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Bogaerts B, Van den Bossche A, Verhaegen B, Delbrassinne L, Mattheus W, Nouws S, Godfroid M, Hoffman S, Roosens NHC, De Keersmaecker SCJ, Vanneste K. Closing the gap: Oxford Nanopore Technologies R10 sequencing allows comparable results to Illumina sequencing for SNP-based outbreak investigation of bacterial pathogens. J Clin Microbiol 2024; 62:e0157623. [PMID: 38441926 PMCID: PMC11077942 DOI: 10.1128/jcm.01576-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 02/09/2024] [Indexed: 03/08/2024] Open
Abstract
Whole-genome sequencing has become the method of choice for bacterial outbreak investigation, with most clinical and public health laboratories currently routinely using short-read Illumina sequencing. Recently, long-read Oxford Nanopore Technologies (ONT) sequencing has gained prominence and may offer advantages over short-read sequencing, particularly with the recent introduction of the R10 chemistry, which promises much lower error rates than the R9 chemistry. However, limited information is available on its performance for bacterial single-nucleotide polymorphism (SNP)-based outbreak investigation. We present an open-source workflow, Prokaryotic Awesome variant Calling Utility (PACU) (https://github.com/BioinformaticsPlatformWIV-ISP/PACU), for constructing SNP phylogenies using Illumina and/or ONT R9/R10 sequencing data. The workflow was evaluated using outbreak data sets of Shiga toxin-producing Escherichia coli and Listeria monocytogenes by comparing ONT R9 and R10 with Illumina data. The performance of each sequencing technology was evaluated not only separately but also by integrating samples sequenced by different technologies/chemistries into the same phylogenomic analysis. Additionally, the minimum sequencing time required to obtain accurate phylogenetic results using nanopore sequencing was evaluated. PACU allowed accurate identification of outbreak clusters for both species using all technologies/chemistries, but ONT R9 results deviated slightly more from the Illumina results. ONT R10 results showed trends very similar to Illumina, and we found that integrating data sets sequenced by either Illumina or ONT R10 for different isolates into the same analysis produced stable and highly accurate phylogenomic results. The resulting phylogenies for these two outbreaks stabilized after ~20 hours of sequencing for ONT R9 and ~8 hours for ONT R10. This study provides a proof of concept for using ONT R10, either in isolation or in combination with Illumina, for rapid and accurate bacterial SNP-based outbreak investigation.
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Affiliation(s)
- Bert Bogaerts
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
| | | | | | | | | | - Stéphanie Nouws
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
| | - Maxime Godfroid
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
| | - Stefan Hoffman
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
| | | | | | - Kevin Vanneste
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
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2
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Tang F, Li C, Li R, Xi L, Wang F, Tian J, Luo W. Antibiotic-Resistance Profiles and Genetic Diversity of Shigella Isolates in China: Implications for Control Strategies. Foodborne Pathog Dis 2024. [PMID: 38557159 DOI: 10.1089/fpd.2023.0138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024] Open
Abstract
The urgent need for comprehensive and systematic analyses of Shigella as the key pathogen led us to meticulously explore the epidemiology and molecular attributes of Shigella isolates. Accordingly, we procured 24 isolates (10 from Xinjiang and 14 from Wuhan, China) and performed serotype identification and antimicrobial susceptibility testing. Resistance gene detection and homology analysis by polymerase chain reaction and pulsed-field gel electrophoresis (PFGE), respectively, were performed for genetic diversity analysis. All isolates were identified as Shigella flexneri, with 70% (35.4-91.9%) and 30% (8.1-64.6%) of the Xinjiang isolates and 85.7% (56.2-97.5%) and 14.3% (2/14, 2.5-43.9%) of the Wuhan isolates belonging to serotype 2a and serotype 2b, respectively. All isolates displayed resistance to at least two antibiotics and complete resistance to ampicillin. Multidrug resistance (MDR) was recorded in 70.8% (48.8-86.6%) of isolates, with Xinjiang isolates exhibiting relatively higher resistance to ampicillin-sulbactam, piperacillin, ceftriaxone, and aztreonam. Conversely, Wuhan isolates displayed higher MDR and resistance to tetracycline, ciprofloxacin, levofloxacin, and cefepime relative to Xinjiang isolates. Molecular scrutiny of antibiotic-resistance determinants revealed that blaTEM was the main mechanism of ampicillin resistance, blaCTX-M was the main gene for resistance to third- and fourth-generation cephalosporins, and tetB was the predominant gene associated with tetracycline resistance. Four Xinjiang and seven Wuhan isolates shared T1-clone types (>85%), and two Xinjiang and one Wuhan isolates were derived from the T6 clone with a high similarity of 87%. Six PFGE patterns (T1, T2, T5, T6-3, T8, and T10) of S. flexneri were associated with MDR. Thus, there is a critical need for robust surveillance and control strategies in managing Shigella infections, along with the development of targeted interventions and antimicrobial stewardship programs tailored to the distinct characteristics of Shigella isolates in different regions of China.
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Affiliation(s)
- Feng Tang
- Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
| | - Changzhen Li
- Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
| | - Ran Li
- Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
| | - Lei Xi
- Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
| | - Fang Wang
- Center for Public Health Laboratory Service, Wuhan Center for Disease Control and Prevention, Wuhan, China
| | - Juling Tian
- Department of Laboratory Medicine, The First People's Hospital of Urumqi, Urumqi, China
| | - Wanjun Luo
- Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
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Shen H, Xie J, Gao W, Wang L, Chen L, Qian H, Yu S, Feng B, Yang F. Detection limit of FT-IR-based bacterial typing based on optimized sample preparation and typing model. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 307:123633. [PMID: 37952427 DOI: 10.1016/j.saa.2023.123633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 11/02/2023] [Accepted: 11/07/2023] [Indexed: 11/14/2023]
Abstract
Accurate and efficient bacterial typing methods are crucial to microbiology. Fourier transform infrared (FT-IR) spectroscopy enables highly distinguishable fingerprint identification of closely related bacterial strains by producing highly specific fingerprints of bacteria, which is increasingly being considered as an alternative to genotypic methods, such as pulsed field gel electrophoresis (PFGE) and whole genome sequencing (WGS), for bacterial typing. Compared with genotypic methods, FT-IR has significant advantages of convenient operation, fast speed, and low cost. Fundamental research into the detection limit based on optimized analytical conditions for FT-IR bacterial typing, which can avoid excessive bacterial culture time or sampling volume, is particularly important, especially in clinical practice. However, the corresponding parameters have not been fully investigated. In this study, we developed a simplified and reliable procedure for sample preparation, optimized the data analysis procedure, and evaluated the FT-IR detection limit based on the above conditions. In particular, we combined the film mold and calcium fluoride plate for sample preparation. We evaluated the detection limit (about 108 CFU/mL) after parameter optimization using hierarchical cluster analysis (HCA) and artificial neural network (ANN). The optimization and evaluation of these key fundamentals will better promote future application of FT-IR-based bacterial typing.
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Affiliation(s)
- Hao Shen
- Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Jinghang Xie
- Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Wenjing Gao
- Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Li Wang
- Kweichow Moutai Group, Renhuai, Guizhou 564501, China
| | | | - Heng Qian
- Shanghai University of Finance and Economics, Shanghai 200433, China
| | - Shaoning Yu
- Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Bin Feng
- Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China.
| | - Fan Yang
- Kweichow Moutai Group, Renhuai, Guizhou 564501, China.
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Hong S, Moon JS, Yoon SS, Kim HY, Lee YJ. Genetic and Phenotypic Diversity of Listeria monocytogenes in Pig Slaughterhouses in Korea. Foodborne Pathog Dis 2024; 21:1-9. [PMID: 37819680 DOI: 10.1089/fpd.2023.0053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023] Open
Abstract
Listeria monocytogenes is a foodborne pathogen that has variable subtypes associated with human listeriosis and occurs in food and processing environments. This study was conducted to provide the genetic and phenotypic characterization of L. monocytogenes in pig carcasses and environments of slaughterhouses in Korea. A total of 22 L. monocytogenes were isolated from eight of 26 pig slaughterhouses between 2020 and 2022, and the most common serotype was 1/2c (40.9%), followed by serotypes 1/2b (31.8%) and 1/2a (27.3%). The isolates showed a significantly high prevalence of virulence genes located in Listeria pathogenicity island-1 (LIPI-1) and internalins (90.9-100%; p < 0.05). However, the prevalence rates of llsX, ptsA, and stress survival islet-1 (SSI-1) located in LIPI-3, LIPI-4, and SSI were only 9.1%, 22.7%, and 31.8%, respectively. In addition, among the epidemic clones (EC), ECI, ECII, ECIII, and ECV, only one isolate was represented as ECV. Isolates identified from the same slaughterhouses were divided into two or more pulsotypes, except for two slaughterhouses. Furthermore, the seven STs were classified into seven clonal complexes (CCs) (CC8, CC9, CC37, CC87, CC121, CC155, and CC288), and all CCs belonged to lineages I (31.8%) and II (68.1%). Interestingly, the isolates showed a high prevalence of oxacillin resistance (59.1%), and most isolates of the serotypes 1/2a and 1/2b exhibited oxacillin resistance, whereas only one of nine serotype 1/2c isolates exhibited oxacillin resistance. These results provide the genetic diversity of L. monocytogenes in pig carcasses and environments of slaughterhouses, and continuous monitoring will be helpful in predicting food safety risks.
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Affiliation(s)
- Serim Hong
- College of Veterinary Medicine and Zoonoses Research Institute, Kyungpook National University, Daegu, Republic of Korea
| | - Jin-San Moon
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon, Republic of Korea
| | - Soon-Seek Yoon
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon, Republic of Korea
| | - Ha-Young Kim
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon, Republic of Korea
| | - Young Ju Lee
- College of Veterinary Medicine and Zoonoses Research Institute, Kyungpook National University, Daegu, Republic of Korea
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5
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Gieroń M, Żarnowiec P, Zegadło K, Gmiter D, Czerwonka G, Kaca W, Kręcisz B. Loop-Mediated Isothermal Amplification of DNA (LAMP) as an Alternative Method for Determining Bacteria in Wound Infections. Int J Mol Sci 2023; 25:411. [PMID: 38203582 PMCID: PMC10778741 DOI: 10.3390/ijms25010411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 12/23/2023] [Accepted: 12/25/2023] [Indexed: 01/12/2024] Open
Abstract
The increasing number of patients with chronic wounds requires the development of quick and accurate diagnostics methods. One of the key and challenging aspects of treating ulcers is to control wound infection. Early detection of infection is essential for the application of suitable treatment methods, such as systemic antibiotics or other antimicrobial agents. Clinically, the most frequently used method for detecting microorganisms in wounds is through a swab and culture on appropriate media. This test has major limitations, such as the long bacterial growth time and the selectivity of bacterial growth. This article presents an overview of molecular methods for detecting bacteria in wounds, including real-time polymerase chain reaction (rtPCR), quantitative polymerase chain reaction (qPCR), genotyping, next-generation sequencing (NGS), and loop-mediated isothermal amplification (LAMP). We focus on the LAMP method, which has not yet been widely used to detect bacteria in wounds, but it is an interesting alternative to conventional detection methods. LAMP does not require additional complicated equipment and provides the fastest detection time for microorganisms (approx. 30 min reaction). It also allows the use of many pairs of primers in one reaction and determination of up to 15 organisms in one sample. Isothermal amplification of DNA is currently the easiest and most economical method for microbial detection in wound infection. Direct visualization of the reaction with dyes, along with omitting DNA isolation, has increased the potential use of this method.
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Affiliation(s)
- Monika Gieroń
- Faculty of Medicine, Jan Kochanowski University in Kielce, 25-369 Kielce, Poland; (M.G.); (B.K.)
- Dermatology Department, Provincial General Hospital, 25-317 Kielce, Poland
| | - Paulina Żarnowiec
- Department of Microbiology, Institute of Biology, Jan Kochanowski University in Kielce, 25-406 Kielce, Poland; (P.Ż.); (K.Z.); (D.G.); (W.K.)
| | - Katarzyna Zegadło
- Department of Microbiology, Institute of Biology, Jan Kochanowski University in Kielce, 25-406 Kielce, Poland; (P.Ż.); (K.Z.); (D.G.); (W.K.)
| | - Dawid Gmiter
- Department of Microbiology, Institute of Biology, Jan Kochanowski University in Kielce, 25-406 Kielce, Poland; (P.Ż.); (K.Z.); (D.G.); (W.K.)
| | - Grzegorz Czerwonka
- Department of Microbiology, Institute of Biology, Jan Kochanowski University in Kielce, 25-406 Kielce, Poland; (P.Ż.); (K.Z.); (D.G.); (W.K.)
| | - Wiesław Kaca
- Department of Microbiology, Institute of Biology, Jan Kochanowski University in Kielce, 25-406 Kielce, Poland; (P.Ż.); (K.Z.); (D.G.); (W.K.)
| | - Beata Kręcisz
- Faculty of Medicine, Jan Kochanowski University in Kielce, 25-369 Kielce, Poland; (M.G.); (B.K.)
- Dermatology Department, Provincial General Hospital, 25-317 Kielce, Poland
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6
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Tran M, Smurthwaite KS, Nghiem S, Cribb DM, Zahedi A, Ferdinand AD, Andersson P, Kirk MD, Glass K, Lancsar E. Economic evaluations of whole-genome sequencing for pathogen identification in public health surveillance and health-care-associated infections: a systematic review. THE LANCET. MICROBE 2023; 4:e953-e962. [PMID: 37683688 DOI: 10.1016/s2666-5247(23)00180-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 05/31/2023] [Accepted: 06/05/2023] [Indexed: 09/10/2023]
Abstract
Whole-genome sequencing (WGS) has resulted in improvements to pathogen characterisation for the rapid investigation and management of disease outbreaks and surveillance. We conducted a systematic review to synthesise the economic evidence of WGS implementation for pathogen identification and surveillance. Of the 2285 unique publications identified through online database searches, 19 studies met the inclusion criteria. The economic evidence to support the broader application of WGS as a front-line pathogen characterisation and surveillance tool is insufficient and of low quality. WGS has been evaluated in various clinical settings, but these evaluations are predominantly investigations of a single pathogen. There are also considerable variations in the evaluation approach. Economic evaluations of costs, effectiveness, and cost-effectiveness are needed to support the implementation of WGS in public health settings.
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Affiliation(s)
- My Tran
- National Centre for Epidemiology and Population Health, Australian National University, Canberra ACT, Australia.
| | - Kayla S Smurthwaite
- National Centre for Epidemiology and Population Health, Australian National University, Canberra ACT, Australia
| | - Son Nghiem
- National Centre for Epidemiology and Population Health, Australian National University, Canberra ACT, Australia
| | - Danielle M Cribb
- National Centre for Epidemiology and Population Health, Australian National University, Canberra ACT, Australia
| | - Alireza Zahedi
- Public Health Microbiology, Forensic and Scientific Services, Queensland Health, Brisbane QLD, Australia
| | - Angeline D Ferdinand
- Microbiological Diagnostic Unit, Peter Doherty Institute, University of Melbourne, Melbourne VIC, Australia
| | - Patiyan Andersson
- Microbiological Diagnostic Unit, Peter Doherty Institute, University of Melbourne, Melbourne VIC, Australia
| | - Martyn D Kirk
- National Centre for Epidemiology and Population Health, Australian National University, Canberra ACT, Australia
| | - Kathryn Glass
- National Centre for Epidemiology and Population Health, Australian National University, Canberra ACT, Australia
| | - Emily Lancsar
- National Centre for Epidemiology and Population Health, Australian National University, Canberra ACT, Australia
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7
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Biguenet A, Bordy A, Atchon A, Hocquet D, Valot B. Introduction and benchmarking of pyMLST: open-source software for assessing bacterial clonality using core genome MLST. Microb Genom 2023; 9. [PMID: 37966168 DOI: 10.1099/mgen.0.001126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023] Open
Abstract
Core genome multilocus sequence typing (cgMLST) has gained in popularity for bacterial typing since whole-genome sequencing (WGS) has become affordable. We introduce here pyMLST, a new complete, stand-alone, free and open source pipeline for cgMLST analysis. pyMLST can create or import a core genome database. For each gene, the first allele is aligned against the bacterial genome of interest using BLAT. Incomplete genes are aligned using MAFT. All data are stored in a SQLite database. pyMLST accepts assembly genomes or raw data (with the option pyMLST-KMA) as input. To evaluate our new tool, we selected three genome collections of major bacterial pathogens (Escherichia coli, Pseudomonas aeruginosa and Staphylococcus aureus) and compared them with pyMLST, pyMLST-KMA, ChewBBACA, SeqSphere and the variant calling approach. We compared the sensitivity, precision and false-positive rate for each method with those of the variant calling approach. Minimal spanning trees were generated with each type of software to evaluate their interest in the context of a bacterial outbreak. We found that pyMLST-KMA is a convenient screening method to avoid assembling large bacterial collections. Our data showed that pyMLST (free, open source, available in Galaxy and pipeline ready) performed similarly to the commercial SeqSphere and performed better than ChewBBACA and pyMLST-KMA.
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Affiliation(s)
- Adrien Biguenet
- CHU de Besançon, Hygiène Hospitalière, F-25030 Besançon, France
- Université de Franche-Comté, CNRS, Chrono-environnement, F-25000 Besançon, France
| | - Augustin Bordy
- Université de Franche-Comté, CNRS, Chrono-environnement, F-25000 Besançon, France
| | - Alban Atchon
- Bioinformatique et Big Data Au Service de La Santé, Université de Franche-Comté, F-25000 Besançon, France
| | - Didier Hocquet
- CHU de Besançon, Hygiène Hospitalière, F-25030 Besançon, France
- Université de Franche-Comté, CNRS, Chrono-environnement, F-25000 Besançon, France
| | - Benoit Valot
- Université de Franche-Comté, CNRS, Chrono-environnement, F-25000 Besançon, France
- Bioinformatique et Big Data Au Service de La Santé, Université de Franche-Comté, F-25000 Besançon, France
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8
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Neupane S, Rao S, Yan WX, Wang PC, Chen SC. First identification, molecular characterization, and pathogenicity assessment of Lactococcus garvieae isolated from cultured pompano in Taiwan. JOURNAL OF FISH DISEASES 2023; 46:1295-1309. [PMID: 37578999 DOI: 10.1111/jfd.13848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 07/28/2023] [Accepted: 07/31/2023] [Indexed: 08/16/2023]
Abstract
Lactococcosis, caused by Lactococcus garvieae, is an acute hemorrhagic septicemia in fish recorded in marine and freshwater aquaculture during the summer months. In 2020-2021, several sea cage Pompano farms recorded sudden fish mortality events. Based on the results of phenotypic and biochemical tests, L. garvieae was predicted to be the cause. PCR with L. garvieae specific primers (pLG1 and pLG2) targeting the 16S rRNA region further confirmed the etiological agent as L. garvieae after amplifying an 1100 base pairs (bp) product. Furthermore, the 16S rRNA sequences of the two representative strains (AOD109-196-2B and AOD110-215-2B) shared 99.81% identity with L. garvieae (GenBank accession number: MT597707.1). The genetic profiles of the strains were classified using pulsed-field gel electrophoresis after digestion with SmaI and ApaI, which clustered our strains under the same pulsotype. Multiplex PCR targeting the capsule gene cluster and serotype-specific PCR collectively showed that the strains were non-capsulated; thus, they belonged to serotype I. An experimental infection was designed to fulfil Koch's postulates by infecting healthy Pompano with case-driven L. garvieae strains (AOD109-196-2B and AOD110-215-2B) with a cumulative mortality of 70%. Overall, L. garvieae infection in Pompano emphasizes the need for better monitoring and control procedures in aquaculture settings.
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Affiliation(s)
- Sandip Neupane
- International Degree Program of Ornamental Fish Technology and Aquatic Animal Health, International College, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Shreesha Rao
- Department of Veterinary Medicine, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Wei-Xiao Yan
- International Degree Program of Ornamental Fish Technology and Aquatic Animal Health, International College, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Pei-Chi Wang
- International Degree Program of Ornamental Fish Technology and Aquatic Animal Health, International College, National Pingtung University of Science and Technology, Pingtung, Taiwan
- Department of Veterinary Medicine, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
- Research Centre for Fish Vaccine and Diseases, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
- Southern Taiwan Fish Diseases Research Centre, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Shih-Chu Chen
- International Degree Program of Ornamental Fish Technology and Aquatic Animal Health, International College, National Pingtung University of Science and Technology, Pingtung, Taiwan
- Department of Veterinary Medicine, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
- Research Centre for Fish Vaccine and Diseases, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
- Southern Taiwan Fish Diseases Research Centre, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
- Research Centre for Animal Biologics, National Pingtung University of Science and Technology, Pingtung, Taiwan
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9
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Zahran M, El-Shabasy RM, Elrashedy A, Mousa W, Nayel M, Salama A, Zaghawa A, Elsify A. Recent progress in the genotyping of bovine tuberculosis and its rapid diagnosis via nanoparticle-based electrochemical biosensors. RSC Adv 2023; 13:31795-31810. [PMID: 37908649 PMCID: PMC10613952 DOI: 10.1039/d3ra05606f] [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: 08/17/2023] [Accepted: 10/16/2023] [Indexed: 11/02/2023] Open
Abstract
Bovine tuberculosis (bTB) is considered a worldwide infectious zoonotic disease. Mycobacterium bovis causes bTB disease. It is one of the Mycobacterium tuberculosis complex (MTBC) members. MTBC is a clonal complex of close relatives with approximately 99.95% similarity. M. bovis is a spillover pathogen that can transmit from animals to humans and rarely from humans to animals with contact. Genotyping techniques are important to discriminate and differentiate between MTBC species. Spoligotyping and mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) are widely used but they have some limitations. As an alternative, whole genome sequencing approaches have been utilized due to their high-resolution power. They are employed in typing M. bovis and explain the evolutionary and phylogenetic relationships between isolates. The control of bTB disease has attracted a large amount of attention. Rapid and proper diagnosis is necessary for monitoring the disease as an initial step for its control and treatment. Nanotechnology has a potential impact on the rapid diagnosis and treatment of bTB through the use of nanocarrier and metal nanoparticles (NPs). Special attention has been paid to voltammetric and impedimetric electrochemical strategies as facile, sensitive, and selective methods for the efficient detection of tuberculosis. The efficacy of these sensors is enhanced in the presence of NPs, which act as recognition and/or redox probes. Gold, silver, copper, cobalt, graphene, and magnetic NPs, as well as polypyrrole nanowires and multiwalled carbon nanotubes have been employed for detecting tuberculosis. Overall, NP-based electrochemical sensors represent a promising tool for the diagnosis of bTB.
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Affiliation(s)
- Moustafa Zahran
- Department of Chemistry, Faculty of Science, Menoufia University Shebin El-Kom 32512 Egypt
- Menoufia Company for Water and Wastewater, Holding Company for Water and Wastewater Menoufia 32514 Egypt
| | - Rehan M El-Shabasy
- Department of Chemistry, Faculty of Science, Menoufia University Shebin El-Kom 32512 Egypt
- Chemistry Department, The American University in Cairo AUC Avenue New Cairo 11835 Egypt
| | - Alyaa Elrashedy
- Department of Animal Medicine and Infectious Diseases, Faculty of Veterinary Medicine, University of Sadat City Egypt
| | - Walid Mousa
- Department of Animal Medicine and Infectious Diseases, Faculty of Veterinary Medicine, University of Sadat City Egypt
| | - Mohamed Nayel
- Department of Animal Medicine and Infectious Diseases, Faculty of Veterinary Medicine, University of Sadat City Egypt
| | - Akram Salama
- Department of Animal Medicine and Infectious Diseases, Faculty of Veterinary Medicine, University of Sadat City Egypt
| | - Ahmed Zaghawa
- Department of Animal Medicine and Infectious Diseases, Faculty of Veterinary Medicine, University of Sadat City Egypt
| | - Ahmed Elsify
- Department of Animal Medicine and Infectious Diseases, Faculty of Veterinary Medicine, University of Sadat City Egypt
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10
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Zhang QB, Zhu P, Zhang S, Rong YJ, Huang ZA, Sun LW, Cai T. Hypervirulent Klebsiella pneumoniae detection methods: a minireview. Arch Microbiol 2023; 205:326. [PMID: 37672079 DOI: 10.1007/s00203-023-03665-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/15/2023] [Accepted: 08/18/2023] [Indexed: 09/07/2023]
Abstract
Hypervirulent Klebsiella pneumoniae (hvKp), characterized by high virulence and epidemic potential, has become a global public health challenge. Therefore, improving the identification of hvKp and enabling earlier and faster detection in the community to support subsequent effective treatment and prevention of hvKp are an urgent issue. To address these issues, a number of assays have emerged, such as String test, Galleria mellonella infection test, PCR, isothermal exponential amplification, and so on. In this paper, we have collected articles on the detection methods of hvKp and conducted a retrospective review based on two aspects: traditional detection technology and biomarker-based detection technology. We summarize the advantages and limitations of these detection methods and discuss the challenges as well as future directions, hoping to provide new insights and references for the rapid detection of hvKp in the future. The aim of this study is to focus on the research papers related to Hypervirulent Klebsiella pneumoniae involving the period from 2012 to 2022. We conducted searches using the keywords "Hypervirulent Klebsiella pneumoniae, biomarkers, detection techniques" on ScienceDirect and Google Scholar. Additionally, we also searched on PubMed, using MeSH terms associated with the keywords (such as Klebsiella pneumoniae, Klebsiella Infections, Virulence, Biomarkers, diagnosis, etc.).
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Affiliation(s)
- Qi-Bin Zhang
- The Affiliated People's Hospital of Ningbo University, Ningbo, China
| | - Peng Zhu
- Ningbo No. 2 Hospital, Ningbo, China
- Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, China
- Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Ningbo, China
| | - Shun Zhang
- Ningbo No. 2 Hospital, Ningbo, China
- Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, China
- Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Ningbo, China
| | - Yan-Jing Rong
- Ningbo No. 2 Hospital, Ningbo, China
- Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Ningbo, China
| | - Zuo-An Huang
- Ningbo No. 2 Hospital, Ningbo, China
- Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Ningbo, China
| | | | - Ting Cai
- Ningbo No. 2 Hospital, Ningbo, China.
- Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, China.
- Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Ningbo, China.
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de-la-Rosa-Martinez D, Bobadilla Del Valle M, Esteban-Kenel V, Zinser Peniche P, Ponce De León Garduño A, Cornejo Juárez P, Sánchez Cruz MN, Camacho-Ortiz A, Vilar-Compte D. Molecular characterization and genotyping of isolates from cancer patients with Clostridioides difficile infection or asymptomatic colonization. J Med Microbiol 2023; 72. [PMID: 37624363 DOI: 10.1099/jmm.0.001748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/26/2023] Open
Abstract
Introduction. Cancer patients with Clostridioides difficile infection (CDI) are at a higher risk for adverse outcomes. In addition, a high prevalence of Clostridioides difficile asymptomatic colonization (CDAC) has been reported in this vulnerable population.Gap Statement. The molecular characteristics and potential role of CDAC in healthcare-related transmission in the cancer population have been poorly explored.Aim. We aimed to compare the molecular and genotypic characteristics of C. difficile isolates from cancer patients with CDAC and CDI.Method. We conducted a prospective cohort study of cancer patients with CDAC or CDI from a referral centre. Molecular characterization, typification and tcdC gene expression of isolates were performed.Results. The hospital-onset and community-onset healthcare facility-associated CDI rates were 4.5 cases/10 000 patient-days and 1.4 cases/1 000 admissions during the study period. Fifty-one C. difficile strains were isolated: 37 (72 %) and 14 (28 %) from patients with CDI or CDAC, respectively. All isolates from symptomatic patients were tcdA+/tcdB+, and four (10 %) were ctdA+/ctdB+. In the CDAC group, 10 (71 %) isolates were toxigenic, and none were ctdA+/ctdB+. The Δ18 in-frame tcdC deletion and two transition mutations were found in five isolates. After bacterial typing, 60 % of toxigenic isolates from asymptomatic carriers were clonal to those from patients with C. difficile-associated diarrhoea. No NAP1/027/BI strains were detected.Conclusions. We found a clonal association between C. difficile isolates from patients with CDAC and CDI. Studies are needed to evaluate the potential role of asymptomatic carriers in the dynamics of nosocomial transmission to support infection control measures and reduce the burden of CDI in high-risk groups.
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Affiliation(s)
- Daniel de-la-Rosa-Martinez
- Plan de Estudios Combinados en Medicina (PECEM), Faculty of Medicine, Universidad Nacional Autonoma de Mexico, México City, Mexico
- Departament of Infectious Diseases, Instituto Nacional de Cancerología, Mexico City, Mexico
| | - Miriam Bobadilla Del Valle
- Laboratory of Clinical Microbiology, Departament of Infectious Diseases, Instituto Nacional de Ciencias Medicas y Nutrición, Mexico City, Mexico
| | - Veronica Esteban-Kenel
- Laboratory of Clinical Microbiology, Departament of Infectious Diseases, Instituto Nacional de Ciencias Medicas y Nutrición, Mexico City, Mexico
| | - Paola Zinser Peniche
- Departament of Infectious Diseases, Instituto Nacional de Cancerología, Mexico City, Mexico
| | - Alfredo Ponce De León Garduño
- Laboratory of Clinical Microbiology, Departament of Infectious Diseases, Instituto Nacional de Ciencias Medicas y Nutrición, Mexico City, Mexico
| | | | - María Nancy Sánchez Cruz
- Laboratory of Clinical Microbiology, Departament of Infectious Diseases, Instituto Nacional de Ciencias Medicas y Nutrición, Mexico City, Mexico
| | - Adrian Camacho-Ortiz
- Department of Infectious Diseases, Department of Internal Medicine, Hospital Universitario Dr. Jose Eleuterio Gonzalez, Universidad Autónoma de Nuevo León, Monterrey, Mexico
| | - Diana Vilar-Compte
- Departament of Infectious Diseases, Instituto Nacional de Cancerología, Mexico City, Mexico
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12
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Dendani Chadi Z, Arcangioli MA. Pulsed-Field Gel Electrophoresis Analysis of Bovine Associated Staphylococcus aureus: A Review. Pathogens 2023; 12:966. [PMID: 37513813 PMCID: PMC10385338 DOI: 10.3390/pathogens12070966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 07/10/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
For decades now, DNA fingerprinting by means of pulsed-field gel electrophoresis (PFGE) continues to be the most widely used to separate large DNA molecules and distinguish between different strains in alternating pulses. This is done by isolating intact chromosomal DNA and using restriction enzymes with specific restriction sites to generate less than 30 restriction fragments from 50 Kb to 10 Mbp. These results make clone-specific band profiles easy to compare. Specialized equipment is required for the optimization of DNA separation and resolution, among which a contour-clamped homogeneous electric field (CHEF) apparatus is the most commonly used. As a result, the PFGE analysis of a bacterial genome provides useful information in terms of epidemiological investigations of different bacterial pathogens. For Staphylococcus aureus subtyping, despite its limitations and the emergence of alternative methods, PFGE analysis has proven to be an adequate choice and the gold standard for determining genetic relatedness, especially in outbreak detection and short-term surveillance in the veterinary field.
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Affiliation(s)
- Zoubida Dendani Chadi
- Laboratory of Biodiversity and Pollution of Ecosystems, Department of Veterinary Medicine, Faculty of Natural Science and Life, University of Chadli Bendjedid, El Tarf 36000, Algeria
| | - Marie-Anne Arcangioli
- VetAgro Sup, Université de Lyon, UMR Mycoplasmoses Animales, 69280 Marcy l'Etoile, France
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Fu Y, M’ikanatha NM, Dudley EG. Whole-Genome Subtyping Reveals Population Structure and Host Adaptation of Salmonella Typhimurium from Wild Birds. J Clin Microbiol 2023; 61:e0184722. [PMID: 37249426 PMCID: PMC10281135 DOI: 10.1128/jcm.01847-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 05/12/2023] [Indexed: 05/31/2023] Open
Abstract
Within-host evolution of bacterial pathogens can lead to host-associated variants of the same species or serovar. Identification and characterization of closely related variants from diverse host species are crucial to public health and host-pathogen adaptation research. However, the work remained largely underexplored at a strain level until the advent of whole-genome sequencing (WGS). Here, we performed WGS-based subtyping and analyses of Salmonella enterica serovar Typhimurium (n = 787) from different wild birds across 18 countries over a 75-year period. We revealed seven avian host-associated S. Typhimurium variants/lineages. These lineages emerged globally over short timescales and presented genetic features distinct from S. Typhimurium lineages circulating among humans and domestic animals. We further showed that, in terms of virulence, host adaptation of these variants was driven by genome degradation. Our results provide a snapshot of the population structure and genetic diversity of S. Typhimurium within avian hosts. We also demonstrate the value of WGS-based subtyping and analyses in unravelling closely related variants at the strain level.
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Affiliation(s)
- Yezhi Fu
- Department of Food Science, The Pennsylvania State University, University Park, Pennsylvania, USA
| | | | - Edward G. Dudley
- Department of Food Science, The Pennsylvania State University, University Park, Pennsylvania, USA
- E. coli Reference Center, The Pennsylvania State University, University Park, Pennsylvania, USA
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Wiktorczyk-Kapischke N, Skowron K, Wałecka-Zacharska E. Genomic and pathogenicity islands of Listeria monocytogenes-overview of selected aspects. Front Mol Biosci 2023; 10:1161486. [PMID: 37388250 PMCID: PMC10300472 DOI: 10.3389/fmolb.2023.1161486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 06/01/2023] [Indexed: 07/01/2023] Open
Abstract
Listeria monocytogenes causes listeriosis, a disease characterized by a high mortality rate (up to 30%). Since the pathogen is highly tolerant to changing conditions (high and low temperature, wide pH range, low availability of nutrients), it is widespread in the environment, e.g., water, soil, or food. L. monocytogenes possess a number of genes that determine its high virulence potential, i.e., genes involved in the intracellular cycle (e.g., prfA, hly, plcA, plcB, inlA, inlB), response to stress conditions (e.g., sigB, gadA, caspD, clpB, lmo1138), biofilm formation (e.g., agr, luxS), or resistance to disinfectants (e.g., emrELm, bcrABC, mdrL). Some genes are organized into genomic and pathogenicity islands. The islands LIPI-1 and LIPI-3 contain genes related to the infectious life cycle and survival in the food processing environment, while LGI-1 and LGI-2 potentially ensure survival and durability in the production environment. Researchers constantly have been searching for new genes determining the virulence of L. monocytogenes. Understanding the virulence potential of L. monocytogenes is an important element of public health protection, as highly pathogenic strains may be associated with outbreaks and the severity of listeriosis. This review summarizes the selected aspects of L. monocytogenes genomic and pathogenicity islands, and the importance of whole genome sequencing for epidemiological purposes.
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Affiliation(s)
- Natalia Wiktorczyk-Kapischke
- Department of Microbiology, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, Toruń, Poland
| | - Krzysztof Skowron
- Department of Microbiology, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, Toruń, Poland
| | - Ewa Wałecka-Zacharska
- Department of Food Hygiene and Consumer Health, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
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15
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Shoaib M, Xu J, Meng X, Wu Z, Hou X, He Z, Shang R, Zhang H, Pu W. Molecular epidemiology and characterization of antimicrobial-resistant Staphylococcus haemolyticus strains isolated from dairy cattle milk in Northwest, China. Front Cell Infect Microbiol 2023; 13:1183390. [PMID: 37265496 PMCID: PMC10230075 DOI: 10.3389/fcimb.2023.1183390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 04/27/2023] [Indexed: 06/03/2023] Open
Abstract
Introduction Non-aureus Staphylococcus (NAS) species are currently the most commonly identified microbial agents causing sub-clinical infections of the udder and are also deemed as opportunistic pathogens of clinical mastitis in dairy cattle. More than 10 NAS species have been identified and studied but little is known about S. haemolyticus in accordance with dairy mastitis. The present study focused on the molecular epidemiology and genotypic characterization of S. haemolyticus isolated from dairy cattle milk in Northwest, China. Methods In this study, a total of 356 milk samples were collected from large dairy farms in three provinces in Northwest, China. The bacterial isolation and presumptive identification were done by microbiological and biochemical methods following the molecular confirmation by 16S rRNA gene sequencing. The antimicrobial susceptibility testing (AST) was done by Kirby-Bauer disk diffusion assay and antibiotic-resistance genes (ARGs) were identified by PCR. The phylogenetic grouping and sequence typing was done by Pulsed Field Gel Electrophoresis (PFGE) and Multi-Locus Sequence Typing (MLST) respectively. Results In total, 39/356 (11.0%) were identified as positive for S. haemolyticus. The overall prevalence of other Staphylococcus species was noted to be 39.6% (141/356), while the species distribution was as follows: S. aureus 14.9%, S. sciuri 10.4%, S. saprophyticus 7.6%, S. chromogenes 4.2%, S. simulans 1.4%, and S. epidermidis 1.1%. The antimicrobial susceptibility of 39 S. haemolyticus strains exhibited higher resistance to erythromycin (92.3%) followed by trimethoprim-sulfamethoxazole (51.3%), ciprofloxacin (43.6%), florfenicol (30.8%), cefoxitin (28.2%), and gentamicin (23.1%). All of the S. haemolyticus strains were susceptible to tetracycline, vancomycin, and linezolid. The overall percentage of multi-drug resistant (MDR) S. haemolyticus strains was noted to be 46.15% (18/39). Among ARGs, mphC was identified as predominant (82.05%), followed by ermB (33.33%), floR (30.77%), gyrA (30.77%), sul1 (28.21%), ermA (23.08%), aadD (12.82%), grlA (12.82%), aacA-aphD (10.26%), sul2 (10.26%), dfrA (7.69%), and dfrG (5.13%). The PFGE categorized 39 S. haemolyticus strains into A-H phylogenetic groups while the MLST categorized strains into eight STs with ST8 being the most predominant while other STs identified were ST3, ST11, ST22, ST32, ST19, ST16, and ST7. Conclusion These findings provided new insights into our understanding of the epidemiology and genetic characteristics of S. haemolyticus in dairy farms to inform interventions limiting the spread of AMR in dairy production.
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Affiliation(s)
- Muhammad Shoaib
- Key Laboratory of New Animal Drug Project, Gansu Province/Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
| | - Jie Xu
- Key Laboratory of New Animal Drug Project, Gansu Province/Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
| | - Xiaoqin Meng
- Lanzhou Center for Animal Disease Control and Prevention, Lanzhou, China
| | - Zhongyong Wu
- Key Laboratory of New Animal Drug Project, Gansu Province/Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
| | - Xiao Hou
- Key Laboratory of New Animal Drug Project, Gansu Province/Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
| | - Zhuolin He
- Key Laboratory of New Animal Drug Project, Gansu Province/Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
| | - Ruofeng Shang
- Key Laboratory of New Animal Drug Project, Gansu Province/Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
| | - Hongjuan Zhang
- Key Laboratory of New Animal Drug Project, Gansu Province/Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
| | - Wanxia Pu
- Key Laboratory of New Animal Drug Project, Gansu Province/Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
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Nguyen P, Nazareth SC, Chen MY, Wang PC, Chen SC. An epidemiological analysis of Nocardia seriolae isolated from a wide range of aquatic animals in Taiwan, based on their genotype and enzymatic activity. JOURNAL OF FISH DISEASES 2023; 46:381-394. [PMID: 36606554 DOI: 10.1111/jfd.13751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 12/19/2022] [Accepted: 12/21/2022] [Indexed: 06/17/2023]
Abstract
Chronic disease following Nocardia seriolae infection in a wide range of aquatic animals has been reported in many Asian countries and recently in America and Mexico. This study aimed to investigate the epidemiological relationship among N. seriolae isolates in Taiwan by investigating their genotype and enzymatic activities. A total of 66 strains isolated from 14 known and four unknown host fish from five sites in Taiwan were characterized using five combined methods. High genotypic diversity was recognized among the isolates with 10 pulsotypes being identified from the pulsed-field gel electrophoresis method and 21 reptypes from the repetitive extragenic palindromic amplification method; however, no natural plasmids were detected in this bacterial population. Pulsotypes A8 and RI analysed by PFGE and repPCR, respectively, were found to be predominant within five sites in Taiwan over 17 years of isolation. Enzymatically, the majority of isolates displayed high leucine arylamidase, β-glucosidase and α-glucosidase activities but were negative for lipase, α-galactosidase, β-glucuronidase, N-acetyl-glucosaminidase, α-mannosidase and α-fucosidase activities. We identified a strong association between genotype and enzymatic activity since the majority of pulsotypes displayed the same type of enzymatic profile. This study provides comprehensive and potential epidemiological data, which will aid the fish farming activities and prevention method development.
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Affiliation(s)
- Phuong Nguyen
- International Degree Program of Ornamental Fish Technology and Aquatic Animal Health, International College, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Sandra Celenia Nazareth
- Department of Veterinary Medicine, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Mei-Yun Chen
- International Degree Program of Ornamental Fish Technology and Aquatic Animal Health, International College, National Pingtung University of Science and Technology, Pingtung, Taiwan
- Department of Veterinary Medicine, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Pei-Chi Wang
- Department of Veterinary Medicine, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
- Southern Taiwan Fish Diseases Research Centre, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Shih-Chu Chen
- International Degree Program of Ornamental Fish Technology and Aquatic Animal Health, International College, National Pingtung University of Science and Technology, Pingtung, Taiwan
- Department of Veterinary Medicine, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
- Southern Taiwan Fish Diseases Research Centre, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
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Hong S, Kang HJ, Lee HY, Jung HR, Moon JS, Yoon SS, Kim HY, Lee YJ. Prevalence and characteristics of foodborne pathogens from slaughtered pig carcasses in Korea. Front Vet Sci 2023; 10:1158196. [PMID: 37065220 PMCID: PMC10103459 DOI: 10.3389/fvets.2023.1158196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 03/14/2023] [Indexed: 04/03/2023] Open
Abstract
The introduction of bacteria into slaughterhouses can lead to microbial contamination in carcasses during slaughter, and the initial level of bacteria in carcasses is important because it directly affects spoilage and the shelf life. This study was conducted to investigate the microbiological quality, and the prevalence of foodborne pathogens in 200 carcasses from 20 pig slaughterhouses across Korea. Distribution of microbial counts were significantly higher for aerobic bacteria at 3.01–4.00 log10 CFU/cm2 (42.0%) and 2.01–3.00 log10 CFU/cm2 (28.5%), whereas most of Escherichia coli showed the counts under 1.00 log10 CFU/cm2 (87.0%) (P < 0.05). The most common pathogen isolated from 200 carcasses was Staphylococcus aureus (11.5%), followed by Yersinia enterocolitica (7.0%). In total, 17 S. aureus isolates from four slaughterhouses were divided into six pulsotypes and seven spa types, and showed the same or different types depending on the slaughterhouses. Interestingly, isolates from two slaughterhouses carried only LukED associated with the promotion of bacterial virulence, whereas, isolates from two other slaughterhouses carried one or more toxin genes associated with enterotoxins including sen. In total, 14 Y. enterocolitica isolates from six slaughterhouses were divided into nine pulsotypes, 13 isolates belonging to biotype 1A or 2 carried only ystB, whereas one isolate belonging to bio-serotype 4/O:3 carried both ail and ystA. This is the first study to investigate microbial quality and the prevalence of foodborne pathogens in carcasses from slaughterhouses nationally, and the findings support the need for ongoing slaughterhouse monitoring to improve the microbiological safety of pig carcasses.
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Affiliation(s)
- Serim Hong
- College of Veterinary Medicine and Zoonoses Research Institute, Kyungpook National University, Daegu, Republic of Korea
| | - Hye Jeong Kang
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon, Republic of Korea
| | - Hye-Young Lee
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon, Republic of Korea
| | - Hye-Ri Jung
- College of Veterinary Medicine and Zoonoses Research Institute, Kyungpook National University, Daegu, Republic of Korea
| | - Jin-San Moon
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon, Republic of Korea
| | - Soon-Seek Yoon
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon, Republic of Korea
| | - Ha-Young Kim
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon, Republic of Korea
- *Correspondence: Ha-Young Kim
| | - Young Ju Lee
- College of Veterinary Medicine and Zoonoses Research Institute, Kyungpook National University, Daegu, Republic of Korea
- Young Ju Lee
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Montone AMI, Cutarelli A, Peruzy MF, La Tela I, Brunetti R, Pirofalo MG, Folliero V, Balestrieri A, Murru N, Capuano F. Antimicrobial Resistance and Genomic Characterization of Salmonella Infantis from Different Sources. Int J Mol Sci 2023; 24:ijms24065492. [PMID: 36982566 PMCID: PMC10049457 DOI: 10.3390/ijms24065492] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/10/2023] [Accepted: 03/10/2023] [Indexed: 03/16/2023] Open
Abstract
The epidemiology of Salmonella Infantis is complex in terms of its distribution and transmission. The continuous collection and analysis of updated data on the prevalence and antimicrobic resistance are essential. The present work aimed to investigate the antimicrobial resistance and the correlation among S. Infantis isolates from different sources through the multiple-locus variable-number of tandem repeat (VNTR) analysis (MLVA). A total of 562 Salmonella strains isolated from 2018 to 2020 from poultry, humans, swine, water buffalo, mussels, cattle, and wild boar were serotyped, and 185 S. Infantis strains (32.92%) were identified. S. Infantis was commonly isolated in poultry and, to a lesser extent, in other sources. The isolates were tested against 12 antimicrobials, and a high prevalence of resistant strains was recorded. S. Infantis showed high resistance against fluoroquinolones, ampicillin, and tetracycline, which are commonly used in human and veterinary medicine. From all S. Infantis isolates, five VNTR loci were amplified. The use of MLVA was not sufficient to understand the complexity of the epidemiological relationships between S. Infantis strains. In conclusion, an alternative methodology to investigate genetic similarities and differences among S. Infantis strains is needed.
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Affiliation(s)
| | - Anna Cutarelli
- Department of Food Inspection, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute 2, 80055 Portici, Italy
| | - Maria Francesca Peruzy
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Via Delpino 1, 80137 Naples, Italy
- Correspondence: ; Tel.: +39-0812536065
| | - Immacolata La Tela
- Salmonella Typing Centre of the Campania Region-Department of Food Microbiology, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute 2, 80055 Portici, Italy
| | - Roberta Brunetti
- Epidemiology and Biostatistics Coordination Department, Experimental Zooprophylactic Institute of Southern, Via Salute 2, 80055 Portici, Italy
| | - Maria Gerarda Pirofalo
- Complex Operative Unit of Pathology and Microbiology, Microbiology Sector, University Hospital San Giovanni di Dio e Ruggi d’ Aragona, Largo Città di Ippocrate, 84131 Salerno, Italy
| | - Veronica Folliero
- Department of Experimental Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy
| | - Anna Balestrieri
- Salmonella Typing Centre of the Campania Region-Department of Food Microbiology, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute 2, 80055 Portici, Italy
| | - Nicoletta Murru
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Via Delpino 1, 80137 Naples, Italy
- Task Force on Microbiome Studies, University of Naples Federico II, 80138 Naples, Italy
| | - Federico Capuano
- Department of Food Inspection, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute 2, 80055 Portici, Italy
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Molecular Detection and Identification of Plant-Associated Lactiplantibacillus plantarum. Int J Mol Sci 2023; 24:ijms24054853. [PMID: 36902287 PMCID: PMC10003612 DOI: 10.3390/ijms24054853] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/27/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023] Open
Abstract
Lactiplantibacillus plantarum is a lactic acid bacterium often isolated from a wide variety of niches. Its ubiquity can be explained by a large, flexible genome that helps it adapt to different habitats. The consequence of this is great strain diversity, which may make their identification difficult. Accordingly, this review provides an overview of molecular techniques, both culture-dependent, and culture-independent, currently used to detect and identify L. plantarum. Some of the techniques described can also be applied to the analysis of other lactic acid bacteria.
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Yang S, He L, Li K, Yu X, Ni L, Hu L, Guo J, Biskup E, Tang L, Wu W. Efficacy of Active Rapid Molecular Screening and IPC Interventions on Carbapenem-Resistant Enterobacterales Infections in Emergency Intensive Care Units without Enough Single-Room Isolation. Infect Drug Resist 2023; 16:1039-1048. [PMID: 36845019 PMCID: PMC9951601 DOI: 10.2147/idr.s396331] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 02/08/2023] [Indexed: 02/22/2023] Open
Abstract
Purpose To investigate whether rapid active molecular screening and infection prevention and control (IPC) interventions can reduce colonization or infection with carbapenem-resistant Enterobacterales (CRE) in a general emergency intensive care unit (EICU) without enough single-room isolation. Methods The study was designed as a before-and-after quasi-experiment. Before the experimental period, the ward was rescheduled and the staff were trained. From May 2018 to April 2021, active screening was performed by seminested real-time fluorescent polymerase chain reaction (PCR) detection with rectal swabs from all patients on admission to the EICU, and the results were reported in 1 hour. Other IPC interventions including hand hygiene, contact precautions, patient isolation, environmental disinfection, environment surveillance, monitoring, auditing and feedback were conducted under strict supervision. The patients' clinical characteristics were collected simultaneously. Results In this 3-year study, 630 patients were enrolled and 19.84% of the patients were initially colonized or infected with CRE as shown by active molecular screening. The average drug resistance ratio to carbapenem shown by clinical culture detection of Klebsiella pneumoniae (KPN) before the study was performed was 71.43% in EICU. The drug resistance ratio decreased significantly from 75%, 66.67% to 46.67% in the next 3 years (p<0.05) during which active screening and IPC interventions were strictly executed. While the ratio gaps between EICU and the whole hospital were narrowed from 22.81%, 21.11% to 4.64%. Patients with invasive devices, skin barrier damage, and the recent use of antibiotics on admission were found to have a higher risk of being colonized or infected with CRE (p<0.05). Conclusion Active rapid molecular screening and other IPC interventions may significantly reduce CRE nosocomial infections even in wards without enough single-room isolation. The key to reduce the spread of CRE in the EICU is the strict execution of IPC interventions by all medical staff and healthcare workers.
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Affiliation(s)
- Simin Yang
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, People’s Republic of China
| | - Lihua He
- Department of Hospital Infection Management, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, People’s Republic of China
| | - Ke Li
- Department of Emergency Intensive Care Unit, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, People’s Republic of China
| | - Xiaoyu Yu
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, People’s Republic of China
| | - Lijun Ni
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, People’s Republic of China
| | - Liang Hu
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, People’s Republic of China
| | - Jian Guo
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, People’s Republic of China
| | - Ewelina Biskup
- Department of Basic and Clinical Medicine, Shanghai University of Medicine and Health Sciences, Shanghai, People’s Republic of China,Department of Internal Medicine, University Hospital of Basel, Basel, Switzerland
| | - Lunxian Tang
- Department of Emergency Intensive Care Unit, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, People’s Republic of China,Correspondence: Lunxian Tang; Wenjuan Wu, Tel +86-15921155750; +86-13386057159, Email ;
| | - Wenjuan Wu
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, People’s Republic of China
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21
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Lan P, Lu Y, Yan R, Fang L, Zhao D, Jiang Y, Yu Y, Du X, Zhou J. Development of a Novel Typing Scheme Based on the Genetic Diversity of Heme/Hemin Uptake System Hmu in Klebsiella pneumoniae Species Complex. Microbiol Spectr 2023; 11:e0106222. [PMID: 36786624 PMCID: PMC10101058 DOI: 10.1128/spectrum.01062-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 01/30/2023] [Indexed: 02/15/2023] Open
Abstract
Iron is essential for the survival and reproduction of Klebsiella pneumoniae. Although K. pneumoniae employs multiple types of siderophores to scavenge iron during infections, the majority of host iron is retained within erythrocytes and carried by hemoglobin that is inaccessible to siderophores. HmuRSTUV is a bacterial hemin/hemoprotein uptake system. However, the genetic background and function of HmuRSTUV in K. pneumoniae remain unknown. We collected 2,242 K. pneumoniae genomes, of which 2,218 (98.9%) had complete hmuRSTUV loci. Based on the 2,218 complete hmuRSTUV sequences, we established a novel typing scheme of K. pneumoniae named hmST, and 446 nonrepetitive hmSTs were identified. In hypervirulent lineages, hmST was diversely distributed and hmST1 mainly existed in ST23 strains. In contrast, hmST was less diversely distributed among multidrug-resistant strains. hmST demonstrated greater genetic diversity in hypervirulent lineages and community-acquired and bloodstream-sourced strains. In vitro and in vivo experiments revealed that an intact hmuRSTUV was essential for hemin uptake, playing an important role in bloodstream infections. This study established a novel typing scheme of hmST based on hmuRSTUV providing new insights into identifying and monitoring the emergence of novel virulence evolution in K. pneumoniae. IMPORTANCE Siderophore is a group of low molecular weight compounds with high affinity for ferric iron, which could facilitate bacterial iron consumption. Similarly, hemin/heme scavenged by the hemin uptake system HmuRSTUV usually act as another critical iron source for K. pneumoniae. This study proved that Hmu system significantly promoted the growth of K. pneumoniae in the presence of hemin and played an important role in bloodstream infections. A novel typing scheme named hmST was established, and the genetic diversity of hmuRSTUV loci was analyzed based on a large number of genomes. This study provides new insights into identifying and monitoring the emergence of novel virulence evolution in K. pneumoniae.
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Affiliation(s)
- Peng Lan
- Department of Critical Care Medicine, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| | - Ye Lu
- Department of Critical Care Medicine, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| | - Rushuang Yan
- Department of Critical Care Medicine, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| | - Lei Fang
- Department of Critical Care Medicine, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| | - Dongdong Zhao
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yan Jiang
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yunsong Yu
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaoxing Du
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jiancang Zhou
- Department of Critical Care Medicine, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
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22
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Wiktorczyk-Kapischke N, Skowron K, Wałecka-Zacharska E, Grudlewska-Buda K, Wnuk K, Buszko K, Gospodarek-Komkowska E. Assessment of the influence of selected stress factors on the growth and survival of Listeria monocytogenes. BMC Microbiol 2023; 23:27. [PMID: 36690941 PMCID: PMC9872351 DOI: 10.1186/s12866-023-02766-4] [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: 10/30/2022] [Accepted: 01/10/2023] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Listeria monocytogenes are Gram-positive rods, which are the etiological factor of listeriosis. L. monocytogenes quickly adapts to changing environmental conditions. Since the main source of rods is food, its elimination from the production line is a priority. The study aimed to evaluate the influence of selected stress factors on the growth and survival of L. monocytogenes strains isolated from food products and clinical material. RESULTS We distinguished fifty genetically different strains of L. monocytogenes (PFGE method). Sixty-two percent of the tested strains represented 1/2a-3a serogroup. Sixty percent of the rods possessed ten examined virulence genes (fbpA, plcA, hlyA, plcB, inlB, actA, iap, inlA, mpl, prfA). Listeria Pathogenicity Island 1 (LIPI-1) was demonstrated among 38 (76.0%) strains. Majority (92.0%) of strains (46) were sensitive to all examined antibiotics. The most effective concentration of bacteriophage (inhibiting the growth of 22 strains; 44.0%) was 5 × 108 PFU. In turn, the concentration of 8% of NaCl was enough to inhibit the growth of 31 strains (62.0%). The clinical strain tolerated the broadest pH range (3 to 10). Five strains survived the 60-min exposure to 70˚C, whereas all were alive at each time stage of the cold stress experiment. During the stress of cyclic freezing-defrosting, an increase in the number of bacteria was shown after the first cycle, and a decrease was only observed after cycle 3. The least sensitive to low nutrients content were strains isolated from frozen food. The high BHI concentration promoted the growth of all groups. CONCLUSIONS Data on survival in stress conditions can form the basis for one of the hypotheses explaining the formation of persistent strains. Such studies are also helpful for planning appropriate hygiene strategies within the food industry.
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Affiliation(s)
- Natalia Wiktorczyk-Kapischke
- Department of Microbiology, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, Toruń, Poland
| | - Krzysztof Skowron
- Department of Microbiology, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, Toruń, Poland.
| | - Ewa Wałecka-Zacharska
- Department of Food Hygiene and Consumer Health, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Katarzyna Grudlewska-Buda
- Department of Microbiology, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, Toruń, Poland
| | - Kacper Wnuk
- Department of Theoretical Foundations of Biomedical Sciences and Medical Computer Science, Ludwik Rydygier Collegium Medium in Bydgoszcz, Nicolaus Copernicus University, Toruń, Poland
| | - Katarzyna Buszko
- Department of Theoretical Foundations of Biomedical Sciences and Medical Computer Science, Ludwik Rydygier Collegium Medium in Bydgoszcz, Nicolaus Copernicus University, Toruń, Poland
| | - Eugenia Gospodarek-Komkowska
- Department of Microbiology, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, Toruń, Poland
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Liu JH, Lan CL, Yao GF, Kong NQ, Luo YW, Li CY, Bi SL. Comparison of pulsed-field gel electrophoresis and a novel amplified intergenic locus polymorphism method for molecular typing of Campylobacter jejuni. Arch Microbiol 2023; 205:49. [PMID: 36595076 DOI: 10.1007/s00203-022-03392-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/25/2022] [Accepted: 12/27/2022] [Indexed: 01/04/2023]
Abstract
Campylobacter is regarded as the leading cause of zoonotic diseases and Campylobacter jejuni (C. jejuni) is one of the predominant pathogenic species. To track C. jejuni infections, various genotyping methods have been used. In this study, amplified intergenic locus polymorphism (AILP) was used to type C. jejuni for the first time. To confirm its feasibility, pulsed-field gel electrophoresis (PFGE) was performed as a control, and the results obtained by the AILP and PFGE methods were compared. Fifty-one isolates were resolved into 34 and 29 different genotypes with Simpson's indices of 0.976 and 0.967 using the AILP and PFGE methods, respectively. The adjusted Rand coefficient of the two approaches was as high as 0.845. In summary, the data showed that the two genotyping methods were similar for discriminating isolates and were both appropriate methods to distinguish whether two isolates were indistinguishable, but the AILP was faster and less costly than PFGE. Therefore, the AILP is a reliable, rapid, and highly discriminative method to genotype C. jejuni collected from poultry meat, which is helpful to effectively monitor C. jejuni.
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Affiliation(s)
- Jin-Hong Liu
- School of Food Science, Guangdong Pharmaceutical University, Zhongshan, 528458, People's Republic of China
| | - Cheng-Lu Lan
- School of Food Science, Guangdong Pharmaceutical University, Zhongshan, 528458, People's Republic of China
| | - Ge-Feng Yao
- School of Food Science, Guangdong Pharmaceutical University, Zhongshan, 528458, People's Republic of China
| | - Nian-Qing Kong
- School of Food Science, Guangdong Pharmaceutical University, Zhongshan, 528458, People's Republic of China
| | - Yong-Wen Luo
- School of South, China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Chu-Yi Li
- School of Food Science, Guangdong Pharmaceutical University, Zhongshan, 528458, People's Republic of China
| | - Shui-Lian Bi
- School of Food Science, Guangdong Pharmaceutical University, Zhongshan, 528458, People's Republic of China.
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24
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Kong N, Luo Y, Liu J, Yao G, Hu Y, Shu S, Li C, Bi S. Subtyping of Campylobacter coli isolated from raw poultry meat in retail markets using amplified intergenic locus polymorphism - A novel rapid subtyping method. J Microbiol Methods 2023; 204:106662. [PMID: 36572193 DOI: 10.1016/j.mimet.2022.106662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/22/2022] [Accepted: 12/22/2022] [Indexed: 12/25/2022]
Abstract
In order to provide more phylogenetic information of Campylobacter coli in large-scale epidemiological investigation, this work was undertaken to develop a novel genotyping method based on amplified intergenic locus polymorphism (AILP), by using pulsed-field gel electrophoresis (PFGE; using SmaI enzymes) as control. Eleven pairs of primers were selected to type C. coli strains for this purpose. A total of 68 C. coli isolates recovered from 51 retail raw chicken and 37 retail raw duck were subtyped. The Simpson's index of diversity (SID) of AILP and PFGE, as well as the adjusted Rand index (AR) and the adjusted Wallace coefficient (AW) between AILP and PFGE, were calculated. The new AILP method differentiated 68 C. coli isolates into 55 different subtypes (SID = 0.993), compared with 46 different profiles obtained from PFGE (SID = 0.980). The SID value of the AILP method was improved with the increasing number of primers, and a combination of 7 loci was selected as the optimal combination. The congruent analysis of the AILP method and PFGE showed moderate congruence between the two methods (AR = 0.462). The AW indicated that if AILP data is the available one can confidently predict the PFGE cluster. The results of this study showed that the AILP method had higher discrimination than PFGE and also allowed for significant reduction in time and cost.
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Affiliation(s)
- Nianqing Kong
- College of Food Science, Guangdong Pharmaceutical University, Zhongshan 528458, Guangdong, China; College of Public Health, Guangdong Pharmaceutical University, Guangzhou 510220, Guangdong, China
| | - Yongwen Luo
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, Guangdong, China
| | - Jinhong Liu
- College of Food Science, Guangdong Pharmaceutical University, Zhongshan 528458, Guangdong, China; College of Public Health, Guangdong Pharmaceutical University, Guangzhou 510220, Guangdong, China
| | - Gefeng Yao
- College of Food Science, Guangdong Pharmaceutical University, Zhongshan 528458, Guangdong, China; College of Public Health, Guangdong Pharmaceutical University, Guangzhou 510220, Guangdong, China
| | - Yilin Hu
- College of Food Science, Guangdong Pharmaceutical University, Zhongshan 528458, Guangdong, China; College of Public Health, Guangdong Pharmaceutical University, Guangzhou 510220, Guangdong, China
| | - Shenghuang Shu
- College of Food Science, Guangdong Pharmaceutical University, Zhongshan 528458, Guangdong, China; College of Public Health, Guangdong Pharmaceutical University, Guangzhou 510220, Guangdong, China
| | - Chuyi Li
- College of Food Science, Guangdong Pharmaceutical University, Zhongshan 528458, Guangdong, China
| | - Shuilian Bi
- College of Food Science, Guangdong Pharmaceutical University, Zhongshan 528458, Guangdong, China.
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25
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Nykrynova M, Barton V, Bezdicek M, Lengerova M, Skutkova H. Identification of highly variable sequence fragments in unmapped reads for rapid bacterial genotyping. BMC Genomics 2022; 23:445. [PMID: 36581824 PMCID: PMC9798552 DOI: 10.1186/s12864-022-08550-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 04/14/2022] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Bacterial genotyping is a crucial process in outbreak investigation and epidemiological studies. Several typing methods such as pulsed-field gel electrophoresis, multilocus sequence typing (MLST) and whole genome sequencing are currently used in routine clinical practice. However, these methods are costly, time-consuming and have high computational demands. An alternative to these methods is mini-MLST, a quick, cost-effective and robust method based on high-resolution melting analysis. Nevertheless, no standardized approach to identify markers suitable for mini-MLST exists. Here, we present a pipeline for variable fragment detection in unmapped reads based on a modified hybrid assembly approach using data from one sequencing platform. RESULTS In routine assembly against the reference sequence, high variable reads are not aligned and remain unmapped. If de novo assembly of them is performed, variable genomic regions can be located in created scaffolds. Based on the variability rates calculation, it is possible to find a highly variable region with the same discriminatory power as seven housekeeping gene fragments used in MLST. In the work presented here, we show the capability of identifying one variable fragment in de novo assembled scaffolds of 21 Escherichia coli genomes and three variable regions in scaffolds of 31 Klebsiella pneumoniae genomes. For each identified fragment, the melting temperatures are calculated based on the nearest neighbor method to verify the mini-MLST's discriminatory power. CONCLUSIONS A pipeline for a modified hybrid assembly approach consisting of reference-based mapping and de novo assembly of unmapped reads is presented. This approach can be employed for the identification of highly variable genomic fragments in unmapped reads. The identified variable regions can then be used in efficient laboratory methods for bacterial typing such as mini-MLST with high discriminatory power, fully replacing expensive methods such as MLST. The results can and will be delivered in a shorter time, which allows immediate and fast infection monitoring in clinical practice.
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Affiliation(s)
- Marketa Nykrynova
- grid.4994.00000 0001 0118 0988Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czechia
| | - Vojtech Barton
- grid.4994.00000 0001 0118 0988Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czechia
| | - Matej Bezdicek
- grid.412554.30000 0004 0609 2751Department of Internal Medicine, Hematology and Oncology, University Hospital Brno, Brno, Czechia
| | - Martina Lengerova
- grid.412554.30000 0004 0609 2751Department of Internal Medicine, Hematology and Oncology, University Hospital Brno, Brno, Czechia
| | - Helena Skutkova
- grid.4994.00000 0001 0118 0988Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czechia
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Detection and identification of Lactobacillus acidophilus species and its commercial probiotic strains using CRISPR loci-based amplicon analysis. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.114166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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27
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Make It Less difficile: Understanding Genetic Evolution and Global Spread of Clostridioides difficile. Genes (Basel) 2022; 13:genes13122200. [PMID: 36553467 PMCID: PMC9778335 DOI: 10.3390/genes13122200] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 11/14/2022] [Accepted: 11/22/2022] [Indexed: 11/25/2022] Open
Abstract
Clostridioides difficile is an obligate anaerobic pathogen among the most common causes of healthcare-associated infections. It poses a global threat due to the clinical outcomes of infection and resistance to antibiotics recommended by international guidelines for its eradication. In particular, C. difficile infection can lead to fulminant colitis associated with shock, hypotension, megacolon, and, in severe cases, death. It is therefore of the utmost urgency to fully characterize this pathogen and better understand its spread, in order to reduce infection rates and improve therapy success. This review aims to provide a state-of-the-art overview of the genetic variation of C. difficile, with particular regard to pathogenic genes and the correlation with clinical issues of its infection. We also summarize the current typing techniques and, based on them, the global distribution of the most common ribotypes. Finally, we discuss genomic surveillance actions and new genetic engineering strategies as future perspectives to make it less difficile.
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28
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Wang D, Wang M, He T, Li D, Zhang L, Zhang D, Feng J, Yang W, Yuan Y. Molecular epidemiology and mechanism of Klebsiella pneumoniae resistance to ertapenem but not to other carbapenems in China. Front Microbiol 2022; 13:974990. [PMID: 36425030 PMCID: PMC9678918 DOI: 10.3389/fmicb.2022.974990] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 10/17/2022] [Indexed: 11/11/2022] Open
Abstract
Resistance to only ertapenem is an unusual phenotype of carbapenem-resistant Klebsiella pneumoniae (CRKP). This study aimed to investigate the molecular epidemiology and underlying mechanism involved in ertapenem resistance of K. pneumoniae strains that are susceptible to meropenem and imipenem. Among the 697 K. pneumoniae strains isolated from 11 grade A hospitals in China, 245 were CRKP strains, of which 18 strains resistant only to ertapenem were isolated. The genotypes, phenotypes, drug resistance homology, and drug sensitivity were analyzed; moreover, the expressions of efflux pump components and outer membrane proteins were assessed. The whole genomes of these 18 strains were sequenced and analyzed for mutations leading to drug resistance. The results revealed that ertapenem resistance may be related to ramR mutation. The function of ramR was confirmed using gene complementation to the original strain to determine the mechanism underlying ertapenem resistance of K. pneumoniae strains. In total, 7.4% of the tested CRKP strains were resistant only to ertapenem. None of these strains contained carbapenemase genes. Of the 18 ertapenem-resistant strains, 17 expressed the efflux pump, and outer membrane protein expression was reduced or absent in 4 strains. Whole-genome sequencing revealed the presence of mutations that introduced premature ramR codons stop in 14 strains (77.78%). When a functional copy of ramR was restored in the 14 strains, the minimum inhibitory concentration of ertapenem decreased, inhibition of efflux pumps was not detected, and the expression of outer membrane protein OmpK35 was either increased or was restored. These findings reveal the existence of ertapenem-resistant K. pneumoniae exhibiting no clonal transmission between strains. Mutations in ramR were demonstrated to cause efflux pump inhibition and over-expression of outer membrane protein OmpK35 in some strains, which is implicated in ertapenem resistance only in K. pneumoniae.
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Affiliation(s)
- Dongliang Wang
- Department of Critical Care Medicine, Gansu Provincial Hospital, Lanzhou, Gansu, China
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
| | - Minggui Wang
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Clinical Pharmacology of Antibiotics, National Health Commission of the People’s Republic of China, Shanghai, China
| | - Tianpeng He
- Department of Critical Care Medicine, Gansu Provincial Hospital, Lanzhou, Gansu, China
| | - Dan Li
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Clinical Pharmacology of Antibiotics, National Health Commission of the People’s Republic of China, Shanghai, China
| | - Liqin Zhang
- Department of Critical Care Medicine, Gansu Provincial Hospital, Lanzhou, Gansu, China
| | - Dongquan Zhang
- Department of Critical Care Medicine, Gansu Provincial Hospital, Lanzhou, Gansu, China
| | - Junshuai Feng
- Department of Critical Care Medicine, Gansu Provincial Hospital, Lanzhou, Gansu, China
| | - Wenli Yang
- Department of Critical Care Medicine, Gansu Provincial Hospital, Lanzhou, Gansu, China
| | - Yuan Yuan
- Department of Critical Care Medicine, Gansu Provincial Hospital, Lanzhou, Gansu, China
- *Correspondence: Yuan Yuan,
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Rahmawaty A, Chen MY, Byadgi OV, Wang PC, Chen SC. Phenotypic and genotypic analysis of Edwardsiella isolates from Taiwan indicates wide variation with a particular reference to Edwardsiella tarda and Edwardsiella anguillarum. JOURNAL OF FISH DISEASES 2022; 45:1659-1672. [PMID: 35916068 DOI: 10.1111/jfd.13688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 07/01/2022] [Accepted: 07/06/2022] [Indexed: 06/15/2023]
Abstract
Edwardsiella spp. is a gram-negative, facultatively anaerobic, intracellular bacteria threatening the aquaculture industry worldwide. Noticeably, E. tarda is now genotypically classified into three distinct groups (E. tarda, E. piscicida and E. anguillarum), but morphologically, it is unclear due to varying degrees of virulence in different fish hosts. Hence, to reclassify E. tarda, we investigated differences in genotypes, phenotypes and pathogenicity. We collected Edwardsiella isolates from five different counties of Taiwan between 2017 and 2021. At first, gyrB gene was amplified for a phylogenetic tree from 40 isolates from different fish and one reference isolate, BCRC10670, from the human. Thirty-nine strains clustered into E. anguillarum, 1 strain into E. piscicida and 1 strain into E. tarda from human strain. Second, all isolates were characterized using various phenotypic (API 20E biochemical profiles) and genotypic (pulsed-field gel electrophoresis [PFGE], and virulence-related gene detection). SpeI digestion revealed 10 pulsotypes and I-CeuI into 7 pulsotypes. Virulent genes (citC, gadB, katB, mukF and fimA) confirmed in 35, 31, 28, 37 and 38 isolates, respectively. Finally, in vivo challenge test in milkfish (Chanos chanos) indicated the highest mortality from E. anguillarum. Overall, results revealed unique features with Edwardsiella spp. genotypes and pathogenicity, which are relevant to the host and provide useful insights for future vaccine development.
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Affiliation(s)
- Atiek Rahmawaty
- International Degree Program of Ornamental Fish Technology and Aquatic Animal Health, International College, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Mei-Yun Chen
- Department of Veterinary Medicine, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Omkar Vijay Byadgi
- International Degree Program of Ornamental Fish Technology and Aquatic Animal Health, International College, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Pei-Chi Wang
- International Degree Program of Ornamental Fish Technology and Aquatic Animal Health, International College, National Pingtung University of Science and Technology, Pingtung, Taiwan
- Department of Veterinary Medicine, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
- Research Centre for Fish Vaccine and Diseases, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
- Southern Taiwan Fish Diseases Research Centre, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Shih-Chu Chen
- International Degree Program of Ornamental Fish Technology and Aquatic Animal Health, International College, National Pingtung University of Science and Technology, Pingtung, Taiwan
- Department of Veterinary Medicine, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
- Research Centre for Fish Vaccine and Diseases, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
- Southern Taiwan Fish Diseases Research Centre, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
- Research Centre for Animal Biologics, National Pingtung University of Science and Technology, Pingtung, Taiwan
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30
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Kong X, Chen J, Yang Y, Li M, Wang J, Jia Q, Wang Y, Yuan Q, Miao Y, Zhao P, You Y, Zhao X, Pei X, Zuo H, Meng J. Phenotypic and genotypic characterization of
salmonella
Enteritidis isolated from two consecutive
Food‐Poisoning
outbreaks in Sichuan, China. J Food Saf 2022. [DOI: 10.1111/jfs.13015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ximei Kong
- Chengdu Center for Disease Control and Prevention Chengdu China
| | - Jingxian Chen
- West China School of Public Health and West China Fourth Hospital Sichuan University Chengdu China
- Food Safety Monitoring and Risk Assessment Key Laboratory of Sichuan Province Chengdu China
| | - Yang Yang
- Chengdu Center for Disease Control and Prevention Chengdu China
| | - Ming Li
- Chengdu Center for Disease Control and Prevention Chengdu China
| | - Jian Wang
- West China School of Public Health and West China Fourth Hospital Sichuan University Chengdu China
- Food Safety Monitoring and Risk Assessment Key Laboratory of Sichuan Province Chengdu China
| | - Qu Jia
- West China School of Public Health and West China Fourth Hospital Sichuan University Chengdu China
- Food Safety Monitoring and Risk Assessment Key Laboratory of Sichuan Province Chengdu China
| | - Yao Wang
- Chengdu Center for Disease Control and Prevention Chengdu China
| | - Qiwu Yuan
- Chengdu Center for Disease Control and Prevention Chengdu China
| | - Yanfang Miao
- Chengdu Center for Disease Control and Prevention Chengdu China
| | - Pinnan Zhao
- Chengdu Center for Disease Control and Prevention Chengdu China
| | - Yiping You
- Chengdu Center for Disease Control and Prevention Chengdu China
| | - Xing Zhao
- West China School of Public Health and West China Fourth Hospital Sichuan University Chengdu China
| | - Xiaofang Pei
- West China School of Public Health and West China Fourth Hospital Sichuan University Chengdu China
- Food Safety Monitoring and Risk Assessment Key Laboratory of Sichuan Province Chengdu China
| | - Haojiang Zuo
- West China School of Public Health and West China Fourth Hospital Sichuan University Chengdu China
- Food Safety Monitoring and Risk Assessment Key Laboratory of Sichuan Province Chengdu China
| | - Jiantong Meng
- Chengdu Center for Disease Control and Prevention Chengdu China
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31
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Ranjan A, Arora J, Chauhan A, Basniwal RK, Kumari A, Rajput VD, Prazdnova EV, Ghosh A, Mukerjee N, Mandzhieva SS, Sushkova S, Minkina T, Jindal T. Advances in characterization of probiotics and challenges in industrial application. Biotechnol Genet Eng Rev 2022:1-44. [PMID: 36200338 DOI: 10.1080/02648725.2022.2122287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 08/05/2022] [Indexed: 11/02/2022]
Abstract
An unbalanced diet and poor lifestyle are common reasons for numerous health complications in humans. Probiotics are known to provide substantial benefits to human health by producing several bioactive compounds, vitamins, short-chain fatty acids and short peptides. Diets that contain probiotics are limited to curd, yoghurt, kefir, kimchi, etc. However, exploring the identification of more potential probiotics and enhancing their commercial application to improve the nutritional quality would be a significant step to utilizing the maximum benefits. The complex evolution patterns among the probiotics are the hurdles in their characterization and adequate application in the industries and dairy products. This article has mainly discussed the molecular methods of characterization that are based on the analysis of ribosomal RNA, whole genome, and protein markers and profiles. It also has critically emphasized the emerging challenges in industrial applications of probiotics.
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Affiliation(s)
- Anuj Ranjan
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, Russia
| | - Jayati Arora
- Amity Institute of Environmental Sciences, Amity University, Noida, India
| | - Abhishek Chauhan
- Amity Institute of Environmental Toxicology Safety and Management, Amity University, Noida, India
| | - Rupesh Kumar Basniwal
- Amity Institute of Advanced Research and Studies (M&D), Amity University, Noida, India
| | - Arpna Kumari
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, Russia
| | - Vishnu D Rajput
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, Russia
| | - Evgeniya V Prazdnova
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, Russia
| | - Arabinda Ghosh
- Microbiology Division, Department of Botany, Gauhati University, Guwahati, India
| | - Nobendu Mukerjee
- Department of Microbiology, Ramakrishna Mission Vivekananda Centenary College, Kolkata, India
- Department of Health Sciences, Novel Global Community Educational Foundation, New South Wales, Australia
| | - Saglara S Mandzhieva
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, Russia
| | - Svetlana Sushkova
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, Russia
| | - Tatiana Minkina
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, Russia
| | - Tanu Jindal
- Amity Institute of Environmental Toxicology Safety and Management, Amity University, Noida, India
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32
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Fujita H, Osaku A, Sakane Y, Yoshida K, Yamada K, Nara S, Mukai T, Su’etsugu M. Enzymatic Supercoiling of Bacterial Chromosomes Facilitates Genome Manipulation. ACS Synth Biol 2022; 11:3088-3099. [PMID: 35998348 PMCID: PMC9486964 DOI: 10.1021/acssynbio.2c00353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The physical stability of bacterial chromosomes is important for their in vitro manipulation, while genetic stability is important in vivo. However, extracted naked chromosomes in the open circular form are fragile due to nicks and gaps. Using a nick/gap repair and negative supercoiling reaction (named SCR), we first achieved the negative supercoiling of the whole genomes extracted from Escherichia coli and Vibrio natriegens cells. Supercoiled chromosomes of 0.2-4.6 megabase (Mb) were separated by size using a conventional agarose gel electrophoresis and served as DNA size markers. We also achieved the enzymatic replication of 1-2 Mb chromosomes using the reconstituted E. coli replication-cycle reaction (RCR). Electroporation-ready 1 Mb chromosomes were prepared by a modified SCR performed at a low salt concentration (L-SCR) and directly introduced into commercial electrocompetent E. coli cells. Since successful electroporation relies on the genetic stability of a chromosome in cells, genetically stable 1 Mb chromosomes were developed according to a portable chromosome format (PCF). Using physically and genetically stabilized chromosomes, the democratization of genome synthetic biology will be greatly accelerated.
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33
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What Can Genetics Do for the Control of Infectious Diseases in Aquaculture? Animals (Basel) 2022; 12:ani12172176. [PMID: 36077896 PMCID: PMC9454762 DOI: 10.3390/ani12172176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/02/2022] [Accepted: 08/22/2022] [Indexed: 11/17/2022] Open
Abstract
Simple Summary Infectious diseases place an economic burden on aquaculture and a limitation to its growth. This state-of-the-art review describes the application of genetics and genomics as novel tools to control infectious disease in aquaculture. Abstract Infectious diseases place an economic burden on aquaculture and a limitation to its growth. An innovative approach to mitigate their impact on production is breeding for disease resistance: selection for domestication, family-based selection, marker-assisted selection, and more recently, genomic selection. Advances in genetics and genomics approaches to the control of infectious diseases are key to increasing aquaculture efficiency, profitability, and sustainability and to reducing its environmental footprint. Interaction and co-evolution between a host and pathogen can, however, turn breeding to boost infectious disease resistance into a potential driver of pathogenic change. Parallel molecular characterization of the pathogen and its virulence and antimicrobial resistance genes is therefore essential to understand pathogen evolution over time in response to host immunity, and to apply appropriate mitigation strategies.
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34
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Li P, Gao M, Feng C, Yan T, Sheng Z, Shi W, Liu S, Zhang L, Li A, Lu J, Lin X, Li K, Xu T, Bao Q, Sun C. Molecular characterization of florfenicol and oxazolidinone resistance in Enterococcus isolates from animals in China. Front Microbiol 2022; 13:811692. [PMID: 35958123 PMCID: PMC9360786 DOI: 10.3389/fmicb.2022.811692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 07/07/2022] [Indexed: 11/24/2022] Open
Abstract
Florfenicol is widely used for the treatment of bacterial infections in domestic animals. The aim of this study was to analyze the molecular mechanisms of florfenicol and oxazolidinone resistance in Enterococcus isolates from anal feces of domestic animals. The minimum inhibitory concentration (MIC) levels were determined by the agar dilution method. Polymerase chain reaction (PCR) was performed to analyze the distribution of the resistance genes. Whole-genome sequencing and comparative plasmid analysis was conducted to analyze the resistance gene environment. A total of 351 non-duplicated enteric strains were obtained. Among these isolates, 22 Enterococcus isolates, including 19 Enterococcus. faecium and 3 Enterococcus. faecalis, were further studied. 31 florfenicol resistance genes (13 fexA, 3 fexB, 12 optrA, and 3 poxtA genes) were identified in 15 of the 19 E. faecium isolates, and no florfenicol or oxazolidinone resistance genes were identified in 3 E. faecalis isolates. Whole-genome sequencing of E. faecium P47, which had all four florfenicol and oxazolidinone resistance genes and high MIC levels for both florfenicol (256 mg/L) and linezolid (8 mg/L), revealed that it contained a chromosome and 3 plasmids (pP47-27, pP47-61, and pP47-180). The four florfenicol and oxazolidinone resistance genes were all related to the insertion sequences IS1216 and located on two smaller plasmids. The genes fexB and poxtA encoded in pP47-27, while fexA and optrA encoded in the conjugative plasmid pP47-61. Comparative analysis of homologous plasmids revealed that the sequences with high identities were plasmid sequences from various Enterococcus species except for the Tn6349 sequence from a Staphylococcus aureus chromosome (MH746818.1). The current study revealed that florfenicol and oxazolidinone resistance genes (fexA, fexB, poxtA, and optrA) were widely distributed in Enterococcus isolates from animal in China. The mobile genetic elements, including the insertion sequences and conjugative plasmid, played an important role in the horizontal transfer of florfenicol and oxazolidinone resistance.
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Affiliation(s)
- Pingping Li
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
- Nursing Department, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
- Department of Clinical Laboratory, Zhoukou Maternal and Child Health Hospital, Zhoukou, China
| | - Mengdi Gao
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Chunlin Feng
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Tielun Yan
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Zhiqiong Sheng
- School of Nursing, Wenzhou Medical University, Wenzhou, China
| | - Weina Shi
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Shuang Liu
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Lei Zhang
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Anqi Li
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Junwan Lu
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Xi Lin
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Kewei Li
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Teng Xu
- Institute of Translational Medicine, Baotou Central Hospital, Baotou, China
- Teng Xu,
| | - Qiyu Bao
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
- Qiyu Bao,
| | - Caixia Sun
- Nursing Department, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
- *Correspondence: Caixia Sun,
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35
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Discrimination and Characterization of Escherichia coli Originating from Clinical Cases of Femoral Head Necrosis in Broilers by MALDI-TOF Mass Spectrometry Confirms Great Heterogeneity of Isolates. Microorganisms 2022; 10:microorganisms10071472. [PMID: 35889191 PMCID: PMC9323188 DOI: 10.3390/microorganisms10071472] [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: 06/17/2022] [Revised: 07/14/2022] [Accepted: 07/19/2022] [Indexed: 02/01/2023] Open
Abstract
Escherichia coli, a major pathogen in poultry production, is involved in femoral head necrosis (FHN) in broiler birds. So far, the characterization and relationship of isolates in context with this disease are mainly based on phenotypic and genotypic characteristics. Previously, an involvement of diverse E. coli isolates was reported. MALDI-TOF MS has been successfully applied investigating the clonality of different bacteria. Therefore, its application to characterize a well-defined selection of E. coli isolates beyond the species level was tested. The isolates were derived from clinical cases of FHN as well as from healthy birds. Reproducibility studies to perform a standardized protocol were done, and LB agar as well as the usage of fresh bacterial cultures proved most appropriate. No distinct clustering in context with the origin of isolates, association with lesions, serotype, or PFGE profile was found. Most of the isolates belonging to phylogroup B2 revealed a characteristic peak shift at 9716 m/z and could be attributed to the same MALDI-TOF MS cluster. The present study confirmed the previously found pheno- and genotypic heterogeneity of E. coli involved in FHN on the proteomic level. The study also highlights the need for standardized protocols when using MALDI-TOF MS for bacterial typing, especially beyond species level.
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36
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Gerace E, Mancuso G, Midiri A, Poidomani S, Zummo S, Biondo C. Recent Advances in the Use of Molecular Methods for the Diagnosis of Bacterial Infections. Pathogens 2022; 11:pathogens11060663. [PMID: 35745518 PMCID: PMC9229729 DOI: 10.3390/pathogens11060663] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 05/31/2022] [Accepted: 06/05/2022] [Indexed: 12/14/2022] Open
Abstract
Infections caused by bacteria have a major impact on public health-related morbidity and mortality. Despite major advances in the prevention and treatment of bacterial infections, the latter continue to represent a significant economic and social burden worldwide. The WHO compiled a list of six highly virulent multidrug-resistant bacteria named ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) responsible for life-threatening diseases. Taken together with Clostridioides difficile, Escherichia coli, Campylobacter spp., (C. jejuni and C. coli), Legionella spp., Salmonella spp., and Neisseria gonorrhoeae, all of these microorganisms are the leading causes of nosocomial infections. The rapid and accurate detection of these pathogens is not only important for the early initiation of appropriate antibiotic therapy, but also for resolving outbreaks and minimizing subsequent antimicrobial resistance. The need for ever-improving molecular diagnostic techniques is also of fundamental importance for improving epidemiological surveillance of bacterial infections. In this review, we aim to discuss the recent advances on the use of molecular techniques based on genomic and proteomic approaches for the diagnosis of bacterial infections. The advantages and limitations of each of the techniques considered are also discussed.
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Affiliation(s)
| | - Giuseppe Mancuso
- Department of Human Pathology, University of Messina, 98125 Messina, Italy; (G.M.); (A.M.); (S.P.); (S.Z.)
| | - Angelina Midiri
- Department of Human Pathology, University of Messina, 98125 Messina, Italy; (G.M.); (A.M.); (S.P.); (S.Z.)
| | - Stefano Poidomani
- Department of Human Pathology, University of Messina, 98125 Messina, Italy; (G.M.); (A.M.); (S.P.); (S.Z.)
| | - Sebastiana Zummo
- Department of Human Pathology, University of Messina, 98125 Messina, Italy; (G.M.); (A.M.); (S.P.); (S.Z.)
| | - Carmelo Biondo
- Department of Human Pathology, University of Messina, 98125 Messina, Italy; (G.M.); (A.M.); (S.P.); (S.Z.)
- Correspondence: ; Tel.: +39-090-2213322
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37
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Feito J, Araújo C, Gómez-Sala B, Contente D, Campanero C, Arbulu S, Saralegui C, Peña N, Muñoz-Atienza E, Borrero J, del Campo R, Hernández PE, Cintas LM. Antimicrobial activity, molecular typing and in vitro safety assessment of Lactococcus garvieae isolates from healthy cultured rainbow trout (Oncorhynchus mykiss, Walbaum) and rearing environment. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.113496] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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38
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RAPD-PCR-Based Fingerprinting Method as a Tool for Epidemiological Analysis of Trueperella pyogenes Infections. Pathogens 2022; 11:pathogens11050562. [PMID: 35631083 PMCID: PMC9147813 DOI: 10.3390/pathogens11050562] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/03/2022] [Accepted: 05/09/2022] [Indexed: 11/30/2022] Open
Abstract
In this study, a Random Amplified Polymorphic DNA-Polymerase Chain Reaction (RAPD-PCR) method for genetic typing of Trueperella pyogenes, an opportunistic bacterial pathogen, was designed. The method optimization was performed for 37 clinical T. pyogenes strains isolated from various infections in different animal species. Optimal conditions for reliable and reproducible DNA fingerprinting were determined according to the modified Taguchi method. The developed method was assessed regarding its typeability, reproducibility, and discriminatory power using the Hunter’s and Gatsons’ index of discrimination. A high degree of genetic diversity was shown between the studied strains, which represented 31 genotypes. The generated RAPD profiles were relatively complex and simultaneously easy to interpret due to the wide size range of amplicons. The discriminatory index of the designed method was sufficiently high; thus, only strains epidemiologically related displayed identical RAPD genotypes. In conclusion, the DNA fingerprinting of T. pyogenes by the developed RAPD-PCR method is a reliable typing tool that may allow a better understanding of the epidemiology as well as pathogenesis of infections caused by this pathogen.
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39
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Prevalence, virulence determinants, and genetic diversity in Yersinia enterocolitica isolated from slaughtered pigs and pig carcasses. Int J Food Microbiol 2022; 376:109756. [DOI: 10.1016/j.ijfoodmicro.2022.109756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 05/17/2022] [Accepted: 05/25/2022] [Indexed: 11/21/2022]
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40
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Detection of emetic Bacillus cereus and the emetic toxin cereulide in food matrices: Progress and perspectives. Trends Food Sci Technol 2022. [DOI: 10.1016/j.tifs.2022.03.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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41
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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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42
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Iglesias MA, Kroning IS, Ramires T, Cunha CEP, Moreira GMSG, Camargo AC, Mendonça M, Nero LA, Conceição FR, Lopes GV, DA Silva WP. Genetic Profiles and Invasion Ability of Listeria monocytogenes Isolated from Bovine Carcasses in Southern Brazil. J Food Prot 2022; 85:591-596. [PMID: 34995347 DOI: 10.4315/jfp-21-345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 01/05/2022] [Indexed: 11/11/2022]
Abstract
ABSTRACT The goals of this study were to evaluate the persistence and the virulence potential of Listeria monocytogenes isolated from beef carcasses obtained in processing facilities in the southern region of Rio Grande do Sul, Brazil, based on pulsed-field gel electrophoresis (PFGE), invasion ability in human colorectal carcinoma cells (HCT-116), internalin A (InlA) expression by Western blot, and identification of mutation points in inlA. PFGE profiles demonstrated that L. monocytogenes isolates were grouped based on their previously identified lineages and serogroups (lineage I: serogroup IIb, n = 2, and serogroup IVb, n = 5; lineage II: serogroup IIc, n = 5). Isolates with indistinguishable genetic profiles through this method were obtained from different slaughterhouses and sampling steps, with as much as a 3-year interval. Seven isolates showed high invasion ability (2.4 to 7.4%; lineage I, n = 6, and lineage II, n = 1) in HCT and expressed InlA. Five isolates showed low cell invasion ability (0.6 to 1.4%; lineage I, n = 1, and lineage II, n = 4) and did not express InlA, and two of them (lineage II, serogroup IIc) presented mutations in inlA that led to premature stop codon type 19 at position 326 (GAA → TAA). The results demonstrated that most L. monocytogenes isolates from lineage I expressed InlA and were the most invasive in HCT, indicating their high virulence potential, whereas most isolates from lineage II showed attenuated invasion because of nonexpression of InlA or the presence of premature stop codon type 19 in inlA. The obtained results demonstrated that L. monocytogenes with indistinguishable PFGE profiles can persist or be reintroduced in beef processing facilities in the studied region and that differences in their virulence potential are based on their lineages and serogroups. HIGHLIGHTS
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Affiliation(s)
- Mariana A Iglesias
- Centro de Desenvolvimento Tecnológico, Núcleo de Biotecnologia, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Isabela S Kroning
- Departamento de Ciência e Tecnologia Agroindustrial, Faculdade de Agronomia, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Tassiana Ramires
- Departamento de Ciência e Tecnologia Agroindustrial, Faculdade de Agronomia, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Carlos E P Cunha
- Centro de Desenvolvimento Tecnológico, Núcleo de Biotecnologia, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Gustavo M S G Moreira
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Anderson C Camargo
- Departamento de Tecnologia de Alimentos, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Marcelo Mendonça
- Programa de Pós-Graduação em Sanidade e Reprodução de Animais de Produção, Universidade Federal Rural do Agreste de Pernambuco, Garanhuns, Pernambuco, Brazil
| | - Luís Augusto Nero
- Departamento de Veterinária, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Fabricio R Conceição
- Centro de Desenvolvimento Tecnológico, Núcleo de Biotecnologia, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Graciela Volz Lopes
- Departamento de Ciência e Tecnologia Agroindustrial, Faculdade de Agronomia, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Wladimir Padilha DA Silva
- Centro de Desenvolvimento Tecnológico, Núcleo de Biotecnologia, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sul, Brazil.,Departamento de Ciência e Tecnologia Agroindustrial, Faculdade de Agronomia, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sul, Brazil
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43
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Li X, Zhu L, Wang X, Li J, Tang B. Evaluation of IR Biotyper for Lactiplantibacillus plantarum Typing and Its Application Potential in Probiotic Preliminary Screening. Front Microbiol 2022; 13:823120. [PMID: 35401469 PMCID: PMC8988154 DOI: 10.3389/fmicb.2022.823120] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 02/24/2022] [Indexed: 12/25/2022] Open
Abstract
IR Biotyper (IRBT), which is a spectroscopic system for microorganism typing based on Fourier transform infrared (FTIR) technology, has been used to detect the spread of clones in clinical microbiology laboratories. However, the use of IRBT to detect probiotics has rarely been reported. Herein, we evaluated the discriminatory power of IRBT to type Lactiplantibacillus plantarum isolates at the strain level and explored its application potential in probiotic preliminary selection. Twenty Lactiplantibacillus isolates collected from pickled radishes during successive fermentation were used to test the robustness of IRBT at the strain level. IRBT was then compared with genotyping methods such as whole-genome sequencing (WGS), pulsed-field gel electrophoresis (PFGE), and multilocus sequence typing (MLST) to evaluate its discrimination power. IRBT distributed the 20 isolates into five clusters, with L. argentoratensis isolate C7-83 being the most distant from the other isolates, which belonged to L. plantarum. IRBT showed good reproducibility, although deviation in the discriminative power of IRBT was found at the strain level across laboratories, probably due to technical variance. All examined methods allowed bacterial identification at the strain level, but IRBT had higher discriminatory power than MLST and was comparable to the WGS and PFGE. In the phenotypic comparison study, we observed that the clustering results of probiotic physiological attributes (e.g., sensitivity to acid and bile salts, hydrophobicity of the cell surface, and resistance to antibiotics) were consistent with the typing results of IRBT. Our results indicated that IRBT is a robust tool for L. plantarum strain typing that could improve the efficiency of probiotic identification and preliminary screening, and can potentially be applied in probiotic traceability and quality control.
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Affiliation(s)
- Xiaoqiong Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Food Sciences, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Liying Zhu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Food Sciences, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xin Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Food Sciences, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Jinjun Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Food Sciences, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- *Correspondence: Jinjun Li,
| | - Biao Tang
- Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- Biao Tang,
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44
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Hu B, Hou P, Teng L, Miao S, Zhao L, Ji S, Li T, Kehrenberg C, Kang D, Yue M. Genomic Investigation Reveals a Community Typhoid Outbreak Caused by Contaminated Drinking Water in China, 2016. Front Med (Lausanne) 2022; 9:753085. [PMID: 35308507 PMCID: PMC8925297 DOI: 10.3389/fmed.2022.753085] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 02/04/2022] [Indexed: 12/27/2022] Open
Abstract
Typhoid fever is a life-threatening disease caused by Salmonella enterica serovar Typhi (S. Typhi) and remains a significant public health burden in developing countries. In China, typhoid fever is endemic with a limited number of reported outbreaks. Recently, Chinese local Center for Disease Prevention and Control is starting to apply whole genome sequencing for tracking the source of outbreak isolates. In this study, we conducted a retrospective investigation into a community outbreak of typhoid fever in Lanling, China, in 2016. A total of 26 S. Typhi isolates were recovered from the drinking water (n = 1) and patients' blood (n = 24) and stool (n = 1). Phylogenetic analysis indicated the persistence of the outbreak isolates in drinking water for more than 3 months. The genomic comparison demonstrated a high similarity between the isolate from water and isolates from patients in their genomic content, virulence gene profiles, and antimicrobial resistance gene profile, indicating the S. Typhi isolate from drinking water was responsible for the examined outbreak. The result of pulsed-field gel electrophoresis (PFGE) revealed these isolates had identical PFGE pattern, indicating they are clonal variants. Additionally, phylogeographical analysis of global S. Typhi isolates suggested the outbreak isolates are evolutionarily linked to the isolates from the United Kingdom and Vietnam. Taken together, this study highlights the drinking water and international travel as critical control points of mitigating the outbreak, emphasizing the necessity of regular monitoring of this pathogen in China.
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Affiliation(s)
- Bin Hu
- Shandong Provincial Center for Disease Control and Prevention, Jinan, China
| | - Peibin Hou
- Shandong Provincial Center for Disease Control and Prevention, Jinan, China
| | - Lin Teng
- Department of Veterinary Medicine, College of Veterinary Medicine, Zhejiang University, Hangzhou, China
| | - Song Miao
- Shandong Medical College, Jinan, China
| | - Lijiang Zhao
- Linyi Center for Disease Control and Prevention, Linyi, China
| | - Shengxiang Ji
- Linyi Center for Disease Control and Prevention, Linyi, China
| | - Tao Li
- Linyi Center for Disease Control and Prevention, Linyi, China
| | - Corinna Kehrenberg
- Institute for Veterinary Food Science, Justus-Liebig-University Giessen, Giessen, Germany
| | - Dianmin Kang
- Shandong Provincial Center for Disease Control and Prevention, Jinan, China
- *Correspondence: Dianmin Kang
| | - Min Yue
- Department of Veterinary Medicine, College of Veterinary Medicine, Zhejiang University, Hangzhou, China
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- The Hainan Institute of Zhejiang University, Sanya, China
- Min Yue
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45
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Krøvel AV, Bernhoff E, Austerheim E, Soma MA, Romstad MR, Löhr IH. Legionella pneumophila in Municipal Shower Systems in Stavanger, Norway; A Longitudinal Surveillance Study Using Whole Genome Sequencing in Risk Management. Microorganisms 2022; 10:microorganisms10030536. [PMID: 35336109 PMCID: PMC8954845 DOI: 10.3390/microorganisms10030536] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 02/25/2022] [Accepted: 02/26/2022] [Indexed: 12/10/2022] Open
Abstract
Following an incidence of Legionnaires disease (LD) in 2007, where a municipal shower system was the likely source of infection, Stavanger municipality initiated a surveillance program for Legionella as part of establishing internal risk evaluation and prevention routines. More than 250 shower systems were examined for cultivatable Legionella pneumophila. The prevalence and diversity of serogroups (sg) and sequence types (STs) of L. pneumophila were mapped using available typing techniques over a period of more than 10 years (2010–2021). The surveillance showed an overall reduction in the L. pneumophila colonisation rate in municipal systems from 11 to 4.5% following prevention measures during the period, with the highest colonisation rate in complex systems (e.g., larger nursing homes and sports complexes). Further, an approximately even distribution between sg1 and 2–14 was seen. Whole genome sequencing (WGS) revealed that only a limited number of STs were detected, and they were consistent at specific locations over time. This study showed that environmental surveillance data in combination with available typing techniques and WGS can give the municipality a better tool for risk management and an overview of ST distributions that can be a valuable asset in future source investigations.
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Affiliation(s)
- Anne Vatland Krøvel
- NORCE—Norwegian Research Centre, Environment Department, Professor Olav Hansenssvei 15, N-4021 Stavanger, Norway;
- National Reference Laboratory for Legionella, Department of Medical Microbiology, Stavanger University Hospital, P.O. Box 8100, N-4068 Stavanger, Norway; (E.B.); (M.A.S.); (M.R.R.); (I.H.L.)
- Correspondence:
| | - Eva Bernhoff
- National Reference Laboratory for Legionella, Department of Medical Microbiology, Stavanger University Hospital, P.O. Box 8100, N-4068 Stavanger, Norway; (E.B.); (M.A.S.); (M.R.R.); (I.H.L.)
| | - Elin Austerheim
- NORCE—Norwegian Research Centre, Environment Department, Professor Olav Hansenssvei 15, N-4021 Stavanger, Norway;
| | - Markus André Soma
- National Reference Laboratory for Legionella, Department of Medical Microbiology, Stavanger University Hospital, P.O. Box 8100, N-4068 Stavanger, Norway; (E.B.); (M.A.S.); (M.R.R.); (I.H.L.)
| | - Monica Regine Romstad
- National Reference Laboratory for Legionella, Department of Medical Microbiology, Stavanger University Hospital, P.O. Box 8100, N-4068 Stavanger, Norway; (E.B.); (M.A.S.); (M.R.R.); (I.H.L.)
| | - Iren Høyland Löhr
- National Reference Laboratory for Legionella, Department of Medical Microbiology, Stavanger University Hospital, P.O. Box 8100, N-4068 Stavanger, Norway; (E.B.); (M.A.S.); (M.R.R.); (I.H.L.)
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46
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Faula LL, Cerqueira MMOP, Madeira JEGC, Souza MR, Souza FN, Amancio GCS. Phenotypic and Genotypic Characterization of Salmonella Isolates Recovered from Foods Linked to Human Salmonellosis Outbreaks in Minas Gerais State, Brazil. J Food Prot 2022; 85:142-154. [PMID: 34525206 DOI: 10.4315/jfp-21-287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 09/10/2021] [Indexed: 11/11/2022]
Abstract
ABSTRACT Salmonella is one of the primary pathogens that causes foodborne diseases worldwide. In the present study, we characterized Salmonella isolates recovered from foods linked to human salmonellosis outbreaks in Minas Gerais, Brazil, from 2003 to 2017. Serotype, antimicrobial susceptibility, presence of virulence genes, and genetic polymorphism as determined by repetitive element sequence-based PCR were determined for 70 Salmonella isolates. Thirteen Salmonella serotypes were identified, and the most prevalent were Enteritidis and Typhimurium, comprising 52 (74.3%) of the 70 isolates. Sixty-five (92.8%) of the isolates were resistant to at least 1 of the 15 antimicrobials tested. Ten isolates (14.2%) had a multidrug resistance phenotype. Isolates were screened for 16 virulence genes, which were found in 75.7 to 100% of the isolates. A statistical difference was found among Salmonella serotypes in the presence of the sipB, sopE, lfpA, sefA, and spvC genes. Based on their DNA fingerprints, 40 isolates of Salmonella Enteritidis from 16 outbreaks were separated into 14 groups and 12 isolates of Salmonella Typhimurium were separated into 6 groups. These serological patterns were similar to those reported by public health centers worldwide. Of concern is the high prevalence among the isolates in this study of both virulence genes and resistance to antimicrobials, especially to critically important drugs. Special attention should be given to Salmonella Enteritidis. Although the genomes of these Salmonella isolates were relatively variable, high genetic similarity was observed among them, and some had identical fingerprints. These results support the hypothesis of clonal circulation of Salmonella isolates causing human infections in Minas Gerais. HIGHLIGHTS
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Affiliation(s)
- Leandro L Faula
- Divisão de Vigilância Sanitária e Ambiental, Laboratório Central de Saúde Pública de Minas Gerais, Fundação Ezequiel Dias, Rua Conde Pereira Carneiro 80, Belo Horizonte 30510-010, Brazil.,Departamento de Tecnologia e Inspeção de Produtos de Origem Animal, Escola de Medicina Veterinária, Universidade Federal de Minas Gerais, Av. Presidente Antônio Carlos 6627, Belo Horizonte 31270-901, Brazil
| | - Monica M O P Cerqueira
- Departamento de Tecnologia e Inspeção de Produtos de Origem Animal, Escola de Medicina Veterinária, Universidade Federal de Minas Gerais, Av. Presidente Antônio Carlos 6627, Belo Horizonte 31270-901, Brazil
| | - Jovita E G C Madeira
- Divisão de Vigilância Sanitária e Ambiental, Laboratório Central de Saúde Pública de Minas Gerais, Fundação Ezequiel Dias, Rua Conde Pereira Carneiro 80, Belo Horizonte 30510-010, Brazil
| | - Marcelo R Souza
- Departamento de Tecnologia e Inspeção de Produtos de Origem Animal, Escola de Medicina Veterinária, Universidade Federal de Minas Gerais, Av. Presidente Antônio Carlos 6627, Belo Horizonte 31270-901, Brazil
| | - Fernando N Souza
- Departamento de Medicina Interna, Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, Av. Prof. Dr. Orlando Marques de Paiva 87, São Paulo 05508-270, Brazil.,Programa de Pós Graduação em Ciência Animal, Universidade Federal da Paraíba, Areia 58397-000, Brazil
| | - Gláucia C S Amancio
- Divisão de Vigilância Sanitária e Ambiental, Laboratório Central de Saúde Pública de Minas Gerais, Fundação Ezequiel Dias, Rua Conde Pereira Carneiro 80, Belo Horizonte 30510-010, Brazil
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47
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Zhang Y, Liu K, Zhang Z, Tian S, Liu M, Li X, Han Y, Zhu K, Liu H, Yang C, Liu H, Du X, Wang Q, Wang H, Yang M, Wang L, Song H, Yang H, Xiang Y, Qiu S. A Severe Gastroenteritis Outbreak of Salmonella enterica Serovar Enteritidis Linked to Contaminated Egg Fried Rice, China, 2021. Front Microbiol 2021; 12:779749. [PMID: 34880847 PMCID: PMC8645860 DOI: 10.3389/fmicb.2021.779749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 10/22/2021] [Indexed: 12/04/2022] Open
Abstract
Salmonella contamination of eggs and egg shells has been identified as a public health problem worldwide. Here, we reported an outbreak of severe gastrointestinal symptoms caused by Salmonella enterica serovar Enteritidis (S. enteritidis) in China. We evaluated the outbreak by using epidemiological surveys, routine laboratory testing methods, and whole genome sequencing (WGS). This outbreak occurred in a canteen in Beijing, during March 9–11, 2021, 225 of the 324 diners who have eaten at the canteen showed gastrointestinal symptoms. The outbreak had characteristical epidemiological and clinical features. It caused a very high attack rate (69.4%) in a short incubation time. All patients developed diarrhea and high fever, accompanied by abdominal pain (62.3%), nausea (50.4%), and vomiting (62.7%). The average frequency of diarrhea was 12.4 times/day, and the highest frequency of diarrhea was as high as 50 times/day. The average fever temperature was 39.4°C, and the highest fever temperature was 42°C. Twenty strains of S. enteritidis were recovered, including 19 from the patients samples, and one from remained egg fried rice. Antibiotic susceptibility test showed that the 20 outbreak strains all had the same resistance pattern. PFGE results demonstrated that all 20 strains bore completely identical bands. Phylogenetic analysis based on WGS revealed that all 20 outbreak strains were tightly clustered together. So the pathogenic source of this food poisoning incident may was contaminated egg fried rice. Resistance gene analysis showed that the outbreak strains are all multi-drug resistant strains. Virulence gene analysis indicated that these outbreak strains carried a large number of virulence genes, including 2 types of Salmonella pathogenicity islands (SPI-1 and SPI-2). Other important virulence genes were also carried by the outbreak strains, such as pefABCD, rck and shdA. And the shdA gene was not in other strains located in the same evolutionary branch as the outbreak strain. We speculated that this is a significant reason for the serious symptoms of gastroenteritis in this outbreak. This outbreak caused by S. enteritidis suggested government should strengthen monitoring of the prevalence of outbreak clone strains, and take measures to mitigate the public health threat posed by contaminated eggs.
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Affiliation(s)
- Yaowen Zhang
- School of Public Health, Zhengzhou University, Zhengzhou, China.,Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Kangkang Liu
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Zhenbiao Zhang
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu, China
| | - Sai Tian
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Meiling Liu
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Xinge Li
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Yiran Han
- School of Public Health, Zhengzhou University, Zhengzhou, China
| | - Kunpeng Zhu
- School of Public Health, Zhengzhou University, Zhengzhou, China
| | - Hongbo Liu
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Chaojie Yang
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Hongbo Liu
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Xinying Du
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Qi Wang
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Hui Wang
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Mingjuan Yang
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Ligui Wang
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Hongbin Song
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Haiyan Yang
- School of Public Health, Zhengzhou University, Zhengzhou, China
| | - Ying Xiang
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Shaofu Qiu
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
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48
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Bedoya-Correa CM, Rincón-Rodríguez RJ, Parada-Sanchez MT. Acidogenic and aciduric properties of Streptococcus mutans serotype c according to its genomic variability. Eur J Oral Sci 2021; 129:e12824. [PMID: 34865249 DOI: 10.1111/eos.12824] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 07/27/2021] [Indexed: 11/24/2022]
Abstract
Streptococcus mutans (S. mutans) has a wide genetic diversity that contributes to its phenotypic heterogeneity, and may be related to attributes associated with acidogenicity and aciduricity. The aim of this study was to evaluate the acidogenic and aciduric properties of S. mutans serotype c isolates from saliva of schoolchildren according to the genomic variability. S. mutans isolates were identified by polymerase chain reaction. Fifty S. mutans serotype c isolates were genotyped by pulsed field gel electrophoresis and tested for their ability to produce and resist acid. Three specific genotypes were identified in the caries-active group and only one in the caries-free group. Although isolates were similarly acidogenic, an exclusive caries-active genotype had the greatest glycolytic activity. In contrast, isolates exhibited variable aciduricity, and three caries-active genotypes were the least aciduric. We concluded that there is genetic variability within serotype c. Acid production was similar regardless of the caries status but correlated with the number of genotypes. In addition, resistance to acid could be an important characteristic for the establishment and colonisation of specific genotypes in children with caries. However, it is important to evaluate children's intrinsic characteristics and other phenotypic properties to explain the physiopathological behaviour of the different genotypes.
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49
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Detection of synergistic antimicrobial resistance mechanisms in clinical isolates of Pseudomonas aeruginosa from post-operative wound infections. Appl Microbiol Biotechnol 2021; 105:9321-9332. [PMID: 34797390 DOI: 10.1007/s00253-021-11680-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/20/2021] [Accepted: 11/02/2021] [Indexed: 12/11/2022]
Abstract
Infections caused by carbapenem-resistant Pseudomonas aeruginosa are life-threatening due to its synergistic resistance mechanisms resulting in the ineffectiveness of the used antimicrobials. This study aimed to characterize P. aeruginosa isolates for antimicrobial susceptibility, biofilm formation virulence genes, and molecular mechanisms responsible for resistance against various antimicrobials. Out of 700 samples, 91 isolates were confirmed as P. aeruginosa which were further classified into 19 non-multidrug-resistant (non-MDR), 7 multidrug-resistant (MDR), 19 extensively drug-resistant (XDR), and 8 pan drug-resistant (PDR) pulsotypes based on standard Kirby Bauer disc diffusion test and pulse field gel electrophoresis. In M9 minimal media, strong biofilms were formed by the XDR and PDR pulsotypes as compared to the non-MDR pulsotypes. The virulence genes, responsible for the worsening of wounds including LasB, plcH, toxA, and exoU, were detected among all MDR, XDR, and PDR pulsotypes. Carbapenemase activity was phenotypically detected in 45% pulsotypes and the responsible genes were found as blaGES (100%), blaVIM (58%), blaIMP (4%), and blaNDM (4%). Real-time polymerase chain reaction showed the concomitant use of multiple mechanisms such as oprD under-expression, enhanced efflux pump activity, and ampC overexpression in the resistant isolates. Polymyxin is found as the only class left with more than 80% susceptibility among the isolates which is an alarming situation suggesting appropriate measures to be taken including alternative therapies. KEY POINTS: • Multidrug-resistant P. aeruginosa isolates formed stronger biofilms in minimal media. • Only polymyxin antimicrobial was found effective against MDR P. aeruginosa isolates. • Under-expression of oprD and overexpression of ampC were found in resistant isolates.
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50
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Woon JJ, Teh CSJ, Chong CW, Abdul Jabar K, Ponnampalavanar S, Idris N. Molecular Characterization of Carbapenem-Resistant Acinetobacter baumannii Isolated from the Intensive Care Unit in a Tertiary Teaching Hospital in Malaysia. Antibiotics (Basel) 2021; 10:antibiotics10111340. [PMID: 34827278 PMCID: PMC8615160 DOI: 10.3390/antibiotics10111340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/21/2021] [Accepted: 10/26/2021] [Indexed: 12/31/2022] Open
Abstract
The emergence of carbapenem-resistant Acinetobacter baumannii (CRAB) has now become a global sentinel event. CRAB infections often instigate severe clinical complications and are potentially fatal, especially for debilitated patients. The present study aimed to conduct molecular characterization on CRAB isolated from patients in the intensive care unit from 2015 to 2016 and determine the risk factors associated with patients’ mortality. One hundred CRAB isolates were retrospectively selected and included in this study. Antimicrobial susceptibility testing showed that all isolates remained susceptible to colistin, even though 62% of them conferred resistance to all other classes of antibiotics tested. OXA carbapenemase gene was found to be the predominant carbapenemase gene, with 99% of the isolates coharbouring blaOXA-23-like and blaOXA-51-like carbapenemase genes. All isolates were carrying intact CarO genes, with the presence of various degree of nucleotide insertion, deletion and substitution. Overall, PFGE subtyped the isolates into 13 distinct pulsotypes, with the presence of 2 predominant pulsotypes. Univariate analysis implied that age, infection/colonization by CRAB, ethnicity, comorbidity and CRAB specimen source were significantly associated with in-hospital mortality. Multivariate analysis identified a higher risk of mortality for patients who are of Chinese ethnicity with diabetes as an underlying disease. As CRAB infection could lead to high rate of mortality, comprehensive infection control measures are needed to minimize the spread of this pathogen.
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Affiliation(s)
- Jia Jie Woon
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur 50603, Malaysia; (J.J.W.); (C.S.J.T.); (K.A.J.)
| | - Cindy Shuan Ju Teh
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur 50603, Malaysia; (J.J.W.); (C.S.J.T.); (K.A.J.)
| | - Chun Wie Chong
- School of Pharmacy, Monash University Malaysia, Subang Jaya 47500, Malaysia
- Correspondence: (C.W.C.); (N.I.); Tel.: +60-379-676-671 (N.I.)
| | - Kartini Abdul Jabar
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur 50603, Malaysia; (J.J.W.); (C.S.J.T.); (K.A.J.)
| | - Sasheela Ponnampalavanar
- Department of Infectious Diseases, University of Malaya Medical Centre, Kuala Lumpur 50603, Malaysia;
| | - Nuryana Idris
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur 50603, Malaysia; (J.J.W.); (C.S.J.T.); (K.A.J.)
- Correspondence: (C.W.C.); (N.I.); Tel.: +60-379-676-671 (N.I.)
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