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Cunningham SA, Eberly AR, Beisken S, Posch AE, Schuetz AN, Patel R. Core Genome Multilocus Sequence Typing and Antibiotic Susceptibility Prediction from Whole-Genome Sequence Data of Multidrug-Resistant Pseudomonas aeruginosa Isolates. Microbiol Spectr 2022; 10:e0392022. [PMID: 36350158 PMCID: PMC9769729 DOI: 10.1128/spectrum.03920-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 10/24/2022] [Indexed: 11/11/2022] Open
Abstract
Over the past decade, whole-genome sequencing (WGS) has overtaken traditional bacterial typing methods for studies of genetic relatedness. Further, WGS data generated during epidemiologic studies can be used in other clinically relevant bioinformatic applications, such as antibiotic resistance prediction. Using commercially available software tools, the relatedness of 38 clinical isolates of multidrug-resistant Pseudomonas aeruginosa was defined by two core genome multilocus sequence typing (cgMLST) methods, and the WGS data of each isolate was analyzed to predict antibiotic susceptibility to nine antibacterial agents. The WGS typing and resistance prediction data were compared with pulsed-field gel electrophoresis (PFGE) and phenotypic antibiotic susceptibility results, respectively. Simpson's Diversity Index and adjusted Wallace pairwise assessments of the three typing methods showed nearly identical discriminatory power. Antibiotic resistance prediction using a trained analytical pipeline examined 342 bacterial-drug combinations with an overall categorical agreement of 92.4% and very major, major, and minor error rates of 3.6, 4.1, and 4.1%, respectively. IMPORTANCE Multidrug-resistant Pseudomonas aeruginosa isolates are a serious public health concern due to their resistance to nearly all or all of the available antibiotics, including carbapenems. Utilizing molecular approaches in conjunction with antibiotic susceptibility prediction software warrants investigation for use in the clinical laboratory workflow. These molecular tools coupled with antibiotic resistance prediction tools offer the opportunity to overcome the extended turnaround time and technical challenges of phenotypic susceptibility testing.
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Affiliation(s)
- Scott A. Cunningham
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Allison R. Eberly
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | | | | | - Audrey N. Schuetz
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
- Division of Public Health, Infectious Diseases, and Occupational Medicine, Mayo Clinic, Rochester, Minnesota, USA
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2
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Mahmoud SF, Fayez M, Swelum AA, Alswat AS, Alkafafy M, Alzahrani OM, Alsunaini SJ, Almuslem A, Al Amer AS, Yusuf S. Genetic Diversity, Biofilm Formation, and Antibiotic Resistance of Pseudomonas aeruginosa Isolated from Cow, Camel, and Mare with Clinical Endometritis. Vet Sci 2022; 9:vetsci9050239. [PMID: 35622767 PMCID: PMC9147788 DOI: 10.3390/vetsci9050239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/07/2022] [Accepted: 05/13/2022] [Indexed: 01/25/2023] Open
Abstract
Pseudomonas aeruginosa is a ubiquitous opportunistic bacterium that causes diseases in animals and humans. This study aimed to investigate the genetic diversity, antimicrobial resistance, biofilm formation, and virulence and antibiotic resistance genes of P. aeruginosa isolated from the uterus of cow, camel, and mare with clinical endometritis and their drinking water. Among the 180 uterine swabs and 90 drinking water samples analysed, 54 (20%) P. aeruginosa isolates were recovered. Isolates were identified biochemically to the genus level by the automated Vitek 2 system and genetically by the amplification of the gyrB gene and the sequencing of the 16S rRNA gene. Multilocus sequence typing identified ten different sequence types for the P. aeruginosa isolates. The identification of ST2012 was significantly (p ≤ 0.05) higher than that of ST296, ST308, ST111, and ST241. The isolates exhibited significantly (p ≤ 0.05) increased resistance to piperacillin (77.8%), ciprofloxacin (59.3%), gentamicin (50%), and ceftazidime (38.9%). Eight (14.8%) isolates showed resistance to imipenem; however, none of the isolates showed resistance to colistin. Multidrug resistance (MDR) was observed in 24 isolates (44.4%) with a multiple antibiotic resistance index ranging from 0.44 to 0.77. MDR was identified in 30 (33.3%) isolates. Furthermore, 38.8% and 9.2% of the isolates exhibited a positive extended-spectrum-β-lactamase (ESBL) and metallo-β-lactamase (MBL) phenotype, respectively. The most prevalent β-lactamase encoding genes were blaTEM and blaCTX-M, however, the blaIPM gene was not detected in any of the isolates. Biofilm formation was observed in 49 (90.7%) isolates classified as: 11.1% weak biofilm producers; 38.9% moderate biofilm producers; 40.7% strong biofilm producers. A positive correlation was observed between the MAR index and biofilm formation. In conclusion, the results highlighted that farm animals with clinical endometritis could act as a reservoir for MDR and virulent P. aeruginosa. The emergence of ESBLs and MBLs producing P. aeruginosa in different farm animals is a public health concern. Therefore, surveillance programs to monitor and control MDR P. aeruginosa in animals are required.
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Affiliation(s)
- Samy F. Mahmoud
- Department of Biotechnology, College of Science, Taif University, Taif 21944, Saudi Arabia; (S.F.M.); (A.S.A.); (M.A.)
| | - Mahmoud Fayez
- Al-Ahsa Veterinary Diagnostic Laboratory, Ministry of Environment, Water and Agriculture, Al-Ahsa 31982, Saudi Arabia; (S.J.A.); (A.A.); (A.S.A.A.)
- Department of Bacteriology, Veterinary Serum and Vaccine Research Institute, Ministry of Agriculture, Cairo 12618, Egypt
- Correspondence:
| | - Ayman A. Swelum
- Department of Theriogenology, Faculty of Veterinary Medicine, Zagazig University, Zagazig 44511, Egypt;
| | - Amal S. Alswat
- Department of Biotechnology, College of Science, Taif University, Taif 21944, Saudi Arabia; (S.F.M.); (A.S.A.); (M.A.)
| | - Mohamed Alkafafy
- Department of Biotechnology, College of Science, Taif University, Taif 21944, Saudi Arabia; (S.F.M.); (A.S.A.); (M.A.)
| | - Othman M. Alzahrani
- Department of Biology, College of Science, Taif University, Taif 21944, Saudi Arabia;
| | - Saleem J. Alsunaini
- Al-Ahsa Veterinary Diagnostic Laboratory, Ministry of Environment, Water and Agriculture, Al-Ahsa 31982, Saudi Arabia; (S.J.A.); (A.A.); (A.S.A.A.)
| | - Ahmed Almuslem
- Al-Ahsa Veterinary Diagnostic Laboratory, Ministry of Environment, Water and Agriculture, Al-Ahsa 31982, Saudi Arabia; (S.J.A.); (A.A.); (A.S.A.A.)
| | - Abdulaziz S. Al Amer
- Al-Ahsa Veterinary Diagnostic Laboratory, Ministry of Environment, Water and Agriculture, Al-Ahsa 31982, Saudi Arabia; (S.J.A.); (A.A.); (A.S.A.A.)
| | - Shaymaa Yusuf
- Department of Microbiology, Faculty of Veterinary Medicine, Assiut University, Assiut 71515, Egypt;
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Oh S, Nam SK, Chang HE, Park KU. Comparative Analysis of Short- and Long-Read Sequencing of Vancomycin-Resistant Enterococci for Application to Molecular Epidemiology. Front Cell Infect Microbiol 2022; 12:857801. [PMID: 35463637 PMCID: PMC9019564 DOI: 10.3389/fcimb.2022.857801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/17/2022] [Indexed: 11/13/2022] Open
Abstract
Vancomycin-resistant enterococci (VRE) are nosocomial pathogens with genetic plasticity and widespread antimicrobial resistance (AMR). To prevent the spread of VRE in the hospital setting, molecular epidemiological approaches such as pulsed-field gel electrophoresis and multilocus sequence typing have been implemented for pathogen outbreak surveillance. However, due to the insufficient discriminatory power of these methods, whole-genome sequencing (WGS), which enables high-resolution analysis of entire genomic sequences, is being used increasingly. Herein, we performed WGS of VRE using both short-read next-generation sequencing (SR-NGS) and long-read next-generation sequencing (LR-NGS). Since standardized workflows and pipelines for WGS-based bacterial epidemiology are lacking, we established three-step pipelines for SR- and LR-NGS, as a standardized WGS-based approach for strain typing and AMR profiling. For strain typing, we analyzed single-nucleotide polymorphisms (SNPs) of VRE isolates and constructed SNP-based maximum-likelihood phylogenies. The phylogenetic trees constructed using short and long reads showed good correspondence. Still, SR-NGS exhibited higher sensitivity for detecting nucleotide substitutions of bacterial sequences. During AMR profiling, we examined AMR genes and resistance-conferring mutations. We also assessed the concordance between genotypic and phenotypic resistance, which was generally better for LR-NGS than SR-NGS. Further validation of our pipelines based on outbreak cases is necessary to ensure the overall performance of pipelines.
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Affiliation(s)
- Sujin Oh
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - Soo Kyung Nam
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - Ho Eun Chang
- Department of Research and Development, PHiCS Institute, Seoul, South Korea
| | - Kyoung Un Park
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, South Korea
- Department of Laboratory Medicine, Seoul National University Bundang Hospital, Seongnam, South Korea
- *Correspondence: Kyoung Un Park,
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4
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Alfouzan W, Dhar R, Mohsin J, Khamis F, Mokaddas E, Abdullah A, Mustafa AS, Otero A, Wanis P, Matar SH, Khalil S, Alekseeva I, Young K. OUP accepted manuscript. JAC Antimicrob Resist 2022; 4:dlac035. [PMID: 35465239 PMCID: PMC9021015 DOI: 10.1093/jacamr/dlac035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 03/07/2022] [Indexed: 11/29/2022] Open
Abstract
Background The treatment options for infections caused by MDR Gram-negative bacteria have been limited, especially for infections caused by bacteria that produce carbapenemases and/or ESBLs. Ceftolozane/tazobactam is a cephalosporin/β-lactamase inhibitor developed to treat Gram-negative bacteria. Methods Ceftolozane/tazobactam and 14 comparators (amikacin, aztreonam, cefepime, cefotaxime, cefoxitin, ceftazidime, ceftriaxone, ciprofloxacin, colistin, ertapenem, imipenem, levofloxacin, meropenem and piperacillin/tazobactam) were evaluated against Pseudomonas aeruginosa and Enterobacterales isolates collected from Kuwait and Oman (n = 606) during 2016–17. In addition, further analysis of resistance mechanisms to ceftolozane/tazobactam was done utilizing WGS. Non-susceptible isolates from ceftolozane/tazobactam surveillance were selected for analysis. Overall, 35 strains underwent WGS. Results Among isolates from Kuwait, susceptibility of P. aeruginosa, Escherichia coli and Klebsiella pneumoniae to ceftolozane/tazobactam was 79.8%, 95.7% and 87.5%, respectively, and from Oman was 92.3%, 93.1% and 88.5%, respectively. No P. aeruginosa with a ceftolozane/tazobactam MIC <32 mg/L encoded β-lactamases besides normal chromosomal enzymes (PDC variants or OXA-50-like) whereas all but one P. aeruginosa isolate with MIC >32 mg/L encoded either MBLs (60%), VEB-1 (19%) or additional OXAs (3.7%). Conclusions Colistin followed by ceftolozane/tazobactam showed the greatest activity against P. aeruginosa. Enterobacterales showed more susceptibility to ceftolozane/tazobactam than to piperacillin/tazobactam, but meropenem and colistin showed better activity.
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Affiliation(s)
- Wadha Alfouzan
- Microbiology Unit, Department of Laboratories, Farwania Hospital, Kuwait City, Kuwait
- Department of Microbiology, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait
- Corresponding author. E-mail:
| | - Rita Dhar
- Microbiology Unit, Department of Laboratories, Farwania Hospital, Kuwait City, Kuwait
| | | | | | - Eiman Mokaddas
- Department of Microbiology, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait
- Microbiology Unit, Department of Laboratories, Ibn Sina Hospital, Kuwait City, Kuwait
| | - Abrar Abdullah
- Microbiology Unit, Department of Laboratories, Amiri hospital, Kuwait City, Kuwait
| | - Abu Salim Mustafa
- Department of Microbiology, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait
| | | | - Paulette Wanis
- Merck Sharp & Dohme IDEA Middle East, Dubai Healthcare City, AlFaris building #39, 4th floor, MSD Office, Dubai, UAE
| | - Samar Hussien Matar
- Merck Sharp & Dohme IDEA Middle East, Dubai Healthcare City, AlFaris building #39, 4th floor, MSD Office, Dubai, UAE
| | - Sherif Khalil
- Merck Sharp & Dohme IDEA Middle East, Dubai Healthcare City, AlFaris building #39, 4th floor, MSD Office, Dubai, UAE
| | - Irina Alekseeva
- Merck Sharp & Dohme IDEA Middle East, Dubai Healthcare City, AlFaris building #39, 4th floor, MSD Office, Dubai, UAE
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5
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Reichler SJ, Murphy SI, Martin NH, Wiedmann M. Identification, subtyping, and tracking of dairy spoilage-associated Pseudomonas by sequencing the ileS gene. J Dairy Sci 2021; 104:2668-2683. [PMID: 33455773 DOI: 10.3168/jds.2020-19283] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 10/25/2020] [Indexed: 11/19/2022]
Abstract
Pseudomonas spp. are important spoilage bacteria that negatively affect the quality of refrigerated fluid milk and uncultured cheese by generating unwanted odors, flavors, and pigments. They are frequently found in dairy plant environments and enter dairy products predominantly as postpasteurization contaminants. Current subtyping and characterization methods for dairy-associated Pseudomonas are often labor-intensive and expensive or provide limited and possibly unreliable classification information (e.g., to the species level). Our goal was to identify a single-copy gene that could be analyzed in dairy spoilage-associated Pseudomonas for preliminary species-level identification, subtyping, and phenotype prediction. We tested 7 genes previously targeted in a Pseudomonas fluorescens multilocus sequence typing scheme for their individual suitability in this application using a set of 113 Pseudomonas spp. isolates representing the diversity of typical pasteurized milk contamination. For each of the 7 candidate genes, we determined the success rate of PCR and sequencing for these 113 isolates as well as the level of discrimination for species identification and subtyping that the sequence data provided. Using these metrics, we selected a single gene, isoleucyl tRNA synthetase (ileS), which had the most suitable traits for simple and affordable single-gene Pseudomonas characterization. This was based on the number of isolates successfully sequenced for ileS (113/113), the number of unique allelic types assigned (83, compared with 50 for 16S rDNA), nucleotide and sequence diversity measures (e.g., number of unique SNP and Simpson index), and tests for genetic recombination. The discriminatory ability of ileS sequencing was confirmed by separation of 99 additional dairy Pseudomonas spp. isolates, which were indistinguishable by 16S rDNA sequencing, into 28 different ileS allelic types. Further, we used whole-genome sequencing data to demonstrate the similarities in ileS-based phylogenetic clustering to whole-genome-based clustering for 27 closely related dairy-associated Pseudomonas spp. isolates and for 178 Pseudomonas type strains. We also found that dairy-associated Pseudomonas within an ileS cluster typically shared the same proteolytic and lipolytic activities. Use of ileS sequencing provides a promising strategy for affordable initial characterization of Pseudomonas isolates, which will help the dairy industry identify, characterize, and track Pseudomonas in their facilities and products.
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Affiliation(s)
- S J Reichler
- Milk Quality Improvement Program, Department of Food Science, Cornell University, Ithaca, NY 14853
| | - S I Murphy
- Milk Quality Improvement Program, Department of Food Science, Cornell University, Ithaca, NY 14853
| | - N H Martin
- Milk Quality Improvement Program, Department of Food Science, Cornell University, Ithaca, NY 14853
| | - M Wiedmann
- Milk Quality Improvement Program, Department of Food Science, Cornell University, Ithaca, NY 14853.
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6
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Wei L, Wu Q, Zhang J, Guo W, Gu Q, Wu H, Wang J, Lei T, Xue L, Zhang Y, Wei X, Zeng X. Prevalence, Virulence, Antimicrobial Resistance, and Molecular Characterization of Pseudomonas aeruginosa Isolates From Drinking Water in China. Front Microbiol 2020; 11:544653. [PMID: 33343513 PMCID: PMC7744469 DOI: 10.3389/fmicb.2020.544653] [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: 03/21/2020] [Accepted: 11/02/2020] [Indexed: 01/26/2023] Open
Abstract
Pseudomonas aeruginosa is an important opportunistic pathogen and remains a major threat to the microbial safety of drinking water. There is a lack of comprehensive data on P. aeruginosa contamination in drinking water in China. Therefore, this study aimed to determine the prevalence, genetic diversity, virulence genes, and antimicrobial resistance of P. aeruginosa isolated from mineral water and spring water in China. From January 2013 to January 2014, 314 drinking water samples were collected from 23 cities in China. Of the collected samples, 77 (24.5%) were contaminated with P. aeruginosa, and these comprised 34 raw water (30.4%), 39 activated carbon-filtered water (30.6%), and four final water product (3.9%). A total of 132 P. aeruginosa isolates were obtained, and all of them showed the presence of virulence genes, with the detection rates of ExoU, ExoS, phzM, toxA, and lasB genes being 7.6, 86.3, 95.5, 89.4, and 100%, respectively. All isolates were sensitive to the 14 antibiotics (ciprofloxacin, levofloxacin, ofloxacin, norfloxacin, gentamicin, tobramycin, amikacin, polymyxin B, imipenem, meropenem, aztreonam, ceftazidime, cefepime, and piperacillin/tazobactam) tested. The 132 isolates were categorized into 42 sequence types according to multilocus sequence typing, and ST235 accounted for 8.3% (11) of the total isolates. Thus, this study provides comprehensive data on the prevalence and characteristics of P. aeruginosa in drinking water in China and can aid in developing preventive measures against contamination during the drinking water treatment process.
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Affiliation(s)
- Lei Wei
- Guangdong Provincial Key Laboratory of Microbiology Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China.,School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China
| | - Qingping Wu
- Guangdong Provincial Key Laboratory of Microbiology Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Jumei Zhang
- Guangdong Provincial Key Laboratory of Microbiology Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Weipeng Guo
- Guangdong Provincial Key Laboratory of Microbiology Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Qihui Gu
- Guangdong Provincial Key Laboratory of Microbiology Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Huiqing Wu
- Guangdong Provincial Key Laboratory of Microbiology Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Juan Wang
- College of Food Science, South China Agricultural University, Guangzhou, China
| | - Tao Lei
- Guangdong Provincial Key Laboratory of Microbiology Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Liang Xue
- Guangdong Provincial Key Laboratory of Microbiology Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Youxiong Zhang
- Guangdong Provincial Key Laboratory of Microbiology Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Xianhu Wei
- Guangdong Provincial Key Laboratory of Microbiology Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Xiaocong Zeng
- Biological Testing and Analysis Department, Guangdong Provincial Institute of Food Inspection, Guangzhou, China
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7
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Development and Application of a Core Genome Multilocus Sequence Typing Scheme for the Health Care-Associated Pathogen Pseudomonas aeruginosa. J Clin Microbiol 2020; 58:JCM.00214-20. [PMID: 32493782 DOI: 10.1128/jcm.00214-20] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 05/28/2020] [Indexed: 12/11/2022] Open
Abstract
Pseudomonas aeruginosa is an opportunistic human pathogen that frequently causes health care-associated infections (HAIs). Due to its metabolic diversity and ability to form biofilms, this Gram-negative nonfermenting bacterium can persist in the health care environment, which can lead to prolonged HAI outbreaks. We describe the creation of a core genome multilocus sequence typing (cgMLST) scheme to provide a stable platform for the rapid comparison of P. aeruginosa isolates using whole-genome sequencing (WGS) data. We used a diverse set of 58 complete P. aeruginosa genomes to curate a set of 4,440 core genes found in each isolate, representing ∼64% of the average genome size. We then expanded the alleles for each gene using 1,991 contig-level genome sequences. The scheme was used to analyze genomes from four historical HAI outbreaks to compare the phylogenies generated using cgMLST to those of other means (traditional MLST, pulsed-field gel electrophoresis [PFGE], and single-nucleotide variant [SNV] analysis). The cgMLST scheme provides sufficient resolution for analyzing individual outbreaks, as well as the stability for comparisons across a variety of isolates encountered in surveillance studies, making it a valuable tool for the rapid analysis of P. aeruginosa genomes.
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8
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Ohadian Moghadam S, Afshar D, Nowroozi MR, Behnamfar A, Farzin A. Molecular Epidemiology of Carbapenemase-Producing Pseudomonas aeruginosa Isolated from an Iranian University Hospital: Evidence for Spread of High-Risk Clones. Infect Drug Resist 2020; 13:1583-1592. [PMID: 32581561 PMCID: PMC7277578 DOI: 10.2147/idr.s253756] [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] [Indexed: 12/24/2022] Open
Abstract
Purpose Given the importance of treatment failure due to multidrug-resistant (MDR) strains, studies on population structure of these organisms are necessary to improve control strategies. Accordingly, the current study aimed to determine the prevalence of carbapenem-resistant P. aeruginosa (CRPA) at a teaching referral hospital in Iran and to analyz their molecular clonality by multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE) for epidemiological purposes. Methods In this study, modified Hodge test (MHT) and double-disk synergy test (DDST) were used for carbapenemase production and metallo-β-lactamases (MBLs) screening, respectively. All P. aeruginosa isolates were tested for antimicrobial resistance. Moreover, MBL genes (blaIMP, blaVIM, blaSPM, blaNDM) were detected by multiplex PCR assay. Results Among 68 P. aeruginosa clinical isolates, 38 (55.88%) isolates were CRPA. Antibiotic susceptibility testing revealed that most of these isolates were MDR. PFGE analyses showed 5 common types and 27 single types among CRPA isolates. MLST analysis revealed three major clusters (MLST-sequence types (STs): 235, 357, and 861) among them. The 30 non-CRPA isolates corresponded mainly to MLST-STs 253, 360, and 446. Conclusion Our results showed that internationally distributed MLST-STs with widely genomic diversity have spread in our hospital, and clonal expansion of MDR strains of P. aeruginosa was described as well.
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Affiliation(s)
| | - Davoud Afshar
- Department of Microbiology and Virology, Zanjan University of Medical Sciences, Zanjan, Iran
| | | | - Amir Behnamfar
- Uro-Oncology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Amirreza Farzin
- Uro-Oncology Research Center, Tehran University of Medical Sciences, Tehran, Iran
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9
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de Sales RO, Migliorini LB, Puga R, Kocsis B, Severino P. A Core Genome Multilocus Sequence Typing Scheme for Pseudomonas aeruginosa. Front Microbiol 2020; 11:1049. [PMID: 32528447 PMCID: PMC7264379 DOI: 10.3389/fmicb.2020.01049] [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: 12/06/2019] [Accepted: 04/28/2020] [Indexed: 12/15/2022] Open
Abstract
Pseudomonas aeruginosa is a ubiquitous microorganism and an important opportunistic pathogen responsible for a broad spectrum of infections mainly in immunosuppressed and critically ill patients. Molecular investigations traditionally rely on pulsed field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). In this work we propose a core genome multilocus sequence typing (cgMLST) scheme for P. aeruginosa, a methodology that combines traditional MLST principles with whole genome sequencing data. All publicly available complete P. aeruginosa genomes, representing the diversity of this species, were used to establish a cgMLST scheme targeting 2,653 genes. The scheme was then tested using genomes available at contig, chromosome and scaffold levels. The proposed cgMLST scheme for P. aeruginosa typed over 99% (2,314/2,325) of the genomes available for this study considering at least 95% of the cgMLST target genes present. The absence of a certain number gene targets at the threshold considered for both the creation and validation steps due to low genome sequence quality is possibly the main reason for this result. The cgMLST scheme was compared with previously published whole genome single nucleotide polymorphism analysis for the characterization of the population structure of the epidemic clone ST235 and results were highly similar. In order to evaluate the typing resolution of the proposed scheme, collections of isolates belonging to two important STs associated with cystic fibrosis, ST146 and ST274, were typed using this scheme, and ST235 isolates associated with an outbreak were evaluated. Besides confirming the relatedness of all the isolates, earlier determined by MLST, the higher resolution of cgMLST denotes that it may be suitable for surveillance programs, overcoming possible shortcomings of classical MLST. The proposed scheme is publicly available at: https://github.com/BioinformaticsHIAEMolecularMicrobiology/cgMLST-Pseudomonas-aeruginosa.
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Affiliation(s)
- Romário Oliveira de Sales
- Hospital Israelita Albert Einstein, Albert Einstein Research and Education Institute, São Paulo, Brazil
| | - Letícia Busato Migliorini
- Hospital Israelita Albert Einstein, Albert Einstein Research and Education Institute, São Paulo, Brazil
| | - Renato Puga
- Hospital Israelita Albert Einstein, Albert Einstein Research and Education Institute, São Paulo, Brazil
| | - Bela Kocsis
- Institute of Medical Microbiology, Semmelweis University, Budapest, Hungary
| | - Patricia Severino
- Hospital Israelita Albert Einstein, Albert Einstein Research and Education Institute, São Paulo, Brazil
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10
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Antimicrobial Resistance, Genetic Diversity and Multilocus Sequence Typing of Escherichia coli from Humans, Retail Chicken and Ground Beef in Egypt. Pathogens 2020; 9:pathogens9050357. [PMID: 32397188 PMCID: PMC7281645 DOI: 10.3390/pathogens9050357] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 04/28/2020] [Accepted: 05/06/2020] [Indexed: 01/02/2023] Open
Abstract
Contamination of retail foods with foodborne pathogens, particularly the antimicrobial resistant ones, poses a persistent threat to human health. There is a dearth of information about the overlapping Escherichia coli (E. coli) lineages circulating among retail foods and humans in Egypt. This study aimed to determine the clonal diversity of 120 E. coli isolates from diarrheic patients (n = 32), retail chicken carcasses (n = 61) and ground beef (n = 27) from Mansoura, Egypt using pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). Simpson’s index of diversity was calculated to compare the results of both typing methods. Antimicrobial resistance phenotypes, genotypes and phylogrouping of the isolates were also determined. Higher frequencies of antimicrobial resistance were found among chicken isolates compared to beef and human isolates; regardless of isolate source, the predominant antimicrobial resistances were found against ampicillin (87/120, 72.5%), tetracycline and sulfisoxazole (82/120, 68.3%, each), and streptomycin (79/120, 65.8%). None of the isolates displayed resistance to meropenem. The prevalent genes detected were tetA (64.2%), blaTEM (62.5%), sul1 (56.7%), floR (53.3%), sul2 (50%), strB (48.3%) and strA (47.5%) corresponding with resistance phenotypes. Alarmingly, blaCTX was detected in 63.9% (39/61) of chicken isolates. The majority of E. coli isolates from humans (90.6%), beef (81.5%) and chicken (70.5%) belonged to commensal phylogroups (A, B1, C). Using PFGE analysis, 16 out of 24 clusters (66.7%) contained isolates from different sources at a similarity level ≥75%. MLST results assigned E. coli isolates into 25, 19 and 13 sequence types (STs) from chicken, human and beef isolates, respectively. Six shared STs were identified including ST1011, ST156, ST48, ST224 (chicken and beef), ST10 (human and chicken) and ST226 (human and beef). Simpson’s index of diversity was higher for MLST (0.98) than PFGE (0.94). In conclusion, the existence of common genetic determinants among isolates from retail foods and humans in Egypt as well as the circulation of shared STs indicates a possible epidemiological link with potential zoonotic hazards.
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Patient-to-Patient Transmission of Acinetobacter baumannii Gastrointestinal Colonization in the Intensive Care Unit. Antimicrob Agents Chemother 2019; 63:AAC.00392-19. [PMID: 31085518 DOI: 10.1128/aac.00392-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 05/07/2019] [Indexed: 12/25/2022] Open
Abstract
Acinetobacter baumannii is an important nosocomial pathogen. The objective of this study was to determine the proportion of A. baumannii infections due to patient-to-patient transmission by analyzing the molecular epidemiology of patients who acquired A. baumannii, using perianal surveillance cultures in a large 2-year intensive care unit (ICU) population. The design was a prospective cohort study. Patients who were admitted to the medical and surgical intensive care units at the University of Maryland Medical Center from 2011 to 2013 underwent admission, weekly, and discharge perianal culture collection. Using multilocus sequence typing (MLST) with subsequent pulsed-field gel electrophoresis (PFGE) for increased discrimination, combined with hospital overlap, the number of patients that acquired A. baumannii due to patient-to-patient transmission was determined. Our cohort consisted of 3,452 patients. In total, 196 cohort patients were colonized with A. baumannii; 130 patients were positive at ICU admission, and 66 patients acquired A. baumannii during their stay. Among the 196 A. baumannii patient isolates, there were 91 unique MLST types. Among the 66 patients who acquired A. baumannii, 31 (50%) were considered genetically related by MLST and/or PFGE type, and 11 (17%) were considered patient-to-patient transmission by genetic relatedness and overlapping hospital stay. Our data show that, of those cases of A. baumannii acquisition, at least 17% were cases of patient-to-patient transmission.
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Sener Okur D, Yuruyen C, Gungor O, Aktas Z, Erturan Z, Akcakaya N, Camcioglu Y, Cokugras H, Koksalan K. Genotypic characterization of Pseudomonas aeruginosa isolates from Turkish children with cystic fibrosis. Infect Drug Resist 2019; 12:675-685. [PMID: 31114258 PMCID: PMC6497484 DOI: 10.2147/idr.s183151] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 02/15/2019] [Indexed: 02/03/2023] Open
Abstract
Objective: To identify epidemic and other transmissible Pseudomonas aeruginosa strains, genotypic analyses are required. The aim of this study was to assess the distribution of P. aeruginosa strains within the Turkish pediatric cystic fibrosis (CF) clinic population. Methods: Eighteen patients attending the pediatric CF clinic of Cerrahpasa Medical Faculty were investigated in the study. Throat swab and/or sputum samples were taken from each patient at 3-month intervals. The isolates of patients were analyzed by pulsed-field gel electrophoresis (PFGE). The intra- and interpatient genotypic heterogeneity of isolates was examined to determine the clonal isolates of P. aeruginosa within the cohort. Results: A total of 108 clinical isolates of P. aeruginosa were obtained from 18 patients between May 2013 and May 2014. The pulsotypes of the first patient’s isolates could not be obtained by PFGE. From the remaining 17 patients and 101 isolates, 55 distinct pulsotypes were detected. The number of pulsotypes observed in more than one patient (minor clonal strains, cluster strains) was 8 (14.5%), and one of them colonized three patients. However, none of them was detected in more than three patients. These pulsotypes were composed of 20 isolates. In addition, with the PFGE analysis of 81 isolates, we detected 47 (85.6%) pulsotypes, which belonged to only one patient. Over different periods of this study, only 2 (11.8%) patients were colonized with the same pulsotype. Conclusion: Our study indicates that there was considerable genomic diversity among the P. aeruginosa isolates in our clinic. The presence of shared pulsotypes supports cross-transmission between patients.
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Affiliation(s)
- Dicle Sener Okur
- Istanbul University Cerrahpasa, Faculty of Medicine, Department of Pediatrics, Division of Pediatric Infectious Diseases, 34098 Kocamustafapasa, Istanbul, Turkey
| | - Caner Yuruyen
- Istanbul University Istanbul, Faculty of Medicine, Department of Microbiology and Clinical Microbiology, 34390 Capa, Istanbul, Turkey
| | - Ozge Gungor
- Istanbul University Istanbul, Faculty of Medicine, Department of Microbiology and Clinical Microbiology, 34390 Capa, Istanbul, Turkey
| | - Zerrin Aktas
- Istanbul University Istanbul, Faculty of Medicine, Department of Microbiology and Clinical Microbiology, 34390 Capa, Istanbul, Turkey
| | - Zayre Erturan
- Istanbul University Istanbul, Faculty of Medicine, Department of Microbiology and Clinical Microbiology, 34390 Capa, Istanbul, Turkey
| | - Necla Akcakaya
- Istanbul University Cerrahpasa, Faculty of Medicine, Department of Pediatrics, Division of Pediatric Infectious Diseases, Clinical Immunology and Allergy, 34098 Kocamustafapasa, Istanbul, Turkey
| | - Yildiz Camcioglu
- Istanbul University Cerrahpasa, Faculty of Medicine, Department of Pediatrics, Division of Pediatric Infectious Diseases, Clinical Immunology and Allergy, 34098 Kocamustafapasa, Istanbul, Turkey
| | - Haluk Cokugras
- Istanbul University Cerrahpasa, Faculty of Medicine, Department of Pediatrics, Division of Pediatric Infectious Diseases, Clinical Immunology and Allergy, 34098 Kocamustafapasa, Istanbul, Turkey
| | - Kaya Koksalan
- Istanbul University, Institute for Medical Experimental Research (DETAE), 34390 Capa, Istanbul, Turkey
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Epidemiology, Biology, and Impact of Clonal Pseudomonas aeruginosa Infections in Cystic Fibrosis. Clin Microbiol Rev 2018; 31:31/4/e00019-18. [PMID: 30158299 DOI: 10.1128/cmr.00019-18] [Citation(s) in RCA: 158] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Chronic lower airway infection with Pseudomonas aeruginosa is a major contributor to morbidity and mortality in individuals suffering from the genetic disease cystic fibrosis (CF). Whereas it was long presumed that each patient independently acquired unique strains of P. aeruginosa present in their living environment, multiple studies have since demonstrated that shared strains of P. aeruginosa exist among individuals with CF. Many of these shared strains, often referred to as clonal or epidemic strains, can be transmitted from one CF individual to another, potentially reaching epidemic status. Numerous epidemic P. aeruginosa strains have been described from different parts of the world and are often associated with an antibiotic-resistant phenotype. Importantly, infection with these strains often portends a worse prognosis than for infection with nonclonal strains, including an increased pulmonary exacerbation rate, exaggerated lung function decline, and progression to end-stage lung disease. This review describes the global epidemiology of clonal P. aeruginosa strains in CF and summarizes the current literature regarding the underlying biology and clinical impact of globally important CF clones. Mechanisms associated with patient-to-patient transmission are discussed, and best-evidence practices to prevent infections are highlighted. Preventing new infections with epidemic P. aeruginosa strains is of paramount importance in mitigating CF disease progression.
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Rutherford V, Yom K, Ozer EA, Pura O, Hughes A, Murphy KR, Cudzilo L, Mitchel D, Hauser AR. Environmental reservoirs for exoS+ and exoU+ strains of Pseudomonas aeruginosa. ENVIRONMENTAL MICROBIOLOGY REPORTS 2018; 10:485-492. [PMID: 29687624 PMCID: PMC6108916 DOI: 10.1111/1758-2229.12653] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 04/15/2018] [Indexed: 06/08/2023]
Abstract
Pseudomonas aeruginosa uses its type III secretion system to inject the effector proteins ExoS and ExoU into eukaryotic cells, which subverts these cells to the bacterium's advantage and contributes to severe infections. We studied the environmental reservoirs of exoS+ and exoU+ strains of P. aeruginosa by collecting water, soil, moist substrates and plant samples from environments in the Chicago region and neighbouring states. Whole-genome sequencing was used to determine the phylogeny and type III secretion system genotypes of 120 environmental isolates. No correlation existed between geographic separation of isolates and their genetic relatedness, which confirmed previous findings of both high genetic diversity within a single site and the widespread distribution of P. aeruginosa clonal complexes. After excluding clonal isolates cultured from the same samples, 74 exoS+ isolates and 16 exoU+ isolates remained. Of the exoS+ isolates, 41 (55%) were from natural environmental sites and 33 (45%) were from man-made sites. Of the exoU+ isolates, only 3 (19%) were from natural environmental sites and 13 (81%) were from man-made sites (p < 0.05). These findings suggest that man-made water systems may be a reservoir from which patients acquire exoU+ P. aeruginosa strains.
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Affiliation(s)
- Victoria Rutherford
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Kelly Yom
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Egon A. Ozer
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Olivia Pura
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Ami Hughes
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Katherine R. Murphy
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Laura Cudzilo
- Department of Biology, St. John’s University, Collegeville, Minnesota
| | - David Mitchel
- Department of Biology, St. John’s University, Collegeville, Minnesota
| | - Alan R. Hauser
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois
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Karami P, Mohajeri P, Yousefi Mashouf R, Karami M, Yaghoobi MH, Dastan D, Alikhani MY. Molecular characterization of clinical and environmental Pseudomonas aeruginosa isolated in a burn center. Saudi J Biol Sci 2018; 26:1731-1736. [PMID: 31762651 PMCID: PMC6864211 DOI: 10.1016/j.sjbs.2018.07.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 06/30/2018] [Accepted: 07/19/2018] [Indexed: 01/09/2023] Open
Abstract
In burn centers, Pseudomonas aeruginosa acts as a major cause of nosocomial infections. Therefore, this study aimed to characterize molecularly P. aeruginosa isolates collected from environmental samples and burn patients. A total of 78 strains (including 58 clinical and 20 environmental isolates) of the P. aeruginosa were collected from Beasat hospital of Hamadan, west of Iran, and was identified using API 20NE. The disk diffusion method according to the CLSI was applied for determination of the antimicrobial resistance. Moreover, the microtiter plate test was used for the quantification of Biofilm formation. The genomic features of the isolated strains was evaluated using Pulsed Field Gel Electrophoresis (PFGE). We found that 94.8% of clinical and 80% environmental isolates were capable of forming biofilm. The rate of MDR in clinical and environmental isolates was 51.7% and 40%, respectively. A significant relationship was observed between biofilm formation capability and multiple drug resistance (p < 0.05). PFGE typing showed 11 different clusters with two major clusters A with 30 (38.5%) and B with 14 (17.9%) members, containing up to 56.4% of all isolates. There was no relationship between biofilm formation ability and antibiotic resistance patterns with PFGE patterns. According to the results, the clonal spread of environmental P. aeruginosa isolates is associated with clinical isolates, and both environmental and clinical isolates are attributed to a high prevalence of the antibiotic resistance and biofilm formation ability. This study highlighted that the prevention programs should be implemented in the hospital environment to control the spread of P. aeruginosa in burn units.
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Affiliation(s)
- Pezhman Karami
- Department of Microbiology, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Parviz Mohajeri
- Department of Microbiology, Faculty of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Rasool Yousefi Mashouf
- Department of Microbiology, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Manoochehr Karami
- Department of Epidemiology, School of Public Health, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Mojtaba Hedayat Yaghoobi
- Department of Infectious Disease, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Dara Dastan
- Department of Pharmacognosy and Pharmaceutical Biotechnology, School of Pharmacy, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Mohammad Yousef Alikhani
- Department of Microbiology, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran.,Brucellosis Research Center, Hamadan University of Medical Sciences, Hamadan, Iran
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Tran-Dinh A, Neulier C, Amara M, Nebot N, Troché G, Breton N, Zuber B, Cavelot S, Pangon B, Bedos JP, Merrer J, Grimaldi D. Impact of intensive care unit relocation and role of tap water on an outbreak of Pseudomonas aeruginosa expressing OprD-mediated resistance to imipenem. J Hosp Infect 2018; 100:e105-e114. [PMID: 29857026 DOI: 10.1016/j.jhin.2018.05.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 05/23/2018] [Indexed: 02/07/2023]
Abstract
BACKGROUND To assess the impact of the incidental relocation of an intensive care unit (ICU) on the risk of colonizations/infections with Pseudomonas aeruginosa exhibiting OprD-mediated resistance to imipenem (PA-OprD). AIM The primary aim was to compare the proportion of PA-OprD among P. aeruginosa samples before and after an incidental relocation of the ICU. The role of tap water as a route of contamination for colonization/infection of patients with PA-OprD was assessed as a secondary aim. METHODS A single-centre, observational, before/after comparison study was conducted from October 2013 to October 2015. The ICU was relocated at the end of October 2014. All P. aeruginosa-positive samples isolated from patients hospitalized ≥48 h in the ICU were included. Tap water specimens were collected every three months in the ICU. PA-OprD strains isolated from patients and tap water were genotyped using pulse-field gel electrophoresis. FINDINGS A total of 139 clinical specimens of P. aeruginosa and 19 tap water samples were analysed. The proportion of PA-OprD strains decreased significantly from 31% to 7.7% after the relocation of the ICU (P = 0.004). All PA-OprD clinical specimens had a distinct genotype. Surprisingly, tap water was colonized with a single PA-OprD strain during both periods, but this single clone has never been isolated from clinical specimens. CONCLUSION Relocation of the ICU was associated with a marked decrease in P. aeruginosa strains resistant to imipenem. The polyclonal character of PA-OprD strains isolated from patients and the absence of tap-water-to-patient contamination highlight the complexity of the environmental impact on the endogenous colonization/infection with P. aeruginosa.
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Affiliation(s)
- A Tran-Dinh
- Service de réanimation, 78150, Centre Hospitalier De Versailles, Le Chesnay, France; Département d'anesthésie et de réanimation chirurgicale, 75018, Centre Hospitalier de Bichat, Paris, France.
| | - C Neulier
- Service de Prévention du Risque Infectieux, Centre Hospitalier de Versailles, Le Chesnay, France
| | - M Amara
- Service de Biologie, Unité de microbiologie, 78157, Centre Hospitalier De Versailles, Le Chesnay, France
| | - N Nebot
- Service de pharmacie, 78150, Centre Hospitalier De Versailles, Le Chesnay, France
| | - G Troché
- Service de réanimation, 78150, Centre Hospitalier De Versailles, Le Chesnay, France
| | - N Breton
- Service de Prévention du Risque Infectieux, Centre Hospitalier de Versailles, Le Chesnay, France
| | - B Zuber
- Service de réanimation, 78150, Centre Hospitalier De Versailles, Le Chesnay, France
| | - S Cavelot
- Service de réanimation, 78150, Centre Hospitalier De Versailles, Le Chesnay, France
| | - B Pangon
- Service de Biologie, Unité de microbiologie, 78157, Centre Hospitalier De Versailles, Le Chesnay, France
| | - J P Bedos
- Service de réanimation, 78150, Centre Hospitalier De Versailles, Le Chesnay, France
| | - J Merrer
- Service de Prévention du Risque Infectieux, Centre Hospitalier de Versailles, Le Chesnay, France
| | - D Grimaldi
- Département de réanimation, CUB-Erasme, Université Libre de Bruxelles (ULB), Bruxelles, Belgium
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Maroui I, Barguigua A, Aboulkacem A, Elhafa H, Ouarrak K, Sbiti M, Louzi L, Timinouni M, Belhaj A. Clonal Analysis of Clinical and Environmental Pseudomonas aeruginosa Isolates from Meknes Region, Morocco. Pol J Microbiol 2017; 66:397-400. [PMID: 29319518 DOI: 10.5604/01.3001.0010.4882] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
From 123 clinical and environmental Pseudomonas aeruginosa isolates, 24 strains were selected for their similar antibioresistance, virulence and biofilm formation profiles, to examine their diversity and occurrence of clones within two hospitals and different natural sites in Meknes (Morocco). Pulsed-field gel electrophoresis, using DraI enzyme, didn't reveal a close relationship between clinical and environmental isolates nor between strains of the two hospitals. 19 genotypes were obtained, including two virulent environmental clones and three clinical clones virulent and resistant to antibiotics. Intra-hospital transmission of high-risk clones detected, in and between wards, constitutes a great public health concern.
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Affiliation(s)
- Itto Maroui
- Ecology and Biodiversity of Wetlands Team, Department of Biology, Faculty of Sciences, Moulay Ismail University, Meknes, Morocco
| | - Abouddihaj Barguigua
- Molecular Bacteriology Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Asmae Aboulkacem
- Ecology and Biodiversity of Wetlands Team, Department of Biology, Faculty of Sciences, Moulay Ismail University, Meknes, Morocco
| | - Hanane Elhafa
- Ecology and Biodiversity of Wetlands Team, Department of Biology, Faculty of Sciences, Moulay Ismail University, Meknes, Morocco
| | - Khadija Ouarrak
- Medical Biology Laboratory of Regional Hospital Mohammed V Meknes, Morocco
| | - Mohammed Sbiti
- Medical Biology Laboratory of Regional Military Hospital Moulay Ismail Meknes, Morocco
| | - Lhoussain Louzi
- Medical Biology Laboratory of Regional Military Hospital Moulay Ismail Meknes, Morocco
| | - Mohammed Timinouni
- Molecular Bacteriology Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Abdelhaq Belhaj
- Ecology and Biodiversity of Wetlands Team, Department of Biology, Faculty of Sciences, Moulay Ismail University, Meknes, Morocco
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18
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Poulsen LL, Thøfner I, Bisgaard M, Christensen JP, Olsen RH, Christensen H. Longitudinal study of transmission of Escherichia coli from broiler breeders to broilers. Vet Microbiol 2017; 207:13-18. [PMID: 28757012 DOI: 10.1016/j.vetmic.2017.05.029] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 05/29/2017] [Accepted: 05/29/2017] [Indexed: 10/19/2022]
Abstract
Escherichia coli is of major importance in industrial broiler production as the main cause of salpingitis and peritonitis in broiler breeders. Furthermore E. coli is the most common cause of first week mortality in broiler chickens. The aim of the present study was to investigate the transmission of E. coli, isolated from broiler breeders with salpingitis, to the progeny and the possibility of subsequent first week mortality. Four parent flocks were followed during the whole production period (20-60 weeks) by post mortem and bacteriological examination of randomly selected dead birds. Newly hatched chickens from each flock were swabbed in the cloaca on four occasions (parent age 30, 40, 50, 60 weeks) and E. coli was isolated. Causes of first week mortality were determined pathologically and bacteriologically. E. coli isolates from parents, newly hatched chickens and first week mortality were selected for Pulsed-Field-Gel-Electrophoresis (PFGE) and Multi-Locus-Sequence-Typing (MLST) to determine their clonal relationships. E. coli was the main cause of both salpingitis in parents and first week mortality in broilers, and E. coli dominated the bacterial flora of the cloaca of newly hatched chickens. PFGE of E. coli showed identical band patterns in isolates from the three different sources indicating a transmission of E. coli from parent birds to chickens. In conclusion, E. coli isolated from salpingitis in broiler parents were found to be transmitted to broilers in which some sequence types contributed to the first week mortality.
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Affiliation(s)
- Louise Ladefoged Poulsen
- University of Copenhagen, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, Stigbøjlen 4, DK, 1870 Frederiksberg, Denmark.
| | - Ida Thøfner
- University of Copenhagen, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, Stigbøjlen 4, DK, 1870 Frederiksberg, Denmark
| | | | - Jens Peter Christensen
- University of Copenhagen, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, Stigbøjlen 4, DK, 1870 Frederiksberg, Denmark
| | - Rikke Heidemann Olsen
- University of Copenhagen, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, Stigbøjlen 4, DK, 1870 Frederiksberg, Denmark
| | - Henrik Christensen
- University of Copenhagen, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, Stigbøjlen 4, DK, 1870 Frederiksberg, Denmark
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20
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Detection and epidemiology of plasmid-mediated AmpC β-lactamase producing Escherichia coli in two Irish tertiary care hospitals. J Glob Antimicrob Resist 2016; 3:242-246. [PMID: 27842867 DOI: 10.1016/j.jgar.2015.06.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 05/01/2015] [Accepted: 06/10/2015] [Indexed: 11/24/2022] Open
Abstract
This study determined the prevalence and distribution of plasmid-mediated AmpC (pAmpC) β-lactamases in Irish Escherichia coli isolates. Clinical E. coli isolates (n=95) that were intermediate or resistant to cefoxitin and/or flagged by VITEK® 2 as potential AmpC-producers underwent confirmation using a MASTDISCS™ ESBL and AmpC Detection Kit. Multiplex PCR capable of detecting family-specific plasmid ampC genes was performed to detect the presence of these genes. Five PCR-negative isolates were selected for promoter analysis. PFGE and MLST were performed on E. coli isolates that harboured a plasmid ampC gene to determine their clonal relatedness. Plasmid ampC genes were detected in 19% (18/95) of phenotypic AmpC producing E. coli isolates. The CIT group was the most common plasmid family type (n=14); DHA (n=3) and ACC (n=1) groups were also detected. Promoter analysis showed that four isolates had multiple point mutations and one had a 1 bp insertion in the -10 box. PFGE demonstrated a polyclonal pattern for E. coli isolates. Furthermore, with the exception of two isolates with an identical sequence type (ST720), MLST analysis revealed that these isolates were not clonally related. This study revealed that there was a marked prevalence of pAmpC E. coli among phenotypic AmpC producing E. coli isolates but no evidence of cross-transmission of a single strain. Establishing the prevalence and clonality of these organisms is important in order to implement evidence-based infection control measures that reduce the spread of pAmpC β-lactamase resistance in the hospital environment.
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Johnson JK, Robinson GL, Zhao L, Harris AD, Stine OC, Thom KA. Comparison of molecular typing methods for the analyses of Acinetobacter baumannii from ICU patients. Diagn Microbiol Infect Dis 2016; 86:345-350. [PMID: 27640081 DOI: 10.1016/j.diagmicrobio.2016.08.024] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 08/18/2016] [Accepted: 08/24/2016] [Indexed: 01/23/2023]
Abstract
Acinetobacter baumannii has emerged as an important cause of healthcare-associated infections causing great morbidity and mortality. Despite its clinical importance, it is still unknown which molecular typing method is the best to determine or confirm institutional outbreaks as well as to identify epidemiologically related isolates from different geographical areas. To determine the most discriminatory molecular typing method, we isolated A. baumannii from perianal swabs collected from intensive care unit (ICU) patients in a cohort study during 2002 and 2008. Strains from each year were analyzed by pulsed-field gel electrophoresis (PFGE), multi-locus sequence typing (MLST), and multi-locus variable-number tandem repeat analysis (MLVA). Genetic relatedness of the isolates was consistent between PFGE and MLST as well as between analyses of loci containing MLVA and MLST. Our data show that PFGE and MLVA are similar when discriminating between isolates and are both good methods to use when questioning whether two isolates are indistinguishable.
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Affiliation(s)
- J Kristie Johnson
- Department of Pathology, University of Maryland School of Medicine Baltimore, MD; Epidemiology and Public Health, University of Maryland School of Medicine Baltimore, MD.
| | - Gwen L Robinson
- Department of Pathology, University of Maryland School of Medicine Baltimore, MD
| | - LiCheng Zhao
- Department of Pathology, University of Maryland School of Medicine Baltimore, MD
| | - Anthony D Harris
- Epidemiology and Public Health, University of Maryland School of Medicine Baltimore, MD
| | - O Colin Stine
- Epidemiology and Public Health, University of Maryland School of Medicine Baltimore, MD
| | - Kerri A Thom
- Epidemiology and Public Health, University of Maryland School of Medicine Baltimore, MD
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Morris DO, Davis MF, Palmeiro BS, O'Shea K, Rankin SC. Molecular and epidemiological characterization of caninePseudomonasotitis using a prospective case-control study design. Vet Dermatol 2016; 28:118-e25. [DOI: 10.1111/vde.12347] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/08/2016] [Indexed: 12/26/2022]
Affiliation(s)
- Daniel O. Morris
- Department of Clinical Studies - Philadelphia; School of Veterinary Medicine; University of Pennsylvania; 3900 Delancey Street Philadelphia PA 19104 USA
| | - Meghan F. Davis
- Department of Environmental Health Sciences; Johns Hopkins Bloomberg School of Public Health; 615 N. Wolfe Street Baltimore MD 21205 USA
| | - Brian S. Palmeiro
- Lehigh Valley Veterinary Dermatology; 4580 Crackersport Road Allentown PA 18104 USA
| | - Kathleen O'Shea
- Department of Pathobiology; School of Veterinary Medicine; University of Pennsylvania; 3900 Delancey Street Philadelphia PA 19104 USA
| | - Shelley C. Rankin
- Department of Pathobiology; School of Veterinary Medicine; University of Pennsylvania; 3900 Delancey Street Philadelphia PA 19104 USA
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Genotypic diversity of Lactobacillus sanfranciscensis strains isolated from French organic sourdoughs. Int J Food Microbiol 2016; 226:13-9. [DOI: 10.1016/j.ijfoodmicro.2016.03.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2015] [Revised: 03/02/2016] [Accepted: 03/11/2016] [Indexed: 11/20/2022]
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Nübling S, Schmidt H, Weiss A. Variation of the Pseudomonas community structure on oak leaf lettuce during storage detected by culture-dependent and -independent methods. Int J Food Microbiol 2016; 216:95-103. [PMID: 26425802 DOI: 10.1016/j.ijfoodmicro.2015.09.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Revised: 08/20/2015] [Accepted: 09/10/2015] [Indexed: 11/29/2022]
Abstract
The genus Pseudomonas plays an important role in the lettuce leaf microbiota and certain species can induce spoilage. The aim of this study was to investigate the occurrence and diversity of Pseudomonas spp. on oak leaf lettuce and to follow their community shift during a six day cold storage with culture-dependent and culture-independent methods. In total, 21 analysed partial Pseudomonas 16S rRNA gene sequences matched closely (> 98.3%) to the different reference strain sequences, which were distributed among 13 different phylogenetic groups or subgroups within the genus Pseudomonas. It could be shown that all detected Pseudomonas species belonged to the P. fluorescens lineage. In the culture-dependent analysis, 73% of the isolates at day 0 and 79% of the isolates at day 6 belonged to the P. fluorescens subgroup. The second most frequent group, with 12% of the isolates, was the P. koreensis subgroup. This subgroup was only detected at day 0. In the culture-independent analysis the P. fluorescens subgroup and P. extremaustralis could not be differentiated by RFLP. Both groups were most abundant and amounted to approximately 46% at day 0 and 79% at day 6. The phytopathogenic species P. salmonii, P. viridiflava and P. marginalis increased during storage. Both approaches identified the P. fluorescens group as the main phylogenetic group. The results of the present study suggest that pseudomonads found by plating methods indeed represent the most abundant part of the Pseudomonas community on oak leaf lettuce.
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Affiliation(s)
- Simone Nübling
- Department of Food Microbiology and Hygiene, Institute of Food Science and Biotechnology, University of Hohenheim, Garbenstrasse 28, 70599 Stuttgart, Germany.
| | - Herbert Schmidt
- Department of Food Microbiology and Hygiene, Institute of Food Science and Biotechnology, University of Hohenheim, Garbenstrasse 28, 70599 Stuttgart, Germany.
| | - Agnes Weiss
- Department of Food Microbiology and Hygiene, Institute of Food Science and Biotechnology, University of Hohenheim, Garbenstrasse 28, 70599 Stuttgart, Germany.
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Ahn S, Sung JY, Kim H, Kim MS, Hwang Y, Jong S, Seo Y, Ha E, Park ES, Choi JY, Yong D, Lee K. Molecular Epidemiology and Characterization of Carbapenemase-ProducingEnterobacteriaceaeIsolated at a University Hospital in Korea during 4-Year Period. ANNALS OF CLINICAL MICROBIOLOGY 2016. [DOI: 10.5145/acm.2016.19.2.39] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- Sunyoung Ahn
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance,Yonsei University College of Medicine, Seoul, Korea
| | - Ji Yeon Sung
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance,Yonsei University College of Medicine, Seoul, Korea
| | - Hyunsoo Kim
- Department of Laboratory Medicine, National Police Hospital, Seoul, Korea
| | - Myung Sook Kim
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance,Yonsei University College of Medicine, Seoul, Korea
| | - Younjee Hwang
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University, Seoul, Korea
| | - Sori Jong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance,Yonsei University College of Medicine, Seoul, Korea
| | - Younghee Seo
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance,Yonsei University College of Medicine, Seoul, Korea
| | - Eunjin Ha
- Department of Infection Control, Severance Hospital, Seoul, Korea
| | - Eun Suk Park
- Department of Infection Control, Severance Hospital, Seoul, Korea
| | - Jun Yong Choi
- Department of Infection Control, Severance Hospital, Seoul, Korea
- Division of Infectious Diseases,Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Dongeun Yong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance,Yonsei University College of Medicine, Seoul, Korea
- Department of Infection Control, Severance Hospital, Seoul, Korea
| | - Kyungwon Lee
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance,Yonsei University College of Medicine, Seoul, Korea
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Next-Generation Sequencing and Comparative Analysis of Sequential Outbreaks Caused by Multidrug-Resistant Acinetobacter baumannii at a Large Academic Burn Center. Antimicrob Agents Chemother 2015; 60:1249-57. [PMID: 26643351 DOI: 10.1128/aac.02014-15] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 12/01/2015] [Indexed: 12/19/2022] Open
Abstract
Next-generation sequencing (NGS) analysis has emerged as a promising molecular epidemiological method for investigating health care-associated outbreaks. Here, we used NGS to investigate a 3-year outbreak of multidrug-resistant Acinetobacter baumannii (MDRAB) at a large academic burn center. A reference genome from the index case was generated using de novo assembly of PacBio reads. Forty-six MDRAB isolates were analyzed by pulsed-field gel electrophoresis (PFGE) and sequenced using an Illumina platform. After mapping to the index case reference genome, four samples were excluded due to low coverage, leaving 42 samples for further analysis. Multilocus sequence types (MLST) and the presence of acquired resistance genes were also determined from the sequencing data. A transmission network was inferred from genomic and epidemiological data using a Bayesian framework. Based on single-nucleotide variant (SNV) differences, this MDRAB outbreak represented three sequential outbreaks caused by distinct clones. The first and second outbreaks were caused by sequence type 2 (ST2), while the third outbreak was caused by ST79. For the second outbreak, the MLST and PFGE results were discordant. However, NGS-based SNV typing detected a recombination event and consequently enabled a more accurate phylogenetic analysis. The distribution of resistance genes varied among the three outbreaks. The first- and second-outbreak strains possessed a blaOXA-23-like group, while the third-outbreak strains harbored a blaOXA-40-like group. NGS-based analysis demonstrated the superior resolution of outbreak transmission networks for MDRAB and provided insight into the mechanisms of strain diversification between sequential outbreaks through recombination.
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Vaez H, Faghri J, Nasr Esfahani B, Moghim S, Fazeli H, Sedighi M, Ghasemian Safaei H. Antibiotic Resistance Patterns and Genetic Diversity in Clinical Isolates of Pseudomonas aeruginosa Isolated From Patients of a Referral Hospital, Isfahan, Iran. Jundishapur J Microbiol 2015; 8:e20130. [PMID: 26468363 PMCID: PMC4600933 DOI: 10.5812/jjm.20130v2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2014] [Revised: 07/30/2014] [Accepted: 09/16/2014] [Indexed: 12/04/2022] Open
Abstract
Background: Pseudomonas aeruginosa is a well-known opportunistic pathogen, which affects hospitalized patients in different wards due to its natural resistance to drugs. Objectives: The purpose of the current study was to determine the antibiotic susceptibility profiles and genetic relatedness in P. aeruginosa isolated from patients admitted to a referral hospital in Isfahan, Iran. Materials and Methods: Out of 150 analyzed samples, 54 P. aeruginosa isolates were recovered and were subjected to antibiotic resistance patterns and genetic diversity determination by Kirby-Bauer’s disk diffusion method and RAPD-PCR, respectively. Results: The highest percentage of resistance was observed against ceftazidime and imipenem with 30 (55.6%) isolates; meanwhile all isolates were sensitive to polymyxin B. Twenty-eight (51.8%) isolates revealed resistance to all applied antibiotics. RAPD-PCR (Random Amplified Polymorphic DNA- Polymerase Chain Reaction) results showed 54 unique genotypes, which were divided into 39 clusters. Conclusions: Although different source of P. aeruginosa may involve in patient colonization, genetically related strains were isolated from different wards and or the same ward of the hospital. Our results pointed to the restriction of currently used antibiotics in studied hospital. We hope that our results cast light on the control and transmission of the infection in the investigated hospital.
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Affiliation(s)
- Hamid Vaez
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, IR Iran
| | - Jamshid Faghri
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, IR Iran
| | - Bahram Nasr Esfahani
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, IR Iran
| | - Sharareh Moghim
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, IR Iran
| | - Hossein Fazeli
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, IR Iran
| | - Mansour Sedighi
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, IR Iran
| | - Hajieh Ghasemian Safaei
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, IR Iran
- Corresponding author: Hajieh Ghasemian Safaei, Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, IR Iran. Tel: +98-3117922469, Fax: +98-3116688597, E-mail:
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Janßen T, Voss M, Kühl M, Semmler T, Philipp HC, Ewers C. A combinational approach of multilocus sequence typing and other molecular typing methods in unravelling the epidemiology of Erysipelothrix rhusiopathiae strains from poultry and mammals. Vet Res 2015. [PMID: 26198736 PMCID: PMC4509749 DOI: 10.1186/s13567-015-0216-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Erysipelothrix rhusiopathiae infections re-emerged as a matter of great concern particularly in the poultry industry. In contrast to porcine isolates, molecular epidemiological traits of avian E. rhusiopathiae isolates are less well known. Thus, we aimed to (i) develop a multilocus sequence typing (MLST) scheme for E. rhusiopathiae, (ii) study the congruence of strain grouping based on pulsed-field gel electrophoresis (PFGE) and MLST, (iii) determine the diversity of the dominant immunogenic protein SpaA, and (iv) examine the distribution of genes putatively linked with virulence among field isolates from poultry (120), swine (24) and other hosts (21), including humans (3). Using seven housekeeping genes for MLST analysis we determined 72 sequence types (STs) among 165 isolates. This indicated an overall high diversity, though 34.5% of all isolates belonged to a single predominant ST-complex, STC9, which grouped strains from birds and mammals, including humans, together. PFGE revealed 58 different clusters and congruence with the sequence-based MLST-method was not common. Based on polymorphisms in the N-terminal hyper-variable region of SpaA the isolates were classified into five groups, which followed the phylogenetic background of the strains. More than 90% of the isolates harboured all 16 putative virulence genes tested and only intI, encoding an internalin-like protein, showed infrequent distribution. MLST data determined E. rhusiopathiae as weakly clonal species with limited host specificity. A common evolutionary origin of isolates as well as shared SpaA variants and virulence genotypes obtained from avian and mammalian hosts indicates common reservoirs, pathogenic pathways and immunogenic properties of the pathogen.
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Affiliation(s)
- Traute Janßen
- Center for Infection Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, Robert-von-Ostertag-Straße 7-13, 14163, Berlin, Germany. .,RIPAC-LABOR GmbH, Am Mühlenberg 11, 14476, Potsdam, Germany.
| | | | - Michael Kühl
- Center for Infection Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, Robert-von-Ostertag-Straße 7-13, 14163, Berlin, Germany. .,Institute of Animal Hygiene and Environmental Health, Freie Universität Berlin, Robert-von-Ostertag-Straße 7-13, 14163, Berlin, Germany.
| | | | - Hans-Christian Philipp
- Boehringer Ingelheim Veterinary Research Center GmbH & Co. KG, Bemeroder Straße 31, 30559, Hannover, Germany.
| | - Christa Ewers
- Institute of Hygiene and Infectious Diseases of Animals, Justus-Liebig-Universität Giessen, Frankfurter Str. 85-89, 35392, Giessen, Germany.
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Calvez S, Fournel C, Douet DG, Daniel P. Pulsed-field gel electrophoresis and multi locus sequence typing for characterizing genotype variability of Yersinia ruckeri isolated from farmed fish in France. Vet Res 2015; 46:73. [PMID: 26104532 PMCID: PMC4477544 DOI: 10.1186/s13567-015-0200-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Accepted: 05/05/2015] [Indexed: 12/11/2022] Open
Abstract
Yersinia ruckeri is a pathogen that has an impact on aquaculture worldwide. The disease caused by this bacterial species, yersiniosis or redmouth disease, generates substantial economic losses due to the associated mortality and veterinary costs. For predicting outbreaks and improving control strategies, it is important to characterize the population structure of the bacteria. The phenotypic and genetic homogeneities described previously indicate a clonal population structure as observed in other fish bacteria. In this study, the pulsed-field gel electrophoresis (PFGE) and multi locus sequence typing (MLST) methods were used to describe a population of isolates from outbreaks on French fish farms. For the PFGE analysis, two enzymes (NotI and AscI) were used separately and together. Results from combining the enzymes showed the great homogeneity of the outbreak population with a similarity > 80.0% but a high variability within the cluster (cut-off value = 80.0%) with a total of 43 pulsotypes described and an index of diversity = 0.93. The dominant pulsotypes described with NotI (PtN4 and PtN7) have already been described in other European countries (Finland, Germany, Denmark, Spain and Italy). The MLST approach showed two dominant sequence types (ST31 and ST36), an epidemic structure of the French Y. ruckeri population and a preferentially clonal evolution for rainbow trout isolates. Our results point to multiple types of selection pressure on the Y. ruckeri population attributable to geographical origin, ecological niche specialization and movements of farmed fish.
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Affiliation(s)
- Ségolène Calvez
- LUNAM Université, Oniris, École nationale vétérinaire, agroalimentaire et de l'alimentation Nantes-Atlantique, UMR1300 Biologie, Épidémiologie et Analyse de Risque en santé animale, F-44307, Nantes, France.
- INRA, UMR1300 BioEpAR, F-44307, Nantes, France.
| | - Catherine Fournel
- LUNAM Université, Oniris, École nationale vétérinaire, agroalimentaire et de l'alimentation Nantes-Atlantique, UMR1300 Biologie, Épidémiologie et Analyse de Risque en santé animale, F-44307, Nantes, France.
- INRA, UMR1300 BioEpAR, F-44307, Nantes, France.
| | - Diane-Gaëlle Douet
- GDSAA, Groupe de Défense Sanitaire Aquacole Aquitain, F-40000, Mont de Marsan, France.
| | - Patrick Daniel
- Laboratoire des Pyrénées et des Landes, F-40000, Mont de Marsan, France.
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Application of whole-genome sequencing for bacterial strain typing in molecular epidemiology. J Clin Microbiol 2015; 53:1072-9. [PMID: 25631811 DOI: 10.1128/jcm.03385-14] [Citation(s) in RCA: 203] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Nosocomial infections pose a significant threat to patient health; however, the gold standard laboratory method for determining bacterial relatedness (pulsed-field gel electrophoresis [PFGE]) remains essentially unchanged 20 years after its introduction. Here, we explored bacterial whole-genome sequencing (WGS) as an alternative approach for molecular strain typing. We compared WGS to PFGE for investigating presumptive outbreaks involving three important pathogens: vancomycin-resistant Enterococcus faecium (n=19), methicillin-resistant Staphylococcus aureus (n=17), and Acinetobacter baumannii (n=15). WGS was highly reproducible (average≤0.39 differences between technical replicates), which enabled a functional, quantitative definition for determining clonality. Strain relatedness data determined by PFGE and WGS roughly correlated, but the resolution of WGS was superior (P=5.6×10(-8) to 0.016). Several discordant results were noted between the methods. A total of 28.9% of isolates which were indistinguishable by PFGE were nonclonal by WGS. For A. baumannii, a species known to undergo rapid horizontal gene transfer, 16.2% of isolate pairs considered nonidentical by PFGE were clonal by WGS. Sequencing whole bacterial genomes with single-nucleotide resolution demonstrates that PFGE is prone to false-positive and false-negative results and suggests the need for a new gold standard approach for molecular epidemiological strain typing.
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AbdulWahab A, Taj-Aldeen SJ, Ibrahim E, Abdulla SH, Muhammed R, Ahmed I, Abdeen Y, Sadek O, Abu-Madi M. Genetic relatedness and host specificity of Pseudomonas aeruginosa isolates from cystic fibrosis and non-cystic fibrosis patients. Infect Drug Resist 2014; 7:309-16. [PMID: 25429232 PMCID: PMC4242404 DOI: 10.2147/idr.s72112] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Pseudomonas aeruginosa is one of the primary pathogens isolated more frequently in cystic fibrosis (CF) and it exhibits innate resistance to a wide range of antibiotics. PURPOSE We sought to determine whether the highly prevalent genotypes of P. aeruginosa are specifically linked to CF patients and have any related multidrug antibiotic resistance. Isolates from hospitalized non-CF patients and from environmental sources were also genotypically analyzed. METHODS Collections of P. aeruginosa from lower respiratory secretions (n=45) were genotyped using pulsed-field gel electrophoresis (PFGE). Phenotypic screening for antibiotic susceptibility was performed for the common antimicrobial agents by E-test and automated Phoenix method. RESULTS P. aeruginosa isolates from CF (n=32), hospitalized non-CF patients (n=13), and environment sources (n=5) were analyzed. The population structure of P. aeruginosa is highly diverse and population-specific. All PFGE results of P. aeruginosa isolates fall among four major clusters. Cluster 1 contained 16 P. aeruginosa isolates from CF patients and two from environmental sources; cluster 2 contained 11 P. aeruginosa isolates from CF and one each from non-CF and environmental sources; cluster 3 contained 12 P. aeruginosa isolates from hospitalized non-CF patients and two P. aeruginosa isolates from one CF patient and one environmental source; and cluster 4 consisted of three isolates from CF patients and one from the environment. The majority of multidrug-resistant P. aeruginosa isolates were in clusters 3 and 4. P. aeruginosa isolates from CF patients were resistant to ciprofloxacin (34.4%) followed by resistance to amikacin and gentamicin (each 28%), whereas the majority of isolates from non-CF patients were resistant to meropenem (69%) and were grouped in cluster 3. CONCLUSION PFGE of P. aeruginosa isolates from CF patients shows a high degree of similarity, suggesting specific adaptation of these clones to CF-affected lungs. The hospitalized non-CF cluster has a different clonal origin, indicating specific clustering in a specific location, suggesting hospital-acquired P. aeruginosa infections.
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Affiliation(s)
- Atqah AbdulWahab
- Department of Pediatrics, Hamad Medical Corporation, Qatar University, Doha, Qatar
| | - Saad J Taj-Aldeen
- Microbiology Division, Department of Laboratory Medicine and Pathology, Hamad Medical Corporation, Qatar University, Doha, Qatar
| | - Emad Ibrahim
- Microbiology Division, Department of Laboratory Medicine and Pathology, Hamad Medical Corporation, Qatar University, Doha, Qatar
| | - Shaikha H Abdulla
- Molecular Biology Unit, Central Food Laboratories, Supreme Council of Health, Qatar University, Doha, Qatar
| | - Ramees Muhammed
- Molecular Biology Unit, Central Food Laboratories, Supreme Council of Health, Qatar University, Doha, Qatar
| | - Irshad Ahmed
- Molecular Biology Unit, Central Food Laboratories, Supreme Council of Health, Qatar University, Doha, Qatar
| | - Yasmine Abdeen
- Department of Health Sciences, College of Arts and Sciences, Qatar University, Doha, Qatar
| | - Omnia Sadek
- Department of Health Sciences, College of Arts and Sciences, Qatar University, Doha, Qatar
| | - Marawan Abu-Madi
- Department of Health Sciences, College of Arts and Sciences, Qatar University, Doha, Qatar
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Selim S, El Kholy I, Hagagy N, El Alfay S, Aziz MA. Rapid identification of Pseudomonas aeruginosa by pulsed-field gel electrophoresis. BIOTECHNOL BIOTEC EQ 2014; 29:152-156. [PMID: 26019629 PMCID: PMC4433924 DOI: 10.1080/13102818.2014.981065] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2014] [Accepted: 05/07/2014] [Indexed: 11/28/2022] Open
Abstract
Twenty clinical Pseudomonas aeruginosa isolates recovered from patients admitted to The General Hospital in Ismailia Governorate (Egypt) were examined in this study. We analysed P. aeruginosa ATCC 9027 (as a control strain) and 19 of the isolates after digestion with SpeI restriction endonuclease. After this we conducted a pulsed-field gel electrophoresis (PFGE) and typed the obtained 10 unique patterns, designated as A, A1, B, B1, C, C1, D, D1, E and F. We evaluated the genetic relatedness between all strains, based on ≥87% band identity. As a result, the isolates were grouped in the 10 clusters as follows: patterns A, A1, B, B1, C contained two strains each and patterns C1, D, D1, E contained a single strain each; the five remaining strains were closely related (genomic pattern F). One isolate belonged to antibiotype ‘b’. The genotype patterns of the P. aeruginosa ATCC 9027 control strain and isolate no. 11 were closely related and had two different antibiotypes ‘d’ and ‘c’, respectively.
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Affiliation(s)
- Samy Selim
- Department of Clinical Laboratory Sciences, College of Applied Medical Science, Aljouf University , Sakaka , Saudi Arabia ; Department of Botany, Faculty of Science, Suez Canal University , Ismailia , Egypt
| | - Iman El Kholy
- Clinical Pathology Department, Ain Shams University Specialized Hospital, Ain Shams University , Cairo , Egypt
| | - Nashwa Hagagy
- Department of Botany, Faculty of Science, Suez Canal University , Ismailia , Egypt
| | - Sahar El Alfay
- Department of Botany, Faculty of Science, Suez Canal University , Ismailia , Egypt
| | - Mohamed Abdel Aziz
- Department of Botany, Faculty of Science, Suez Canal University , Ismailia , Egypt
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Multilocus sequence typing scheme versus pulsed-field gel electrophoresis for typing Mycobacterium abscessus isolates. J Clin Microbiol 2014; 52:2881-91. [PMID: 24899019 DOI: 10.1128/jcm.00688-14] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Outbreaks of infections by rapidly growing mycobacteria following invasive procedures, such as ophthalmological, laparoscopic, arthroscopic, plastic, and cardiac surgeries, mesotherapy, and vaccination, have been detected in Brazil since 1998. Members of the Mycobacterium chelonae-Mycobacterium abscessus group have caused most of these outbreaks. As part of an epidemiological investigation, the isolates were typed by pulsed-field gel electrophoresis (PFGE). In this project, we performed a large-scale comparison of PFGE profiles with the results of a recently developed multilocus sequence typing (MLST) scheme for M. abscessus. Ninety-three isolates were analyzed, with 40 M. abscessus subsp. abscessus isolates, 47 M. abscessus subsp. bolletii isolates, and six isolates with no assigned subspecies. Forty-five isolates were obtained during five outbreaks, and 48 were sporadic isolates that were not associated with outbreaks. For MLST, seven housekeeping genes (argH, cya, glpK, gnd, murC, pta, and purH) were sequenced, and each isolate was assigned a sequence type (ST) from the combination of obtained alleles. The PFGE patterns of DraI-digested DNA were compared with the MLST results. All isolates were analyzable by both methods. Isolates from monoclonal outbreaks showed unique STs and indistinguishable or very similar PFGE patterns. Thirty-three STs and 49 unique PFGE patterns were identified among the 93 isolates. The Simpson's index of diversity values for MLST and PFGE were 0.69 and 0.93, respectively, for M. abscessus subsp. abscessus and 0.96 and 0.97, respectively, for M. abscessus subsp. bolletii. In conclusion, the MLST scheme showed 100% typeability and grouped monoclonal outbreak isolates in agreement with PFGE, but it was less discriminative than PFGE for M. abscessus.
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González-Arenzana L, Santamaría P, López R, López-Alfaro I. Oenococcus oeni strain typification by combination of Multilocus Sequence Typing and Pulsed Field Gel Electrophoresis analysis. Food Microbiol 2014; 38:295-302. [DOI: 10.1016/j.fm.2013.07.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Revised: 07/26/2013] [Accepted: 07/30/2013] [Indexed: 10/26/2022]
Affiliation(s)
- Lucía González-Arenzana
- ICVV, Instituto de Ciencias de la Vid y del Vino (Gobierno de La Rioja, Universidad de La Rioja and CSIC), C/Madre de Dios 51, 26006 Logroño, La Rioja, Spain
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Qi J, Li L, Du Y, Wang S, Wang J, Luo Y, Che J, Lu J, Liu H, Hu G, Li J, Gong Y, Wang G, Hu M, Shiganyan, Liu Y. The identification, typing, and antimicrobial susceptibility of Pseudomonas aeruginosa isolated from mink with hemorrhagic pneumonia. Vet Microbiol 2014; 170:456-61. [PMID: 24629901 DOI: 10.1016/j.vetmic.2014.02.025] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Revised: 02/10/2014] [Accepted: 02/13/2014] [Indexed: 10/25/2022]
Abstract
The biological characteristics and molecular epidemiology of Pseudomonas aeruginosa associated with mink hemorrhagic pneumonia from Shandong province of eastern China were determined in this study. From 2010 to 2011, 30 mink P. aeruginosa isolates were identified from lung, fecal and feed samples of clinical cases and subjected to serotyping, antimicrobial susceptibility testing and pulsed-field gel electrophoresis (PFGE) using SpeI. The P. aeruginosa isolates belonged to four serotypes-21 of type G, four of type I, three of type M, one of type B, and one non-typable strain. The strains were divided into four large groups as determined by PFGE. Isolates from the group 2 were highly homologous and were obtained from the same region as an epidemic. All of the isolates were sensitive to piperacillin, piperacillin/tazobactam, ceftazidime, cefepime, imipenem, amikacin, gentamicin and tobramycin and resistant to ampicillin, cefuroxime and cefuroxime axetil. A high frequency of resistance was found to ampicillin/sulbactam, cefazolin, cefotetan, ceftriaxone, nitrofurantoin, and trimethoprim/sulfamethoxazole (96.7%). Resistance to ticarcillin/clavulanic acid, ciprofloxacin and levofloxacin was less common (13.3%). There was no relationship between antibiotic resistance and serotype distribution of the isolates. The epidemic serotype of P. aeruginosa from the mink hemorrhagic pneumonia in Shandong province was type G, which was a clone of commonly found in this province. These findings reveal the genetic similarities and antimicrobial susceptibility profiles of P. aeruginosa from clinical cases of mink hemorrhagic pneumonia and will facilitate the prevention and control of the disease in Shandong province of China.
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Affiliation(s)
- Jing Qi
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China; College of Life Sciences, Shandong University, Jinan 250100, China
| | - Lulu Li
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Yijun Du
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China; College of Life Sciences, Shandong University, Jinan 250100, China
| | - Shourong Wang
- College of Agricultural Sciences, Liaocheng University, Liaocheng 252059, China
| | - Jinwen Wang
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China; College of Life Sciences, Shandong University, Jinan 250100, China
| | - Yanbo Luo
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Jie Che
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Jinxing Lu
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Hui Liu
- Jinan Municipal Center for Disease Control & Prevention, Jinan 250021, China
| | - Guangchun Hu
- Jinan Municipal Center for Disease Control & Prevention, Jinan 250021, China
| | - Jixia Li
- Jinan Military General Hospital, Jinan 250031, China
| | - Yanwen Gong
- Jinan Military General Hospital, Jinan 250031, China
| | - Guisheng Wang
- College of Life Sciences, Shandong University, Jinan 250100, China; Shandong Provincial Center for Animal Disease Control and Prevention, Jinan 250022, China
| | - Ming Hu
- College of Life Sciences, Shandong University, Jinan 250100, China
| | - Shiganyan
- College of Life Sciences, Shandong University, Jinan 250100, China
| | - Yuqing Liu
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China; College of Life Sciences, Shandong University, Jinan 250100, China.
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Abstract
Genotyping allows for the identification of bacterial isolates to the strain level and provides basic information about the evolutionary biology, population biology, taxonomy, ecology, and genetics of bacteria. Depending on the underlying question and available resources, Pseudomonas aeruginosa strains may be typed by anonymous fingerprinting techniques or electronically portable sequence-based typing methods such as multiple locus variable number tandem repeat (VNTR) analysis (MLVA), multilocus sequence typing, or oligonucleotide microarray. Macrorestriction fragment pattern analysis is a genotyping method that is globally applicable to all bacteria and hence has been and still is the reference method for strain typing in bacteriology. Agarose-embedded chromosomal DNA is cleaved with a rare-cutting restriction endonuclease and the generated 20-70 fragments are then separated by pulsed-field gel electrophoresis. The chapter provides a detailed step-by-step manual for SpeI genome fingerprinting of Pseudomonas chromosomes that has been optimized for SpeI fragment pattern analysis of P. aeruginosa.
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Affiliation(s)
- Burkhard Tümmler
- Clinical Research Group, Clinic for Pediatric Pneumology, Allergology and Neonatology, Hanover Medical School, Hanover, Germany,
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Two copies of bla NDM-1 gene are present in NDM-1 producing Pseudomonas aeruginosa isolates from Serbia. Antonie van Leeuwenhoek 2013; 105:613-8. [DOI: 10.1007/s10482-013-0094-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 12/07/2013] [Indexed: 10/25/2022]
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Maâtallah M, Bakhrouf A, Habeeb MA, Turlej-Rogacka A, Iversen A, Pourcel C, Sioud O, Giske CG. Four genotyping schemes for phylogenetic analysis of Pseudomonas aeruginosa: comparison of their congruence with multi-locus sequence typing. PLoS One 2013; 8:e82069. [PMID: 24349186 PMCID: PMC3859543 DOI: 10.1371/journal.pone.0082069] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 10/21/2013] [Indexed: 11/28/2022] Open
Abstract
Several molecular typing schemes have been proposed to differentiate among isolates and clonal groups, and hence establish epidemiological or phylogenetic links. It has been widely accepted that multi-locus sequence typing (MLST) is the gold standard for phylogenetic typing/long-term epidemiological surveillance, but other recently described methods may be easier to carry out, especially in settings with limited access to DNA sequencing. Comparing the performance of such techniques to MLST is therefore of relevance. A study was therefore carried out with a collection of P. aeruginosa strains (n = 133) typed by four typing schemes: MLST, multiple-locus variable number tandem repeat analysis (MLVA), pulsed-field gel electrophoresis (PFGE) and the commercial DiversiLab microbial typing system (DL). The aim of this study was to compare the results of each typing method with MLST. The Simpson's indices of diversity were 0.989, 0.980, 0.961 and 0.906 respectively for PFGE, MLVA, DL and MLST. The congruence between techniques was measured by the adjusted Wallace index (W): this coefficient indicates the probability that a pair of isolates which is assigned to the same type by one typing method is also typed as identical by the other. In this context, the congruence between techniques was recorded as follow: MLVA-type to predict MLST-type (93%), PFGE to MLST (92%), DL to MLST (64.2%), PFGE to MLVA (63.5%) and PFGE to DL (61.7%). Conversely, for all above combinations, prediction was very poor. The congruence was increased at the clonal complex (CC) level. MLST is regarded the gold standard for phylogenetic classification of bacteria, but is rather laborious to carry out in many settings. Our data suggest that MLVA can predict the MLST-type with high accuracy, and even higher when studying the clonal complex level. Of the studied three techniques MLVA was therefore the best surrogate method to predict MLST.
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Affiliation(s)
- Makaoui Maâtallah
- Laboratoire d'Analyse, Traitement et Valorisation des Polluants de l'Environnement et des Produits, Faculté de Pharmacie, Monastir, Tunisia
| | - Amina Bakhrouf
- Laboratoire d'Analyse, Traitement et Valorisation des Polluants de l'Environnement et des Produits, Faculté de Pharmacie, Monastir, Tunisia
| | - Muhammed Asif Habeeb
- Clinical Microbiology L2:02, MTC – Karolinska Institutet, Karolinska University Hospital Solna, Stockholm, Sweden
| | - Agata Turlej-Rogacka
- Clinical Microbiology L2:02, MTC – Karolinska Institutet, Karolinska University Hospital Solna, Stockholm, Sweden
| | - Aina Iversen
- Clinical Microbiology L2:02, MTC – Karolinska Institutet, Karolinska University Hospital Solna, Stockholm, Sweden
| | - Christine Pourcel
- Univ Paris-Sud, Institut de Génétique et Microbiologie, Orsay, France
- CNRS, Orsay, France
| | - Olfa Sioud
- Laboratoire de Microbiologie CHU Fattouma Bourguiba, Monastir, Tunisia
| | - Christian G. Giske
- Clinical Microbiology L2:02, MTC – Karolinska Institutet, Karolinska University Hospital Solna, Stockholm, Sweden
- * E-mail:
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39
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Sefraoui I, Berrazeg M, Drissi M, Rolain JM. Molecular epidemiology of carbapenem-resistant Pseudomonas aeruginosa clinical strains isolated from western Algeria between 2009 and 2012. Microb Drug Resist 2013; 20:156-61. [PMID: 24320688 DOI: 10.1089/mdr.2013.0161] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Infections caused by carbapenem-resistant Pseudomonas aeruginosa strains represent a major therapeutic and epidemiological problem. The aim of this study was to characterize carbapenem resistance in 89 clinical strains of P. aeruginosa isolated from three hospitals in western Algeria between October 2009 and November 2012. Minimum inhibitory concentrations (MICs) of imipenem were determined by the Etest method. Screening for metallo-β-lactamase (MβL) was performed using Etest MβL strips, and a PCR was conducted to detect carbapenemase-encoding genes. The amplification of the oprD gene followed by a sequencing reaction was performed for all strains resistant to imipenem. The clonality of 53 P. aeruginosa strains was demonstrated using multilocus sequence typing (MLST). Among the 89 isolates, 35 (39.33%) were found to be resistant to IMP (MICs ≥16 μg/ml). The blaVIM-2 gene was detected in two strains. The remaining imipenem-resistant isolates showed the presence of oprD mutations. The MLST analysis differentiated strains into various clones and the strains from the same clone had an identical sequence of the oprD gene. We report the second detection in 2010 of blaVIM-2 in Algerian P. aeruginosa strains. We also found that oprD mutations were the major determinant of high-level imipenem resistance. We demonstrate that these oprD mutations can be used as a tool to study the clonality in P. aeruginosa isolates.
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Affiliation(s)
- Imane Sefraoui
- 1 Aix-Marseille Université , Unité de Recherche en Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63, CNRS 7278, IRD 198, Inserm 1095, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Marseille, France
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40
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Diversity among strains of Pseudomonas aeruginosa from manure and soil, evaluated by multiple locus variable number tandem repeat analysis and antibiotic resistance profiles. Res Microbiol 2013; 165:2-13. [PMID: 24140790 DOI: 10.1016/j.resmic.2013.10.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 09/03/2013] [Indexed: 01/08/2023]
Abstract
The results of a multiple locus variable number of tandem repeat (VNTR) analysis (MLVA)-based study designed to understand the genetic diversity of soil and manure-borne Pseudomonas aeruginosa isolates, and the relationship between these isolates and a set of clinical and environmental isolates, are hereby reported. Fifteen described VNTR markers were first selected, and 62 isolates recovered from agricultural and industrial soils in France and Burkina Faso, and from cattle and horse manure, along with 26 snake-related isolates and 17 environmental and clinical isolates from international collections, were genotyped. Following a comparison with previously published 9-marker MLVA schemes, an optimal 13-marker MLVA scheme (MLVA13-Lyon) was identified that was found to be the most efficient, as it showed high typability (90%) and high discriminatory power (0.987). A comparison of MLVA with PFGE for typing of the snake-related isolates confirmed the MLVA13-Lyon scheme to be a robust method for quickly discriminating and inferring genetic relatedness among environmental isolates. The 62 isolates displayed wide diversity, since 41 MLVA types (i.e. MTs) were observed, with 26 MTs clustered in 10 MLVA clonal complexes (MCs). Three and eight MCs were found among soil and manure isolates, respectively. Only one MC contained both soil and manure-borne isolates. No common MC was observed between soil and manure-borne isolates and the snake-related or environmental and clinical isolates. Antibiotic resistance profiles were performed to determine a potential link between resistance properties and the selective pressure that might be present in the various habitats. Except for four soil and manure isolates resistant to ticarcillin and ticarcillin/clavulanic acid and one isolate from a hydrocarbon-contaminated soil resistant to imipenem, all environmental isolates showed wild-type antibiotic profiles.
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41
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Moustafa AM, Bennett MD, Edwards J, Azim K, Mesaik MA, Choudhary MI, Pathanasophon P, Worarach A, Ali Q, Abubakar M, Anjum R. Molecular typing of haemorrhagic septicaemia-associated Pasteurella multocida isolates from Pakistan and Thailand using multilocus sequence typing and pulsed-field gel electrophoresis. Res Vet Sci 2013; 95:986-90. [PMID: 23916592 DOI: 10.1016/j.rvsc.2013.07.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Revised: 05/17/2013] [Accepted: 07/08/2013] [Indexed: 11/25/2022]
Abstract
A comparative genetic study of 23 field isolates and vaccine strains of Pasteurella multocida associated with haemorrhagic septicaemia cases from Pakistan and Thailand was done using pulsed field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). The MLST sequence type (ST) for all 20 of the 23 isolates tested was 122. The PFGE results showed one band difference between the Pakistani and the Thai isolates. Sequence type 122 is the dominant associated profile with haemorrhagic septicaemia (HS) cases in South Asia. The study supports the concept of using PFGE for short-term epidemiology and MLST for long-term epidemiology.
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Affiliation(s)
- Ahmed M Moustafa
- School of Veterinary and Life Sciences, Murdoch University, South Street, Murdoch, Western Australia 6150, Australia
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42
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Gomila M, Del Carmen Gallegos M, Fernández-Baca V, Pareja A, Pascual M, Díaz-Antolín P, García-Valdés E, Lalucat J. Genetic diversity of clinical Pseudomonas aeruginosa isolates in a public hospital in Spain. BMC Microbiol 2013; 13:138. [PMID: 23773707 PMCID: PMC3706262 DOI: 10.1186/1471-2180-13-138] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2012] [Accepted: 06/13/2013] [Indexed: 12/29/2022] Open
Abstract
Background Pseudomonas aeruginosa is an important nosocomial pathogen that exhibits multiple resistances to antibiotics with increasing frequency, making patient treatment more difficult. The aim of the study is to ascertain the population structure of this clinical pathogen in the Hospital Son Llàtzer, Spain. Results A significant set (56) of randomly selected clinical P. aeruginosa isolates, including multidrug and non-multidrug resistant isolates, were assigned to sequence types (STs) and compared them with their antibiotic susceptibility profile classified as follows: extensively drug resistant (XDR), multidrug resistant (MDR) and non-multidrug resistant (non-MDR). The genetic diversity was assessed by applying the multilocus sequence typing (MLST) scheme developed by Curran and collaborators, and by the phylogenetic analysis of a concatenated tree. The analysis of seven loci, acsA, aroE, guaA, mutL, nuoD, ppsA and trpE, demonstrated that the prevalent STs were ST-175, ST-235 and ST-253. The majority of the XDR and MDR isolates were included in ST-175 and ST-235. ST-253 is the third in frequency and included non-MDR isolates. The 26 singleton sequence types corresponded mainly to non-MDR isolates. Twenty-two isolates corresponded to new sequence types (not previously defined) of which 12 isolates were non-MDR and 10 isolates were MDR or XDR. Conclusions The population structure of clinical P. aeruginosa present in our hospital indicates the coexistence of nonresistant and resistant isolates with the same sequence type. The multiresistant isolates studied are grouped in the prevalent sequence types found in other Spanish hospitals and at the international level, and the susceptible isolates correspond mainly to singleton sequence types.
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Affiliation(s)
- Margarita Gomila
- Microbiología, Hospital Son Llàtzer, Palma de Mallorca, Illes Balears 07198, Spain.
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43
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Li L, Abu Al-Soud W, Bergmark L, Riber L, Hansen LH, Magid J, Sørensen SJ. Investigating the Diversity of Pseudomonas spp. in Soil Using Culture Dependent and Independent Techniques. Curr Microbiol 2013; 67:423-30. [DOI: 10.1007/s00284-013-0382-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 03/13/2013] [Indexed: 11/30/2022]
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44
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Salomonsen C, Themudo G, Jelsbak L, Molin S, Høiby N, Hammer A. Typing of Pseudomonas aeruginosa from hemorrhagic pneumonia in mink (Neovison vison). Vet Microbiol 2013; 163:103-9. [DOI: 10.1016/j.vetmic.2012.12.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Revised: 12/03/2012] [Accepted: 12/04/2012] [Indexed: 10/27/2022]
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45
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Hall AJ, Fothergill JL, Kaye SB, Neal TJ, McNamara PS, Southern KW, Winstanley C. Intraclonal genetic diversity amongst cystic fibrosis and keratitis isolates of Pseudomonas aeruginosa. J Med Microbiol 2013; 62:208-216. [DOI: 10.1099/jmm.0.048272-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Affiliation(s)
- Amanda J. Hall
- Institute of Infection and Global Health, University of Liverpool, Liverpool L69 3BX, UK
| | - Joanne L. Fothergill
- Institute of Infection and Global Health, University of Liverpool, Liverpool L69 3BX, UK
| | - Stephen B. Kaye
- St Paul’s Eye Unit, Royal Liverpool University Hospital, Liverpool L7 8XP, UK
| | - Timothy J. Neal
- Department of Medical Microbiology, Royal Liverpool University Hospital, Liverpool L7 8XP, UK
| | | | | | - Craig Winstanley
- Institute of Infection and Global Health, University of Liverpool, Liverpool L69 3BX, UK
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46
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Abstract
Strain-typing technology in support of outbreak identification and resolution has evolved from phenotypic analysis, such as serology and biotypes, to much-more-robust molecular genetic approaches, such as pulsed-field gel electrophoresis (PFGE) and whole-genome sequencing. Whole-genome mapping (WGM) has been recently applied to subtyping analysis, and it bridges the gap between PFGE (∼20 bands sorted by size) and whole-genome sequencing. WGM utilizes restriction site analysis but arranges 200 to 500 bands in the order they appear on the chromosome. WGM is able to quickly and cost-effectively generate high-resolution, ordered whole-genome maps of bacteria.
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47
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Mechergui A, Achour W, Giorgini D, Baaboura R, Taha MK, Hassen AB. Molecular typing ofNeisseria perflavaclinical isolates. APMIS 2012; 121:843-7. [DOI: 10.1111/apm.12042] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2012] [Accepted: 11/20/2012] [Indexed: 11/24/2022]
Affiliation(s)
| | | | - Dario Giorgini
- Institut Pasteur; Unité postulante des infections bactériennes invasives; Paris; France
| | | | - Muhamed-Kheir Taha
- Institut Pasteur; Unité postulante des infections bactériennes invasives; Paris; France
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48
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Liu ZH, Xu Y, Duo LB, Liu Y, Xu ZZ, Burns JL, Liu GR, Yang BF, Liu SL. Pseudomonas aeruginosa isolates of distinct sub-genotypes exhibit similar potential of antimicrobial resistance by drugs exposure. Antonie van Leeuwenhoek 2012; 103:797-807. [PMID: 23224438 DOI: 10.1007/s10482-012-9862-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Accepted: 11/29/2012] [Indexed: 10/27/2022]
Abstract
Pseudomonas aeruginosa, a wide-spread opportunistic pathogen, often complicates clinical treatments due to its resistance to a large variety of antimicrobials, especially in immune compromised patients, occasionally leading to death. However, the resistance to antimicrobials varies greatly among the P. aeruginosa isolates, which raises a question on whether some sub-lineages of P. aeruginosa might have greater potential to develop antimicrobial resistance than others. To explore this question, we divided 160 P. aeruginosa isolates collected from cities of USA and China into distinct genotypes using I-CeuI, a special endonuclease that had previously been proven to reveal phylogenetic relationships among bacteria reliably due to the highly conserved 26-bp recognition sequence. We resolved 10 genotypes by I-CeuI analysis and further divided them into 82 sub-genotypes by endonuclease cleavage with SpeI. Eight of the 10 genotypes contained both multi-drug resistant (MDR) and less resistant isolates based on comparisons of their antimicrobial resistance profiles (ARPs). When the less resistant or susceptible isolates from different genotypes were exposed to eight individual antimicrobials, they showed similar potential to become resistant with minor exceptions. This is to our knowledge the first report to examine correlations between phylogenetic sub-lineages of P. aeruginosa and their potential to become resistant to antimicrobials. This study further alerts the importance and urgency of antimicrobial abuse control.
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Affiliation(s)
- Zhen-Hong Liu
- Department of Pharmacology, Harbin Medical University, Harbin, China
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49
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Pseudomonas aeruginosa exhibits frequent recombination, but only a limited association between genotype and ecological setting. PLoS One 2012; 7:e44199. [PMID: 22970178 PMCID: PMC3435406 DOI: 10.1371/journal.pone.0044199] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Accepted: 07/30/2012] [Indexed: 01/12/2023] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen and an important cause of infection, particularly amongst cystic fibrosis (CF) patients. While specific strains capable of patient-to-patient transmission are known, many infections appear to be caused by unique and unrelated strains. There is a need to understand the relationship between strains capable of colonising the CF lung and the broader set of P. aeruginosa isolates found in natural environments. Here we report the results of a multilocus sequence typing (MLST)-based study designed to understand the genetic diversity and population structure of an extensive regional sample of P. aeruginosa isolates from South East Queensland, Australia. The analysis is based on 501 P. aeruginosa isolates obtained from environmental, animal and human (CF and non-CF) sources with particular emphasis on isolates from the Lower Brisbane River and isolates from CF patients obtained from the same geographical region. Overall, MLST identified 274 different sequence types, of which 53 were shared between one or more ecological settings. Our analysis revealed a limited association between genotype and environment and evidence of frequent recombination. We also found that genetic diversity of P. aeruginosa in Queensland, Australia was indistinguishable from that of the global P. aeruginosa population. Several CF strains were encountered frequently in multiple ecological settings; however, the most frequently encountered CF strains were confined to CF patients. Overall, our data confirm a non-clonal epidemic structure and indicate that most CF strains are a random sample of the broader P. aeruginosa population. The increased abundance of some CF strains in different geographical regions is a likely product of chance colonisation events followed by adaptation to the CF lung and horizontal transmission among patients.
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50
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Waters V, Zlosnik JEA, Yau YCW, Speert DP, Aaron SD, Guttman DS. Comparison of three typing methods for Pseudomonas aeruginosa isolates from patients with cystic fibrosis. Eur J Clin Microbiol Infect Dis 2012; 31:3341-50. [PMID: 22843295 DOI: 10.1007/s10096-012-1701-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2012] [Accepted: 07/10/2012] [Indexed: 10/28/2022]
Abstract
The aim of this study was to compare two traditional pattern matching techniques, pulsed-field gel electrophoresis (PFGE) and random amplified polymorphic DNA (RAPD), with the more reproducible technique of multilocus sequence typing (MLST) to genotype a blinded sample of Pseudomonas aeruginosa isolates from cystic fibrosis (CF) patients. A blinded sample of 48 well-characterized CF P. aeruginosa isolates was genotyped by PFGE, RAPD, and MLST, each performed in a different laboratory. The discriminatory power and congruence between the methods were compared using the Simpson's index, Rand index, and Wallace coefficient. PFGE and MLST had the greatest congruence with the highest Rand index (0.697). The discriminatory power of PFGE, RAPD, and MLST were comparable, with high Simpson's indices (range 0.973-0.980). MLST identified the most clonal relationships. When clonality was defined as agreement between two or more methods, MLST had the greatest predictive value (100 %) in labeling strains as unique, while PFGE had the greatest predictive value (96 %) in labeling strains as clonal. This study demonstrated the highest level of agreement between PFGE and MLST in genotyping P. aeruginosa isolates from CF patients. MLST had the greatest predictive value in identifying strains as unique and, thus, has the potential to be a cost-efficient, high-throughput, first-pass typing method.
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Affiliation(s)
- V Waters
- Division of Infectious Diseases, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, 555 University Avenue, Toronto, Ontario, M5G 1X8, Canada.
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