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Sonalio K, Boyen F, Devriendt B, Chantziaras I, Beuckelaere L, Biebaut E, Haesebrouck F, Santamarta I, de Oliveira LG, Maes D. Rationalizing the use of common parameters and technological tools to follow up Mycoplasma hyopneumoniae infections in pigs. Porcine Health Manag 2024; 10:31. [PMID: 39180129 PMCID: PMC11342468 DOI: 10.1186/s40813-024-00381-x] [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: 01/05/2024] [Accepted: 08/05/2024] [Indexed: 08/26/2024] Open
Abstract
BACKGROUND Mycoplasma (M.) hyopneumoniae is associated with respiratory disease in pigs and is the primary agent of enzootic pneumonia. Quantification of M. hyopneumoniae-related outcome parameters can be difficult, expensive, and time-consuming, in both research and field settings. In addition to well-established methods, technological tools are becoming available to monitor various aspects of relevant animal- and environment-related features, often in real-time. Therefore, this study aimed to assess whether certain parameters, such as animal movement and body temperature using microchips (IMT), correlate with established parameters and whether the currently used parameters can be rationalized. RESULTS The percentage of movement was significantly reduced by M. hyopneumoniae infection in pigs (p < 0.05), where the M. hyopneumoniae-infected group showed a lower percentage of movement (1.9%) when compared to the negative control group (6.9%). On the other hand, macroscopic (MLCL) and microscopic (MLL) lung lesions, respiratory disease score (RDS), M. hyopneumoniae-DNA load, and anti-M. hyopneumoniae antibody levels increased significantly in the M. hyopneumoniae-infected group 28 days post-inoculation (p < 0.05). Moderate (r > 0.30) to very strong correlations (> 0.80) were observed between the abovementioned parameters (p < 0.05), except for IMT. A significant and moderate correlation was reported between IMT and rectal temperature (r = 0.49; p < 0.05). Last, the average daily weight gain and the percentage of air in the lung were not affected by M. hyopneumoniae infection (p > 0.05). CONCLUSIONS M. hyopneumoniae infection significantly reduced the movement of piglets and increased lung lesions, M. hyopneumoniae-DNA load, and anti-M. hyopneumoniae antibody levels; and, good correlations were observed between most parameters, indicating a direct relationship between them. Thus, we suggest that changes in movement might be a reliable indicator of M. hyopneumoniae infection in pigs, and that a selected group of parameters-specifically RDS, MLCL, MLL, M. hyopneumoniae-DNA load, anti-M. hyopneumoniae antibody levels, and movement-are optimal to assess M. hyopneumoniae infection under experimental conditions.
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Affiliation(s)
- Karina Sonalio
- Department of Internal Medicine, Reproduction and Population Medicine, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium.
- Department of Veterinary Clinic and Surgery, School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), Jaboticabal, Brazil.
| | - Filip Boyen
- Department of Pathobiology, Pharmacology and Zoological Medicine, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Bert Devriendt
- Department of Translational Physiology, Infectiology and Public Health, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Ilias Chantziaras
- Department of Internal Medicine, Reproduction and Population Medicine, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Lisa Beuckelaere
- Department of Internal Medicine, Reproduction and Population Medicine, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Evelien Biebaut
- Department of Internal Medicine, Reproduction and Population Medicine, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Freddy Haesebrouck
- Department of Pathobiology, Pharmacology and Zoological Medicine, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | | | - Luís Guilherme de Oliveira
- Department of Veterinary Clinic and Surgery, School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), Jaboticabal, Brazil
| | - Dominiek Maes
- Department of Internal Medicine, Reproduction and Population Medicine, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
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Ahmed S, Albahri J, Shams S, Sosa-Portugal S, Lima C, Xu Y, McGalliard R, Jones T, Parry CM, Timofte D, Carrol ED, Muhamadali H, Goodacre R. Rapid Classification and Differentiation of Sepsis-Related Pathogens Using FT-IR Spectroscopy. Microorganisms 2024; 12:1415. [PMID: 39065183 PMCID: PMC11279078 DOI: 10.3390/microorganisms12071415] [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: 06/12/2024] [Revised: 07/05/2024] [Accepted: 07/09/2024] [Indexed: 07/28/2024] Open
Abstract
Sepsis is a life-threatening condition arising from a dysregulated host immune response to infection, leading to a substantial global health burden. The accurate identification of bacterial pathogens in sepsis is essential for guiding effective antimicrobial therapy and optimising patient outcomes. Traditional culture-based bacterial typing methods present inherent limitations, necessitating the exploration of alternative diagnostic approaches. This study reports the successful application of Fourier-transform infrared (FT-IR) spectroscopy in combination with chemometrics as a potent tool for the classification and discrimination of microbial species and strains, primarily sourced from individuals with invasive infections. These samples were obtained from various children with suspected sepsis infections with bacteria and fungi originating at different sites. We conducted a comprehensive analysis utilising 212 isolates from 14 distinct genera, comprising 202 bacterial and 10 fungal isolates. With the spectral analysis taking several weeks, we present the incorporation of quality control samples to mitigate potential variations that may arise between different sample plates, especially when dealing with a large sample size. The results demonstrated a remarkable consistency in clustering patterns among 14 genera when subjected to principal component analysis (PCA). Particularly, Candida, a fungal genus, was distinctly recovered away from bacterial samples. Principal component discriminant function analysis (PC-DFA) allowed for distinct discrimination between different bacterial groups, particularly Gram-negative and Gram-positive bacteria. Clear differentiation was also observed between coagulase-negative staphylococci (CNS) and Staphylococcus aureus isolates, while methicillin-resistant S. aureus (MRSA) was also separated from methicillin-susceptible S. aureus (MSSA) isolates. Furthermore, highly accurate discrimination was achieved between Enterococcus and vancomycin-resistant enterococci isolates with 98.4% accuracy using partial least squares-discriminant analysis. The study also demonstrates the specificity of FT-IR, as it effectively discriminates between individual isolates of Streptococcus and Candida at their respective species levels. The findings of this study establish a strong groundwork for the broader implementation of FT-IR and chemometrics in clinical and microbiological applications. The potential of these techniques for enhanced microbial classification holds significant promise in the diagnosis and management of invasive bacterial infections, thereby contributing to improved patient outcomes.
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Affiliation(s)
- Shwan Ahmed
- Centre for Metabolomics Research, Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK; (S.A.); (J.A.); (S.S.); (C.L.); (Y.X.)
- Department of Environment and Quality Control, Kurdistan Institution for Strategic Studies and Scientific Research, Sulaymaniyah, Kurdistan Region, Iraq
| | - Jawaher Albahri
- Centre for Metabolomics Research, Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK; (S.A.); (J.A.); (S.S.); (C.L.); (Y.X.)
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Khalid University, Abha 62529, Saudi Arabia
| | - Sahand Shams
- Centre for Metabolomics Research, Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK; (S.A.); (J.A.); (S.S.); (C.L.); (Y.X.)
| | - Silvana Sosa-Portugal
- Department of Veterinary Anatomy, Physiology and Pathology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Neston CH64 7TE, UK; (S.S.-P.); (D.T.)
| | - Cassio Lima
- Centre for Metabolomics Research, Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK; (S.A.); (J.A.); (S.S.); (C.L.); (Y.X.)
| | - Yun Xu
- Centre for Metabolomics Research, Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK; (S.A.); (J.A.); (S.S.); (C.L.); (Y.X.)
| | - Rachel McGalliard
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 7BE, UK; (R.M.); (T.J.); (E.D.C.)
| | - Trevor Jones
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 7BE, UK; (R.M.); (T.J.); (E.D.C.)
| | - Christopher M. Parry
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool L7 8XZ, UK;
| | - Dorina Timofte
- Department of Veterinary Anatomy, Physiology and Pathology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Neston CH64 7TE, UK; (S.S.-P.); (D.T.)
| | - Enitan D. Carrol
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 7BE, UK; (R.M.); (T.J.); (E.D.C.)
| | - Howbeer Muhamadali
- Centre for Metabolomics Research, Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK; (S.A.); (J.A.); (S.S.); (C.L.); (Y.X.)
| | - Royston Goodacre
- Centre for Metabolomics Research, Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK; (S.A.); (J.A.); (S.S.); (C.L.); (Y.X.)
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Wang SX, Park M, Kim SG. Complete genome sequence of Delftia tsuruhatensis strain HA60 isolated from a commercial hydroxyapatite nano-particle product (nano-hydroxyapatite). Microbiol Resour Announc 2024; 13:e0017124. [PMID: 38700346 PMCID: PMC11237730 DOI: 10.1128/mra.00171-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 04/22/2024] [Indexed: 05/05/2024] Open
Abstract
Delftia tsuruhatensis is a Gram-negative rod-shaped aerobic bacterium with environmental remediation functions. D. tsuruhatensis strain HA60 was isolated from a commercial nano-particle product, nano-hydroxyapatite. We report that the genome of D. tsuruhatensis strain HA60 has a circular genome of 6,922,195 base pairs with a G+C content of 66.45%.
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Affiliation(s)
- Sharon X. Wang
- Surveillance/Diagnostic Laboratory, Office of Scientific Coordination, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
| | - Miseon Park
- Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
| | - Sung Guk Kim
- Surveillance/Diagnostic Laboratory, Office of Scientific Coordination, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
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Morimura A, Taniguchi M, Takei H, Sakamoto O, Naono N, Akeda Y, Onozuka D, Yoshimura J, Tomono K, Kutsuna S, Hamaguchi S. Using novel micropore technology combined with artificial intelligence to differentiate Staphylococcus aureus and Staphylococcus epidermidis. Sci Rep 2024; 14:6994. [PMID: 38523156 PMCID: PMC10961322 DOI: 10.1038/s41598-024-55773-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 02/27/2024] [Indexed: 03/26/2024] Open
Abstract
Methods for identifying bacterial pathogens are broadly categorised into conventional culture-based microbiology, nucleic acid-based tests, and mass spectrometry. The conventional method requires several days to isolate and identify bacteria. Nucleic acid-based tests and mass spectrometry are relatively rapid and reliable, but they require trained technicians. Moreover, mass spectrometry requires expensive equipment. The development of a novel, inexpensive, and simple technique for identifying bacterial pathogens is needed. Through combining micropore technology and assembly machine learning, we developed a novel classifier whose receiver operating characteristic (ROC) curve showed an area under the ROC curve of 0.94, which rapidly differentiated between Staphylococcus aureus and Staphylococcus epidermidis in this proof-of-concept study. Morphologically similar bacteria belonging to an identical genus can be distinguished using our method, which requires no specific training, and may facilitate the diagnosis and treatment of patients with bacterial infections in remote areas and in developing countries.
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Affiliation(s)
- Ayumi Morimura
- Department of Infection Control and Prevention, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Masateru Taniguchi
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan
| | - Hiroyasu Takei
- Aipore Inc., 26-1 Sakuraoka-cho, Shibuya-ku, Tokyo, 150-8512, Japan
| | - Osamu Sakamoto
- Aipore Inc., 26-1 Sakuraoka-cho, Shibuya-ku, Tokyo, 150-8512, Japan
| | - Norihiko Naono
- Aipore Inc., 26-1 Sakuraoka-cho, Shibuya-ku, Tokyo, 150-8512, Japan
| | - Yukihiro Akeda
- Department of Bacteriology I, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan
| | - Daisuke Onozuka
- Department of Oral Microbe Control, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Jumpei Yoshimura
- Department of Traumatology and Acute Critical Medicine, Graduate School of Medicine, Osaka University, 2-15 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Kazunori Tomono
- Osaka Institute of Public Health, 1-3-3 Nakamichi, Higashinari-ku, Osaka, 537-0025, Japan
| | - Satoshi Kutsuna
- Department of Infection Control and Prevention, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
- Department of Oral Microbe Control, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
- Division of Infection Control and Prevention, Osaka University Hospital, 2-15 Yamadaoka, Suita, Osaka, 565-0871, Japan
- Division of Fostering Required Medical Human Resources, Center for Infectious Disease Education and Research (CiDER), Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Shigeto Hamaguchi
- Division of Infection Control and Prevention, Osaka University Hospital, 2-15 Yamadaoka, Suita, Osaka, 565-0871, Japan.
- Division of Fostering Required Medical Human Resources, Center for Infectious Disease Education and Research (CiDER), Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.
- Department of Transformative Analysis for Human Specimen, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.
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5
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Li D, Duan L, Zhang X, Cao J. Clinical significance of rapid detection and diagnosis of Listeria infection in blood with mass spectrometry. J Obstet Gynaecol Res 2024; 50:508-515. [PMID: 38087434 DOI: 10.1111/jog.15859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 11/30/2023] [Indexed: 03/04/2024]
Abstract
OBJECTIVE Listeriosis is caused by the bacterium, Listeria monocytogenes, and is a significant health concern because of high hospitalization and mortality rates. This study reports seven cases of pregnancy-associated listeriosis diagnosed with matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry performed on infection-positive blood culture. METHODS Blood culture-positive samples of seven patients whose pregnancy was complicated by Listeria infection and treated at Xuanwu Hospital of Capital Medical University between January 2016 and December 2021 were analyzed retrospectively. Strains identified by MALDI-TOF mass spectrometry were compared with colony identification results. Identification accuracy and consistency were assessed. RESULTS A total of seven strains of Listeria were collected from seven pregnant women presented with fever (37.6-39.9°C). Clinical abnormalities included abnormal liver function, emaciation, hypoalbuminemia, hypocalcemia, hypokalemia, hyponatremia, ketosis, mild to moderate anemia, leukopenia, and thrombocytopenia. Compared with the traditional culture method, MALDI-TOF mass spectrometry led to much earlier identification (4-6 h vs. 3-4 days) with 100% identification accuracy. Of the seven pregnancies complicated by Listeria, only two led to live births. Of the five fetal deaths, three occurred in the second trimester. CONCLUSION In this series of pregnancy-associated listeriosis cases, the fetal mortality rate was 71%. MALDI-TOF mass spectrometry is a valuable method that can identify Listeria from blood culture rapidly and accurately.
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Affiliation(s)
- Dan Li
- Department of Obstetrics and Gynecology, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Linyan Duan
- Education Section, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Xiaoyan Zhang
- Education Section, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Jingrong Cao
- Department of Clinical Laboratory, Xuanwu Hospital of Capital Medical University, Beijing, China
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Song M, Li Q, Liu C, Wang P, Qin F, Zhang L, Fan Y, Shao H, Chen G, Yang M. A comprehensive technology strategy for microbial identification and contamination investigation in the sterile drug manufacturing facility-a case study. Front Microbiol 2024; 15:1327175. [PMID: 38410390 PMCID: PMC10895062 DOI: 10.3389/fmicb.2024.1327175] [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: 10/24/2023] [Accepted: 01/30/2024] [Indexed: 02/28/2024] Open
Abstract
Objective A comprehensive strategy for microbial identification and contamination investigation during sterile drug manufacturing was innovatively established in this study, mainly based on MALDI-TOF MS for the identification and complemented by sequencing technology on strain typing. Methods It was implemented to monitor the bacterial contamination of a sterile drug manufacturing facility, including its bacterial distribution features and patterns. In three months, two hundred ninety-two samples were collected covering multiple critical components of raw materials, personnel, environment, and production water. Results Based on our strategy, the bacterial profile across the production process was determined: 241/292 bacterial identities were obtained, and Staphylococcus spp. (40.25%), Micrococcus spp.(11.20%), Bacillus spp. (8.30%), Actinobacteria (5.81%), and Paenibacillus spp. (4.56%) are shown to be the most dominant microbial contaminants. With 75.8% species-level and 95.4% genus-level identification capability, MALDI-TOF MS was promising to be a first-line tool for environmental monitoring routine. Furthermore, to determine the source of the most frequently occurring Staphylococcus cohnii, which evidenced a widespread presence in the entire process, a more discriminating S. cohnii whole-genome SNP typing method was developed to track the transmission routes. Phylogenetic analysis based on SNP results indicated critical environment contamination is highly relevant to personnel flow in this case. The strain typing results provide robust and accurate information for the following risk assessment step and support effective preventive and corrective measures. Conclusion In general, the strategy presented in this research will facilitate the development of improved production and environmental control processes for the pharmaceutical industry, and give insights about how to provide more sound and reliable evidence for the optimization of its control program.
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Affiliation(s)
- Minghui Song
- NMPA Key Laboratory for Testing Technology of Pharmaceutical Microbiology, Shanghai Institute for Food and Drug Control, Shanghai, China
- Shanghai Quality Inspection and Testing Center for Innovative Biological Products, Shanghai, China
| | - Qiongqiong Li
- NMPA Key Laboratory for Testing Technology of Pharmaceutical Microbiology, Shanghai Institute for Food and Drug Control, Shanghai, China
- Shanghai Quality Inspection and Testing Center for Innovative Biological Products, Shanghai, China
| | - Chengzhi Liu
- Hangzhou Digital-Micro Biotech Co., Ltd., Hangzhou, China
| | - Peien Wang
- NMPA Key Laboratory for Testing Technology of Pharmaceutical Microbiology, Shanghai Institute for Food and Drug Control, Shanghai, China
- Shanghai Quality Inspection and Testing Center for Innovative Biological Products, Shanghai, China
| | - Feng Qin
- NMPA Key Laboratory for Testing Technology of Pharmaceutical Microbiology, Shanghai Institute for Food and Drug Control, Shanghai, China
| | - Lichun Zhang
- Shanghai SPH New Asia Pharmaceutical Co., Ltd., Shanghai, China
| | - Yiling Fan
- NMPA Key Laboratory for Testing Technology of Pharmaceutical Microbiology, Shanghai Institute for Food and Drug Control, Shanghai, China
- Shanghai Quality Inspection and Testing Center for Innovative Biological Products, Shanghai, China
- China State Institute of Pharmaceutical Industry Co., Ltd., Shanghai, China
| | - Hong Shao
- NMPA Key Laboratory for Testing Technology of Pharmaceutical Microbiology, Shanghai Institute for Food and Drug Control, Shanghai, China
- Shanghai Quality Inspection and Testing Center for Innovative Biological Products, Shanghai, China
| | - Guiliang Chen
- China State Institute of Pharmaceutical Industry Co., Ltd., Shanghai, China
- Shanghai Center for Drug Evaluation and Inspection, Shanghai, China
| | - Meicheng Yang
- NMPA Key Laboratory for Testing Technology of Pharmaceutical Microbiology, Shanghai Institute for Food and Drug Control, Shanghai, China
- China State Institute of Pharmaceutical Industry Co., Ltd., Shanghai, China
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Chukwu S, Munn A, Wilson JC, Ibrahim H, Gosling D, Love RM, Bakr MM. Efficacy of an impression disinfectant solution after repeated use: An in vitro study. Heliyon 2024; 10:e23792. [PMID: 38223712 PMCID: PMC10784168 DOI: 10.1016/j.heliyon.2023.e23792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/30/2023] [Accepted: 12/13/2023] [Indexed: 01/16/2024] Open
Abstract
Statement of problem There are very few studies using Benzalkonium Chloride (BAC) as an active disinfection agent for immersion techniques and there are no studies investigating the efficacy of repeated use of a disinfectant solution. Purpose This study evaluated an impression disinfectant by testing bacterial contamination of disinfectant batches used in a clinical setting after repeated use. Materials and methods Liquid samples were collected from impression disinfectant solutions used to disinfect dental impressions taken at a university dental clinic. The experimental samples (500 ml from 1 L of solution) were collected from teaching and professional clinics and the in-house commercial processing laboratory and stored at room temperature each day of clinic operation over five weeks. To determine to what extent the disinfectant efficacy of the active product decreased over time, the following tests were carried out: a. Inoculation b. Gram staining technique c. Matrix Assisted Laser Desorption/Ionization Mass spectrometry (MALDI- MS). Microbial growth was monitored and photographed. A culture revival was made from colonies grown on sheep blood agar, to isolate pure colonies incubated for 24 h at 37 °C. Each morphologically distinct type of colony was gram stained and MALDI spectrometry analysis was performed using the VITEK MS (BioMerieux Inc.). Results Evidence of growth of bacteria was detected in teaching clinics' samples, and no growth from the professional clinic or the commercial laboratory. Conclusions The study demonstrated that impression disinfectanat solution tested is effective against common oral bacteria, despite some rare species such as Bacillus circulans, Bacillus horneckiae, Bacillus altitudinis/pumilus and Bacillus cereus showing evidence of survival in solutions used for disinfection of impressions. However, in a high use teaching clinic environment its efficacy deteriorated. Though a second level disinfection protocol in the commercial laboratory-maintained impression disinfection.
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Affiliation(s)
- Simon Chukwu
- Clinical Dental technologist, L & T Dental Laboratory Bridgend, Wales, UK
| | - Alan Munn
- Senior Lecturer in Biochemistry, School of Pharmacy and Medical Sciences, Griffith University, Queensland, Australia
| | - Jennifer C. Wilson
- Associate Professor, School of Pharmacy and Medical Sciences, Griffith University, Queensland, Australia
| | - Hadeel Ibrahim
- Lecturer in Prosthodontics, University of Melbourne, Prosthodontist at the Royal Dental Hospital of Melbourne, Australia
| | - Dean Gosling
- Advanced Scientist - Laboratory Operations Manager, Queensland Public Health and Scientific Services (QPHaSS), Queensland Health, Queensland, Australia
| | - Robert M. Love
- Dean of Dentistry, School of Medicine and Dentistry, Griffith University, Queensland, Australia
| | - Mahmoud M. Bakr
- Director of Clinical Education, Senior lecturer in General Dental Practice, School of Medicine and Dentistry, Griffith University, Queensland, Australia
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Williams A, Webster WZ, Cai C, Milgrom A, Al-Hasan M, Bookstaver PB. Evaluation of the diagnostic utility of metagenomic next-generation sequencing testing for pathogen identification in infected hosts: a retrospective cohort study. Ther Adv Infect Dis 2024; 11:20499361241232854. [PMID: 38404751 PMCID: PMC10893884 DOI: 10.1177/20499361241232854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 01/30/2024] [Indexed: 02/27/2024] Open
Abstract
Background Metagenomic next-generation sequencing (mNGS) testing identifies thousands of potential pathogens in a single blood test, though data on its real-world diagnostic utility are lacking. Objectives Determine the diagnostic utility of mNGS testing in practice and factors associated with high clinical utility. Design Retrospective cohort study of mNGS tests ordered from June 2018 through May 2020 at a community teaching hospital. Methods Tests were included if ordered for diagnostic purposes in patients with probable or high clinical suspicion of infection. Exclusions included patient expiration, hospice care, or transfer outside of the institution. Utility criteria were established a priori by the research team. Two investigators independently reviewed each test and categorized it to either high or low diagnostic utility. Reviewer discordance was referred to a third investigator. The stepwise multiple regression method was used to identify clinical factors associated with high diagnostic utility. Results Among 96 individual tests from 82 unique patients, 80 tests met the inclusion criteria for analysis. At least one potential pathogen was identified in 58% of tests. Among 112 pathogens identified, there were 74 bacteria, 25 viruses, 12 fungi, and 1 protozoon. In all, 46 tests (57.5%) were determined to be of high diagnostic utility. Positive mNGS tests were identified in 36 (78.3%) and 11 (32.4%) of high and low diagnostic utility tests, respectively (p < 0.001). Antimicrobials were changed after receiving test results in 31 (67.4%) of high utility tests and 4 (11.8%) of low utility tests (p < 0.0001). In the multiple regression model, a positive test [odds ratio (OR) = 10.9; 95% confidence interval (CI), 3.2-44.4] and consultation with the company medical director (OR = 3.6; 95% CI, 1.1-13.7) remained significantly associated with high diagnostic utility. Conclusion mNGS testing resulted in high clinical utility in most cases. Positive mNGS tests were associated with high diagnostic utility. Consultation with the Karius® medical director is recommended to maximize utility.
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Affiliation(s)
- Austin Williams
- Department of Pharmacy, Prisma Health Midlands, Columbia, SC, USA
| | - William Zach Webster
- Division of Infectious Diseases, Wake Forest Baptist Medical Center, Winston-Salem, NC, USA
| | - Chao Cai
- Department of Clinical Pharmacy and Outcomes Sciences, University of South Carolina College of Pharmacy, Columbia, SC, USA
| | - Alexander Milgrom
- Division of Infectious Diseases, Prisma Health Richland, Columbia, SC, USA
| | - Majdi Al-Hasan
- Division of Infectious Diseases, Prisma Health Richland, Columbia, SC, USA
| | - P. Brandon Bookstaver
- Department of Clinical Pharmacy and Outcomes Sciences, University of South Carolina College of Pharmacy, Columbia, SC 29208, USA
- Department of Pharmacy, Prisma Health Richland, 5 Medical Park Dr., Columbia, SC 29203, USA
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Sababadichetty L, Miltgen G, Vincent B, Guilhaumon F, Lenoble V, Thibault M, Bureau S, Tortosa P, Bouvier T, Jourand P. Microplastics in the insular marine environment of the Southwest Indian Ocean carry a microbiome including antimicrobial resistant (AMR) bacteria: A case study from Reunion Island. MARINE POLLUTION BULLETIN 2024; 198:115911. [PMID: 38103498 DOI: 10.1016/j.marpolbul.2023.115911] [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: 06/29/2023] [Revised: 11/13/2023] [Accepted: 12/05/2023] [Indexed: 12/19/2023]
Abstract
The increasing threats to ecosystems and humans from marine plastic pollution require a comprehensive assessment. We present a plastisphere case study from Reunion Island, a remote oceanic island located in the Southwest Indian Ocean, polluted by plastics. We characterized the plastic pollution on the island's coastal waters, described the associated microbiome, explored viable bacterial flora and the presence of antimicrobial resistant (AMR) bacteria. Reunion Island faces plastic pollution with up to 10,000 items/km2 in coastal water. These plastics host microbiomes dominated by Proteobacteria (80 %), including dominant genera such as Psychrobacter, Photobacterium, Pseudoalteromonas and Vibrio. Culturable microbiomes reach 107 CFU/g of microplastics, with dominance of Exiguobacterium and Pseudomonas. Plastics also carry AMR bacteria including β-lactam resistance. Thus, Southwest Indian Ocean islands are facing serious plastic pollution. This pollution requires vigilant monitoring as it harbors a plastisphere including AMR, that threatens pristine ecosystems and potentially human health through the marine food chain.
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Affiliation(s)
- Loik Sababadichetty
- Université de La Réunion, UMR ENTROPIE, 15 Avenue René Cassin, CS 92003, 97744 Saint Denis Cedex 9, La Réunion, France; CHU, Laboratoire de Bactériologie, CHU Félix Guyon, Allée des Topazes, 97400 Saint-Denis, La Réunion, France
| | - Guillaume Miltgen
- CHU, Laboratoire de Bactériologie, CHU Félix Guyon, Allée des Topazes, 97400 Saint-Denis, La Réunion, France; Université de La Réunion, UMR PIMIT Processus Infectieux en Milieu Insulaire Tropical, CNRS 9192, INSERM 1187, IRD 249, Plateforme de recherche CYROI, 2 rue Maxime Rivière, 97490 Ste Clotilde, La Réunion, France
| | - Bryan Vincent
- CIRAD, UMR040 LSTM, Campus Agro Environnemental Caraïbe, BP 214-97285, Cedex 2 le Lamentin, Martinique, Antilles Françaises, France
| | - François Guilhaumon
- IRD, UMR ENTROPIE, 15 Avenue René Cassin, CS 92003, 97744 Saint Denis Cedex 9, La Réunion, France
| | - Veronique Lenoble
- Université de Toulon, Aix Marseille Université, CNRS, IRD, UMR MIO, 83 Toulon, France
| | - Margot Thibault
- Université de La Réunion, UMR ENTROPIE, 15 Avenue René Cassin, CS 92003, 97744 Saint Denis Cedex 9, La Réunion, France; The Ocean Cleanup, Rotterdam, the Netherlands; CNRS, Université Toulouse III, Laboratoire des Interactions Moléculaires et Réactivité Chimique et Photochimique (IMRCP), UMR 5623, Toulouse, France
| | - Sophie Bureau
- Université de La Réunion, UMR ENTROPIE, 15 Avenue René Cassin, CS 92003, 97744 Saint Denis Cedex 9, La Réunion, France
| | - Pablo Tortosa
- Université de La Réunion, UMR PIMIT Processus Infectieux en Milieu Insulaire Tropical, CNRS 9192, INSERM 1187, IRD 249, Plateforme de recherche CYROI, 2 rue Maxime Rivière, 97490 Ste Clotilde, La Réunion, France
| | - Thierry Bouvier
- UMR MARBEC, Université Montpellier, CNRS, Ifremer, IRD, Montpellier, France
| | - Philippe Jourand
- IRD, UMR ENTROPIE, 15 Avenue René Cassin, CS 92003, 97744 Saint Denis Cedex 9, La Réunion, France.
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10
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Coenye T. Biofilm antimicrobial susceptibility testing: where are we and where could we be going? Clin Microbiol Rev 2023; 36:e0002423. [PMID: 37812003 PMCID: PMC10732061 DOI: 10.1128/cmr.00024-23] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 07/27/2023] [Indexed: 10/10/2023] Open
Abstract
Our knowledge about the fundamental aspects of biofilm biology, including the mechanisms behind the reduced antimicrobial susceptibility of biofilms, has increased drastically over the last decades. However, this knowledge has so far not been translated into major changes in clinical practice. While the biofilm concept is increasingly on the radar of clinical microbiologists, physicians, and healthcare professionals in general, the standardized tools to study biofilms in the clinical microbiology laboratory are still lacking; one area in which this is particularly obvious is that of antimicrobial susceptibility testing (AST). It is generally accepted that the biofilm lifestyle has a tremendous impact on antibiotic susceptibility, yet AST is typically still carried out with planktonic cells. On top of that, the microenvironment at the site of infection is an important driver for microbial physiology and hence susceptibility; but this is poorly reflected in current AST methods. The goal of this review is to provide an overview of the state of the art concerning biofilm AST and highlight the knowledge gaps in this area. Subsequently, potential ways to improve biofilm-based AST will be discussed. Finally, bottlenecks currently preventing the use of biofilm AST in clinical practice, as well as the steps needed to get past these bottlenecks, will be discussed.
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Affiliation(s)
- Tom Coenye
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
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11
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Sarr M, Alou MT, Padane A, Diouf FS, Beye M, Sokhna C, Fenollar F, Mboup S, Raoult D, Million M. A review of the literature of Listeria monocytogenes in Africa highlights breast milk as an overlooked human source. Front Microbiol 2023; 14:1213953. [PMID: 38173673 PMCID: PMC10761537 DOI: 10.3389/fmicb.2023.1213953] [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: 04/28/2023] [Accepted: 11/29/2023] [Indexed: 01/05/2024] Open
Abstract
According to the latest WHO estimates (2015) of the global burden of foodborne diseases, Listeria monocytogenes is responsible for one of the most serious foodborne infections and commonly results in severe clinical outcomes. The 2013 French MONALISA prospective cohort identified that women born in Africa has a 3-fold increase in the risk of maternal neonatal listeriosis. One of the largest L. monocytogenes outbreaks occurred in South Africa in 2017-2018 with over 1,000 cases. Moreover, recent findings identified L. monocytogenes in human breast milk in Mali and Senegal with its relative abundance positively correlated with severe acute malnutrition. These observations suggest that the carriage of L. monocytogenes in Africa should be further explored, starting with the existing literature. For that purpose, we searched the peer-reviewed and grey literature published dating back to 1926 to date using six databases. Ultimately, 225 articles were included in this review. We highlighted that L. monocytogenes is detected in various sample types including environmental samples, food samples as well as animal and human samples. These studies were mostly conducted in five east African countries, four west African countries, four north African countries, and two Southern African countries. Moreover, only ≈ 0.2% of the Listeria monocytogenes genomes available on NCBI were obtained from African samples, contracted with its detection. The pangenome resulting from the African Listeria monocytogenes samples revealed three clusters including two from South-African strains as well as one consisting of the strains isolated from breast milk in Mali and Senegal and, a vaginal post-miscarriage sample. This suggests there was a clonal complex circulating in Mali and Senegal. As this clone has not been associated to infections, further studies should be conducted to confirm its circulation in the region and explore its association with foodborne infections. Moreover, it is apparent that more resources should be allocated to the detection of L. monocytogenes as only 15/54 countries have reported its detection in the literature. It seems paramount to map the presence and carriage of L. monocytogenes in all African countries to prevent listeriosis outbreaks and the related miscarriages and confirm its association with severe acute malnutrition.
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Affiliation(s)
- Marièma Sarr
- Aix Marseille University, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
- Campus Commun UCAD-IRD of Hann, Dakar, Senegal
- Institut de Recherche en Santé, de Surveillance Épidémiologique et de Formation (IRESSEF), Dakar, Senegal
| | - Maryam Tidjani Alou
- Aix Marseille University, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - Abdou Padane
- Institut de Recherche en Santé, de Surveillance Épidémiologique et de Formation (IRESSEF), Dakar, Senegal
| | - Fatou Samba Diouf
- Aix Marseille University, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
- Campus Commun UCAD-IRD of Hann, Dakar, Senegal
| | - Mamadou Beye
- Aix Marseille University, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - Cheikh Sokhna
- Campus Commun UCAD-IRD of Hann, Dakar, Senegal
- Aix Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - Florence Fenollar
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - Souleymane Mboup
- Institut de Recherche en Santé, de Surveillance Épidémiologique et de Formation (IRESSEF), Dakar, Senegal
| | - Didier Raoult
- Aix Marseille University, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - Matthieu Million
- Aix Marseille University, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
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12
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Didouh N, Khadidja M, Campos C, Sampaio-Maia B, Boumediene MB, Araujo R. Assessment of biofilm, enzyme production and antibiotic susceptibility of bacteria from milk pre- and post-pasteurization pipelines in Algeria. Int J Food Microbiol 2023; 407:110389. [PMID: 37708608 DOI: 10.1016/j.ijfoodmicro.2023.110389] [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: 05/17/2023] [Revised: 09/01/2023] [Accepted: 09/02/2023] [Indexed: 09/16/2023]
Abstract
Bacterial biofilm is a major concern of dairy industry due to its association with milk contamination and its derived products. Algerian pasteurized milk shelf-life does not exceed one day, which may reflect the high level of contamination of this product and presence of extracellular enzymes such as lipases and proteases. This work aimed to investigate the microbial biodiversity in milk-processing surfaces of a dairy plant in Algeria. Therefore, stainless steel cylinders were placed in piping system of the dairy system before and after pasteurization of the milk, being removed after 7 days, for biofilm maturation and microorganism isolation and identification by mass spectrometry. Fifty-nine Gram-positive isolates were identified, namely Bacillus altitudinis, Bacillus cereus, Bacillus pumilus, Bacillus subtilis, Bacillus weithenstephanensis, Enterococcus casseliflavus, Enterococcus faecium, and Staphylococcus epidermidis. In addition, twenty-four Gram-negative isolates were identified, namely Acinetobacter schindleri Enterobacter cloacae, Enterobacter xiangfangensis, Leclercia adecarboxylata, and Raoultella ornithinolytica. Bacterial isolates showed ability for production of extracellular enzymes, being 49 % capable of both proteolytic and lipolytic activities. Milk isolates were tested for the ability to form biofilms on stainless steel. The cell numbers recovered on plate count agar plates from stainless steel biofilms ranged from 3.52 to 6.92 log10 CFU/cm2, being the maximum number detected for Enterococcus casseliflavus. Bacterial isolates showed intermediate and/or resistant profiles to multiple antibiotics. Resistance to amoxicillin, cefoxitin and/or erythromycin was commonly found among the bacterial isolates.
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Affiliation(s)
- Nassima Didouh
- Université Abou Bekr Belkaid Tlemcen, Algeria; Laboratoire de Microbiologie Appliqué à l'Agroalimentaire au Biomédical et à l'Environnement, 13000 Tlemcen, Algeria
| | - Medjahdi Khadidja
- Université Abou Bekr Belkaid Tlemcen, Algeria; Laboratoire de Microbiologie Appliqué à l'Agroalimentaire au Biomédical et à l'Environnement, 13000 Tlemcen, Algeria; Université Hassiba Benbouali Chlef, Algeria
| | - Carla Campos
- Instituto Português de Oncologia (IPO) do Porto Francisco Gentil, Porto, Portugal
| | - Benedita Sampaio-Maia
- Nephrology & Infectious Diseases R&D Group, INEB - Instituto de Engenharia Biomédica, i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal; Faculdade de Medicina Dentária, Universidade do Porto, Porto, Portugal
| | - Moussa Boudjemaa Boumediene
- Université Abou Bekr Belkaid Tlemcen, Algeria; Laboratoire de Microbiologie Appliqué à l'Agroalimentaire au Biomédical et à l'Environnement, 13000 Tlemcen, Algeria
| | - Ricardo Araujo
- Nephrology & Infectious Diseases R&D Group, INEB - Instituto de Engenharia Biomédica, i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.
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13
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Tamai S, Suzuki Y. Diversity of Fecal Indicator Enterococci among Different Hosts: Importance to Water Contamination Source Tracking. Microorganisms 2023; 11:2981. [PMID: 38138125 PMCID: PMC10745335 DOI: 10.3390/microorganisms11122981] [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: 10/24/2023] [Revised: 12/04/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023] Open
Abstract
Enterococcus spp. are common bacteria present in the intestinal tracts of animals and are used as fecal indicators in aquatic environments. On the other hand, enterococci are also known as opportunistic pathogens. Elucidating their composition in the intestinal tracts of domestic animals can assist in estimating the sources of fecal contamination in aquatic environments. However, information on the species and composition of enterococci in animal hosts (except humans) is still lacking. In this study, enterococci were isolated from the feces of cattle, pigs, birds, and humans using selective media. Enterococcal species were identified using mass spectrometry technology, and each host was characterized by diversity and cluster analysis. The most dominant species were E. hirae in cattle, E. faecium in birds, and E. faecalis in pigs and humans. Cattle had the highest alpha diversity, with high interindividual and livestock farm diversity. The dominant enterococcal species in pigs and humans were identical, and cluster analysis showed that the majority of the two hosts' species clustered together.
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Affiliation(s)
| | - Yoshihiro Suzuki
- Department of Civil and Environmental Engineering, Faculty of Engineering, University of Miyazaki, Miyazaki 889-2192, Japan;
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14
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Wang Z, Zhou Y, Guo G, Li Q, Yu Y, Zhang W. Promising potential of machine learning-assisted MALDI-TOF MS as an effective detector for Streptococcus suis serotype 2 and virulence thereof. Appl Environ Microbiol 2023; 89:e0128423. [PMID: 37861326 PMCID: PMC10686076 DOI: 10.1128/aem.01284-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 09/01/2023] [Indexed: 10/21/2023] Open
Abstract
IMPORTANCE To the best of our knowledge, this study reveals a strong correlation between mass spectra pattern and virulence phenotype among S. suis for the first time. In order to make the findings applicable and to excavate the intrinsic information in the spectra, the classifiers based on the machine learning algorithms were established, and RF (Random Forest)-based models have achieved an accuracy of over 90%. Overall, this study will pave the way for virulent SS2 (Streptococcus suis serotype 2) rapid detection, and the important findings on the association between genotype and mass spectrum may provide a new idea for the genotype-dependent detection of specific pathogens.
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Affiliation(s)
- Zhuohao Wang
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- OIE Reference Lab for Swine Streptococcosis, Nanjing, China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, China
- The Sanya Institute of Nanjing Agriculture University, Sanya, China
| | - Yu Zhou
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- OIE Reference Lab for Swine Streptococcosis, Nanjing, China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, China
- The Sanya Institute of Nanjing Agriculture University, Sanya, China
| | - Genglin Guo
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- OIE Reference Lab for Swine Streptococcosis, Nanjing, China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, China
- The Sanya Institute of Nanjing Agriculture University, Sanya, China
| | - Quan Li
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Yanfei Yu
- Key Laboratory of Veterinary Biological Engineering and Technology of Ministry of Agriculture, Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Wei Zhang
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- OIE Reference Lab for Swine Streptococcosis, Nanjing, China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, China
- The Sanya Institute of Nanjing Agriculture University, Sanya, China
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15
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Laurence Yehouenou C, Bogaerts B, Vanneste K, De Keersmaecker SCJ, Roosens NHC, Kpangon AA, Affolabi D, Simon A, Dossou FM, Dalleur O. Whole-Genome Sequencing-Based Screening of MRSA in Patients and Healthcare Workers in Public Hospitals in Benin. Microorganisms 2023; 11:1954. [PMID: 37630513 PMCID: PMC10459514 DOI: 10.3390/microorganisms11081954] [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: 06/27/2023] [Revised: 07/11/2023] [Accepted: 07/14/2023] [Indexed: 08/27/2023] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) constitutes a serious public health concern, with a considerable impact on patients' health, and substantial healthcare costs. In this study, patients and healthcare workers (HCWs) from six public hospitals in Benin were screened for MRSA. Strains were identified as MRSA using conventional microbiological methods in Benin, and confirmed using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry in Belgium. Whole-genome sequencing (WGS) was used on the confirmed MRSA isolates, to characterize their genomic content and study their relatedness. Amongst the 305 isolates (304 wound swabs and 61 nasal swabs) that were collected from patients and HCWs, we detected 32 and 15 cases of MRSA, respectively. From this collection, 27 high-quality WGS datasets were obtained, which carried numerous genes and mutations associated with antimicrobial resistance. The mecA gene was detected in all the sequenced isolates. These isolates were assigned to five sequence types (STs), with ST8 (55.56%, n = 15/27), ST152 (18.52%, n = 5/27), and ST121 (18.52%, n = 5/27) being the most common. These 27 isolates carried multiple virulence genes, including the genes encoding the Panton-Valentine leukocidin toxin (48.15%, n = 13/27), and the tst gene (29.63%, n = 8/27), associated with toxic shock syndrome. This study highlights the need to implement a multimodal strategy for reducing the risk of the cross-transmission of MRSA in hospitals.
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Affiliation(s)
- Carine Laurence Yehouenou
- Clinical Pharmacy Research Group (CLIP), Louvain Drug Research Institute (LDRI), Université Catholique de Louvain UCLouvain, Avenue Mounier 73, 1200 Brussels, Belgium;
- Laboratoire de Référence des Mycobactéries (LRM), Cotonou BP 817, Benin;
- Faculté des Sciences de la Santé (FSS), Université d’Abomey Calavi (UAC), Cotonou 01 BP 188, Benin
| | - Bert Bogaerts
- Transversal Activities in Applied Genomics, Sciensano, Juliette Wytsmanstraat 14, 1050 Brussels, Belgium; (B.B.); (K.V.); (S.C.J.D.K.); (N.H.C.R.)
| | - Kevin Vanneste
- Transversal Activities in Applied Genomics, Sciensano, Juliette Wytsmanstraat 14, 1050 Brussels, Belgium; (B.B.); (K.V.); (S.C.J.D.K.); (N.H.C.R.)
| | - Sigrid C. J. De Keersmaecker
- Transversal Activities in Applied Genomics, Sciensano, Juliette Wytsmanstraat 14, 1050 Brussels, Belgium; (B.B.); (K.V.); (S.C.J.D.K.); (N.H.C.R.)
| | - Nancy H. C. Roosens
- Transversal Activities in Applied Genomics, Sciensano, Juliette Wytsmanstraat 14, 1050 Brussels, Belgium; (B.B.); (K.V.); (S.C.J.D.K.); (N.H.C.R.)
| | - Arsène A. Kpangon
- Ecole Nationale des Techniciens Supérieurs en Santé Publique et Surveillance Épidémiologique, Université de Parakou, Parakou, Benin;
| | - Dissou Affolabi
- Laboratoire de Référence des Mycobactéries (LRM), Cotonou BP 817, Benin;
- Faculté des Sciences de la Santé (FSS), Université d’Abomey Calavi (UAC), Cotonou 01 BP 188, Benin
- Centre National Hospitalier et Universitaire Hubert Koutoukou Maga (CNHU-HKM), Cotonou BP 386, Benin
| | - Anne Simon
- Centres Hospitaliers Jolimont, Prévention et Contrôle des Infections, Groupe Jolimont Asbl, Rue Ferrer 159, 7100 Haine-Saint-Paul, Belgium;
| | - Francis Moise Dossou
- Department of Surgery and Surgical Specialties, Faculty of Health Sciences, Campus Universitaire, Champs de Foire, Cotonou 01 BP 118, Benin;
| | - Olivia Dalleur
- Clinical Pharmacy Research Group (CLIP), Louvain Drug Research Institute (LDRI), Université Catholique de Louvain UCLouvain, Avenue Mounier 73, 1200 Brussels, Belgium;
- Pharmacy, Clinique Universitaire Saint-Luc, Université Catholique de Louvain (UCLouvain), Avenue Hippocrate 10, 1200 Brussels, Belgium
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16
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Akinyemi KO, Fakorede CO, Linde J, Methner U, Wareth G, Tomaso H, Neubauer H. Whole genome sequencing of Salmonella enterica serovars isolated from humans, animals, and the environment in Lagos, Nigeria. BMC Microbiol 2023; 23:164. [PMID: 37312043 DOI: 10.1186/s12866-023-02901-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 05/17/2023] [Indexed: 06/15/2023] Open
Abstract
BACKGROUND Salmonella infections remain an important public health issue worldwide. Some serovars of non-typhoidal Salmonella (NTS) have been associated with bloodstream infections and gastroenteritis, especially in children in Sub-Saharan Africa with circulating S. enterica serovars with drug resistance and virulence genes. This study identified and verified the clonal relationship of Nigerian NTS strains isolated from humans, animals, and the environment. METHODS In total, 2,522 samples were collected from patients, animals (cattle and poultry), and environmental sources between December 2017 and May 2019. The samples were subjected to a standard microbiological investigation. All the isolates were identified using Microbact 24E, and MALDI-TOF MS. The isolates were serotyped using the Kauffmann-White scheme. Antibiotic susceptibility testing was conducted using the disc diffusion method and the Vitek 2 compact system. Virulence and antimicrobial resistance genes, sequence type, and cluster analysis were investigated using WGS data. RESULTS Forty-eight (48) NTS isolates (1.9%) were obtained. The prevalence of NTS from clinical sources was 0.9%, while 4% was recorded for animal sources. The serovars identified were S. Cotham (n = 17), S. Give (n = 16), S. Mokola (n = 6), S. Abony (n = 4), S. Typhimurium (n = 4), and S. Senftenberg (n = 1). All 48 Salmonella isolates carried intrinsic and acquired resistant genes such as aac.6…Iaa, mdf(A), qnrB, qnrB19 genes and golT, golS, pcoA, and silP, mediated by plasmid Col440I_1, incFIB.B and incFII. Between 100 and 118 virulence gene markers distributed across several Salmonella pathogenicity islands (SPIs), clusters, prophages, and plasmid operons were found in each isolate. WGS revealed that strains of each Salmonella serovar could be assigned to a single 7-gene MLST cluster, and strains within the clusters were identical strains and closely related as defined by the 0 and 10 cgSNPs and likely shared a common ancestor. The dominant sequence types were S. Give ST516 and S. Cotham ST617. CONCLUSION We found identical Salmonella sequence types in human, animal, and environmental samples in the same locality, which demonstrates the great potential of the applied tools to trace back outbreak strains. Strategies to control and prevent the spread of NTS in the context of one's health are essential to prevent possible outbreaks.
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Affiliation(s)
| | | | - Jörg Linde
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institute, Jena, Germany
| | - Ulrich Methner
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institute, Jena, Germany
| | - Gamal Wareth
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institute, Jena, Germany
- Department of Bacteriology, Immunology, and Mycology, Faculty of Veterinary Medicine, Benha University, PO Box 13736, Toukh, Moshtohor, Egypt
- Institute of Infectious Diseases and Infection Control, Jena University Hospital, Am Klinikum 1, 07747, Jena, Germany
| | - Herbert Tomaso
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institute, Jena, Germany
| | - Heinrich Neubauer
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institute, Jena, Germany
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17
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Qiao J, Chen Y, Ge H, Xu H, Guo X, Liu R, Li C, Chen R, Gou J, Chen M, Zheng B. Coexistence of blaIMP-4, blaNDM-1 and blaOXA-1 in blaKPC-2-producing Citrobacter freundii of clinical origin in China. Front Microbiol 2023; 14:1074612. [PMID: 37378293 PMCID: PMC10291173 DOI: 10.3389/fmicb.2023.1074612] [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: 10/19/2022] [Accepted: 05/19/2023] [Indexed: 06/29/2023] Open
Abstract
Purpose To explore the genetic characteristics of the IMP-4, NDM-1, OXA-1, and KPC-2 co-producing multidrug-resistant (MDR) clinical isolate, Citrobacter freundii wang9. Methods MALDI-TOF MS was used for species identification. PCR and Sanger sequencing analysis were used to identify resistance genes. In addition to agar dilution, broth microdilution was used for antimicrobial susceptibility testing (AST). We performed whole genome sequencing (WGS) of the strains and analyzed the resulting data for drug resistance genes and plasmids. Phylogenetic trees were constructed with maximum likelihood, plotted using MAGA X, and decorated by iTOL. Results Citrobacter freundii carrying blaKPC-2, blaIMP-4, blaOXA-1, and blaNDM-1 are resistant to most antibiotics, intermediate to tigecycline, and only sensitive to polymyxin B, amikacin, and fosfomycin. The blaIMP-4 coexists with the blaNDM-1 and the blaOXA-1 on a novel transferable plasmid variant pwang9-1, located on the integron In1337, transposon TnAS3, and integron In2054, respectively. The gene cassette sequence of integron In1337 is IntI1-blaIMP-4-qacG2-aacA4'-catB3Δ, while the gene cassette sequence of In2054 is IntI1-aacA4cr-blaOXA-1-catB3-arr3-qacEΔ1-sul1. The blaNDM-1 is located on the transposon TnAS3, and its sequence is IS91-sul-ISAba14-aph (3')-VI-IS30-blaNDM-1-ble-trpF-dsbD-IS91. The blaKPC-2 is located on the transposon Tn2 of plasmid pwang9-1, and its sequence is klcA-korC-ISkpn6-blaKPC-2-ISkpn27-tnpR-tnpA. Phylogenetic analysis showed that most of the 34\u00B0C. freundii isolates from China were divided into three clusters. Among them, wang1 and wang9 belong to the same cluster as two strains of C. freundii from environmental samples from Zhejiang. Conclusion We found C. freundii carrying blaIMP-4, blaNDM-1, blaOXA-1, and blaKPC-2 for the first time, and conducted in-depth research on its drug resistance mechanism, molecular transfer mechanism and epidemiology. In particular, we found that blaIMP-4, blaOXA-1, and blaNDM-1 coexisted on a new transferable hybrid plasmid that carried many drug resistance genes and insertion sequences. The plasmid may capture more resistance genes, raising our concern about the emergence of new resistance strains.
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Affiliation(s)
- Jie Qiao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Department of Laboratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yingying Chen
- Department of Neurosurgery, Shaoxing People’s Hospital (Shaoxing Hospital, Zhejiang University School of Medicine), Shaoxing, China
| | - Haoyu Ge
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Department of Laboratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Hao Xu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Xiaobing Guo
- Department of Laboratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ruishan Liu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Chenyu Li
- Department of Laboratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ruyan Chen
- Department of Laboratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jianjun Gou
- Department of Laboratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Mantao Chen
- Department of Neurosurgery, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Beiwen Zheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Department of Structure and Morphology, Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
- Research Units of Infectious Diseases and Microecology, Chinese Academy of Medical Sciences, Beijing, China
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Mohammad N, Normand AC, Nabet C, Godmer A, Brossas JY, Blaize M, Bonnal C, Fekkar A, Imbert S, Tannier X, Piarroux R. Improving the Detection of Epidemic Clones in Candida parapsilosis Outbreaks by Combining MALDI-TOF Mass Spectrometry and Deep Learning Approaches. Microorganisms 2023; 11:microorganisms11041071. [PMID: 37110493 PMCID: PMC10146746 DOI: 10.3390/microorganisms11041071] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/11/2023] [Accepted: 04/17/2023] [Indexed: 04/29/2023] Open
Abstract
Identifying fungal clones propagated during outbreaks in hospital settings is a problem that increasingly confronts biologists. Current tools based on DNA sequencing or microsatellite analysis require specific manipulations that are difficult to implement in the context of routine diagnosis. Using deep learning to classify the mass spectra obtained during the routine identification of fungi by MALDI-TOF mass spectrometry could be of interest to differentiate isolates belonging to epidemic clones from others. As part of the management of a nosocomial outbreak due to Candida parapsilosis in two Parisian hospitals, we studied the impact of the preparation of the spectra on the performance of a deep neural network. Our purpose was to differentiate 39 otherwise fluconazole-resistant isolates belonging to a clonal subset from 56 other isolates, most of which were fluconazole-susceptible, collected during the same period and not belonging to the clonal subset. Our study carried out on spectra obtained on four different machines from isolates cultured for 24 or 48 h on three different culture media showed that each of these parameters had a significant impact on the performance of the classifier. In particular, using different culture times between learning and testing steps could lead to a collapse in the accuracy of the predictions. On the other hand, including spectra obtained after 24 and 48 h of growth during the learning step restored the good results. Finally, we showed that the deleterious effect of the device variability used for learning and testing could be largely improved by including a spectra alignment step during preprocessing before submitting them to the neural network. Taken together, these experiments show the great potential of deep learning models to identify spectra of specific clones, providing that crucial parameters are controlled during both culture and preparation steps before submitting spectra to a classifier.
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Affiliation(s)
- Noshine Mohammad
- Groupe Hospitalier Pitié-Salpêtrière, Service de Parasitologie Mycologie, AP-HP, 75013 Paris, France
- INSERM, Institut Pierre-Louis d'Épidémiologie et de Santé Publique, Sorbonne Université, 75013 Paris, France
| | - Anne-Cécile Normand
- Groupe Hospitalier Pitié-Salpêtrière, Service de Parasitologie Mycologie, AP-HP, 75013 Paris, France
| | - Cécile Nabet
- Groupe Hospitalier Pitié-Salpêtrière, Service de Parasitologie Mycologie, AP-HP, 75013 Paris, France
- INSERM, Institut Pierre-Louis d'Épidémiologie et de Santé Publique, Sorbonne Université, 75013 Paris, France
| | - Alexandre Godmer
- CIMI-Paris, Centre d'Immunologie et des Maladies Infectieuses, UMR 1135, Sorbonne Université, 75013 Paris, France
- Département de Bactériologie, Hôpital Saint-Antoine, AP-HP, Sorbonne Université, 75012 Paris, France
| | - Jean-Yves Brossas
- Groupe Hospitalier Pitié-Salpêtrière, Service de Parasitologie Mycologie, AP-HP, 75013 Paris, France
| | - Marion Blaize
- Groupe Hospitalier Pitié-Salpêtrière, Service de Parasitologie Mycologie, AP-HP, 75013 Paris, France
- CIMI-Paris, Centre d'Immunologie et des Maladies Infectieuses, CNRS, INSERM, Sorbonne Université, 75013 Paris, France
| | - Christine Bonnal
- Service de Parasitologie Mycologie, Hôpital Bichat-Claude Bernard, AP-HP, 75018 Paris, France
| | - Arnaud Fekkar
- Groupe Hospitalier Pitié-Salpêtrière, Service de Parasitologie Mycologie, AP-HP, 75013 Paris, France
- CIMI-Paris, Centre d'Immunologie et des Maladies Infectieuses, CNRS, INSERM, Sorbonne Université, 75013 Paris, France
| | - Sébastien Imbert
- Service de Parasitologie Mycologie, Centre Hospitalier Universitaire de Bordeaux, 33075 Bordeaux, France
| | - Xavier Tannier
- Sorbonne Université, Inserm, Laboratoire d'Informatique Médicale et d'Ingénierie des Connaissances en e-Santé, LIMICS, 75013 Paris, France
| | - Renaud Piarroux
- Groupe Hospitalier Pitié-Salpêtrière, Service de Parasitologie Mycologie, AP-HP, 75013 Paris, France
- INSERM, Institut Pierre-Louis d'Épidémiologie et de Santé Publique, Sorbonne Université, 75013 Paris, France
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19
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Li J, Fan W, Zou X, Dai X, Zhao Y, Pan H, Wu S, Li X, Huang H. Clinical evaluation of polymerase chain reaction coupled with quantum dot fluorescence analysis in the identification of bacteria and yeasts in patients with suspected bloodstream infections. Microb Biotechnol 2023; 16:827-837. [PMID: 36722318 PMCID: PMC10034622 DOI: 10.1111/1751-7915.14226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 12/18/2022] [Accepted: 01/16/2023] [Indexed: 02/02/2023] Open
Abstract
Bloodstream infections are serious and complex infectious diseases that often require a rapid diagnosis. Polymerase chain reaction coupled with quantum dot fluorescence analysis (PCR-QDFA) is a novel diagnostic technique. This study aimed to evaluate the diagnostic performance of PCR-QDFA for pathogen detection in patients with suspected bloodstream infections (BSIs). It evaluates 29 kinds of common pathogens (24 bacteria and 5 yeasts) from blood culture bottles. The results of PCR-QDFA identification and traditional microbial laboratory identification were compared, and the latter was used as the 'gold standard' to analyse the diagnostic performance of the PCR-QDFA. In total, 517 blood culture bottles were included in this study. The PCR-QDFA identified microorganisms in 368/422 (87.2%) samples with monomicrobial growth. For the pathogens on the PCR-QDFA list, the assay showed a higher sensitivity of 97.4% (368/378). When polymicrobial growth was analysed, the PCR-QDFA successfully detected 19/25 (76%) microorganisms on the PCR-QDFA list. In addition, 82/82 negative blood culture bottles also showed no pathogens by PCR-QDFA with a specificity of 100%. In conclusion, the PCR-QDFA assay could identify a majority of the common pathogens encountered in clinical practice, showing excellent diagnostic performance for pathogen detection in patients with suspected BSIs.
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Affiliation(s)
- Jie Li
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Department of Infectious Disease, Zhejiang Provincial People's Hospital, Hangzhou, China
| | - Wenjia Fan
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Department of Infectious Disease, Zhejiang Provincial People's Hospital, Hangzhou, China
| | - Xuehan Zou
- Department of Infectious Disease, Zhejiang Provincial People's Hospital, Hangzhou, China
| | - Xuan Dai
- Department of Infectious Disease, Zhejiang Provincial People's Hospital, Hangzhou, China
| | - Yueyue Zhao
- Department of Infectious Disease, Zhejiang Provincial People's Hospital, Hangzhou, China
| | - Hongying Pan
- Department of Infectious Disease, Zhejiang Provincial People's Hospital, Hangzhou, China
| | - Shijin Wu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Xi Li
- Centre of Laboratory Medicine, Zhejiang Provincial People's Hospital, Hangzhou, China
| | - Haijun Huang
- Department of Infectious Disease, Zhejiang Provincial People's Hospital, Hangzhou, China
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20
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Asare PT, Lee CH, Hürlimann V, Teo Y, Cuénod A, Akduman N, Gekeler C, Afrizal A, Corthesy M, Kohout C, Thomas V, de Wouters T, Greub G, Clavel T, Pamer EG, Egli A, Maier L, Vonaesch P. A MALDI-TOF MS library for rapid identification of human commensal gut bacteria from the class Clostridia. Front Microbiol 2023; 14:1104707. [PMID: 36896425 PMCID: PMC9990839 DOI: 10.3389/fmicb.2023.1104707] [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: 11/21/2022] [Accepted: 01/31/2023] [Indexed: 02/25/2023] Open
Abstract
Introduction Microbial isolates from culture can be identified using 16S or whole-genome sequencing which generates substantial costs and requires time and expertise. Protein fingerprinting via Matrix-assisted Laser Desorption Ionization-time of flight mass spectrometry (MALDI-TOF MS) is widely used for rapid bacterial identification in routine diagnostics but shows a poor performance and resolution on commensal bacteria due to currently limited database entries. The aim of this study was to develop a MALDI-TOF MS plugin database (CLOSTRI-TOF) allowing for rapid identification of non-pathogenic human commensal gastrointestinal bacteria. Methods We constructed a database containing mass spectral profiles (MSP) from 142 bacterial strains representing 47 species and 21 genera within the class Clostridia. Each strain-specific MSP was constructed using >20 raw spectra measured on a microflex Biotyper system (Bruker-Daltonics) from two independent cultures. Results For validation, we used 58 sequence-confirmed strains and the CLOSTRI-TOF database successfully identified 98 and 93% of the strains, respectively, in two independent laboratories. Next, we applied the database to 326 isolates from stool of healthy Swiss volunteers and identified 264 (82%) of all isolates (compared to 170 (52.1%) with the Bruker-Daltonics library alone), thus classifying 60% of the formerly unknown isolates. Discussion We describe a new open-source MSP database for fast and accurate identification of the Clostridia class from the human gut microbiota. CLOSTRI-TOF expands the number of species which can be rapidly identified by MALDI-TOF MS.
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Affiliation(s)
- Paul Tetteh Asare
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.,Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland.,Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Chi-Hsien Lee
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.,Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Vera Hürlimann
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Youzheng Teo
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Aline Cuénod
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland.,Clinical Bacteriology and Mycology, University Hospital of Basel, Basel, Switzerland
| | - Nermin Akduman
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, University of Tübingen, Tübingen, Germany.,Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, Tübingen, Germany
| | - Cordula Gekeler
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, University of Tübingen, Tübingen, Germany.,Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, Tübingen, Germany
| | - Afrizal Afrizal
- Functional Microbiome Research Group, Institute of Medical Microbiology, RWTH University Hospital, Aachen, Germany
| | - Myriam Corthesy
- Institute of Microbiology of the University of Lausanne, University Hospital Centre (CHUV), Lausanne, Switzerland
| | - Claire Kohout
- Duchossois Family Institute, Division of Infectious Diseases and Global Health, University of Chicago, Chicago, IL, United States
| | | | | | - Gilbert Greub
- Institute of Microbiology of the University of Lausanne, University Hospital Centre (CHUV), Lausanne, Switzerland
| | - Thomas Clavel
- Functional Microbiome Research Group, Institute of Medical Microbiology, RWTH University Hospital, Aachen, Germany
| | - Eric G Pamer
- Duchossois Family Institute, Division of Infectious Diseases and Global Health, University of Chicago, Chicago, IL, United States
| | - Adrian Egli
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland.,Clinical Bacteriology and Mycology, University Hospital of Basel, Basel, Switzerland
| | - Lisa Maier
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, University of Tübingen, Tübingen, Germany.,Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, Tübingen, Germany
| | - Pascale Vonaesch
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.,Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
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21
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Guadalupe Armas GDC, Martel-Benítez CJ, Alayón-Afonso R, Clavo B, Bordes Benítez A, González-Martín JM, Torres-Mata LB, Martín-Barrasa JL. In vitro antimicrobial activity of ozonated sunflower oil in milk against Escherichia coli: comparative study in cow, goat and sheep. JOURNAL OF APPLIED ANIMAL RESEARCH 2022. [DOI: 10.1080/09712119.2022.2147186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Gloria del Carmen Guadalupe Armas
- Research Unit Hospital Universitario de Gran Canaria, Dr. Negrín, Fundación Instituto de Investigación Sanitaria de Canarias (FIISC), Las Palmas de Gran Canaria, Spain
| | - Carlos José Martel-Benítez
- Research Unit Hospital Universitario de Gran Canaria, Dr. Negrín, Fundación Instituto de Investigación Sanitaria de Canarias (FIISC), Las Palmas de Gran Canaria, Spain
- Group of Fish Health and Infectious Diseases, University Institute of Animal Health and Food Safety (IUSA), University of Las Palmas de Gran Canaria, Arucas, Spain
| | - Rafael Alayón-Afonso
- Research Unit Hospital Universitario de Gran Canaria, Dr. Negrín, Fundación Instituto de Investigación Sanitaria de Canarias (FIISC), Las Palmas de Gran Canaria, Spain
- Group of Fish Health and Infectious Diseases, University Institute of Animal Health and Food Safety (IUSA), University of Las Palmas de Gran Canaria, Arucas, Spain
| | - Bernardino Clavo
- Research Unit Hospital Universitario de Gran Canaria, Dr. Negrín, Fundación Instituto de Investigación Sanitaria de Canarias (FIISC), Las Palmas de Gran Canaria, Spain
- Fundación Canaria del Instituto de Investigación Sanitaria de Canarias (FIISC), Las Palmas de Gran Canaria, Spain
- BioPharm Group, Instituto Universitario de Investigaciones Biomédicas y Sanitarias (IUIBS), Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias, Universidad de La Laguna, La Laguna, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Ana Bordes Benítez
- Microbiology Department, Hospital Universitario de Gran Canaria, Dr. Negrín, Las Palmas de Gran Canaria, Spain
| | - Jesús María González-Martín
- Research Unit Hospital Universitario de Gran Canaria, Dr. Negrín, Fundación Instituto de Investigación Sanitaria de Canarias (FIISC), Las Palmas de Gran Canaria, Spain
- Fundación Canaria del Instituto de Investigación Sanitaria de Canarias (FIISC), Las Palmas de Gran Canaria, Spain
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias, Universidad de La Laguna, La Laguna, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Laura B Torres-Mata
- Research Unit Hospital Universitario de Gran Canaria, Dr. Negrín, Fundación Instituto de Investigación Sanitaria de Canarias (FIISC), Las Palmas de Gran Canaria, Spain
- Fundación Canaria del Instituto de Investigación Sanitaria de Canarias (FIISC), Las Palmas de Gran Canaria, Spain
- BioPharm Group, Instituto Universitario de Investigaciones Biomédicas y Sanitarias (IUIBS), Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain
- Chemical Engineering & Materials Department, Universidad Complutense, Madrid, Spain
| | - José Luis Martín-Barrasa
- Research Unit Hospital Universitario de Gran Canaria, Dr. Negrín, Fundación Instituto de Investigación Sanitaria de Canarias (FIISC), Las Palmas de Gran Canaria, Spain
- Group of Fish Health and Infectious Diseases, University Institute of Animal Health and Food Safety (IUSA), University of Las Palmas de Gran Canaria, Arucas, Spain
- Fundación Canaria del Instituto de Investigación Sanitaria de Canarias (FIISC), Las Palmas de Gran Canaria, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- Animal Facility, Research Unit, Hospital Universitario de Gran Canaria, Dr. Negrín, Fundación Instituto de Investigación Sanitaria de Canarias (FIISC), Las Palmas de Gran Canaria, Spain
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22
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A Practical Workflow for the Identification of Aspergillus, Fusarium, Mucorales by MALDI-TOF MS: Database, Medium, and Incubation Optimization. J Clin Microbiol 2022; 60:e0103222. [PMID: 36326257 PMCID: PMC9769873 DOI: 10.1128/jcm.01032-22] [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: 11/06/2022] Open
Abstract
There is an increasing body of literature on the utility of MALDI-TOF MS in the identification of filamentous fungi. However, the process still lacks standardization. In this study, we attempted to establish a practical workflow for the identification of three clinically important molds: Aspergillus, Fusarium, and Mucorales using MALDI-TOF MS. We evaluated the performance of Bruker Filamentous Fungi database v3.0 for the identification of these fungi, highlighting when there would be a benefit of using an additional database, the MSI-2 for further identification. We also examined two other variables, namely, medium effect and incubation time on the accuracy of fungal identification. The Bruker database achieved correct species level identification in 85.7% of Aspergillus and 90% of Mucorales, and correct species-complex level in 94.4% of Fusarium. Analysis of spectra using the MSI-2 database would also offer additional value for species identification of Aspergillus species, especially when suspecting species with known identification limits within the Bruker database. This issue would only be of importance in selected cases where species-level identification would impact therapeutic options. Id-Fungi plates (IDFP) had almost equivalent performance to Sabouraud dextrose agar (SDA) for species-level identification of isolates and enabled an easier harvest of the isolates with occasional faster identification. Our study showed accurate identification at 24 h for Fusarium and Mucorales species, but not for Aspergillus species, which generally required 48 h.
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MALDI-TOF Mass Spectrometry for the Diagnosis of Citrus Canker Caused by Xanthomonas citri subsp. citri. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27248947. [PMID: 36558076 PMCID: PMC9781495 DOI: 10.3390/molecules27248947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/09/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
Citrus canker, caused by the bacterium Xanthomonas citri subsp. citri (Xcc), is a disease that causes serious problems to the global citrus industry. Matrix-Assisted Laser Desorption/Ionization Time-of-Flight (MALDI-TOF) Mass Spectrometry (MS) has been used in human medicine to diagnose various diseases caused by both fungi and bacteria. In agriculture, this technique has potential for the diagnosis of diseases due to the low cost of large-scale analysis and quickness. This study showed that MALDI-TOF MS combined with chemometric analysis was effective for differentiating the macromolecule profile of orange leaves with canker lesions, healthy leaves, and leaves with phytotoxicity symptoms, proving that this technique may be used for the rapid diagnosis of citrus canker.
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Zhang XD, Gu B, Usman M, Tang JW, Li ZK, Zhang XQ, Yan JW, Wang L. Recent Progress in the Diagnosis of Staphylococcus in Clinical Settings. Infect Dis (Lond) 2022. [DOI: 10.5772/intechopen.108524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Staphylococci are mainly found on the skin or in the nose. These bacteria are typically friendly, causing no harm to healthy individuals or resulting in only minor issues that can go away on their own. However, under certain circumstances, staphylococcal bacteria could invade the bloodstream, affect the entire body, and lead to life-threatening problems like septic shock. In addition, antibiotic-resistant Staphylococcus is another issue because of its difficulty in the treatment of infections, such as the notorious methicillin-resistant Staphylococcus aureus (MRSA) which is resistant to most of the currently known antibiotics. Therefore, rapid and accurate diagnosis of Staphylococcus and characterization of the antibiotic resistance profiles are essential in clinical settings for efficient prevention, control, and treatment of the bacteria. This chapter highlights recent advances in the diagnosis of Staphylococci in clinical settings with a focus on the advanced technique of surface-enhanced Raman spectroscopy (SERS), which will provide a framework for the real-world applications of novel diagnostic techniques in medical laboratories via bench-top instruments and at the bedside through point-of-care devices.
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25
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Citterio F, Zanotto E, Pellegrini G, Annaratore L, Barbui AM, Dellavia C, Baima G, Romano F, Aimetti M. Comparison of Different Chemical and Mechanical Modalities for Implant Surface Decontamination: Activity against Biofilm and Influence on Cellular Regrowth—An In Vitro Study. Front Surg 2022; 9:886559. [PMID: 36248376 PMCID: PMC9562851 DOI: 10.3389/fsurg.2022.886559] [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: 02/28/2022] [Accepted: 03/05/2022] [Indexed: 11/14/2022] Open
Abstract
Objectives The aim of this in vitro study was to compare the efficacy of chemical and mechanical methods for decontamination of titanium dental implant surfaces previously infected with polymicrobial biofilms in a model simulating a peri-implant defect. Furthermore, the effect of each decontamination protocol on MG-63 osteoblast-like cells morphology and adhesion to the treated implants was assessed. Background Peri-implantitis is a growing issue in dentistry, and evidence about implant surface decontamination procedures is lacking and inconclusive. Methods A total of 40 previously biofilm-contaminated implants were placed into a custom-made model simulating a peri-implant defect and randomly assigned to five treatment groups: (C) control (no treatment); (AW) air abrasion without any powder; (ESC) air abrasion with powder of erythritol, amorphous silica, and 0.3% chlorhexidine; (HBX) decontamination with a sulfonic/sulfuric acid solution in gel; and (HBX + ESC) a combination of HBX and ESC. Microbiological analysis was performed on five implants per treatment group, and the residual viable bacterial load measured in log 10 CFU/mL was counted for each bacterial strain and for the total number of colonies. The remaining three implants per group and three noncontaminated (NC) implants were used to assess surface biocompatibility using a scanning electron microscope and a backscattered electron microscope after seeding with MG-63 cells. Results A significant decontaminant effect was achieved using HBX or HBX + ESC, while no differences were observed among other groups. The percentage of implant surface covered by adherent MG-63 cells was influenced by the treatment method. Progressive increases in covered surfaces were observed in groups C, AW, ESC, HBX, HBX + ESC, and NC. Conclusions A combination of mechanical and chemical decontamination may provide more predictable results than mechanical cleaning alone.
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Affiliation(s)
- Filippo Citterio
- Department of Surgical Sciences, Section of Periodontology, C.I.R. Dental School, Università di Torino, Turin, Italy
- Correspondence: Filippo Citterio
| | - Elisa Zanotto
- Microbiology and Virology Unit, University Hospital City of Health and Science of Turin, Turin, Italy
| | - Gaia Pellegrini
- Department of Biomedical Surgical and Dental Sciences, Università degli Studi di Milano, Milan, Italy
| | - Laura Annaratore
- Department of Medical Sciences, Pathology Unit, Università degli Studi di Torino, Turin, Italy
- Pathology Unit, Candiolo Cancer Institute, FPO IRCCS, Candiolo, Italy
| | - Anna Maria Barbui
- Microbiology and Virology Unit, University Hospital City of Health and Science of Turin, Turin, Italy
| | - Claudia Dellavia
- Department of Biomedical Surgical and Dental Sciences, Università degli Studi di Milano, Milan, Italy
| | - Giacomo Baima
- Department of Surgical Sciences, Section of Periodontology, C.I.R. Dental School, Università di Torino, Turin, Italy
| | - Federica Romano
- Department of Surgical Sciences, Section of Periodontology, C.I.R. Dental School, Università di Torino, Turin, Italy
| | - Mario Aimetti
- Department of Surgical Sciences, Section of Periodontology, C.I.R. Dental School, Università di Torino, Turin, Italy
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Wang H, Zhang W, Tang YW. Clinical Microbiology in Detection and Identification of Emerging Microbial Pathogens: Past, Present and Future. Emerg Microbes Infect 2022; 11:2579-2589. [PMID: 36121351 PMCID: PMC9639501 DOI: 10.1080/22221751.2022.2125345] [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: 11/21/2022]
Abstract
Clinical microbiology has possessed a marvellous past, an important present and a bright future. Western medicine modernization started with the discovery of bacterial pathogens, and from then, clinical bacteriology became a cornerstone of diagnostics. Today, clinical microbiology uses standard techniques including Gram stain morphology, in vitro culture, antigen and antibody assays, and molecular biology both to establish a diagnosis and monitor the progression of microbial infections. Clinical microbiology has played a critical role in pathogen detection and characterization for emerging infectious diseases as evidenced by the ongoing COVID-19 pandemic. Revolutionary changes are on the way in clinical microbiology with the application of “-omic” techniques, including transcriptomics and metabolomics, and optimization of clinical practice configurations to improve outcomes of patients with infectious diseases.
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Affiliation(s)
- Hui Wang
- Department of Laboratory Medicine, Peking University People's Hospital, Beijing 100044, China
| | - Wenhong Zhang
- Department of Infectious Diseases, Fudan University Huashan Hospital, Shanghai 200040, China
| | - Yi-Wei Tang
- Medical Affairs, Danaher Diagnostic Platform China/Cepheid, Shanghai 200325, China
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Occurrence, Phenotypic and Molecular Characteristics of Extended-Spectrum Beta-Lactamase-Producing Escherichia coli in Healthy Turkeys in Northern Egypt. Antibiotics (Basel) 2022; 11:antibiotics11081075. [PMID: 36009944 PMCID: PMC9404839 DOI: 10.3390/antibiotics11081075] [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: 07/21/2022] [Revised: 07/29/2022] [Accepted: 08/03/2022] [Indexed: 12/01/2022] Open
Abstract
Poultry is one of the most important reservoirs for zoonotic multidrug-resistant pathogens. The indiscriminate use of antimicrobials in poultry production is a leading factor for development and dissemination of antimicrobial resistance. This study aimed to describe the prevalence and antimicrobial resistance of E. coli isolated from healthy turkey flocks of different ages in Nile delta region, Egypt. In the current investigation, 250 cloacal swabs were collected from 12 turkey farms in five governorates in the northern Egypt. Collected samples were cultivated on BrillianceTM ESBL agar media supplemented with cefotaxime (100 mg/L). The E. coli isolates were identified using MALDI-TOF-MS and confirmed by a conventional PCR assay targeting 16S rRNA-DNA. The phenotypic antibiogram against 14 antimicrobial agents was determined using the broth micro-dilution method. DNA-microarray-based assay was applied for genotyping and determination of both, virulence and resistance-associated gene markers. Multiplex real-time PCR was additionally applied for all isolates for detection of the actual most relevant Carbapenemase genes. The phenotypic identification of colistin resistance was carried out using E-test. A total of 26 E. coli isolates were recovered from the cloacal samples. All isolates were defined as multidrug-resistant. Interestingly, two different E. coli strains were isolated from one sample. Both strains had different phenotypic and genotypic profiles. All isolates were phenotypically susceptible to imipenem, while resistant to penicillin, rifampicin, streptomycin, and erythromycin. None of the examined carbapenem resistance genes was detected among isolates. At least one beta-lactamase gene was identified in most of isolates, where blaTEM was the most commonly identified determinant (80.8%), in addition to blaCTX-M9 (23.1%), blaSHV (19.2%) and blaOXA-10 (15.4%). Genes associated with chloramphenicol resistance were floR (65.4%) and cmlA1 (46.2%). Tetracycline- and quinolone-resistance-associated genes tetA and qnrS were detected in (57.7%) and (50.0%) of isolates, respectively. The aminoglycoside resistance associated genes aadA1 (65.4%), aadA2 (53.8%), aphA (50.0%), strA (69.2%), and strB (65.4%), were detected among isolates. Macrolide resistance associated genes mph and mrx were also detected in (53.8%) and (34.6%). Moreover, colistin resistance associated gene mcr-9 was identified in one isolate (3.8%). The class 1 integron integrase intI1 (84.6%), transposase for the transposon tnpISEcp1 (34.6%) and OqxB -integral membrane and component of RND-type multidrug efflux pump oqxB (7.7%) were identified among the isolates. The existing high incidence of ESBL/colistin-producing E. coli identified in healthy turkeys is a major concern that demands prompt control; otherwise, such strains and their resistance determinants could be transmitted to other bacteria and, eventually, to people via the food chain.
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Kim G, Ahn D, Kang M, Park J, Ryu D, Jo Y, Song J, Ryu JS, Choi G, Chung HJ, Kim K, Chung DR, Yoo IY, Huh HJ, Min HS, Lee NY, Park Y. Rapid species identification of pathogenic bacteria from a minute quantity exploiting three-dimensional quantitative phase imaging and artificial neural network. LIGHT, SCIENCE & APPLICATIONS 2022; 11:190. [PMID: 35739098 PMCID: PMC9226356 DOI: 10.1038/s41377-022-00881-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 06/03/2022] [Accepted: 06/09/2022] [Indexed: 05/14/2023]
Abstract
The healthcare industry is in dire need of rapid microbial identification techniques for treating microbial infections. Microbial infections are a major healthcare issue worldwide, as these widespread diseases often develop into deadly symptoms. While studies have shown that an early appropriate antibiotic treatment significantly reduces the mortality of an infection, this effective treatment is difficult to practice. The main obstacle to early appropriate antibiotic treatments is the long turnaround time of the routine microbial identification, which includes time-consuming sample growth. Here, we propose a microscopy-based framework that identifies the pathogen from single to few cells. Our framework obtains and exploits the morphology of the limited sample by incorporating three-dimensional quantitative phase imaging and an artificial neural network. We demonstrate the identification of 19 bacterial species that cause bloodstream infections, achieving an accuracy of 82.5% from an individual bacterial cell or cluster. This performance, comparable to that of the gold standard mass spectroscopy under a sufficient amount of sample, underpins the effectiveness of our framework in clinical applications. Furthermore, our accuracy increases with multiple measurements, reaching 99.9% with seven different measurements of cells or clusters. We believe that our framework can serve as a beneficial advisory tool for clinicians during the initial treatment of infections.
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Affiliation(s)
- Geon Kim
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon, 34141, Republic of Korea
| | - Daewoong Ahn
- Tomocube Inc., Daejeon, 34109, Republic of Korea
| | - Minhee Kang
- Smart Healthcare & Device Research Center, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351, Republic of Korea
| | - Jinho Park
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon, 34141, Republic of Korea
| | - DongHun Ryu
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon, 34141, Republic of Korea
| | - YoungJu Jo
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon, 34141, Republic of Korea
- Tomocube Inc., Daejeon, 34109, Republic of Korea
- Department of Applied Physics, Stanford University, Stanford, CA, 94305, USA
| | - Jinyeop Song
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon, 34141, Republic of Korea
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Jea Sung Ryu
- Graduate School of Nanoscience and Technology, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Gunho Choi
- Tomocube Inc., Daejeon, 34109, Republic of Korea
| | - Hyun Jung Chung
- Graduate School of Nanoscience and Technology, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Kyuseok Kim
- Department of Emergency Medicine, Bundang CHA Hospital, Seongnam-si, Gyeonggi-Do, 13496, Korea
| | - Doo Ryeon Chung
- Division of Infectious Diseases, Department of Internal Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351, Republic of Korea
| | - In Young Yoo
- Department of Laboratory Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea
| | - Hee Jae Huh
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351, Republic of Korea
| | | | - Nam Yong Lee
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351, Republic of Korea.
| | - YongKeun Park
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.
- KAIST Institute for Health Science and Technology, KAIST, Daejeon, 34141, Republic of Korea.
- Tomocube Inc., Daejeon, 34109, Republic of Korea.
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Honsig C, Selitsch B, Hollenstein M, Vossen MG, Spettel K, Willinger B. Identification of Filamentous Fungi by MALDI-TOF Mass Spectrometry: Evaluation of Three Different Sample Preparation Methods and Validation of an In-House Species Cutoff. J Fungi (Basel) 2022; 8:jof8040383. [PMID: 35448614 PMCID: PMC9025689 DOI: 10.3390/jof8040383] [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: 03/12/2022] [Revised: 04/06/2022] [Accepted: 04/07/2022] [Indexed: 12/04/2022] Open
Abstract
Invasive infections caused by filamentous fungi constitute a leading cause of morbidity and mortality in immunocompromised patients. Rapid and reliable identification of filamentous fungi is essential for the early initiation of appropriate treatment. In the present study, 230 filamentous fungi isolates identified by conventional methods were investigated using MALDI-TOF MS (Bruker Daltonics, Bremen, Germany) in combination with the Filamentous Fungi Library 3.0 provided by the manufacturer. Three different sample preparation methods were applied as recommended by the manufacturer and identification rates were compared using the criteria provided by the manufacturer. Application of the more time-consuming sample preparation methods clearly improved identification at the species level. Thus, the identification rate increased from 48.9% using the simplest method to 76.1% with the most laborious procedure. Misidentifications did not occur. Furthermore, the reliability of an in-house threshold for species identification was investigated. The reduced threshold increased the rate of isolates correctly identified at the species level by up to 86.4%. As no misidentification was made at the genus level and only one misidentification of minor significance occurred at the species level, this threshold could be validated for routine use in our laboratory. In conclusion, regarding the high identification rates achieved, this commercial platform proved suitable for implementation in routine diagnosis.
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Affiliation(s)
- Claudia Honsig
- Division of Clinical Microbiology, Department of Laboratory Medicine, Medical University of Vienna, 1090 Vienna, Austria; (C.H.); (B.S.); (K.S.)
| | - Brigitte Selitsch
- Division of Clinical Microbiology, Department of Laboratory Medicine, Medical University of Vienna, 1090 Vienna, Austria; (C.H.); (B.S.); (K.S.)
| | - Marlene Hollenstein
- Department of Laboratory Medicine, Medical University of Vienna, 1090 Vienna, Austria;
| | - Matthias G. Vossen
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine I, Medical University of Vienna, 1090 Vienna, Austria;
| | - Kathrin Spettel
- Division of Clinical Microbiology, Department of Laboratory Medicine, Medical University of Vienna, 1090 Vienna, Austria; (C.H.); (B.S.); (K.S.)
| | - Birgit Willinger
- Division of Clinical Microbiology, Department of Laboratory Medicine, Medical University of Vienna, 1090 Vienna, Austria; (C.H.); (B.S.); (K.S.)
- Correspondence: ; Tel.: +43-1-40400-51560
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Wen H, Xie S, Liang Y, Liu Y, Wei H, Sun Q, Wang W, Wen B, Zhao J. Direct Identification, Antimicrobial Susceptibility Testing, and Extended-Spectrum β-Lactamase and Carbapenemase Detection in Gram-Negative Bacteria Isolated from Blood Cultures. Infect Drug Resist 2022; 15:1587-1599. [PMID: 35418761 PMCID: PMC8995151 DOI: 10.2147/idr.s350612] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 03/23/2022] [Indexed: 12/21/2022] Open
Abstract
Purpose To shorten the turnaround time for blood culture (BC) analyses, a rapid method was developed for the direct identification, antimicrobial susceptibility testing (AST), and multidrug resistance testing of bacteria-positive BCs. Materials and Methods The mixtures in BC bottles were treated with the multistep centrifugation method developed here and the conventional culture-based method. The bacterial sediment obtained after centrifugation was analyzed directly with MALDI-TOF MS and Vitek 2 Compact, and AST was performed directly with the Kirby–Bauer (K–B) disk diffusion, VITEK 2 Compact, and E-test methods. Extended spectrum lactamases (ESBLs) were detected with discs containing cefotaxime, cefotaxime/clavulanate, ceftazidime, and ceftazidime/clavulanate, and carbapenemase was detected with the modified carbapenem inactivation method (mCIM) and EDTA-mCIM (eCIM). Results All the results of direct testing were compared to those of the conventional methods, to evaluate the accuracy of the direct methods. The accuracies of the direct Vitek 2 Compact and MALDI-TOF MS methods were 95.5% (214/224) and 90.2% (202/224), respectively. Direct AST with K–B, Vitek 2, and E-test showed category agreement of 96.0% (2611/2721), 96.1% (2614/2721), and 97.4% (2650/2721), respectively, and the major errors and very major errors were < 2% for all three methods. In the direct determination of ESBLs, the results for cefotaxime combined with cefotaxime/clavulanate were completely consistent with those after the standard isolation method. The carbapenemase detection rate with direct mCIM and eCIM was exactly the same as that with the standard method. Conclusion These direct procedures based on multistep centrifugation are not only highly accurate but are appropriate for clinical laboratory use because the turnaround time is shorter.
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Affiliation(s)
- Hainan Wen
- The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, People’s Republic of China
| | - Shoujun Xie
- Clinical Laboratory, the Affiliated Hospital of Chengde Medical University, Chengde, Hebei, People’s Republic of China
| | - Yueyi Liang
- Clinical Laboratory, the Affiliated Hospital of Chengde Medical University, Chengde, Hebei, People’s Republic of China
| | - Yanchao Liu
- Clinical Laboratory, the Affiliated Hospital of Chengde Medical University, Chengde, Hebei, People’s Republic of China
| | - Honglian Wei
- The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, People’s Republic of China
| | - Qian Sun
- The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, People’s Republic of China
| | - Weigang Wang
- The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, People’s Republic of China
- Hebei Provincial Center for Clinical Laboratories, Shijiazhuang, Hebei, People’s Republic of China
| | - Baojiang Wen
- The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, People’s Republic of China
- Hebei Provincial Center for Clinical Laboratories, Shijiazhuang, Hebei, People’s Republic of China
| | - Jianhong Zhao
- The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, People’s Republic of China
- Hebei Provincial Center for Clinical Laboratories, Shijiazhuang, Hebei, People’s Republic of China
- Correspondence: Jianhong Zhao, The Second Hospital of Hebei Medical University, 215 West Heping Road, Shijiazhuang, Hebei Province, 050051, People’s Republic of China, Tel +86 158 03210790, Fax +86 311 66002851, Email
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31
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MALDI-Based Mass Spectrometry in Clinical Testing: Focus on Bacterial Identification. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12062814] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The term “proteome” refers to the total of all proteins expressed in an organism. The term “proteomics” refers to the field of research that includes not only information on the expression levels of individual proteins, but also their higher-order structures, intermolecular interactions, and post-translational modifications. The core technology, matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS), is available for protein analysis thanks to the work of Koichi Tanaka and John Fenn, who were awarded the Nobel Prize in Chemistry in 2002. The most successful proteome analysis in clinical practice is rapid microbial identification. This method determines the bacterial species by comparing the proteome profile of the bacteria obtained by matrix-assisted laser desorption ionization-time of flight MS (MALDI-TOF MS) with a database. MS is superior in simplicity, speed, and accuracy to classic speciation by staining and phenotyping. In clinical microbiology, MS has had a large impact on the diagnosis and treatment of infectious disease. Early diagnosis and treatment of infectious disease are important, and rapid identification by MALDI-TOF MS has made a major contribution to this field.
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Xie J, Tian S, Liu J, Cao R, Yue P, Cai X, Shang Q, Yang M, Han L, Zhang DK. Dual role of the nasal microbiota in neurological diseases—An unignorable risk factor or a potential therapy carrier. Pharmacol Res 2022; 179:106189. [DOI: 10.1016/j.phrs.2022.106189] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 03/06/2022] [Accepted: 03/17/2022] [Indexed: 12/11/2022]
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OUP accepted manuscript. J AOAC Int 2022; 105:1468-1474. [DOI: 10.1093/jaoacint/qsac036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 03/02/2022] [Accepted: 03/06/2022] [Indexed: 11/13/2022]
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Isolation and probiotic potential of lactic acid bacteria from swine feces for feed additive composition. Arch Microbiol 2021; 204:61. [PMID: 34940898 PMCID: PMC8702511 DOI: 10.1007/s00203-021-02700-0] [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: 06/10/2021] [Revised: 11/08/2021] [Accepted: 11/09/2021] [Indexed: 12/05/2022]
Abstract
Animal microbiota is becoming an object of interest as a source of beneficial bacteria for commercial use. Moreover, the escalating problem of bacterial resistance to antibiotics is threatening animals and humans; therefore, in the last decade intensive search for alternative antimicrobials has been observed. In this study, lactic acid bacteria (LAB) were isolated from suckling and weaned pigs feces (376) and characterized to determine their functional properties and usability as pigs additives. Selection of the most promising LAB was made after each stage of research. Isolates were tested for their antimicrobial activity (376) and susceptibility to antibiotics (71). Selected LAB isolates (41) were tested for the production of organic acids, enzymatic activity, cell surface hydrophobicity and survival in gastrointestinal tract. Isolates selected for feed additive (5) were identified by MALDI-TOF mass spectrometry and partial sequence analysis of 16S rRNA gene, represented by Lentilactobacillus, Lacticaseibacillus (both previously classified as Lactobacillus) and Pediococcus genus. Feed additive prototype demonstrated high viability after lyophilization and during storage at 4 °C and − 20 °C for 30 days. Finally, feed additive was tested for survival in simulated alimentary tract of pigs, showing viability at the sufficient level to colonize the host. Studies are focused on obtaining beneficial strains of LAB with probiotic properties for pigs feed additive.
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Sun B, Kang X, Yue S, Lan L, Li R, Chen C, Zhang W, He S, Zhang C, Fan Y, Wang P, Zheng G, Hong W. A rapid procedure for bacterial identification and antimicrobial susceptibility testing directly from positive blood cultures. Analyst 2021; 147:147-154. [PMID: 34860216 DOI: 10.1039/d1an01210j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
There is an urgent need to develop a rapid procedure that can rapidly identify and obtain antimicrobial susceptibility testing (AST) results directly from positive blood cultures. Here, we report a semi-automatic bacterial diagnosis procedure, which includes (1) a bacterial concentration process to isolate bacteria from a positive blood culture bottle (PBCB), (2) an identification process using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS), and (3) a rapid AST process based on stimulated Raman scattering imaging of deuterium oxide (D2O) incorporation in bacteria. A total of 105 samples were tested for bacterial identification, and a bacterial identification accuracy of 92.3% was achieved. AST takes about 2.5 h after identification. This semi-automatic procedure only takes 3.5 h, which is demonstrated to be the fastest process to obtain identification and AST results starting from PBCBs.
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Affiliation(s)
- Bo Sun
- Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, China. .,Laboratory Diagnosis Center, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.
| | - Xixiong Kang
- Laboratory Diagnosis Center, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.
| | - Shuhua Yue
- Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, China.
| | - Lu Lan
- Vibronix Inc., West Lafayette, IN, USA
| | - Rui Li
- Vibronix Inc., West Lafayette, IN, USA
| | - Chen Chen
- Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, China.
| | - Weifeng Zhang
- Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, China.
| | - Shipei He
- Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, China.
| | - Chenxi Zhang
- Laboratory Diagnosis Center, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.
| | - Yubo Fan
- Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, China. .,School of Medical Science and Engineering, Beihang University, Beijing, China
| | - Pu Wang
- Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, China.
| | - Guanghui Zheng
- Laboratory Diagnosis Center, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.
| | - Weili Hong
- Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, China.
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Achek R, El-Adawy H, Hotzel H, Hendam A, Tomaso H, Ehricht R, Neubauer H, Nabi I, Hamdi TM, Monecke S. Molecular Characterization of Staphylococcus aureus Isolated from Human and Food Samples in Northern Algeria. Pathogens 2021; 10:pathogens10101276. [PMID: 34684225 PMCID: PMC8537606 DOI: 10.3390/pathogens10101276] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 09/23/2021] [Accepted: 09/28/2021] [Indexed: 01/04/2023] Open
Abstract
Staphylococcus aureus is a commensal resident of the skin and nasal cavities of humans and can cause various infections. Some toxigenic strains can contaminate food matrices and cause foodborne intoxications. The present study aimed to provide relevant information (clonal complex lineages, agr types, virulence and antimicrobial resistance-associated genes) based on DNA microarray analyses as well as the origins and dissemination of several circulating clones of 60 Staphylococcus aureus isolated from food matrices (n = 24), clinical samples (n = 20), and nasal carriers (n = 16) in northern Algeria. Staphylococcus aureus were genotyped into 14 different clonal complexes. Out of 60 S. aureus, 13 and 10 isolates belonged to CC1-MSSA and CC97-MSSA, respectively. The CC 80-MRSA-IV was the predominant S. aureus strain in clinical isolates. The accessory gene regulator allele agr group III was mainly found among clinical isolates (70.4%). Panton–Valentine leukocidin genes lukF/lukS-PV were detected in 13.3% of isolates that all belonged to CC80-MRSA. The lukF/S-hlg, hlgA, and hla genes encoding for hemolysins and leucocidin components were detected in all Staphylococcusaureus isolates. Clinical and food isolates harbored more often the antibiotic resistance genes markers. Seventeen (28.3%) methicillin-resistant Staphylococcus aureus carrying the mecA gene localized on a SCCmec type IV element were identified. The penicillinase operon (blaZ/I/R) was found in 71.7% (43/60) of isolates. Food isolates belonging to CC97-MSSA carried several antibiotic resistance genes (blaZ, ermB, aphA3, sat, tetM, and tetK). The results of this study showed that all clones were found in their typical host, but interestingly, some nasal carriers had isolates assigned to CC705 thought to be absent in humans. The detection of MRSA strains among food isolates should be considered as a potential public health risk. Therefore, controlling the antibiotics prescription for a rational use in human and animal infections is mandatory.
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Affiliation(s)
- Rachid Achek
- Faculty of Nature and Life and Earth Sciences, Djilali-Bounaama University, Soufay, Khemis-Miliana 44225, Algeria;
- Laboratory of Food Hygiene and Quality Assurance System, High National Veterinary School, Oued Smar, Algiers 16059, Algeria;
| | - Hosny El-Adawy
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, 07743 Jena, Germany; (H.H.); (H.T.); (H.N.)
- Faculty of Veterinary Medicine, Kafrelsheikh University, Kafr El-Sheikh 35516, Egypt
- Correspondence:
| | - Helmut Hotzel
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, 07743 Jena, Germany; (H.H.); (H.T.); (H.N.)
| | - Ashraf Hendam
- Climate Change Information Center, Renewable Energy and Expert Systems (CCICREES), Agricultural Research Center, 9 Algamaa Street, Giza 12619, Egypt;
| | - Herbert Tomaso
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, 07743 Jena, Germany; (H.H.); (H.T.); (H.N.)
| | - Ralf Ehricht
- Leibniz Institute of Photonic Technology (IPHT), 07745 Jena, Germany; (R.E.); (S.M.)
- InfectoGnostics Research Campus Jena e. V., 07743 Jena, Germany
- Institute of Physical Chemistry, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Heinrich Neubauer
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, 07743 Jena, Germany; (H.H.); (H.T.); (H.N.)
| | - Ibrahim Nabi
- Faculty of Sciences, Yahia Farès University, Urban Pole, Médéa 26000, Algeria;
| | - Taha Mossadak Hamdi
- Laboratory of Food Hygiene and Quality Assurance System, High National Veterinary School, Oued Smar, Algiers 16059, Algeria;
| | - Stefan Monecke
- Leibniz Institute of Photonic Technology (IPHT), 07745 Jena, Germany; (R.E.); (S.M.)
- InfectoGnostics Research Campus Jena e. V., 07743 Jena, Germany
- Institute for Medical Microbiology and Virology, Dresden University Hospital, 01307 Dresden, Germany
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Barrera-Galicia GC, Peniche-Pavía HA, Peña-Cabriales JJ, Covarrubias SA, Vera-Núñez JA, Délano-Frier JP. Metabolic Footprints of Burkholderia Sensu Lato Rhizosphere Bacteria Active against Maize Fusarium Pathogens. Microorganisms 2021; 9:microorganisms9102061. [PMID: 34683382 PMCID: PMC8538949 DOI: 10.3390/microorganisms9102061] [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: 08/12/2021] [Revised: 09/20/2021] [Accepted: 09/24/2021] [Indexed: 11/16/2022] Open
Abstract
Consistent with their reported abundance in soils, several Burkholderia sensu lato strains were isolated from the rhizosphere of maize plants cultivated at different sites in central México. Comparative analysis of their 16S rRNA gene sequences permitted their separation into three distinctive clades, which were further subdivided into six other clusters by their close resemblance to (1) Trinickia dinghuensis; (2) Paraburkholderia kirstenboschensis, P. graminis, P. dilworthii and P. rhynchosiae; (3) B. gladioli; (4) B. arboris; (5) B. contaminans, or (6) B. metallica representative species. Direct confrontation assays revealed that these strains inhibited the growth of pathogenic Fusarium oxysporum f. sp. radicis-lycopersici, and F. verticillioides within a roughly 3-55% inhibition range. The use of a DIESI-based non-targeted mass spectroscopy experimental strategy further indicated that this method is an option for rapid determination of the pathogen inhibitory capacity of Burkholderia sensu lato strains based solely on the analysis of their exometabolome. Furthermore, it showed that the highest anti-fungal activity observed in B. contaminans and B. arboris was associated with a distinctive abundance of certain m/z ions, some of which were identified as components of the ornbactin and pyochelin siderophores. These results highlight the chemical diversity of Burkholderia sensu lato bacteria and suggest that their capacity to inhibit the Fusarium-related infection of maize in suppressive soils is associated with siderophore synthesis.
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Affiliation(s)
- Guadalupe C. Barrera-Galicia
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Irapuato, Irapuato 36824, Guanajuato, Mexico; (G.C.B.-G.); (H.A.P.-P.); (J.J.P.-C.)
| | - Héctor A. Peniche-Pavía
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Irapuato, Irapuato 36824, Guanajuato, Mexico; (G.C.B.-G.); (H.A.P.-P.); (J.J.P.-C.)
| | - Juan José Peña-Cabriales
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Irapuato, Irapuato 36824, Guanajuato, Mexico; (G.C.B.-G.); (H.A.P.-P.); (J.J.P.-C.)
| | - Sergio A. Covarrubias
- Área de Ciencias de la Salud, Ciudad Universitaria Campus Siglo XXI, Universidad Autónoma de Zacatecas, Zacatecas 98160, Zacatecas, Mexico; (S.A.C.); (J.A.V.-N.)
| | - José A. Vera-Núñez
- Área de Ciencias de la Salud, Ciudad Universitaria Campus Siglo XXI, Universidad Autónoma de Zacatecas, Zacatecas 98160, Zacatecas, Mexico; (S.A.C.); (J.A.V.-N.)
| | - John P. Délano-Frier
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Irapuato, Irapuato 36824, Guanajuato, Mexico; (G.C.B.-G.); (H.A.P.-P.); (J.J.P.-C.)
- Correspondence: ; Tel.: +52-462-623-9600
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Nakamura T, Ishikawa K, Matsuo T, Kawai F, Uehara Y, Mori N. Enterococcus hirae bacteremia associated with acute pyelonephritis in a patient with alcoholic cirrhosis: a case report and literature review. BMC Infect Dis 2021; 21:999. [PMID: 34556047 PMCID: PMC8461981 DOI: 10.1186/s12879-021-06707-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 09/16/2021] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Infections caused by Enterococcus hirae are common in animals, with instances of transmission to humans being rare. Further, few cases have been reported in humans because of the difficulty in identifying the bacteria. Herein, we report a case of pyelonephritis caused by E. hirae bacteremia and conduct a literature review on E. hirae bacteremia. CASE PRESENTATION A 57-year-old male patient with alcoholic cirrhosis and neurogenic bladder presented with fever and chills that had persisted for 3 days. Physical examination revealed tenderness of the right costovertebral angle. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) of the patient's blood and urine samples revealed the presence of E. hirae, and pyelonephritis was diagnosed. The patient was treated successfully with intravenous ampicillin followed by oral linezolid for a total of three weeks. CONCLUSION The literature review we conducted revealed that E. hirae bacteremia is frequently reported in urinary tract infections, biliary tract infections, and infective endocarditis and is more likely to occur in patients with diabetes, liver cirrhosis, and chronic kidney disease. However, mortality is not common because of the high antimicrobial susceptibility of E. hirae. With the advancements in MALDI-TOF MS, the number of reports of E. hirae infections has also increased, and clinicians need to consider E. hirae as a possible causative pathogen of urinary tract infections in patients with known risk factors.
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Affiliation(s)
- Tomoaki Nakamura
- Department of Infectious Diseases, St. Luke's International Hospital, 9-1, Akashi-cho, Chuo-ku, Tokyo, Japan.
| | - Kazuhiro Ishikawa
- Department of Infectious Diseases, St. Luke's International Hospital, 9-1, Akashi-cho, Chuo-ku, Tokyo, Japan
| | - Takahiro Matsuo
- Department of Infectious Diseases, St. Luke's International Hospital, 9-1, Akashi-cho, Chuo-ku, Tokyo, Japan
| | - Fujimi Kawai
- St. Luke's International University Library, Tokyo, Japan
| | - Yuki Uehara
- Department of Infectious Diseases, St. Luke's International Hospital, 9-1, Akashi-cho, Chuo-ku, Tokyo, Japan
- Department of Clinical Laboratory, St. Luke's International Hospital, Tokyo, Japan
- Department of Microbiology, Faculty of Medicine, Juntendo University, Tokyo, Japan
- Department of General Medicine, Faculty of Medicine, Juntendo University, Tokyo, Japan
| | - Nobuyoshi Mori
- Department of Infectious Diseases, St. Luke's International Hospital, 9-1, Akashi-cho, Chuo-ku, Tokyo, Japan
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Liu S, Xu H, Guo X, Li S, Wang Q, Li Y, Liu R, Gou J. Emergence and Genetic Characterization of Plasmid-Encoded VIM-2-Producing Pseudomonas stutzeri with Novel Integron In 1998 Isolated from Cerebrospinal Fluid. Infect Drug Resist 2021; 14:3415-3424. [PMID: 34466007 PMCID: PMC8402987 DOI: 10.2147/idr.s320294] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 07/07/2021] [Indexed: 11/23/2022] Open
Abstract
Purpose To investigate the genomic and plasmid characteristics of a newly discovered Pseudomonas stutzeri strain with a bla VIM-2-carrying plasmid and novel integron In1998 isolated from a cerebrospinal fluid specimen in a teaching hospital. Methods Species identification was performed by MALDI-TOF MS, and bla VIM-2 was identified by PCR and Sanger sequencing. Whole-genome sequencing analysis was conducted using the Illumina NovaSeq 6000 and Oxford Nanopore platforms. Integron detection was performed using INTEGRALL. The phylogenetic tree was constructed by using kSNP3.0. Plasmid characteristics were assessed by S1-pulsed-field gel electrophoresis (S1-PFGE), Southern blotting, conjugation experiments, and whole-genome sequencing analysis. Comparative genomics analysis of the plasmid and genetic context of bla VIM-2 were conducted by using BLAST Ring Image Generator (BRIG) and Easyfig 2.3, respectively. Results ZDHY95, an MDR strain of P. stutzeri harboring bla VIM-2, was identified. It was sensitive only to amikacin and was resistant to carbapenems, β-lactams, aztreonam, fluoroquinolones, and aminoglycosides. Joint S1-PFGE, Southern blot, conjugation assay, and whole-genome sequencing experiments confirmed that the bla VIM-2 gene was located within class I integron In1722 of the plasmid and that the surrounding genetic environment was 5'CS-aacA4'-30-bla VIM-2-aacA4'-3'CS. The novel class I integron In1998 was detected on the chromosome of P. stutzeri ZDHY95, and the gene cassette array was 5'CS-aacA3-aadA13-cmlA8-bla OXA-246-arr3-dfrA27-3'CS. Phylogenetic analysis showed that antimicrobial resistance gene-carrying P. stutzeri isolates were divided into two clusters, mainly containing isolates from the USA and Pakistan. Conclusion A novel bla VIM-2-carrying conjugative plasmid, pZDHY95-VIM-2, was reported for the first time in P. stutzeri, elucidating the genetic environment and transfer mechanism. The gene structure of the novel class I integron In1998 was also clarified. We explored the phylogenetic relationship of P. stutzeri with drug resistance genes and suggested that Pseudomonas with metallo-β-lactamases (MBLs) in the hospital environment may cause infection in patients with long-term intubation or after interventional surgery.
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Affiliation(s)
- Shuxiu Liu
- Department of Laboratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, People's Republic of China.,State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, 310003, People's Republic of China
| | - Hao Xu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, 310003, People's Republic of China
| | - Xiaobing Guo
- Department of Laboratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, People's Republic of China
| | - Shuang Li
- Department of Obstetrics and Gynecology, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, 450052, People's Republic of China
| | - Qian Wang
- Department of Laboratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, People's Republic of China.,State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, 310003, People's Republic of China
| | - Yuan Li
- Department of Nuclear Medicine, The First Affiliated Hospital of ZhengZhou University, Zhengzhou, 450052, People's Republic of China
| | - Ruishan Liu
- Department of Laboratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, People's Republic of China.,State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, 310003, People's Republic of China
| | - Jianjun Gou
- Department of Laboratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, People's Republic of China
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Salvagno GL, Danese E, Lippi G. Mass spectrometry and total laboratory automation: opportunities and drawbacks. Clin Chem Lab Med 2021; 58:994-1001. [PMID: 32191622 DOI: 10.1515/cclm-2019-0723] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 02/14/2020] [Indexed: 11/15/2022]
Abstract
The diffusion of laboratory automation, initiated nearly 50 years ago with consolidation of preanalytical, clinical chemistry and immunochemistry workstations, is now also gradually embracing mass spectrometry (MS). As for other diagnostic disciplines, the automation of MS carries many advantages, such as efficient personnel management (i.e. improving working atmosphere by decreasing manual activities, lowering health risks, simplifying staff training), better organization (i.e. reducing workloads, improving inventory handling, increasing analytical process standardization) and the possibility to reduce the number of platforms. The development and integration of different technologies into automated MS analyzers will also generate technical and practical advantages, such as prepackaged and ready-to-use reagents, automated dispensing, incubation and measurement, automated sample processing (e.g. system fit for many models of laboratory automation, bar code readers), multiplex testing, automatic data processing, also including quality control assessment, and automated validation/interpretation (e.g. autoverification). A new generation of preanalytical workstations, which can be directly connected to MS systems, will allow the automation of manual extraction and elimination of time-consuming activities, such as tube labeling and capping/decapping. The use of automated liquid-handling platform for pipetting samples, along with addition of internal standards, may then enable the optimization of some steps of extraction and protein precipitation, thus decreasing turnaround time and increasing throughput in MS testing. Therefore, this focused review is aimed at providing a brief update on the importance of consolidation and integration of MS platforms in laboratory automation.
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Affiliation(s)
| | - Elisa Danese
- Section of Clinical Biochemistry, University of Verona, Verona, Italy
| | - Giuseppe Lippi
- Section of Clinical Biochemistry, University of Verona, Verona, Italy
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Deng Z, Lam TJGM, Hogeveen H, Koop G. Regularly fluctuating somatic cell count pattern in dairy herds. J Dairy Sci 2021; 104:11126-11134. [PMID: 34275629 DOI: 10.3168/jds.2020-20063] [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: 12/21/2020] [Accepted: 06/04/2021] [Indexed: 11/19/2022]
Abstract
Online somatic cell count (SCC) measurement is widely used in dairy herds milked with automatic milking systems (AMS) and gives the opportunity to closely monitor individual cow udder health. Using automated SCC data, we observed cows displaying a remarkably regularly fluctuating SCC (rfSCC) pattern, which is described in this study. We aimed to (1) estimate the prevalence of rfSCC in cows milked by AMS, (2) characterize the rfSCC pattern, and (3) identify factors potentially associated with the rfSCC pattern. We analyzed 30-d episodes of composite SCC recordings of 1,000 cows from 55 dairy herds from 6 countries using an AMS with automated SCC measurement, and we identified the rfSCC pattern in 4.7% (95% CI: 3.5-6.2%) of these episodes. The rfSCC episodes had a median SCC of 701 × 1,000 cells/mL (2.5-97.5% quantile: 539-1,162), a median amplitude of 552 × 1,000 cells/mL (2.5-97.5% quantile: 409-886), and a median cycle length of 4.1 d (2.5-97.5% quantile: 3.7-4.9). Bacteriological culture data from quarter-milk samples collected every 2 wk in 1 Dutch AMS herd were analyzed, yielding no clear association between pathogen species and the rfSCC pattern found in that herd. Altogether, we described an intriguing phenomenon, present in almost 5% of the cows during a 1-mo study period. Further work is needed to quantify its importance in terms of udder health, but also to elucidate the mechanism behind this remarkable SCC pattern.
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Affiliation(s)
- Z Deng
- Department Population Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 7, 3584 CL Utrecht, the Netherlands.
| | - T J G M Lam
- Department Population Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 7, 3584 CL Utrecht, the Netherlands; Royal GD, PO Box 9, 7400 AA Deventer, the Netherlands
| | - H Hogeveen
- Department Population Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 7, 3584 CL Utrecht, the Netherlands; Chair Group Business Economics, Wageningen University and Research, PO Box 8130, 6700 EW Wageningen, the Netherlands
| | - G Koop
- Department Population Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 7, 3584 CL Utrecht, the Netherlands
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Screening of New Potential Probiotics Strains against Photobacterium damselae Subsp. piscicida for Marine Aquaculture. Animals (Basel) 2021; 11:ani11072029. [PMID: 34359157 PMCID: PMC8300301 DOI: 10.3390/ani11072029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 06/20/2021] [Accepted: 07/05/2021] [Indexed: 11/16/2022] Open
Abstract
On intensive fish farms, 10% of the population dies exclusively from pathogens, and Photobacterium damselae subsp. Piscicida (Ph. damselae subsp. Piscicida), the bacteria causing pasteurellosis in marine aquaculture, is one of the major pathogens involved. The objective of this study was to obtain new probiotic strains against pasteurellosis in order to limit the use of chemotherapy, avoiding the environmental repercussions generated by the abusive use of these products. In this study, 122 strains were isolated from the gills and intestines of different marine fish species and were later evaluated in vitro to demonstrate the production of antagonistic effects, the production of antibacterial substances, adhesion and growth to mucus, resistance to bile and resistance to pH gradients, as well as its harmlessness and the dynamic of expression of immune-related genes by real-time PCR after administration of the potential probiotic in the fish diet. Only 1/122 strains showed excellent results to be considered as a potential probiotic strain and continue its characterization against Ph. damselae subsp. piscicida to determine its protective effect and elucidating in future studies its use as a possible probiotic strain for marine aquaculture.
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An Improved Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry Data Analysis Pipeline for the Identification of Carbapenemase-Producing Klebsiella pneumoniae. J Clin Microbiol 2021; 59:e0080021. [PMID: 33952594 DOI: 10.1128/jcm.00800-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The increasing emergence of carbapenemase-producing Klebsiella pneumoniae (CPK) isolates is a global health alarm. Rapid methods that require minimum sample preparation and rapid data analysis are urgently required. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has recently been used by clinical laboratories for identification of antibiotic-resistant bacteria; however, discrepancies have arisen regarding biological and technical issues. The aim of this study was to standardize an operating procedure and data analysis for identification of CPK by MALDI-TOF MS. To evaluate this approach, a series of 162 K. pneumoniae isolates (112 CPK and 50 non-CPK) were processed in the MALDI BioTyper system (Bruker Daltonik, Germany) following a standard operating procedure. The study was conducted in two stages; the first is denominated the "reproducibility stage" and the second "CPK identification." The first stage was designed to evaluate the biological and technical variation associated with the entire analysis of CPK and the second stage to assess the final accuracy of MALDI-TOF MS for the identification of CPK. Therefore, we present an improved MALDI-TOF MS data analysis pipeline using neural network analysis implemented in Clover MS Data Analysis Software (Clover Biosoft, Spain) that is designed to reduce variability, guarantee interlaboratory reproducibility, and maximize the information selected from the bacterial proteome. Using the random forest (RF) algorithm, 100% of CPK isolates were correctly identified when all the peaks in the spectra were selected as input features and total ion current (TIC) normalization was applied. Thus, we have demonstrated that real-time direct tracking of CPK is possible using MALDI-TOF MS.
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Meena S, Mohanty A, Kaistha N, Sasirekha U, Meena J. Comparative Assessment of Matrix-assisted Laser Desorption Ionization-time of Flight Mass Spectrometry (MALDI-TOF-MS) and Conventional Methods in the Identification of Clinically Relevant Yeasts. Cureus 2021; 13:e15607. [PMID: 34277227 PMCID: PMC8273367 DOI: 10.7759/cureus.15607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/11/2021] [Indexed: 11/20/2022] Open
Abstract
Background: Candida species are generally identified by conventional methods such as germ tube or morphological appearance on cornmeal agar (CMA), biochemical methods using API kits, and molecular biological techniques. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF-MS) has revolutionized the identification of fungi reducing the turnaround time of days to minutes. Purpose: To compare the performance of MALDI-TOF MS and conventional methods in the identification of clinically relevant yeasts. Materials and methods: In this study, Candida identifications on CMA are compared with the results obtained on MALDI-TOF MS (Bruker Daltonics, Bremen, Germany). Discrepant results were confirmed by sequencing internal transcribed spacer (ITS) regions of rDNA. Results: A total of 114 clinical Candida species isolated from blood cultures were isolated and identified with conventional methods as well as with the MALDI-TOF-MS system. The agreement between the two test results were analyzed using Inter-rater reliability analysis (Cohen's Kappa) in SPSS Software Version 24 (IBM Corp., Armonk, NY). Overall, there was substantial agreement (Cohen's kappa=0.763) between the two methods. A value between 0.61 and 0.80 is classified under substantial. The most frequently isolated bloodstream Candida species included Candida albicans, C. tropicalis, C. parapsilosis, C.lusitaniae, C. glabrata which were accurately identified by MALDI-TOF-MS. When compared with conventional identification methods, MALDI-TOF-MS results are more reliable and rapid for Candida identification.
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Affiliation(s)
- Suneeta Meena
- Lab Medicine, All India Institute of Medical Sciences New Delhi, New Delhi, IND
| | - Aroop Mohanty
- Microbiology, All India Institute of Medical Sciences Gorakhpur, Gorakhpur, IND
| | - Neelam Kaistha
- Microbiology, All India Institute of Medical Sciences Rishikesh, Rishikesh, IND
| | - U Sasirekha
- Microbiology, All India Institute of Medical Sciences Rishikesh, Rishikesh, IND
| | - Jitendra Meena
- Preventive Oncology, National Cancer Institute, All India Institute of Medical Sciences Jhajjar, Haryana, IND
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Tambong JT, Xu R, Gerdis S, Daniels GC, Chabot D, Hubbard K, Harding MW. Molecular Analysis of Bacterial Isolates From Necrotic Wheat Leaf Lesions Caused by Xanthomonas translucens, and Description of Three Putative Novel Species, Sphingomonas albertensis sp. nov., Pseudomonas triticumensis sp. nov. and Pseudomonas foliumensis sp. nov. Front Microbiol 2021; 12:666689. [PMID: 34093484 PMCID: PMC8170138 DOI: 10.3389/fmicb.2021.666689] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 03/22/2021] [Indexed: 11/13/2022] Open
Abstract
Xanthomonas translucens is the etiological agent of the wheat bacterial leaf streak (BLS) disease. The isolation of this pathogen is usually based on the Wilbrink's-boric acid-cephalexin semi-selective medium which eliminates 90% of other bacteria, some of which might be novel species. In our study, a general purpose nutrient agar was used to isolate 49 bacterial strains including X. translucens from necrotic wheat leaf tissues. Maximum likelihood cluster analysis of 16S rRNA sequences grouped the strains into 10 distinct genera. Pseudomonas (32.7%) and Pantoea (28.6%) were the dominant genera while Xanthomonas, Clavibacter and Curtobacterium had 8.2%, each. Erwinia and Sphingomonas had two strains, each. BLAST and phylogenetic analyses of multilocus sequence analysis (MLSA) of specific housekeeping genes taxonomically assigned all the strains to validly described bacterial species, except three strains (10L4B, 12L4D and 32L3A) of Pseudomonas and two (23L3C and 15L3B) of Sphingomonas. Strains 10L4B and12L4D had Pseudomonas caspiana as their closest known type strain while strain 32L3A was closest to Pseudomonas asturiensis. Sphingomonas sp. strains 23L3C and 15L3B were closest to S. faeni based on MLSA analysis. Our data on MLSA, whole genome-based cluster analysis, DNA-DNA hybridization and average nucleotide identity, matrix-assisted laser desorption/ionization-time-of-flight, chemotaxonomy and phenotype affirmed that these 5 strains constitute three novel lineages and are taxonomically described in this study. We propose the names, Sphingomonas albertensis sp. nov. (type strain 23L3CT = DOAB 1063T = CECT 30248T = LMG 32139T), Pseudomonas triticumensis sp. nov. (type strain 32L3AT = DOAB 1067T = CECT 30249T = LMG 32140T) and Pseudomonas foliumensis sp. nov. (type strain 10L4BT = DOAB 1069T = CECT 30250T = LMG 32142T). Comparative genomics of these novel species, relative to their closest type strains, revealed unique repertoires of core secretion systems and secondary metabolites/antibiotics. Also, the detection of CRISPR-Cas systems in the genomes of these novel species suggests an acquired mechanism for resistance against foreign mobile genetic elements. The results presented here revealed a cohabitation, within the BLS lesions, of diverse bacterial species, including novel lineages.
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Affiliation(s)
- James T Tambong
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Renlin Xu
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Suzanne Gerdis
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Greg C Daniels
- Crop Diversification Centre South, Alberta Agriculture and Forestry, Brooks, AB, Canada
| | - Denise Chabot
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Keith Hubbard
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Michael W Harding
- Crop Diversification Centre South, Alberta Agriculture and Forestry, Brooks, AB, Canada
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Transmission dynamics of Staphylococcus aureus and Streptococcus agalactiae in a Dutch dairy herd using an automatic milking system. Prev Vet Med 2021; 192:105384. [PMID: 34033990 DOI: 10.1016/j.prevetmed.2021.105384] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 05/06/2021] [Accepted: 05/15/2021] [Indexed: 11/19/2022]
Abstract
Staphylococcus aureus and Streptococcus agalactiae are important contagious mastitis pathogens and are considered to mainly transmit between cows through the milking machine. Controlling contagious mastitis on dairy farms requires a reduction of the transmission rate or the duration of intramammary infections (IMI), or both. These parameters may differ in dairy herds milked with an automatic milking system (AMS) as compared to those milked with a conventional milking system (CMS). The aims of this prospective longitudinal study were to estimate the transmission rate, the median duration of IMI and the basic reproduction number (R0) of Staph. aureus and Strep. agalactiae in a Dutch AMS herd. Bacteriological cultures of quarter milk samples were collected every 2 wks. Using 3 different definitions of IMI, we estimated the transmission rate for Staph. aureus to be within the range of 0.002 (95 % CI: 0-0.005) quarter-day-1 to 0.019 (95 % CI: 0.010-0.032) quarter-day-1, and for Strep. agalactiae of 0.007 (95 % CI: 0.005-0.010) quarter-day-1 to 0.019 (95 % CI: 0.011-0.032) quarter-day-1, the median duration of chronic IMI at 95 (95 % CI: 72-125) days for Staph. aureus and at 86 (95 % CI: 67-111) days for Strep. agalactiae, and the R0 between 0.16 (95 % CI: 0.05-0.27) and 0.34 (95 % CI: 0.20-0.48) for Staph. aureus, and between 0.64 (95 % CI: 0.41-0.87) and 0.68 (95 % CI: 0.48-0.88) for Strep. agalactiae. Transmission of these two contagious pathogens in this herd was limited and theoretically the IMI would not sustain, given that R0 of both pathogens was lower than 1. The estimated transmission rate of Staph. aureus in this AMS herd was found to be comparable to those described for CMS herds, while for Strep. agalactiae, it was slightly higher than in CMS herds. The duration of Staph. aureus IMI was in line with results from CMS farms, while the duration of Strep. agalactiae was lower than what has been described in CMS herds. The R0 of these contagious pathogens was found to be lower than the estimates in CMS herds. Our study suggests that the transmission rate of these two contagious pathogens in this AMS herd were comparable to what has been reported about well-performing CMS herds that have a low rate of transmission.
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Benyahia H, Ouarti B, Diarra AZ, Boucheikhchoukh M, Meguini MN, Behidji M, Benakhla A, Parola P, Almeras L. Identification of Lice Stored in Alcohol Using MALDI-TOF MS. JOURNAL OF MEDICAL ENTOMOLOGY 2021; 58:1126-1133. [PMID: 33346344 DOI: 10.1093/jme/tjaa266] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Indexed: 06/12/2023]
Abstract
Lice pose major public and veterinary health problems with economic consequences. Their identification is essential and requires the development of an innovative strategy. MALDI-TOF MS has recently been proposed as a quick, inexpensive, and accurate tool for the identification of arthropods. Alcohol is one of the most frequently used storage methods and makes it possible to store samples for long periods at room temperature. Several recent studies have reported that alcohol alters protein profiles resulting from MS analysis. After preliminary studies on frozen lice, the purpose of this research was to evaluate the influence of alcohol preservation on the accuracy of lice identification by MALDI-TOF MS. To this end, lice stored in alcohol for variable periods were submitted for MS analysis and sample preparation protocols were optimized. The reproducibility and specificity of the MS spectra obtained on both these arthropod families allowed us to implement the reference MS spectra database (DB) with protein profiles of seven lice species stored in alcohol. Blind tests revealed a correct identification of 93.9% of Pediculus humanus corporis (Linnaeus, 1758) and 98.4% of the other lice species collected in the field. This study demonstrated that MALDI-TOF MS could be successfully used for the identification of lice stored in alcohol for different lengths of time.
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Affiliation(s)
- Hanene Benyahia
- Aix Marseille Univ, IRD, SSA, AP-HM, VITROME, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - Basma Ouarti
- Aix Marseille Univ, IRD, SSA, AP-HM, VITROME, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - Adama Zan Diarra
- Aix Marseille Univ, IRD, SSA, AP-HM, VITROME, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - Mehdi Boucheikhchoukh
- Department of Veterinary Sciences, Chadli Bendjedid University, El-Tarf, 36000, Algeria
| | - Mohamed Nadir Meguini
- Institute of Veterinary and Agronomic Sciences, Mohamed Cherif Messaadia University, Souk-Ahras, Algeria
| | - Makhlouf Behidji
- Institute of Veterinary and Agronomic Sciences, Mohamed Cherif Messaadia University, Souk-Ahras, Algeria
| | - Ahmed Benakhla
- Department of Veterinary Sciences, Chadli Bendjedid University, El-Tarf, 36000, Algeria
| | - Philippe Parola
- Aix Marseille Univ, IRD, SSA, AP-HM, VITROME, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - Lionel Almeras
- Aix Marseille Univ, IRD, SSA, AP-HM, VITROME, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
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Wang G, Song G, Xu Y. A Rapid Antimicrobial Susceptibility Test for Klebsiella pneumoniae Using a Broth Micro-Dilution Combined with MALDI TOF MS. Infect Drug Resist 2021; 14:1823-1831. [PMID: 34025124 PMCID: PMC8132464 DOI: 10.2147/idr.s305280] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 04/22/2021] [Indexed: 12/27/2022] Open
Abstract
Background Matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) is a novel method that can be used to identify pathogens and has potential applications in the detection of drug-resistant bacteria. Purpose To evaluate the ability of a MALDI-TOF MS-based broth micro-dilution method in detecting the minimum inhibitory concentration (MIC) values of Klebsiella pneumoniae to ceftriaxone and imipenem. Materials and Methods Sixty strains of K. pneumoniae with different levels of resistance to carbapenems and cephalosporins were randomly collected. The 0.5 McFarland (Mc) concentration of the bacterial suspension was inoculated in cation-adjusted Mueller-Hinton broth (CAMHB) with a final cell turbidity of 5×105 CFU/mL. The broth was incubated with serial concentrations of antibiotics. After centrifuging the bacterial suspensions, the lysed cells were analyzed by MALDI-TOF MS to identify the growth-promoting or inhibitory effects on K. pneumoniae. The molecular mechanisms of resistance were investigated by PCR and DNA sequencing analysis. Results The expression of known resistance genes (blaKPC, blaFOX, blaDHA, blaCTX-M and blaTEM) was detected in the 30 carbapenems-resistant strains. The agreement between the MIC values derived from the MALDI-TOF MS analysis and from the broth micro-dilution method was 61.7% for ceftriaxone and 71.7% for imipenem. According to the Clinical and Laboratory Standards Institute (CLSI) breakpoint of resistance to ceftriaxone and imipenem, the 60 isolates were accurately classified as resistant or susceptible isolates with 100% sensitivity and 100% specificity. Conclusion The transmission and infection of multidrug-resistant bacteria could be better managed and treated with the rapid identification of strains and antimicrobial susceptibility. A MALDI-TOF MS-based susceptibility test could be used to identify resistance of K. pneumoniae within a short time-frame. This approach could potentially be used as a supplementary antimicrobial susceptibility test that could be investigated on more bacterial species combined with different antibiotics.
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Affiliation(s)
- Gang Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui Province, People's Republic of China
| | - Guobin Song
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui Province, People's Republic of China.,Department of Clinical Laboratory, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Yuanhong Xu
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui Province, People's Republic of China
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Yoo IY, Han J, Ha SI, Cha YJ, Pil SD, Park YJ. Clinical performance of ASTA SepsiPrep kit in direct bacterial identification and antimicrobial susceptibility test using MicroIDSys Elite and VITEK-2 system. J Clin Lab Anal 2021; 35:e23744. [PMID: 33939213 PMCID: PMC8183931 DOI: 10.1002/jcla.23744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/21/2021] [Accepted: 02/09/2021] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND Rapid and accurate microbial identification and antimicrobial susceptibility testing (AST) are essential for timely use of appropriate antimicrobial agents for bloodstream infection. To shorten the time for isolating colonies from the positive blood culture, various preparation methods for direct identification using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) system were developed. Here, we evaluated the SepsiPrep kit (ASTA Corp.) for direct identification of microorganisms and AST from positive blood cultures using MicroIDSys Elite MALDI-TOF MS system (ASTA Corp.) and VITEK-2 system (bioMérieux). METHODS For direct identification, a total of 124 prospective monomicrobial positive blood culture bottles were included. For direct identification, the pellet was prepared by centrifugation and washing twice. For direct AST, the pellet was suspended in 0.45% saline and adjusted to McFarland 0.5. The results from the direct identification and AST using MicroIDSys Elite and VITEK-2 system were compared to those from the conventional method performed with pure colony subcultured on agar plate. RESULTS Compared to the conventional method using pure colony, correct direct identification rate was 96.5% and 98.5% for 57 gram-positive isolates and 67 gram-negative isolates, respectively. For direct AST, among the 55 gram-positive isolates, the categorical agreement (CA) for staphylococci, streptococci, and enterococci was 96.7%, 98.4%, and 94.1%, respectively. For 66 gram-negative isolates, the CA for Enterobacterales and non-fermentative gram-negative rods was 99.0% and 96.6%, respectively. CONCLUSIONS The SepsiPrep kit was easy to use combined with MicroIDSys Elite and VITEK-2 system and also, the correct identification and AST rate were very high.
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Affiliation(s)
- In Young Yoo
- Department of Laboratory Medicine, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Korea
| | - Jayho Han
- Department of Laboratory Medicine, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Korea
| | - Sung Il Ha
- Department of Laboratory Medicine, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Korea
| | - Young Jong Cha
- Department of Laboratory Medicine, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Korea
| | - Shin Dong Pil
- Department of Laboratory Medicine, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Korea
| | - Yeon-Joon Park
- Department of Laboratory Medicine, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Korea
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Hassen B, Abbassi MS, Ruiz-Ripa L, Mama OM, Ibrahim C, Benlabidi S, Hassen A, Torres C, Hammami S. Genetic characterization of extended-spectrum β-lactamase-producing Enterobacteriaceae from a biological industrial wastewater treatment plant in Tunisia with detection of the colistin-resistance mcr-1 gene. FEMS Microbiol Ecol 2021; 97:5986610. [PMID: 33202005 DOI: 10.1093/femsec/fiaa231] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 11/13/2020] [Indexed: 12/14/2022] Open
Abstract
This study evaluated the occurrence of extended-spectrum β-lactamases (ESBL) and associated resistance genes, integrons, and plasmid types, as well as the genetic relatedness of enterobacterial isolates in the wastewater treatment plant (WWTP) of La Charguia, Tunis City (Tunisia). A total of 100 water samples were collected at different points of the sewage treatment process during 2017-2019. Antimicrobial susceptibility was conducted by the disc-diffusion method. blaCTX-M, blaTEM and blaSHV genes as well as those encoding non-β-lactam resistance, the plasmid types, occurrence of class1 integrons and phylogenetic groups of Escherichia coli isolates were determined by PCR/sequencing. Genomic relatedness was determined by multi-locus sequence typing (MLST) for selected isolates. In total, 57 ESBL-producer isolates were recovered (47 E. coli, eight Klebsiella pneumoniae, 1 of the Citrobacter freundii complex and 1 of the Enterobacter cloacae complex). The CTX-M-15 enzyme was the most frequently detected ESBL, followed by CTX-M-27, CTX-M-55 and SHV-12. One E. coli isolate harboured the mcr-1 gene. The following phylogroups/sequence types (STs) were identified among ESBL-producing E. coli isolates: B2/ST131 (subclade-C1), A/ST3221, A/ST8900, D/ST69, D/ST2142, D/ST38, B1/ST2460 and B1/ST6448. High numbers of isolates harboured the class 1 integrons with various gene cassette arrays as well as IncP-1 and IncFIB plasmids. Our findings confirm the importance of WWTPs as hotspot collectors of ESBL-producing Enterobacteriaceae with a high likelihood of spread to human and natural environments.
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Affiliation(s)
- Bilel Hassen
- Université de Tunis El Manar, Institut de la Recherche Vétérinaire de Tunisie, 20 rue Jebel Lakhdhar, Bab Saadoun, Tunis 1006, Tunisia
| | - Mohamed Salah Abbassi
- Université de Tunis El Manar, Institut de la Recherche Vétérinaire de Tunisie, 20 rue Jebel Lakhdhar, Bab Saadoun, Tunis 1006, Tunisia.,Université de Tunis El Manar, Faculté de Médecine de Tunis, Laboratoire de résistance aux antibiotiques LR99ES09, Tunisia
| | - Laura Ruiz-Ripa
- Departamento de Agricultura y Alimentación, Universidad de La Rioja, 26006 Logroño, Spain
| | - Olouwafemi M Mama
- Departamento de Agricultura y Alimentación, Universidad de La Rioja, 26006 Logroño, Spain
| | - Chourouk Ibrahim
- Laboratoire de Traitement et de Valorisation des rejets hydriques, Centre des Recherches et des Technologies des Eaux (CERTE), Technopole Borj-Cédria, BP 273, 8020, Soliman, Tunisia
| | - Saloua Benlabidi
- Université de Tunis El Manar, Institut de la Recherche Vétérinaire de Tunisie, 20 rue Jebel Lakhdhar, Bab Saadoun, Tunis 1006, Tunisia
| | - Abdennaceur Hassen
- Laboratoire de Traitement et de Valorisation des rejets hydriques, Centre des Recherches et des Technologies des Eaux (CERTE), Technopole Borj-Cédria, BP 273, 8020, Soliman, Tunisia
| | - Carmen Torres
- Departamento de Agricultura y Alimentación, Universidad de La Rioja, 26006 Logroño, Spain
| | - Salah Hammami
- Université de la Manouba, IRESA, École Nationale de Médecine Vétérinaire de Sidi Thabet, Sidi Thabet 2020, Sidi Thabet, Ariana, Tunisia
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