Microbiology, Dorevitch Pathology, Vic, Australia
| | - James Knox
- Department of Microbiology, Dorevitch Pathology, Vic, Australia
| | - Lai-Yang Lee
- Department of Microbiology, Dorevitch Pathology, Vic, Australia
| |
Collapse
|
3
|
de Oliveira AS, Inácio MM, de Oliveira LS, Elias Moreira AL, Alves Silva GA, Silva LOS, de Oliveira MAP, Giambiagi-deMarval M, Borges CL, Soares CMDA, Parente-Rocha JA. Immunoproteomic and immunoinformatic approaches identify secreted antigens and epitopes from Staphylococcus saprophyticus. Microb Pathog 2023:106171. [PMID: 37244490 DOI: 10.1016/j.micpath.2023.106171] [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: 08/16/2022] [Revised: 05/19/2023] [Accepted: 05/22/2023] [Indexed: 05/29/2023]
Abstract
Urinary tract infections (UTIs) are common human infections that compromise women's health around the world, even though they can affect men and women of all ages. Bacterial species are the primary causative agents of UTIs, while Staphylococcus saprophyticus, a gram-positive bacterium, is especially important for uncomplicated infections in young women. Despite the number of antigenic proteins identified in Staphylococcus aureus and other bacteria of the genus, there is no immunoproteomic study in S. saprophyticus. In this context, since pathogenic microorganisms secrete important proteins that interact with hosts during infection, the present work aims to identify the exoantigens from S. saprophyticus ATCC 15305 by immunoproteomic and immunoinformatic approaches. We identified 32 antigens on the exoproteome of S. saprophyticus ATCC 15305 by immunoinformatic tools. By using 2D-IB immunoproteomic analysis, it was possible to identify 3 antigenic proteins: transglycosylase IsaA, enolase and the secretory antigen Q49ZL8. In addition, 5 antigenic proteins were detected by immunoprecipitation (IP) approach, where the most abundant were bifunctional autolysin and transglycosylase IsaA proteins. The transglycosylase IsaA was the only protein detected by all the tools approaches used in this study. In this work it was possible to describe a total of 36 S. saprophyticus exoantigens. Immunoinformatic analysis allowed the identification of 5 exclusive linear B cell epitopes from S. saprophyticus and 5 epitopes presenting homology with other bacteria that cause UTIs. This work describes, for the first time, the profile of exoantigens secreted by S. saprophyticus and can contribute to the identification of new diagnostic targets of UTIs, as well as to develop vaccines and immunotherapies against bacterial urinary infections.
Collapse
Affiliation(s)
- Andrea Santana de Oliveira
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Brazil.
| | - Moisés Morais Inácio
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Brazil.
| | - Lucas Silva de Oliveira
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Brazil.
| | - André Luís Elias Moreira
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Brazil.
| | - Guilherme Algusto Alves Silva
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Brazil.
| | - Lana O'Hara Souza Silva
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Brazil.
| | | | - Marcia Giambiagi-deMarval
- Laboratório de Microbiologia Molecular, Instituto de Microbiologia Prof. Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Clayton Luiz Borges
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Brazil.
| | - Célia Maria de Almeida Soares
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Brazil.
| | - Juliana Alves Parente-Rocha
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Brazil.
| |
Collapse
|
4
|
Somorin YM, Weir NJM, Pattison SH, Crockard MA, Hughes CM, Tunney MM, Gilpin DF. Antimicrobial resistance in urinary pathogens and culture-independent detection of trimethoprim resistance in urine from patients with urinary tract infection. BMC Microbiol 2022; 22:144. [PMID: 35610571 PMCID: PMC9128081 DOI: 10.1186/s12866-022-02551-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 02/21/2022] [Indexed: 11/24/2022] Open
Abstract
Background Although urinary tract infections (UTIs) are extremely common, isolation of causative uropathogens is not always routinely performed, with antibiotics frequently prescribed empirically. This study determined the susceptibility of urinary isolates from two Health and Social Care Trusts (HSCTs) in Northern Ireland to a range of antibiotics commonly used in the treatment of UTIs. Furthermore, we determined if detection of trimethoprim resistance genes (dfrA) could be used as a potential biomarker for rapid detection of phenotypic trimethoprim resistance in urinary pathogens and from urine without culture. Methods Susceptibility of E. coli and Klebsiella spp. isolates (n = 124) to trimethoprim, amoxicillin, ceftazidime, ciprofloxacin, co-amoxiclav and nitrofurantoin in addition to susceptibility of Proteus mirabilis (n = 61) and Staphylococcus saprophyticus (n = 17) to trimethoprim was determined by ETEST® and interpreted according to EUCAST breakpoints. PCR was used to detect dfrA genes in bacterial isolates (n = 202) and urine samples(n = 94). Results Resistance to trimethoprim was observed in 37/124 (29.8%) E. coli and Klebsiella spp. isolates with an MIC90 > 32 mg/L. DfrA genes were detected in 29/37 (78.4%) trimethoprim-resistant isolates. Detection of dfrA was highly sensitive (93.6%) and specific (91.4%) in predicting phenotypic trimethoprim resistance among E. coli and Klebsiella spp. isolates. The dfrA genes analysed were detected using a culture-independent PCR method in 16/94 (17%) urine samples. Phenotypic trimethoprim resistance was apparent in isolates cultured from 15/16 (94%) dfrA-positive urine samples. There was a significant association (P < 0.0001) between the presence of dfrA and trimethoprim resistance in urine samples containing Gram-negative bacteria (Sensitivity = 75%; Specificity = 96.9%; PPV = 93.8%; NPV = 86.1%). Conclusions This study demonstrates that molecular detection of dfrA genes is a good indicator of trimethoprim resistance without the need for culture and susceptibility testing. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02551-9.
Collapse
Affiliation(s)
- Yinka M Somorin
- School of Pharmacy, Queen's University Belfast, 97 Lisburn Road, Belfast, Northern Ireland
| | - Nichola-Jane M Weir
- School of Pharmacy, Queen's University Belfast, 97 Lisburn Road, Belfast, Northern Ireland
| | - Sally H Pattison
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, 97 Lisburn Road,, Belfast, Northern Ireland
| | - Martin A Crockard
- Randox Laboratories Ltd, 55 The Diamond Road, Crumlin, Northern Ireland
| | - Carmel M Hughes
- School of Pharmacy, Queen's University Belfast, 97 Lisburn Road, Belfast, Northern Ireland
| | - Michael M Tunney
- School of Pharmacy, Queen's University Belfast, 97 Lisburn Road, Belfast, Northern Ireland
| | - Deirdre F Gilpin
- School of Pharmacy, Queen's University Belfast, 97 Lisburn Road, Belfast, Northern Ireland.
| |
Collapse
|
5
|
Fatima S, Ali K, Ahmed B, Al Kheraif AA, Syed A, Elgorban AM, Musarrat J, Lee J. Titanium Dioxide Nanoparticles Induce Inhibitory Effects against Planktonic Cells and Biofilms of Human Oral Cavity Isolates of Rothia mucilaginosa, Georgenia sp. and Staphylococcus saprophyticus. Pharmaceutics 2021; 13:1564. [PMID: 34683856 PMCID: PMC8540964 DOI: 10.3390/pharmaceutics13101564] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 09/16/2021] [Accepted: 09/23/2021] [Indexed: 11/17/2022] Open
Abstract
Multi-drug resistant (MDR) bacterial cells embedded in biofilm matrices can lead to the development of chronic cariogenesis. Here, we isolated and identified three Gram-positive MDR oral cocci, (1) SJM-04, (2) SJM-38, and (3) SJM-65, and characterized them morphologically, biochemically, and by 16S rRNA gene-based phylogenetic analysis as Georgenia sp., Staphylococcus saprophyticus, and Rothia mucilaginosa, respectively. These three oral isolates exhibited antibiotic-resistance against nalidixic acid, tetracycline, cefuroxime, methicillin, and ceftazidime. Furthermore, these Gram positive MDR oral cocci showed significant (p < 0.05) variations in their biofilm forming ability under different physicochemical conditions, that is, at temperatures of 28, 30, and 42 °C, pH of 6.4, 7.4, and 8.4, and NaCl concentrations from 200 to 1000 µg/mL. Exposure of oral isolates to TiO2NPs (14.7 nm) significantly (p < 0.05) reduced planktonic cell viability and biofilm formation in a concentration-dependent manner, which was confirmed by observing biofilm architecture by scanning electron microscopy (SEM) and optical microscopy. Overall, these results have important implications for the use of tetragonal anatase phase TiO2NPs (size range 5-25 nm, crystalline size 13.7 nm, and spherical shape) as an oral antibiofilm agent against Gram positive cocci infections. We suggest that TiO2NPs pave the way for further applications in oral mouthwash formulations and antibiofilm dental coatings.
Collapse
Affiliation(s)
- Saher Fatima
- Faculty of Agricultural Sciences, Department of Agricultural Microbiology, Aligarh Muslim University, Aligarh 202002, India; (S.F.); (J.M.)
| | - Khursheed Ali
- Faculty of Agricultural Sciences, Department of Agricultural Microbiology, Aligarh Muslim University, Aligarh 202002, India; (S.F.); (J.M.)
| | - Bilal Ahmed
- School of Chemical Engineering, Yeungnam University, Gyeongsan 38541, Korea;
| | - Abdulaziz A. Al Kheraif
- Dental Health Department, College of Applied Medical Sciences, King Saud University, P.O. Box 10219, Riyadh 11433, Saudi Arabia;
| | - Asad Syed
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia; (A.S.); (A.M.E.)
| | - Abdallah M. Elgorban
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia; (A.S.); (A.M.E.)
| | - Javed Musarrat
- Faculty of Agricultural Sciences, Department of Agricultural Microbiology, Aligarh Muslim University, Aligarh 202002, India; (S.F.); (J.M.)
| | - Jintae Lee
- School of Chemical Engineering, Yeungnam University, Gyeongsan 38541, Korea;
| |
Collapse
|
6
|
Lawal OU, Fraqueza MJ, Bouchami O, Worning P, Bartels MD, Gonçalves ML, Paixão P, Gonçalves E, Toscano C, Empel J, Urbaś M, Domínguez MA, Westh H, de Lencastre H, Miragaia M. Foodborne Origin and Local and Global Spread of Staphylococcus saprophyticus Causing Human Urinary Tract Infections. Emerg Infect Dis 2021; 27:880-893. [PMID: 33622483 PMCID: PMC7920669 DOI: 10.3201/eid2703.200852] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Staphylococcus saprophyticus is a primary cause of community-acquired urinary tract infections (UTIs) in young women. S. saprophyticus colonizes humans and animals but basic features of its molecular epidemiology are undetermined. We conducted a phylogenomic analysis of 321 S. saprophyticus isolates collected from human UTIs worldwide during 1997–2017 and 232 isolates from human UTIs and the pig-processing chain in a confined region during 2016–2017. We found epidemiologic and genomic evidence that the meat-production chain is a major source of S. saprophyticus causing human UTIs; human microbiota is another possible origin. Pathogenic S. saprophyticus belonged to 2 lineages with distinctive genetic features that are globally and locally disseminated. Pangenome-wide approaches identified a strong association between pathogenicity and antimicrobial resistance, phages, platelet binding proteins, and an increased recombination rate. Our study provides insight into the origin, transmission, and population structure of pathogenic S. saprophyticus and identifies putative new virulence factors.
Collapse
|
7
|
Staphylococcus saprophyticus Causing Infections in Humans Is Associated with High Resistance to Heavy Metals. Antimicrob Agents Chemother 2021; 65:e0268520. [PMID: 33941519 DOI: 10.1128/aac.02685-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Staphylococcus saprophyticus is a common pathogen of the urinary tract, a heavy metal-rich environment, but information regarding its heavy metal resistance is unknown. We investigated 422 S. saprophyticus isolates from human infection and colonization/contamination, animals, and environmental sources for resistance to copper, zinc, arsenic, and cadmium using the agar dilution method. To identify the genes associated with metal resistance and assess possible links to pathogenicity, we accessed the whole-genome sequence of all isolates and used in silico and pangenome-wide association approaches. The MIC values for copper and zinc were uniformly high (1,600 mg/liter). Genes encoding copper efflux pumps (copA, copB, copZ, mco, and csoR) and zinc transporters (zinT, czrAB, znuBC, and zur) were abundant in the population (20 to 100%). Arsenic and cadmium showed various susceptibility levels. Genes encoding the ars operon (arsRDABC), an ABC transporter and a two-component permease, were linked to resistance to arsenic (MICs ≥ 1,600 mg/liter; 14% [58/422]; P < 0.05). At least three cad genes (cadA or cadC and cadD-cadX or czrC) and genes encoding multidrug efflux pumps and hyperosmoregulation in acidified conditions were associated with resistance to cadmium (MICs ≥ 200 mg/liter; 20% [85/422]; P < 0.05). These resistance genes were frequently carried by mobile genetic elements. Resistance to arsenic and cadmium were linked to human infection and a clonal lineage originating in animals (P < 0.05). Altogether, S. saprophyticus was highly resistant to heavy metals and accumulated multiple metal resistance determinants. The highest arsenic and cadmium resistance levels were associated with infection, suggesting resistance to these metals is relevant for S. saprophyticus pathogenicity.
Collapse
|
8
|
Ahmad F, Farooq A, Khan MUG. Deep Learning Model for Pathogen Classification Using Feature Fusion and Data Augmentation. Curr Bioinform 2021. [DOI: 10.2174/1574893615999200707143535] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
Bacterial pathogens are deadly for animals and humans. The ease of their dissemination, coupled
with their high capacity for ailment and death in infected individuals, makes them a threat to society.
Objective:
Due to high similarity among genera and species of pathogens, it is sometimes difficult for microbiologists to
differentiate between them. Their automatic classification using deep-learning models can help in reliable, and accurate
outcomes.
Method:
Deep-learning models, namely; AlexNet, GoogleNet, ResNet101, and InceptionV3 are used with numerous
variations including training model from scratch, fine-tuning without pre-trained weights, fine-tuning along with freezing
weights of initial layers, fine-tuning along with adjusting weights of all layers and augmenting the dataset by random
translation and reflection. Moreover, as the dataset is small, fine-tuning and data augmentation strategies are applied to
avoid overfitting and produce a generalized model. A merged feature vector is produced using two best-performing models
and accuracy is calculated by xgboost algorithm on the feature vector by applying cross-validation.
Results:
Fine-tuned models where augmentation is applied produces the best results. Out of these, two-best-performing
deep models i.e. (ResNet101, and InceptionV3) selected for feature fusion, produced a similar validation accuracy of 95.83
with a loss of 0.0213 and 0.1066, and a testing accuracy of 97.92 and 93.75, respectively. The proposed model used xgboost
to attained a classification accuracy of 98.17% by using 35-folds cross-validation.
Conclusion:
The automatic classification using these models can help experts in the correct identification of pathogens.
Consequently, they can help in controlling epidemics and thereby minimizing the socio-economic impact on the community.
Collapse
Affiliation(s)
- Fareed Ahmad
- Department of Computer Science and Engineering, Faculty of Electrical Engineering, University of Engineering and Technology, Lahore, Pakistan
| | - Amjad Farooq
- Department of Computer Science and Engineering, Faculty of Electrical Engineering, University of Engineering and Technology, Lahore, Pakistan
| | - Muhammad Usman Ghani Khan
- Department of Computer Science and Engineering, Faculty of Electrical Engineering, University of Engineering and Technology, Lahore, Pakistan
| |
Collapse
|
9
|
Jackson N, Borges CA, Tarlton NJ, Resendez A, Milton AK, de Boer TR, Butcher CR, Murthy N, Riley LW. A rapid, antibiotic susceptibility test for multidrug-resistant, Gram-negative bacterial uropathogens using the biochemical assay, DETECT. J Microbiol Methods 2021; 182:106160. [PMID: 33548393 DOI: 10.1016/j.mimet.2021.106160] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 01/04/2021] [Accepted: 01/31/2021] [Indexed: 12/26/2022]
Abstract
The increasing prevalence of extended spectrum β-lactamases (ESBLs) and plasmid-mediated AmpC (pAmpC) β-lactamases among Enterobacterales threatens our ability to treat urinary tract infections (UTIs). These organisms are resistant to most β-lactam antibiotics and are frequently multidrug-resistant (MDR). Consequently, they are often resistant to antibiotics used to empirically treat UTIs. The lack of rapid diagnostic and antibiotic susceptibility tests (AST) makes clinical management of UTIs caused by such organisms difficult, as standard culture and susceptibility assays require several days. We have adapted a biochemical detection assay, termed dual-enzyme trigger-enabled cascade technology (DETECT) for rapid detection of resistance (time-to-result of 3 h) to other antibiotics commonly used in treatment of UTIs. DETECT is activated by the presence of CTX-M and pAmpC β-lactamases. In this proof-of-concept study, the adapted DETECT assay (AST-DETECT) has been performed on pure-cultures of Klebsiella pneumoniae and Escherichia coli (48 isolates) expressing ESBL or pAmpC β-lactamases to perform AST for ciprofloxacin (sensitivity 96.9%, specificity 100%, accuracy 97.9%) nitrofurantoin (sensitivity 95.7%, specificity 91.7%, accuracy 94%) and trimethoprim/sulfamethoxazole (sensitivity 83.3%, specificity 100%, accuracy 89.4%). These results suggest that AST-DETECT may be adapted as a potential diagnostic platform to rapidly detect multidrug-resistant E. coli and K. pneumoniae that cause UTI.
Collapse
Affiliation(s)
- Nicole Jackson
- School of Public Health, Department of Infectious Diseases and Vaccinology, University of California Berkeley, Berkeley, CA, USA.
| | - Clarissa A Borges
- School of Public Health, Department of Infectious Diseases and Vaccinology, University of California Berkeley, Berkeley, CA, USA
| | - Nicole J Tarlton
- Department of Microbiology, BioAmp Diagnostics, Inc., San Carlos, CA, USA
| | - Angel Resendez
- Department of Chemistry, BioAmp Diagnostics, Inc., San Carlos, CA, USA
| | | | - Tara R de Boer
- Department of Chemistry, BioAmp Diagnostics, Inc., San Carlos, CA, USA
| | - Cheyenne R Butcher
- School of Public Health, Department of Infectious Diseases and Vaccinology, University of California Berkeley, Berkeley, CA, USA
| | - Niren Murthy
- Department of Bioengineering, University of California Berkeley, Berkeley, CA, USA
| | - Lee W Riley
- School of Public Health, Department of Infectious Diseases and Vaccinology, University of California Berkeley, Berkeley, CA, USA.
| |
Collapse
|
10
|
Wu C, Zhang X, Liang J, Li Q, Lin H, Lin C, Liu H, Zhou D, Lu W, Sun Z, Lin X, Zhang H, Li K, Xu T, Bao Q, Lu J. Characterization of florfenicol resistance genes in the coagulase-negative Staphylococcus (CoNS) isolates and genomic features of a multidrug-resistant Staphylococcus lentus strain H29. Antimicrob Resist Infect Control 2021; 10:9. [PMID: 33413633 PMCID: PMC7791814 DOI: 10.1186/s13756-020-00869-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 12/11/2020] [Indexed: 02/08/2023] Open
Abstract
Background With the wide use of florfenicol to prevent and treat the bacterial infection of domestic animals, the emergence of the florfenicol resistance bacteria is increasingly serious. It is very important to elucidate the molecular mechanism of the bacteria’s resistance to florfenicol. Methods The minimum inhibitory concentration (MIC) levels were determined by the agar dilution method, and polymerase chain reaction was conducted to analyze the distribution of florfenicol resistance genes in 39 CoNS strains isolated from poultry and livestock animals and seafood. The whole genome sequence of one multidrug resistant strain, Staphylococcus lentus H29, was characterized, and comparative genomics analysis of the resistance gene-related sequences was also performed. Results As a result, the isolates from the animals showed a higher resistance rate (23/28, 82.1%) and much higher MIC levels to florfenicol than those from seafood. Twenty-seven animal isolates carried 37 florfenicol resistance genes (including 26 fexA, 6 cfr and 5 fexB genes) with one carrying a cfr gene, 16 each harboring a fexA gene, 5 with both a fexA gene and a fexB gene and the other 5 with both a fexA gene and a cfr gene. On the other hand, all 11 isolates from seafood were sensitive to florfenicol, and only 3 carried a fexA gene each. The whole genome sequence of S. lentus H29 was composed of a chromosome and two plasmids (pH29-46, pH29-26) and harbored 11 resistance genes, including 6 genes [cfr, fexA, ant(6)-Ia, aacA-aphD, mecA and mph(C)] encoded on the chromosome, 4 genes [cfr, fexA, aacA-aphD and tcaA] on pH29-46 and 1 gene (fosD) on pH29-26. We found that the S. lentus H29 genome carried two identical copies of the gene arrays of radC-tnpABC-hp-fexA (5671 bp) and IS256-cfr (2690 bp), of which one copy of the two gene arrays was encoded on plasmid pH29-46, while the other was encoded on the chromosome. Conclusions The current study revealed the wide distribution of florfenicol resistance genes (cfr, fexA and fexB) in animal bacteria, and to the best of our knowledge, this is the first report that one S. lentus strain carried two identical copies of florfenicol resistance-related gene arrays.
Collapse
Affiliation(s)
- Chongyang Wu
- School of Laboratory Medicine and Life Science/Institute of Biomedical Informatics, Wenzhou Medical University, Chashan University Town, Wenzhou, 325035, Zhejiang, China.,The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China.,Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Xueya Zhang
- School of Laboratory Medicine and Life Science/Institute of Biomedical Informatics, Wenzhou Medical University, Chashan University Town, Wenzhou, 325035, Zhejiang, China.,The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
| | - Jialei Liang
- The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
| | - Qiaoling Li
- School of Laboratory Medicine and Life Science/Institute of Biomedical Informatics, Wenzhou Medical University, Chashan University Town, Wenzhou, 325035, Zhejiang, China.,The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
| | - Hailong Lin
- School of Laboratory Medicine and Life Science/Institute of Biomedical Informatics, Wenzhou Medical University, Chashan University Town, Wenzhou, 325035, Zhejiang, China.,The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
| | - Chaoqin Lin
- The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
| | - Hongmao Liu
- The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
| | - Danying Zhou
- School of Laboratory Medicine and Life Science/Institute of Biomedical Informatics, Wenzhou Medical University, Chashan University Town, Wenzhou, 325035, Zhejiang, China
| | - Wei Lu
- School of Laboratory Medicine and Life Science/Institute of Biomedical Informatics, Wenzhou Medical University, Chashan University Town, Wenzhou, 325035, Zhejiang, China
| | - Zhewei Sun
- School of Laboratory Medicine and Life Science/Institute of Biomedical Informatics, Wenzhou Medical University, Chashan University Town, Wenzhou, 325035, Zhejiang, China
| | - Xi Lin
- School of Laboratory Medicine and Life Science/Institute of Biomedical Informatics, Wenzhou Medical University, Chashan University Town, Wenzhou, 325035, Zhejiang, China
| | - Hailin Zhang
- The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
| | - Kewei Li
- School of Laboratory Medicine and Life Science/Institute of Biomedical Informatics, Wenzhou Medical University, Chashan University Town, Wenzhou, 325035, Zhejiang, China
| | - Teng Xu
- Institute of Translational Medicine, Baotou Central Hospital, Baotou, 014040, China.
| | - Qiyu Bao
- School of Laboratory Medicine and Life Science/Institute of Biomedical Informatics, Wenzhou Medical University, Chashan University Town, Wenzhou, 325035, Zhejiang, China.
| | - Junwan Lu
- School of Laboratory Medicine and Life Science/Institute of Biomedical Informatics, Wenzhou Medical University, Chashan University Town, Wenzhou, 325035, Zhejiang, China.
| |
Collapse
|
11
|
Rossato AM, Primon-Barros M, Rocha LDL, Reiter KC, Dias CAG, d’Azevedo PA. Resistance profile to antimicrobials agents in methicillin-resistant Staphylococcus aureus isolated from hospitals in South Brazil between 2014-2019. Rev Soc Bras Med Trop 2020; 53:e20200431. [PMID: 33174961 PMCID: PMC7670760 DOI: 10.1590/0037-8682-0431-2020] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 08/12/2020] [Indexed: 02/07/2023] Open
Abstract
INTRODUCTION Methicillin-resistant Staphylococcus aureus (MRSA) is a common pathogen causing healthcare-associated infections. Owing to the restricted use of beta-lactams in MRSA infections, non-beta-lactam antimicrobials are required for treatment. However, MRSA can develop resistance mechanisms to non-beta-lactam antimicrobials, which reduces viable treatment options. Here, we evaluated the antimicrobial susceptibility and resistance genes of MRSA isolated from hospitalized patients in South Brazil. METHODS The antimicrobial susceptibilities of hospital MRSA (217) isolates were determined by disk diffusion or microdilution methods. Additionally, the presence of 14 resistance genes and SCCmec typing was performed by PCR. RESULTS Among the antimicrobials tested, we observed high erythromycin (74.2%), ciprofloxacin (64.5%), and clindamycin (46.1%) resistance rates and complete susceptibility to linezolid and vancomycin. Seventeen different patterns of MRSA antimicrobial resistance were observed, of which 42.9% represented multidrug resistance. Among erythromycin-resistant MRSA, 53.4%, 45.3%, 37.9%, 13.0%, and 6.8% carried ermA, msrA, msrB, ermC, and ermB genes, respectively. Among clindamycin-resistant MRSA, 83%, 17%, 10%, 4%, and 2% carried ermA, ermC, ermB, linA, and linB genes, respectively. Among gentamicin-resistant MRSA, 96.8%, 83.9%, and 9.7% carried aac(6')/aph(2''), aph(3')-IIIa, and ant(4')-Ia genes, respectively. Among tetracycline-resistant MRSA, 6.5% and 93.5% carried tetK and tetM genes, respectively. Lastly, among trimethoprim/sulfamethoxazole-resistant MRSA, 13.3% and 100% carried dfrA and dfrG genes, respectively. The SCCmec type IV isolates were detected more frequently, whereas the SCCmec type III isolates exhibited higher multidrug resistance. CONCLUSIONS The study data provides information regarding the MRSA resistance profile in South Brazil that is associated with the clinical conditions of patients and can contribute to clinical decision-making.
Collapse
Affiliation(s)
- Adriana Medianeira Rossato
- Universidade Federal de Ciências da Saúde de Porto Alegre,
Programa de Pós-graduação em Ciências da Saúde, Porto Alegre, RS, Brasil
| | - Muriel Primon-Barros
- Universidade Federal de Ciências da Saúde de Porto Alegre,
Programa de Pós-graduação em Ciências da Saúde, Porto Alegre, RS, Brasil
| | - Lisiane da Luz Rocha
- Universidade Federal de Ciências da Saúde de Porto Alegre,
Programa de Pós-graduação em Ciências da Saúde, Porto Alegre, RS, Brasil
| | - Keli Cristine Reiter
- Universidade Federal de Ciências da Saúde de Porto Alegre,
Programa de Pós-graduação em Ciências da Saúde, Porto Alegre, RS, Brasil
| | - Cícero Armídio Gomes Dias
- Universidade Federal de Ciências da Saúde de Porto Alegre,
Programa de Pós-graduação em Ciências da Saúde, Porto Alegre, RS, Brasil
| | - Pedro Alves d’Azevedo
- Universidade Federal de Ciências da Saúde de Porto Alegre,
Programa de Pós-graduação em Ciências da Saúde, Porto Alegre, RS, Brasil
| |
Collapse
|
12
|
Mann AE, Mitchell EA, Zhang Y, Curtis-Robles R, Thapa S, Hamer SA, Allen MS. Comparison of the Bacterial Gut Microbiome of North American Triatoma spp. With and Without Trypanosoma cruzi. Front Microbiol 2020; 11:364. [PMID: 32231645 PMCID: PMC7082358 DOI: 10.3389/fmicb.2020.00364] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 02/18/2020] [Indexed: 12/20/2022] Open
Abstract
Chagas disease, caused by the hemoflagellate protist Trypanosoma cruzi, affects nearly 6 million people worldwide, mainly in Latin America. Hematophagous triatomine insects (“kissing bugs”) are the primary vectors of T. cruzi throughout the Americas and feed on a variety of animals, including humans. Control of triatomines is central to the control of T. cruzi infection. Recent advances in mitigation of other insect-borne diseases via the manipulation of insect-associated bacteria as a way to halt or slow disease transmission has opened questions to the applicability of these methods to Chagas disease vectors. Few studies have examined the hindgut microbiome of triatomines found in North America. In the current study, two species of triatomines were collected across Texas, United States, screened for the presence of T. cruzi, and analyzed for the bacterial composition of their hindguts using a 16S rRNA gene-fragment metabarcoding approach. We compared diversity of microbial community profiles across 74 triatomine insects to address the hypothesis that the richness and abundance of bacterial groups differ by T. cruzi infection and strain type, blood meal engorgement status, insect species, sex, and collection location. The gut microbial community of individual triatomines was characterized by low intraindividual taxonomic diversity and high interindividual variation that was weakly predicted by triatomine species, and was not predicted by triatomine sex, collection location, T. cruzi infection status, or blood meal score. However, we did find bacterial groups enriched in T. cruzi-positive individuals, including Enterobacterales, and Petrimonas. Additionally, we detected Salmonella enterica subspecies diarizonae in three triatomine individuals; this species is commonly associated with reptiles and domesticated animals and is a pathogen of humans. These data suggest that Triatoma spp. in Texas have variable patterns of colonized and transient bacteria, and may aid in development of novel means to interfere with transmission of the Chagas disease parasite T. cruzi. Deeper understanding of the effects of parasite infection on diverse insect vector microbiomes may highlight disease transmission risk and facilitate discovery of possible intervention strategies for biological control of this emerging vector-borne disease of global health significance.
Collapse
Affiliation(s)
- Allison E Mann
- Tick-Borne Disease Research Laboratory, Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, TX, United States
| | - Elizabeth A Mitchell
- Tick-Borne Disease Research Laboratory, Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, TX, United States
| | - Yan Zhang
- Tick-Borne Disease Research Laboratory, Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, TX, United States
| | - Rachel Curtis-Robles
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, United States
| | - Santosh Thapa
- Tick-Borne Disease Research Laboratory, Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, TX, United States.,Texas Children's Microbiome Center, Texas Children's Hospital, Houston, TX, United States.,Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, United States
| | - Sarah A Hamer
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, United States
| | - Michael S Allen
- Tick-Borne Disease Research Laboratory, Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, TX, United States
| |
Collapse
|
13
|
Silva KCS, Silva LOS, Silva GAA, Borges CL, Novaes E, Paccez JD, Fontes W, Giambiagi-deMarval M, Soares CMDA, Parente-Rocha JA. Staphylococcus saprophyticus Proteomic Analyses Elucidate Differences in the Protein Repertories among Clinical Strains Related to Virulence and Persistence. Pathogens 2020; 9:pathogens9010069. [PMID: 31963821 PMCID: PMC7169411 DOI: 10.3390/pathogens9010069] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 01/06/2020] [Accepted: 01/10/2020] [Indexed: 02/07/2023] Open
Abstract
Staphylococcus saprophyticus is a Gram-positive and coagulase negative cocci that composes the skin microbiota and can act as an opportunistic agent causing urinary tract infections, being more frequent in sexually active young women. The ability of a pathogen to cause infection in the host is associated to its ability to adhere to host cells and to survive host immune defenses. In this work, we presented the comparative proteomic profile of three S. saprophyticus strains. It was possible to characterize differences in the proteome content, specially related to expression of virulence factors. We compiled this data and previous data and we detected one strain (9325) possessing higher production and secretion of proteins related to virulence. Our results show that phenotypic, genotypic, and proteomic differences reflect in the ability to survive during interaction with host cells, since the 9325 strain presented a higher survival rate after macrophage interaction. In counterpart, the 7108 strain that possesses lower content of proteins related to virulence presented higher ability to form biofilm suggesting that this strain can be better adapted to persist in the host and in the environment. Our work describes, for the first time, proteomic flexibility among S. saprophyticus strains, reflecting in virulence and persistence.
Collapse
Affiliation(s)
- Karla Christina Sousa Silva
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia-GO 74690-900, Brazil; (K.C.S.S.); (L.O.S.S.); (G.A.A.S.); (C.L.B.); (J.D.P.); (C.M.d.A.S.)
| | - Lana O’Hara Souza Silva
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia-GO 74690-900, Brazil; (K.C.S.S.); (L.O.S.S.); (G.A.A.S.); (C.L.B.); (J.D.P.); (C.M.d.A.S.)
| | - Guilherme Algusto Alves Silva
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia-GO 74690-900, Brazil; (K.C.S.S.); (L.O.S.S.); (G.A.A.S.); (C.L.B.); (J.D.P.); (C.M.d.A.S.)
| | - Clayton Luiz Borges
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia-GO 74690-900, Brazil; (K.C.S.S.); (L.O.S.S.); (G.A.A.S.); (C.L.B.); (J.D.P.); (C.M.d.A.S.)
| | - Evandro Novaes
- Departamento de Biologia, Universidade Federal de Lavras, Lavras 37200-900, Brazil;
| | - Juliano Domiraci Paccez
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia-GO 74690-900, Brazil; (K.C.S.S.); (L.O.S.S.); (G.A.A.S.); (C.L.B.); (J.D.P.); (C.M.d.A.S.)
| | - Wagner Fontes
- Laboratório de Química de Proteínas, Instituto de Biologia, Universidade de Brasília, UnB-Brasilia 70910-900, Brazil;
| | - Marcia Giambiagi-deMarval
- Laboratório de Microbiologia Molecular, Instituto de Microbiologia Prof. Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro-RJ 21941-902, Brazil;
| | - Célia Maria de Almeida Soares
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia-GO 74690-900, Brazil; (K.C.S.S.); (L.O.S.S.); (G.A.A.S.); (C.L.B.); (J.D.P.); (C.M.d.A.S.)
| | - Juliana Alves Parente-Rocha
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia-GO 74690-900, Brazil; (K.C.S.S.); (L.O.S.S.); (G.A.A.S.); (C.L.B.); (J.D.P.); (C.M.d.A.S.)
- Correspondence:
| |
Collapse
|
14
|
Oliveira ASD, Rosa IIR, Novaes E, Oliveira LSD, Baeza LC, Borges CL, Marlinghaus L, Soares CMDA, Giambiagi-deMarval M, Parente-Rocha JA. The exoproteome profiles of three Staphylococcus saprophyticus strains reveal diversity in protein secretion contents. Microbiol Res 2018; 216:85-96. [PMID: 30269860 DOI: 10.1016/j.micres.2018.08.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 08/07/2018] [Accepted: 08/21/2018] [Indexed: 12/24/2022]
Abstract
Staphylococcus saprophyticus is a gram-positive microorganism responsible for urinary tract infections (UTIs). Although some virulence factors are characterized, such as urease, autolysins, adhesins and hemagglutinins, large-scale proteomic studies have not been performed within this species. We performed the characterization of the exoproteome from three S. saprophyticus strains: the reference strain ATCC 15,305, a non-capsular strain 7108 and the 9325 strain containing a thick capsule which were cultured in BHI medium and culture supernatants were analysed by using mass spectrometry approach. We observed a core of 72 secreted proteins. In addition, it was possible to detect diversity in the protein profiles of the exoproteomes. Interestingly, strain 7108 presented no secretion of three antigenic proteins, including the classical SsaA antigen. In addition, the level of antigenic proteins secreted by strain 9325 was higher than in ATCC 15,305. This result was confirmed by Western blot analysis using anti-SsaA polyclonal antibodies, and no production/ secretion of SsaA was detected in strain 7108. Transcriptional data shows that 7108 strain produces transcripts encoding SsaA, suggesting post-transcriptional regulation occurs in this strain. Moreover, when compared with the other strains that were analyzed, it was possible to detect higher levels of proteases secreted by strain 7108 and higher levels of antigenic proteins and transglycosylases secreted by 9325 strain. The results reveal diversity in protein secretion among strains. This research is an important first step towards understanding the variability in S. saprophyticus exoproteome profile and could be significant in explaining differences among strains.
Collapse
Affiliation(s)
- Andrea Santana de Oliveira
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Isabella Inês Rodrigues Rosa
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Evandro Novaes
- Escola de Agronomia, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Lucas Silva de Oliveira
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Lilian Cristiane Baeza
- Centro de Ciências Médicas e Farmacêuticas, Universidade Estadual do Oeste do Paraná, Cascavel, Brazil
| | - Clayton Luiz Borges
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | | | - Célia Maria de Almeida Soares
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Marcia Giambiagi-deMarval
- Laboratório de Microbiologia Molecular, Instituto de Microbiologia Prof. Paulo de Góes, Universidade Federal do Rio de Janeiro - Rio de Janeiro, Rio de Janeiro, Brazil
| | - Juliana Alves Parente-Rocha
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, Brazil.
| |
Collapse
|
15
|
Stavropoulou DA, De Vuyst L, Leroy F. Nonconventional starter cultures of coagulase-negative staphylococci to produce animal-derived fermented foods, a SWOT analysis. J Appl Microbiol 2018; 125:1570-1586. [PMID: 30053335 DOI: 10.1111/jam.14054] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 07/15/2018] [Accepted: 07/17/2018] [Indexed: 01/03/2023]
Abstract
Coagulase-negative staphylococci (CNS) are ubiquitous micro-organisms that are commonly present on animal skin and animal-derived foods. They are members of the beneficial microbial consortia of several fermented food products where they contribute to quality. Currently, only a few CNS species are included in commercial starter cultures, although many other ones with promising properties have been isolated from diverse food ecosystems. In the present study, a Strengths-Weaknesses-Opportunities-Threats (SWOT) analysis of the potential use of unconventional CNS starter cultures for the fermentation of animal-derived foods is carried out. An overview of both their desirable and worrisome metabolic traits is given. In general, the application of innovative CNS-based starter cultures offers opportunities to modulate flavour, improve the safety and health aspects and develop novel colour development strategies for clean label products. Yet, their implementation is often not straightforward as nontrivial obstacles or threats are encountered, which relate to technological, food safety and legal concerns. As most of the desirable and undesirable characteristics of CNS species are strain dependent, a case-by-case evaluation is needed when evaluating specific strains for their potential use as novel starter cultures.
Collapse
Affiliation(s)
- D A Stavropoulou
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - L De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - F Leroy
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| |
Collapse
|
16
|
de Paiva-Santos W, de Sousa VS, Giambiagi-deMarval M. Occurrence of virulence-associated genes among Staphylococcus saprophyticus isolated from different sources. Microb Pathog 2018; 119:9-11. [PMID: 29604423 DOI: 10.1016/j.micpath.2018.03.054] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 03/09/2018] [Accepted: 03/28/2018] [Indexed: 11/27/2022]
Abstract
Staphylococcus saprophyticus is an important pathogen responsible for community urinary tract infections (UTI). Besides composing the human microbiota, this species is widely distributed in the environment and the origins of this organism for human infection is not fully characterized. Although some virulence determinants are known, such as d-serine deaminase (DsdA), urease and cell-wall associated proteins, few studies investigated the distribution of virulence-associated genes and analyzed the pathogenic potential of S. saprophyticus strains from different sources. The aim of the present study was to detect the presence of S. saprophyticus genes encoding surface proteins UafA, Aas, Ssp, SdrI, SssF as well as the DsdA and urease enzymes. A total of 142 S. saprophyticus strains were obtained from four sources: UTI, colonization, water and food. It was found, in every tested strain, the presence of genes encoding the surface proteins UafA, Aas, Ssp and SssF and the DsdA and urease enzymes. In contrast, the gene encoding SdrI surface protein was not detected in any of the strains of S. saprophyticus. These results provide a better understanding of the characteristics of S. saprophyticus strains and suggest that isolates from non-human sources have a potential to colonize the urinary tract.
Collapse
Affiliation(s)
- Weslley de Paiva-Santos
- Departamento de Microbiologia Médica, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Centro de Ciências da Saúde (CCS), Av. Carlos Chagas Filho, 373, Bloco I, Cidade Universitária, 21941-920, Rio de Janeiro, RJ, Brazil
| | - Viviane Santos de Sousa
- Departamento de Microbiologia Médica, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Centro de Ciências da Saúde (CCS), Av. Carlos Chagas Filho, 373, Bloco I, Cidade Universitária, 21941-920, Rio de Janeiro, RJ, Brazil
| | - Marcia Giambiagi-deMarval
- Departamento de Microbiologia Médica, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Centro de Ciências da Saúde (CCS), Av. Carlos Chagas Filho, 373, Bloco I, Cidade Universitária, 21941-920, Rio de Janeiro, RJ, Brazil.
| |
Collapse
|
17
|
Subhan F, Shahzad R, Tauseef I, Haleem KS, Rehman AU, Mahmood S, Lee IJ. Isolation, identification, and pathological effects of beach sand bacterial extract on human skin keratinocytes in vitro. PeerJ 2018; 6:e4245. [PMID: 29441229 PMCID: PMC5807979 DOI: 10.7717/peerj.4245] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 12/18/2017] [Indexed: 01/22/2023] Open
Abstract
Background Beaches are recreational spots for people. However, beach sand contains harmful microbes that affect human health, and there are no established methods for either sampling and identifying beach-borne pathogens or managing the quality of beach sand. Method This study was conducted with the aim of improving human safety at beaches and augmenting the quality of the beach experience. Beach sand was used as a resource to isolate bacteria due to its distinctive features and the biodiversity of the beach sand biota. A selected bacterial isolate termed FSRS was identified as Pseudomonas stutzeri using 16S rRNA sequencing and phylogenetic analysis, and the sequence was deposited in the NCBI GenBank database under the accession number MF599548. The isolated P. stutzeri bacterium was cultured in Luria-Bertani growth medium, and a crude extract was prepared using ethyl acetate to examine the potential pathogenic effect of P. stutzeri on human skin. A human skin keratinocyte cell line (HaCaT) was used to assess cell adhesion, cell viability, and cell proliferation using a morphological analysis and a WST-1 assay. Result The crude P. stutzeri extract inhibited cell adhesion and decreased cell viability in HaCaT cells. We concluded that the crude extract of P. stutzeri FSRS had a strong pathological effect on human skin cells. Discussion Beach visitors frequently get skin infections, but the exact cause of the infections is yet to be determined. The beach sand bacterium P. stutzeri may, therefore, be responsible for some of the dermatological problems experienced by people visiting the beach.
Collapse
Affiliation(s)
- Fazli Subhan
- Department of Microbiology, Hazara University, Mansehra, Pakistan
| | - Raheem Shahzad
- School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Isfahan Tauseef
- Department of Microbiology, Hazara University, Mansehra, Pakistan
| | | | - Atta-Ur Rehman
- Department of Zoology, Hazara University, Mansehra, Pakistan
| | - Sajid Mahmood
- Department of Zoology, Hazara University, Mansehra, Pakistan
| | - In-Jung Lee
- School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea.,Research Institute for Dok-do and Ulleung-do Island, Kyungpook National University, Daegu, Republic of Korea
| |
Collapse
|