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Lee RT, Evanowski RL, Greenbaum HE, Pawloski DA, Wiedmann M, Martin NH. Troubleshooting high laboratory pasteurization counts in organic raw milk requires characterization of dominant thermoduric bacteria, which includes nonsporeformers as well as sporeformers. J Dairy Sci 2024; 107:3478-3491. [PMID: 38246545 DOI: 10.3168/jds.2023-24330] [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: 10/19/2023] [Accepted: 12/15/2023] [Indexed: 01/23/2024]
Abstract
Laboratory pasteurization count (LPC) enumerates thermoduric bacteria and is one parameter used to assess raw milk quality. No regulatory limit has presently been set for LPC, but LPC data are used by some dairy processors and cooperatives to designate raw milk quality premiums paid to farmers and may also be used for troubleshooting bacterial contamination issues. Although it is occasionally used as a proxy for levels of bacterial spores in raw milk, limited knowledge is available on the types of organisms that are enumerated by LPC in contemporary raw milk supplies. Although historical studies have reported that thermoduric bacteria quantified by LPC may predominantly represent gram-positive cocci, updated knowledge on microbial populations enumerated by LPC in contemporary organic raw milk supplies is needed. To address this gap, organic raw milk samples from across the United States (n = 94) were assessed using LPC, and bacterial isolates were characterized. LPC ranged from below detection (<0.70 log cfu/mL) to 4.07 log cfu/mL, with a geometric mean of 1.48 log cfu/mL. Among 380 isolates characterized by 16S rDNA sequencing, 52.6%, 44.5%, and 2.4% were identified as gram-positive sporeformers, gram-positive nonsporeformers, and gram-negatives, respectively; 0.5% could not be categorized into those groups because they could only be assigned a higher level of taxonomy. Isolates identified as gram-positive sporeformers were predominantly Bacillus (168/200), and gram-positive nonsporeformers were predominantly Brachybacterium (56/169) and Kocuria (47/169). To elucidate if the LPC level can be an indicator of the type of thermoduric (e.g., sporeforming bacteria) present in raw milk, we evaluated the proportion of sporeformers in raw milk samples with LPC of ≤100 cfu/mL, 100 to 200 cfu/mL, and ≥200 cfu/mL (51%, 67%, and 35%), showing a trend for sporeformers to represent a smaller proportion of the total thermoduric population when LPC increases, although overall linear regression showed no significant association between the proportion of sporeformers and the LPC concentration. Hence, LPC level alone provides no insight into the makeup of the thermoduric population in raw milk, and further characterization is needed to elucidate the bacterial drivers of elevated LPC in raw milk. We therefore further characterized the isolates from this study using MALDI-TOF mass spectrometry (MALDI-TOF MS), a rapid microbial identification tool that is more readily available to dairy producers than 16S rDNA PCR and sequencing. Although our data indicated agreement between 16S rDNA sequencing and MALDI-TOF MS for 66.6% of isolates at the genus level, 24.2% and 9.2% could not be reliably identified or were mischaracterized using MALDI-TOF MS, respectively. This suggests that further optimization of this method is needed to allow for accurate characterization of thermoduric organisms commonly found in raw milk. Ultimately, our study provides a contemporary perspective on thermoduric bacteria selected by the LPC method and establishes that the LPC alone is not sufficient for identifying the bacterial drivers of LPC levels. Further development of rapid characterization methods that are accessible to producers, cooperatives, and processors will support milk quality troubleshooting efforts and ultimately improve outcomes for dairy industry community members.
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Affiliation(s)
- Renee T Lee
- Milk Quality Improvement Program, Department of Food Science, Cornell University, Ithaca, NY 14853
| | - Rachel L Evanowski
- Milk Quality Improvement Program, Department of Food Science, Cornell University, Ithaca, NY 14853
| | - Halle E Greenbaum
- Milk Quality Improvement Program, Department of Food Science, Cornell University, Ithaca, NY 14853
| | - Deborah A Pawloski
- Quality Milk Production Services, Animal Health Diagnostic Center, Cornell University, Cobleskill, NY 12043
| | - Martin Wiedmann
- Milk Quality Improvement Program, Department of Food Science, Cornell University, Ithaca, NY 14853
| | - Nicole H Martin
- Milk Quality Improvement Program, Department of Food Science, Cornell University, Ithaca, NY 14853.
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2
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Shelef O, Kopp T, Tannous R, Arutkin M, Jospe-Kaufman M, Reuveni S, Shabat D, Fridman M. Enzymatic Activity Profiling Using an Ultrasensitive Array of Chemiluminescent Probes for Bacterial Classification and Characterization. J Am Chem Soc 2024; 146:5263-5273. [PMID: 38362863 PMCID: PMC10910560 DOI: 10.1021/jacs.3c11790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 02/02/2024] [Accepted: 02/05/2024] [Indexed: 02/17/2024]
Abstract
Identification and characterization of bacterial species in clinical and industrial settings necessitate the use of diverse, labor-intensive, and time-consuming protocols as well as the utilization of expensive and high-maintenance equipment. Furthermore, while cutting-edge identification technologies such as mass spectrometry and PCR are highly effective in identifying bacterial pathogens, they fall short in providing additional information for identifying bacteria not present in the databases upon which these methods rely. In response to these challenges, we present a robust and general approach to bacterial identification based on their unique enzymatic activity profiles. This method delivers results within 90 min, utilizing an array of highly sensitive and enzyme-selective chemiluminescent probes. Leveraging our recently developed technology of chemiluminescent luminophores, which emit light under physiological conditions, we have crafted an array of probes designed to rapidly detect various bacterial enzymatic activities. The array includes probes for detecting resistance to the important and large class of β-lactam antibiotics. The analysis of chemiluminescent fingerprints from a diverse range of prominent bacterial pathogens unveiled distinct enzymatic activity profiles for each strain. The reported universally applicable identification procedure offers a highly sensitive and expeditious means to delineate bacterial enzymatic activity fingerprints. This opens new avenues for characterizing and identifying pathogens in research, clinical, and industrial applications.
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Affiliation(s)
| | | | | | - Maxence Arutkin
- School of Chemistry, Raymond
& Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Moriah Jospe-Kaufman
- School of Chemistry, Raymond
& Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Shlomi Reuveni
- School of Chemistry, Raymond
& Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Doron Shabat
- School of Chemistry, Raymond
& Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Micha Fridman
- School of Chemistry, Raymond
& Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
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3
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Cerca NF, DePaula J, Calado VMA, Antônio L Miguel M, Farah A. Bioactive profile and microbiological safety of Coffea arabica and Coffea canephora beverages obtained by innovative cold extraction methods (cold brews). Food Res Int 2023; 174:113667. [PMID: 37981379 DOI: 10.1016/j.foodres.2023.113667] [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: 07/19/2023] [Revised: 10/27/2023] [Accepted: 11/03/2023] [Indexed: 11/21/2023]
Abstract
Coffee cold brews have been gaining prominence and popularity among consumers worldwide. However, only a few studies have systematically analyzed their chemical composition or evaluated microbiological safety aspects. This study aimed to evaluate the survival of Bacillus cereus and Escherichia coli in cold brews prepared from roasted and ground Coffea arabica and C. canephora seeds using the following preparation methods: immersion without filter (INF), immersion in a cotton filter bag (ICF), vacuum (Vac.) and cold dripping (Drip.). Traditional hot dripping methods using filter paper (HDFP) and cotton filter (HDCF) were also tested for comparison. Water at 4 °C or 25 °C was intentionally contaminated (105 CFU/mL) with cells of Escherichia coli ATCC 25922 (EC) and Bacillus cereus F4433 (BC) before coffee extraction and refrigeration at 4 °C. Coffee concentrations of 5, 10, and 15% were tested. Analyses of pH, soluble solids, nine chlorogenic acids and two lactones (CGA), caffeine, trigonelline, and melanoidins were performed. Results were compared by ANOVA, followed by the Fisher's test, Pearson correlation, Variable Importance in Projection (VIP), and Cluster analyses, with a significance level of 5%. EC and BC were not detected (<10 CFU/mL and < 1 CFU/mL, respectively) after preparing C. arabica and C. canephora hot brews. In cold brews, the higher the extraction of soluble solids and bioactive compounds (with the highest occurring at 25 °C), the lower the counts of inoculated microorganisms during 24 h of storage. BC was not detected after 24 h of extraction and/or storage in the drinks obtained by ICF and Drip. at 5%, 10%, and 15% and INF and Vac. at 15%. EC was not detected in ICF and Drip. at 10 and 15%, and in INF at 15%. C. canephora brews exhibited higher levels of soluble solids, CGA, caffeine, and melanoidins than C. arabica brews. Based on these results, it can be concluded that in the absence of thermal processing as in hot brews, more concentrated cold brews, such as 15%, produced at 25 °C by dripping and immersion methods, are preferable for later dilution due to the higher content of soluble solids and bioactive compounds that contribute reducing the number of microorganisms in the beverage.
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Affiliation(s)
- Nathália F Cerca
- Food Chemistry and Bioactivity Laboratory & Coffee Research Core (NUPECAFÉ), Nutrition Institute, Federal University of Rio de Janeiro (UFRJ), Brazil; Food Microbiology Laboratory, Institute of Microbiology, UFRJ, Brazil.
| | - Juliana DePaula
- Food Chemistry and Bioactivity Laboratory & Coffee Research Core (NUPECAFÉ), Nutrition Institute, Federal University of Rio de Janeiro (UFRJ), Brazil.
| | | | | | - Adriana Farah
- Food Chemistry and Bioactivity Laboratory & Coffee Research Core (NUPECAFÉ), Nutrition Institute, Federal University of Rio de Janeiro (UFRJ), Brazil.
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4
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Janiszewska D, Złoch M, Pomastowski P, Szultka-Młyńska M. Implications of Sample Preparation Methods on the MALDI-TOF MS Identification of Spore-Forming Bacillus Species from Food Samples: A Closer Look at Bacillus licheniformis, Peribacillus simplex, Lysinibacillus fusiformis, Bacillus flexus, and Bacillus marisflavi. ACS OMEGA 2023; 8:34982-34994. [PMID: 37779958 PMCID: PMC10536843 DOI: 10.1021/acsomega.3c04354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 08/30/2023] [Indexed: 10/03/2023]
Abstract
This research underscores the criticality of tailored culture conditions and incubation periods for effective and accurate identification of spore-forming bacteria: Bacillus licheniformis, Peribacillus simplex, Lysinibacillus fusiformis, Bacillus flexus, and Bacillus marisflav, isolated from food samples, utilizing the MALDI-TOF MS technique. All isolated strains were confirmed as Gram-positive bacteria from diverse genera through 16S rDNA gene sequencing. To enhance the accuracy of the identification process, the study employed an optimization strategy involving a varied incubation time (ranging from 1 to 48 h) and two distinct sample preparation approaches-direct transfer facilitated by formic acid and protein extraction via ethanol. It was observed that matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) could successfully identify approximately 47% of the samples following a 24 h incubation period. The study emphasizes the critical role of sample preparation methods in enabling precise bacterial identification. Our findings reveal the necessity of tailoring the incubation time for each sample, as the optimum period for accurate identification fluctuated between 1 and 12 h. Further demonstrating the interplay between incubation time and spore quantity, our study used the Schaeffer-Fulton staining method to show that the lowest spore counts were detected between 5 and 8 h of incubation. This provides evidence that spore formation impacts bacterial identification. Our research thus deepens the understanding of spore-forming bacteria identification using MALDI-TOF MS and illuminates the various factors affecting the dependability and accuracy of this technique. Future research may explore additional variables, such as the effect of varying culture media, to further augment identification accuracy and gain a holistic understanding of spore-forming bacterial behavior in food samples. By enhancing our knowledge, these findings can substantially contribute to improving food safety and quality assurance strategies by enabling the more accurate and efficient identification of spore-forming bacteria in the food industry, thereby elevating the standards of food safety.
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Affiliation(s)
- Daria Janiszewska
- Department
of Environmental Chemistry and Bioanalytics, Gagarina 7, 87-100 Torun, Poland
| | - Michał Złoch
- Centre
for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wilenska 4, 87-100 Torun, Poland
| | - Paweł Pomastowski
- Centre
for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wilenska 4, 87-100 Torun, Poland
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5
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Nellessen CM, Nehl DB. An easy adjustment of instrument settings ('Peak MALDI') improves identification of organisms by MALDI-ToF mass spectrometry. Sci Rep 2023; 13:15018. [PMID: 37700004 PMCID: PMC10497524 DOI: 10.1038/s41598-023-42328-2] [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: 06/06/2023] [Accepted: 09/08/2023] [Indexed: 09/14/2023] Open
Abstract
Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-ToF MS) is a mature technolaogy with 'auto-execute' instrument settings and peak processing parameters tailored for rapid bacterial identification. Adoption for other organisms has been problematic, with optimisation efforts focusing on sample preparation. Using the Bruker MALDI Biotyper, we demonstrate 'Peak MALDI': easily-applied settings that immediately enhance sensitivity, improve spectrum quality, and increase identification confidence for any target, establishing its potential value for all MALDI-ToF MS systems.
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Affiliation(s)
| | - David B Nehl
- Department of Agriculture, Fisheries and Forestry, Sydney, Australia
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Rossy T, Distler T, Meirelles LA, Pezoldt J, Kim J, Talà L, Bouklas N, Deplancke B, Persat A. Pseudomonas aeruginosa type IV pili actively induce mucus contraction to form biofilms in tissue-engineered human airways. PLoS Biol 2023; 21:e3002209. [PMID: 37527210 PMCID: PMC10393179 DOI: 10.1371/journal.pbio.3002209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 06/21/2023] [Indexed: 08/03/2023] Open
Abstract
The opportunistic pathogen Pseudomonas aeruginosa causes antibiotic-recalcitrant pneumonia by forming biofilms in the respiratory tract. Despite extensive in vitro experimentation, how P. aeruginosa forms biofilms at the airway mucosa is unresolved. To investigate the process of biofilm formation in realistic conditions, we developed AirGels: 3D, optically accessible tissue-engineered human lung models that emulate the airway mucosal environment. AirGels recapitulate important factors that mediate host-pathogen interactions including mucus secretion, flow and air-liquid interface (ALI), while accommodating high-resolution live microscopy. With AirGels, we investigated the contributions of mucus to P. aeruginosa biofilm biogenesis in in vivo-like conditions. We found that P. aeruginosa forms mucus-associated biofilms within hours by contracting luminal mucus early during colonization. Mucus contractions facilitate aggregation, thereby nucleating biofilms. We show that P. aeruginosa actively contracts mucus using retractile filaments called type IV pili. Our results therefore suggest that, while protecting epithelia, mucus constitutes a breeding ground for biofilms.
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Affiliation(s)
- Tamara Rossy
- Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Tania Distler
- Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Lucas A Meirelles
- Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Joern Pezoldt
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Jaemin Kim
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, New York, United States of America
| | - Lorenzo Talà
- Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Nikolaos Bouklas
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, New York, United States of America
| | - Bart Deplancke
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Alexandre Persat
- Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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7
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Li S, Han D, Chen X, Zheng D, Cai Y, Lin D, Zhang X, Ke P, Qu P, Chen C. Evaluation of the Zybio EXS3000 mass spectrometry in routine identification of Clinical isolates. Heliyon 2023; 9:e18990. [PMID: 37600400 PMCID: PMC10432711 DOI: 10.1016/j.heliyon.2023.e18990] [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: 02/28/2023] [Revised: 07/25/2023] [Accepted: 08/04/2023] [Indexed: 08/22/2023] Open
Abstract
The matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has been widely applied in routine clinical microbiology laboratories as an efficient and reliable technique for diagnostic purpose. In this work, we evaluated the performance of the newly developed Zybio EXS3000 (Zybio Inc., China) in microbial identification and compared it with VITEK MS (bioMérieux, France). For this study, a total of 1340 isolates from various clinical specimens were collected. These isolates were analyzed simultaneously on both EXS3000 and VITEK MS. The inconsistent or unidentifiable data were further identified using the help of either 16S rRNA gene or ITS region sequencing. During the study, we observed that EXS3000 and VITEK MS provided positive confirmatory diagnostics for 95.0% and 96.5% of the isolates, respectively, which were consistent with the sequencing results. However, it is worth noting that the EXS3000 system needs to improve the identification performance of Candida albicans in the follow-up. There are no significant differences between the two devices in terms of microbial identification performance. The advantage of EXS3000 over VITEK MS is in its ability to perform in significantly lesser time period. In conclusion, the results of this investigation showed that EXS3000 can be used to identify microorganisms in clinical microbiology laboratories.
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Affiliation(s)
- Song Li
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
- Department of Clinical Laboratory, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Dexing Han
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xiaowei Chen
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Dexiang Zheng
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
- Department of Clinical Laboratory, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Yimei Cai
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
- Department of Clinical Laboratory, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Dongling Lin
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
- Department of Clinical Laboratory, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Xuan Zhang
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
- Department of Clinical Laboratory, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Peifeng Ke
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
- Department of Clinical Laboratory, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Pinghua Qu
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
- Department of Clinical Laboratory, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Cha Chen
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
- Department of Clinical Laboratory, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
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8
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Bopp TC, Marchesi M, Zihlmann R, Sax H, Wolfensberger A. Identifying patients at high risk for multidrug-resistant organisms after hospitalization abroad. Infect Control Hosp Epidemiol 2023; 44:1281-1288. [PMID: 36912341 DOI: 10.1017/ice.2022.256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2023]
Abstract
OBJECTIVES We quantified the percentage of multidrug-resistant organism (MDRO) carriers among repatriated patients. We identified factors associated with MDRO carriage, and we evaluated the yield of MDRO detection per screened body site. DESIGN Retrospective cohort study. SETTING A tertiary-care center in Switzerland. PATIENTS Adult patients after a stay in a healthcare institution abroad. METHODS Patients were screened for MDRO carriage. Standard sites, including nose and throat, groins, and (since mid-2018) rectum, and risk-based sites (wounds, urine, tracheal secretion) were sampled. MDROs were defined as methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant Enterococcus (VRE), extended-spectrum β-lactamase (ESBL)- and carbapenemase-producing Enterobacterales (CPE), multidrug-resistant (MDR) Enterobacterales, and MDR nonfermenting gram-negative rods. Risk factors for MDRO carriage were assessed using multivariate logistic regression. RESULTS Between May 2017 and April 2019, 438 patients were screened and 107 (24.4%) tested positive for an MDRO, predominantly ESBL-producing and MDR Enterobacterales. Risk factors for MDRO colonization were the length of stay in hospital abroad, antibiotic treatment with 'Watch' and 'Reserve' antibiotics, and region of hospitalization abroad. Rectal swabs had the highest yield for detecting patients with MDR intestinal bacteria, but nose/throat and groins, or wound samples were more sensitive for MRSA or nonfermenting gram-negative organisms, respectively. CONCLUSIONS We identified risk factors for MDRO carriage and body sites with the highest yield for a specific MDRO, which might help to target screening and isolation and reduce screening costs.
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Affiliation(s)
- Tamara C Bopp
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, University of Zurich, Zurich, Switzerland
| | - Martina Marchesi
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Reto Zihlmann
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, University of Zurich, Zurich, Switzerland
- Seminar for Statistics, ETH Zurich, Zurich, Switzerland
| | - Hugo Sax
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, University of Zurich, Zurich, Switzerland
- Department of Infectious Diseases, Bern University Hospital and University of Bern, Bern, Switzerland
| | - Aline Wolfensberger
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, University of Zurich, Zurich, Switzerland
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9
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Kolesnik-Goldmann N, Seth-Smith HMB, Haldimann K, Imkamp F, Roloff T, Zbinden R, Hobbie SN, Egli A, Mancini S. Comparison of Disk Diffusion, E-Test, and Broth Microdilution Methods for Testing In Vitro Activity of Cefiderocol in Acinetobacter baumannii. Antibiotics (Basel) 2023; 12:1212. [PMID: 37508308 PMCID: PMC10376138 DOI: 10.3390/antibiotics12071212] [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: 06/20/2023] [Revised: 07/14/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023] Open
Abstract
The reference method for cefiderocol antimicrobial susceptibility testing is broth microdilution (BMD) with iron-depleted-Mueller-Hinton (ID-MH) medium, whereas breakpoints recommended for disk diffusion (DD) are based on MH-agar plates. We aimed to compare the performance of the commercial BMD tests ComASP (Liofilchem) and UMIC (Bruker), and DD and E-test using MH- and ID-MH-agar plates with the reference BMD method using 100 carbapenem-resistant-A. baumannii isolates. Standard BMD was performed according to the EUCAST guidelines; DD and E-test were carried out using two commercial MH-agar plates (BioMérieux and Liofilchem) and an in-house ID-MH-agar plate, while ComASP and UMIC were performed according to the manufacturer's guidelines. DD performed with the ID-MH-agar plates led to a higher categorical agreement (CA, 95.1%) with standard BMD and fewer categorization errors compared to the commercial MH-agar plates (CA BioMérieux 91.1%, Liofilchem 89.2%). E-test on ID-MH-agar plates exhibited a significantly higher essential agreement (EA, 75%) with standard BMD compared to the two MH-agar plates (EA BioMérieux 57%, Liofilchem 44%), and showed a higher performance in detecting high-level resistance than ComASP and UMIC (mean log2 difference with standard BMD for resistant isolates of 0.5, 2.83, and 2.08, respectively). In conclusion, DD and E-test on ID-MH-agar plates exhibit a higher diagnostic performance than on MH-agar plates and the commercial BMD methods. Therefore, we recommend using ID-MH-agar plates for cefiderocol susceptibility testing of A. baumannii.
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Affiliation(s)
| | - Helena M B Seth-Smith
- Institute of Medical Microbiology, University Zurich, Gloriastrasse 28/30, 8006 Zurich, Switzerland
| | - Klara Haldimann
- Institute of Medical Microbiology, University Zurich, Gloriastrasse 28/30, 8006 Zurich, Switzerland
| | - Frank Imkamp
- Institute of Medical Microbiology, University Zurich, Gloriastrasse 28/30, 8006 Zurich, Switzerland
| | - Tim Roloff
- Institute of Medical Microbiology, University Zurich, Gloriastrasse 28/30, 8006 Zurich, Switzerland
| | - Reinhard Zbinden
- Institute of Medical Microbiology, University Zurich, Gloriastrasse 28/30, 8006 Zurich, Switzerland
| | - Sven N Hobbie
- Institute of Medical Microbiology, University Zurich, Gloriastrasse 28/30, 8006 Zurich, Switzerland
| | - Adrian Egli
- Institute of Medical Microbiology, University Zurich, Gloriastrasse 28/30, 8006 Zurich, Switzerland
| | - Stefano Mancini
- Institute of Medical Microbiology, University Zurich, Gloriastrasse 28/30, 8006 Zurich, Switzerland
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10
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Meile S, Du J, Staubli S, Grossmann S, Koliwer-Brandl H, Piffaretti P, Leitner L, Matter CI, Baggenstos J, Hunold L, Milek S, Guebeli C, Kozomara-Hocke M, Neumeier V, Botteon A, Klumpp J, Marschall J, McCallin S, Zbinden R, Kessler TM, Loessner MJ, Dunne M, Kilcher S. Engineered reporter phages for detection of Escherichia coli, Enterococcus, and Klebsiella in urine. Nat Commun 2023; 14:4336. [PMID: 37474554 PMCID: PMC10359277 DOI: 10.1038/s41467-023-39863-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 07/03/2023] [Indexed: 07/22/2023] Open
Abstract
The rapid detection and species-level differentiation of bacterial pathogens facilitates antibiotic stewardship and improves disease management. Here, we develop a rapid bacteriophage-based diagnostic assay to detect the most prevalent pathogens causing urinary tract infections: Escherichia coli, Enterococcus spp., and Klebsiella spp. For each uropathogen, two virulent phages were genetically engineered to express a nanoluciferase reporter gene upon host infection. Using 206 patient urine samples, reporter phage-induced bioluminescence was quantified to identify bacteriuria and the assay was benchmarked against conventional urinalysis. Overall, E. coli, Enterococcus spp., and Klebsiella spp. were each detected with high sensitivity (68%, 78%, 87%), specificity (99%, 99%, 99%), and accuracy (90%, 94%, 98%) at a resolution of ≥103 CFU/ml within 5 h. We further demonstrate how bioluminescence in urine can be used to predict phage antibacterial activity, demonstrating the future potential of reporter phages as companion diagnostics that guide patient-phage matching prior to therapeutic phage application.
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Affiliation(s)
- Susanne Meile
- Institute of Food Nutrition and Health, ETH, Zurich, Switzerland
| | - Jiemin Du
- Institute of Food Nutrition and Health, ETH, Zurich, Switzerland
| | - Samuel Staubli
- Institute of Food Nutrition and Health, ETH, Zurich, Switzerland
| | | | | | | | - Lorenz Leitner
- Department of Neuro-Urology, Balgrist University Hospital, University of Zurich, Zurich, Switzerland
| | | | | | - Laura Hunold
- Institute of Food Nutrition and Health, ETH, Zurich, Switzerland
| | - Sonja Milek
- Department of Neuro-Urology, Balgrist University Hospital, University of Zurich, Zurich, Switzerland
| | | | | | - Vera Neumeier
- Department of Neuro-Urology, Balgrist University Hospital, University of Zurich, Zurich, Switzerland
| | - Angela Botteon
- Institute of Food Nutrition and Health, ETH, Zurich, Switzerland
| | - Jochen Klumpp
- Institute of Food Nutrition and Health, ETH, Zurich, Switzerland
| | - Jonas Marschall
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, MO, US
| | - Shawna McCallin
- Department of Neuro-Urology, Balgrist University Hospital, University of Zurich, Zurich, Switzerland
| | - Reinhard Zbinden
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Thomas M Kessler
- Department of Neuro-Urology, Balgrist University Hospital, University of Zurich, Zurich, Switzerland
| | | | - Matthew Dunne
- Institute of Food Nutrition and Health, ETH, Zurich, Switzerland.
| | - Samuel Kilcher
- Institute of Food Nutrition and Health, ETH, Zurich, Switzerland.
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11
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Linn-Peirano SC, Hepworth-Warren K, Kinsella H, Diaz-Campos D, Brenseke BM, Cianciolo RE, Schroeder E, Schreeg ME. Ingesta-associated choledocholithiasis in horses: 2 cases and literature review. J Vet Diagn Invest 2023; 35:417-424. [PMID: 37232550 PMCID: PMC10331394 DOI: 10.1177/10406387231177251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023] Open
Abstract
Equine ingesta-associated choledocholithiasis is a rare cause of morbidity and mortality. We describe here the clinical, gross, histologic, and microbiologic features of this condition in 2 horses and compare the features to 2 previous cases. Case 1 was a 4-y-old Thoroughbred mare with colic. Case 2 was an 18-y-old American Paint Horse mare with colic, chronic weight loss, and inappropriate mentation. Both had elevated biochemical markers of hepatocellular injury and cholestasis and were euthanized given a poor prognosis. Case 1 had a well-formed 5-cm choledocholith surrounding a piece of hay, and had chronic neutrophilic cholangiohepatitis, bridging fibrosis, and extrahepatic obstruction. Case 2 had an ill-formed choledocholith with occasional hay fragments, wood stick, and twigs, and had regionally extensive hepatocellular necrosis with mild neutrophilic cholangiohepatitis and bridging fibrosis. Enterococcus casseliflavus and Escherichia coli were isolated in both cases; Clostridium spp. were also isolated from case 2. All 4 reported cases had increased activity of cholestatic enzymes, hyperbilirubinemia, portal inflammation, and bridging fibrosis. Colic, pyrexia, leukocytosis with neutrophilia, and elevated hepatocellular enzyme activity were documented in 3 cases. Foreign material in all 4 cases was plant origin (choledochophytolithiasis), including hay (n = 2), sticks/twigs (n = 2), and grass awns (n = 1). Ingesta-associated choledocholithiasis may be considered as a cause of colic, pyrexia, and elevated cholestatic biomarkers in horses.
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Affiliation(s)
| | - Kate Hepworth-Warren
- College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - Hannah Kinsella
- College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA
| | | | - Bonnie M. Brenseke
- College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
- Jerry M. Wallace School of Osteopathic Medicine, Campbell University, Buies Creek, NC, USA
| | - Rachel E. Cianciolo
- College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA
- Zoetis, Parsippany, NJ, USA
| | - Eric Schroeder
- College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA
| | - Megan E. Schreeg
- College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA
- College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
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12
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Maki JJ, Howard M, Connelly S, Pettengill MA, Hardy DJ, Cameron A. Species Delineation and Comparative Genomics within the Campylobacter ureolyticus Complex. J Clin Microbiol 2023; 61:e0004623. [PMID: 37129508 PMCID: PMC10204631 DOI: 10.1128/jcm.00046-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 04/06/2023] [Indexed: 05/03/2023] Open
Abstract
Campylobacter ureolyticus is an emerging pathogen increasingly appreciated as a common cause of gastroenteritis and extra-intestinal infections in humans. Outside the setting of gastroenteritis, little work has been done to describe the genomic content and relatedness of the species, especially regarding clinical isolates. We reviewed the epidemiology of clinical C. ureolyticus cultured by our institution over the past 10 years. Fifty-one unique C. ureolyticus isolates were identified between January 2010 and August 2022, mostly originating from abscesses and blood cultures. To clarify the taxonomic relationships between isolates and to attribute specific genes with different clinical manifestations, we sequenced 19 available isolates from a variety of clinical specimen types and conducted a pangenomic analysis with publicly available C. ureolyticus genomes. Digital DNA:DNA hybridization suggested that these C. ureolyticus comprised a species complex of 10 species clusters (SCs) and several subspecies clusters. Although some orthologous genes or gene functions were enriched in isolates found in different SCs and clinical specimens, no association was significant. Nearly a third of the isolates possessed antimicrobial resistance genes, including the ermA resistance gene, potentially conferring resistance to macrolides, the treatment of choice for severe human campylobacteriosis. This work effectively doubles the number of publicly available C. ureolyticus genomes, provides further clarification of taxonomic relationships within this bacterial complex, and identifies target SCs for future analysis.
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Affiliation(s)
- Joel J. Maki
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, New York, USA
| | - Mondraya Howard
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, New York, USA
| | - Sara Connelly
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, New York, USA
| | - Matthew A. Pettengill
- Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Dwight J. Hardy
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, New York, USA
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
| | - Andrew Cameron
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, New York, USA
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13
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Imkamp F, Kolesnik-Goldmann N, Bodendoerfer E, Zbinden R, Mancini S. Detection of Extended-Spectrum β-Lactamases (ESBLs) and AmpC in Class A and Class B Carbapenemase-Producing Enterobacterales. Microbiol Spectr 2022; 10:e0213722. [PMID: 36287018 PMCID: PMC9769508 DOI: 10.1128/spectrum.02137-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 09/30/2022] [Indexed: 01/06/2023] Open
Abstract
In carbapenemase-producing Enterobacterales (CPE) additional β-lactam resistance mechanisms such as extended-spectrum-β-lactamases (ESBL) and/or AmpC-β-lactamases are generally difficult to detect by phenotypical methods. Recently, a modified version of the CLSI ESBL confirmatory combination disc diffusion (CDD) test, which involves the addition of boronic acid and EDTA on discs containing ESBL and AmpC substrates ± inhibitors, has been proposed for the detection of ESBL in class A and class B CPE. Here, the performance of the modified CDD test was evaluated using 121 genotypically characterized class A and class B CPE. Also, the effectiveness of the NG-Test CTX-M-MULTI lateral flow immunoassay was evaluated for ESBL detection. For class A CPE (n = 47), the modified CDD method exhibited an equal specificity (95.7%) and a higher sensitivity (100%) compared to the standard method (91.7%). The CTX-M-MULTI test detected ESBL in all CTX-M-type ESBL producers (n = 23), whereas it was negative for all CTX-M-type ESBL-negative isolates (n = 24). For class B CPE (n = 71), the modified method significantly improved both sensitivity (95%) and specificity (100%) in detecting ESBL compared to the standard method (17.5% sensitivity and 83.9% specificity). In comparison, the CTX-M-MULTI led to identification of ESBL in all CTX-M-ESBL-producers (n = 39) and no false-positive signal was generated with the CTX-M-type-ESBL-negative isolates (n = 30). Furthermore, the modified CDD improved the robustness of the method for AmpC detection (inconclusive results were produced in 53/57 and 10/57 cases with the standard and modified method, respectively), although the sensitivity of the test was poor (23.5%). Here, we propose a practical and cost-effective approach combining the modified CDD and the CTX-M-MULTI test for detection of ESBL and/or AmpC in class A and B CPE. IMPORTANCE Antimicrobial resistance is a growing public health threat of broad concern worldwide. Timely detection of antibiotic resistance mechanisms can help to monitor and to curb the spread of resistant bacteria within the hospital setting as well as in the environment. In this work we report an accurate and affordable method to phenotypically identify difficult-to-detect resistance determinants in highly resistant (carbapenemase-producing) bacteria. This method may be implemented in any diagnostic microbiology lab and may reduce the underreporting of relevant resistance mechanisms.
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Affiliation(s)
- Frank Imkamp
- Institute of Medical Microbiology, University Zurich, Zurich, Switzerland
| | | | - Elias Bodendoerfer
- Institute of Medical Microbiology, University Zurich, Zurich, Switzerland
| | - Reinhard Zbinden
- Institute of Medical Microbiology, University Zurich, Zurich, Switzerland
| | - Stefano Mancini
- Institute of Medical Microbiology, University Zurich, Zurich, Switzerland
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14
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Djebala S, Coria E, Munaut F, Gille L, Eppe J, Moula N, Taminiau B, Daube G, Bossaert P. Bacterial Contamination of the Surgical Site at the Time of Elective Caesarean Section in Belgian Blue Cows-Part 1: Identified by Bacterial Culture. Vet Sci 2022; 9:vetsci9120687. [PMID: 36548847 PMCID: PMC9785745 DOI: 10.3390/vetsci9120687] [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: 11/20/2022] [Revised: 12/05/2022] [Accepted: 12/07/2022] [Indexed: 12/13/2022] Open
Abstract
To improve the efficacy of preoperative antibiotics used in elective caesarean section (CS), we aimed to identify the bacteria contaminating the surgical site during this surgery. A study was conducted on 76 Belgian Blue cows. Bacteriology was performed on cotton swab sampled from the visceral and parietal peritoneum of each cow during the CS. Most of samples showed a negative culture (55/76; 72.37%), 19/76 (25%) were positive (p < 0.0001) and two samples were contaminated. In total, 32 isolates belonging to 18 species were identified. Most of them are aerobic (17/18; 94.44%) and half of them were gram-negative (G-). The most encountered bacteria were Acinetobacter sp. (6/32; 18.75%), Pseudomonas sp. (4/32; 12.5%), Aerococcus viridans (4/32; 12.5%), Psychrobacter sp. (3/32; 9.37%), and Escherichia coli (2/32; 6.25%). Among the identified isolates, 31/32 (96.87%) were aerobic and 1/32 (3.12%) was anaerobic (p = 0.0001). Furthermore, 20/32 (62.50%) strains were G− while 12/32 (37.5%) were gram-positive (G+) (p = 0.012). In fact, most of cultured strains were aerobic G− (20/32), 11/32 were aerobic G+ and 1/32 is anaerobic G+ (p < 0.0001). In conclusion, most of samples showed a negative bacteriology; however, aerobic G− strains were the most identified in positive swabs. Therefore, preoperative antibiotics should be aimed against these bacteria.
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Affiliation(s)
- Salem Djebala
- Clinical Department of Ruminants, University of Liège, Quartier Vallée 2, Avenue de Cureghem 7A-7D, 4000 Liège, Belgium
- Murphy and Leslie Veterinary Centre (Private Practice), Muckerstaff Granard, N39AN52 Co Longford, Ireland
- Correspondence: ; Tel.: +32-493-33-35-91 or +353-87-115-12-58
| | - Elise Coria
- Clinical Department of Ruminants, University of Liège, Quartier Vallée 2, Avenue de Cureghem 7A-7D, 4000 Liège, Belgium
| | - Florian Munaut
- Clinical Department of Ruminants, University of Liège, Quartier Vallée 2, Avenue de Cureghem 7A-7D, 4000 Liège, Belgium
| | - Linde Gille
- Clinical Department of Ruminants, University of Liège, Quartier Vallée 2, Avenue de Cureghem 7A-7D, 4000 Liège, Belgium
| | - Justine Eppe
- Clinical Department of Ruminants, University of Liège, Quartier Vallée 2, Avenue de Cureghem 7A-7D, 4000 Liège, Belgium
| | - Nassim Moula
- Department of animal production, University of Liege, Quartier Vallée 2, Avenue de Cureghem 6, 4000 Liège, Belgium
- GIGA, Animal Facilities, ULiège, B 34, 4000 Liège, Belgium
| | - Bernard Taminiau
- Fundamental and Applied Research for Animal and Health (FARAH), University of Liege, 4000 Liege, Belgium
- Food Microbiology, Department of Food Sciences, Faculty of Veterinary Medicine, University of Liege, 4000 Liege, Belgium
| | - Georges Daube
- Fundamental and Applied Research for Animal and Health (FARAH), University of Liege, 4000 Liege, Belgium
- Food Microbiology, Department of Food Sciences, Faculty of Veterinary Medicine, University of Liege, 4000 Liege, Belgium
| | - Philippe Bossaert
- Faculty of Veterinary Medicine, University of Namur, Rue de Bruxelles 61, 5000 Namur, Belgium
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15
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Andrzejewska M, Grudlewska-Buda K, Śpica D, Skowron K, Ćwiklińska-Jurkowska M, Szady-Grad M, Indykiewicz P, Wiktorczyk-Kapischke N, Klawe JJ. Genetic relatedness, virulence, and drug susceptibility of Campylobacter isolated from water and wild birds. Front Cell Infect Microbiol 2022; 12:1005085. [PMID: 36506026 PMCID: PMC9732551 DOI: 10.3389/fcimb.2022.1005085] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/31/2022] [Indexed: 11/27/2022] Open
Abstract
Introduction This study aimed to identify the characteristics of Campylobacter isolated from wild birds (Black-headed gulls Chroicocephalus ridibundus and Great tits Parus major) and collect surface water samples (from rivers, ponds, ornamental lakes, freshwater beaches). Research material included 33 Campylobacter isolates. All the strains were isolated by different monitoring and surveillance plans. Methods The prevalence of selected genes (flaA, cadF, iam, cdtB, wlaN, sodB, tet0) encoding virulence factors and resistance among Campylobacter spp. was assessed by the PCR method. The genetic similarities of isolates were determined by Pulsed-Field Gel Electrophoresis (PFGE). The susceptibility of Campylobacter isolates to clinically important antimicrobials: erythromycin, tetracycline, and ciprofloxacin, previously assessed by E-test, was presented in the form of drug susceptibility profiles depending on the origin of the isolates. Results The cadF, flaA, cdtB, and sodB genes exhibited the highest detection rate. Statistically significant differences between the presence of wlaN virulence genes were noted among different species of the isolates. No genetically identical isolates were found. The most numerous antibiotic susceptibility profile included strains susceptible to all antibiotics studied (profile A-33.3%). The second most common were the tetracycline - and ciprofloxacin-resistant (profile B-27.2%), and tetracycline-resistant profile (C-24.2%) respectively. Discussion The study revealed the virulent properties of Campylobacter isolated from water samples, and wild birds, and high resistance rates to tetracycline, and fluoroquinolones. The lack of genetic relatedness among strains isolated from water, and birds may indicate other sources of surface water contamination with Campylobacter bacteria than birds. The presence of Campylobacter spp. in wild birds could also have other environmental origins.
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Affiliation(s)
- Małgorzata Andrzejewska
- Department of Hygiene, Epidemiology, Ergonomy and Postgraduate Education, Ludwik Rydygier Collegium Medicum in Bydgoszcz Nicolaus Copernicus University in Torun, Bydgoszcz, Poland,*Correspondence: Małgorzata Andrzejewska,
| | - Katarzyna Grudlewska-Buda
- Department of Microbiology, Ludwik Rydygier Collegium Medicum in Bydgoszcz Nicolaus Copernicus University in Torun, Bydgoszcz, Poland
| | - Dorota Śpica
- Department of Hygiene, Epidemiology, Ergonomy and Postgraduate Education, Ludwik Rydygier Collegium Medicum in Bydgoszcz Nicolaus Copernicus University in Torun, Bydgoszcz, Poland
| | - Krzysztof Skowron
- Department of Microbiology, Ludwik Rydygier Collegium Medicum in Bydgoszcz Nicolaus Copernicus University in Torun, Bydgoszcz, Poland
| | - Małgorzata Ćwiklińska-Jurkowska
- Department of Biostatistics and Theory of Biomedical Systems, Ludwik Rydygier Collegium Medicum in Bydgoszcz Nicolaus Copernicus University in Torun, Bydgoszcz, Poland
| | - Małgorzata Szady-Grad
- Department of Hygiene, Epidemiology, Ergonomy and Postgraduate Education, Ludwik Rydygier Collegium Medicum in Bydgoszcz Nicolaus Copernicus University in Torun, Bydgoszcz, Poland
| | - Piotr Indykiewicz
- Department of Biology and Animal Environment, Bydgoszcz University of Science and Technology, Bydgoszcz, Poland
| | - Natalia Wiktorczyk-Kapischke
- Department of Microbiology, Ludwik Rydygier Collegium Medicum in Bydgoszcz Nicolaus Copernicus University in Torun, Bydgoszcz, Poland
| | - Jacek J. Klawe
- Department of Hygiene, Epidemiology, Ergonomy and Postgraduate Education, Ludwik Rydygier Collegium Medicum in Bydgoszcz Nicolaus Copernicus University in Torun, Bydgoszcz, Poland
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16
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Wiktorczyk-Kapischke N, Skowron K, Kwiecińska-Piróg J, Białucha A, Wałecka-Zacharska E, Grudlewska-Buda K, Kraszewska Z, Gospodarek-Komkowska E. Flies as a potential vector of selected alert pathogens in a hospital environment. INTERNATIONAL JOURNAL OF ENVIRONMENTAL HEALTH RESEARCH 2022; 32:1868-1887. [PMID: 33926318 DOI: 10.1080/09603123.2021.1919605] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 04/16/2021] [Indexed: 06/12/2023]
Abstract
Multi-drug resistant pathogens are a global problem. Flies are a potential vector of multi-drug resistant pathogens, which can be particularly dangerous in the hospital environment. This study aimed to evaluate flies as vectors of alert pathogens. The research material consisted of 100 flies (Musca domestica (46.0%), Lucilia sericata (28.0%), and Calliphora vicina (26.0%)) collected at the University Hospital No. 1 dr. A. Jurasz in Bydgoszcz (Poland) in 2018-2019 (summer months). The presence of bacteria of the genera: Enterococcus, Staphylococcus, Escherichia, Leclercia, Citrobacter, Hafnia, Providencia, Proteus, Enterobacter, Klebsiella, Raoultella, Morganella, Moellerella, Bordetella, Pantoea, Serratia, Plesiomonas, Wohlfahrimonas, and Lelliottia was confirmed. The most frequently isolated species included: Enterococcus faecalis (n = 64), Escherichia coli (n = 43) and Moellerella wisconsensis (n = 24). The infection rate and antibiotic resistance of bacteria were assessed. One strain of Proteus mirabilis (isolated from Calliphora vicina) produced ESBLs (extended-spectrum beta-lactamases). The infection rate was 0.38%, 0.26%, and 0.20% for Musca domestica, Lucilia sericata, and Calliphora vicina, respectively. The flies from a hospital area were not a vector of alert pathogens. Monitoring flies as potential vectors of pathogens is an important aspect of public health, especially for hospitalized patients.
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Affiliation(s)
- Natalia Wiktorczyk-Kapischke
- Department of Microbiology, Nicolaus Copernicus University in Toruń, Collegium Medicum of L. Rydygier in Bydgoszcz Poland
| | - Krzysztof Skowron
- Department of Microbiology, Nicolaus Copernicus University in Toruń, Collegium Medicum of L. Rydygier in Bydgoszcz Poland
| | - Joanna Kwiecińska-Piróg
- Department of Microbiology, Nicolaus Copernicus University in Toruń, Collegium Medicum of L. Rydygier in Bydgoszcz Poland
| | - Agata Białucha
- Department of Microbiology, Nicolaus Copernicus University in Toruń, Collegium Medicum of L. Rydygier in Bydgoszcz Poland
| | - Ewa Wałecka-Zacharska
- Department of Food Hygiene and Consumer Health, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Katarzyna Grudlewska-Buda
- Department of Microbiology, Nicolaus Copernicus University in Toruń, Collegium Medicum of L. Rydygier in Bydgoszcz Poland
| | - Zuzanna Kraszewska
- Department of Microbiology, Nicolaus Copernicus University in Toruń, Collegium Medicum of L. Rydygier in Bydgoszcz Poland
| | - Eugenia Gospodarek-Komkowska
- Department of Microbiology, Nicolaus Copernicus University in Toruń, Collegium Medicum of L. Rydygier in Bydgoszcz Poland
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Besedin D, Turner BJ, Deo P, Lopes MDB, Williams CR. Effect of captivity and water salinity on culture-dependent frog skin microbiota and Batrachochytrium dendrobatidis ( Bd) infection. T ROY SOC SOUTH AUST 2022. [DOI: 10.1080/03721426.2022.2086358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Darislav Besedin
- UniSA Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Brandon J. Turner
- UniSA Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Permal Deo
- UniSA Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia
- Health and Biomedical Innovation, UniSA Clinical and Health Science, University of South Australia, Adelaide, South Australia, Australia
| | - Miguel De Barros Lopes
- UniSA Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia
- Health and Biomedical Innovation, UniSA Clinical and Health Science, University of South Australia, Adelaide, South Australia, Australia
| | - Craig R. Williams
- UniSA Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia
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18
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Torres-Sangiao E, Lamas Rodriguez B, Cea Pájaro M, Carracedo Montero R, Parajó Pazos N, García-Riestra C. Direct Urine Resistance Detection Using VITEK 2. Antibiotics (Basel) 2022; 11:antibiotics11050663. [PMID: 35625307 PMCID: PMC9138041 DOI: 10.3390/antibiotics11050663] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 05/10/2022] [Accepted: 05/12/2022] [Indexed: 02/01/2023] Open
Abstract
Urinary tract infections (UTIs) are the most common infectious diseases in both communities and hospitals. With non-anatomical or functional abnormalities, UTIs are usually self-limiting, though women suffer more reinfections throughout their lives. Certainly, antibiotic treatment leads to a more rapid resolution of symptoms, but also it selects resistant uropathogens and adversely affects the gut and vaginal microbiota. As uropathogens are increasingly becoming resistant to currently available antibiotics, it could be time to explore alternative strategies for managing UTIs. Rapid identification and antimicrobial susceptibility testing (AST) allow fast and precise treatment. The objective of this study was to shorten the time of diagnosis of UTIs by combining pathogen screening through flow cytometry, microbial identification by matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF MS), and the VITEK 2 system for the direct analysis of urine samples. First, we selected positive urine samples by flow cytometry using UF5000, establishing the cut-off for positive at 150 bacteria/mL. After confirming the identification using MALDI-TOF MS and filtering the urine samples for Escherichia coli, we directly tested the AST N388 card using VITEK 2. We tested a total of 211 E. coli from urine samples. Cefoxitin, ertapenem, imipenem, gentamicin, nalidixic acid, ciprofloxacin, fosfomycin, and nitrofurantoin had no major important errors (MIE), and ampicillin, cefuroxime, and tobramycin showed higher MIEs. Cefepime, imipenem, and tobramycin had no major errors (ME). Fosfomycin was the antibiotic with the most MEs. The antibiotic with the most minor errors (mE) was ceftazidime. The total categorical agreement (CA) was 97.4% with a 95% CI of (96.8–97.9)95%. The direct AST from the urine samples proposed here was shorter by one day, without significant loss of sensibility regarding the standard diagnosis. Therefore, we hypothesize that this method is more realistic and better suited to human antibiotic concentrations.
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Affiliation(s)
- Eva Torres-Sangiao
- Grupo Escherichia coli, Fundación Instituto de InvestigaciónSanitaria (FIDIS), Hospital Clínico Universitario de Santiago de Compostela (CHUS), 15706 Santiago de Compostela, Spain
- Clinical Microbiology Lab, University Hospital Marqués de Valdecilla, 39008 Santander, Spain
- Instituto de Investigación Sanitaria Marqués de Valdecilla (IDIVAL), 39011 Santander, Spain
- Correspondence: (E.T.-S.); (C.G.-R.)
| | - Brais Lamas Rodriguez
- Dto Microbiology at Medical School, University of Santiago de Compostela, 15705 Santiago de Compostela, Spain;
| | - María Cea Pájaro
- Clinical Microbiology Lab, Hospital Clínico Universitario de Santiago de Compostela (CHUS), 15706 Santiago de Compostela, Spain; (M.C.P.); (R.C.M.); (N.P.P.)
| | - Raquel Carracedo Montero
- Clinical Microbiology Lab, Hospital Clínico Universitario de Santiago de Compostela (CHUS), 15706 Santiago de Compostela, Spain; (M.C.P.); (R.C.M.); (N.P.P.)
| | - Noelia Parajó Pazos
- Clinical Microbiology Lab, Hospital Clínico Universitario de Santiago de Compostela (CHUS), 15706 Santiago de Compostela, Spain; (M.C.P.); (R.C.M.); (N.P.P.)
| | - Carlos García-Riestra
- Grupo Escherichia coli, Fundación Instituto de InvestigaciónSanitaria (FIDIS), Hospital Clínico Universitario de Santiago de Compostela (CHUS), 15706 Santiago de Compostela, Spain
- Dto Microbiology at Medical School, University of Santiago de Compostela, 15705 Santiago de Compostela, Spain;
- Clinical Microbiology Lab, Hospital Clínico Universitario de Santiago de Compostela (CHUS), 15706 Santiago de Compostela, Spain; (M.C.P.); (R.C.M.); (N.P.P.)
- Correspondence: (E.T.-S.); (C.G.-R.)
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19
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Walser F, Prinz J, Rahm S, Zingg PO, Mancini S, Imkamp F, Zbinden R, Achermann Y. Antimicrobial susceptibility testing is crucial when treating Finegoldia magna infections. Eur J Clin Microbiol Infect Dis 2022:10.1007/s10096-022-04439-y. [PMID: 35391578 DOI: 10.1007/s10096-022-04439-y] [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: 10/01/2021] [Accepted: 03/24/2022] [Indexed: 11/03/2022]
Abstract
Finegoldia magna is an anaerobic gram-positive bacterium that can cause invasive human infections. Recently, a 52-year-old patient suffering from a periprosthetic joint infection (PJI) due to F. magna was treated with cefepime on hemodialysis; however, treatment failed due to relapse caused by antibiotic-resistant strains. Reports on the antimicrobial susceptibility of F. magna clinical isolates are rare. We collected 57 clinical F. magna isolates from Zurich, Switzerland, between September 2019 and July 2020 and tested their antimicrobial susceptibility to investigate the local resistance pattern. Antimicrobial susceptibility testing (AST) was evaluated for nine antibiotics (benzylpenicillin, amoxicillin/clavulanic acid, cefuroxime, cefepime, levofloxacin, rifampicin, metronidazole, doxycycline, and clindamycin) by E-test according to CLSI guidelines. All F. magna strains were susceptible to benzylpenicillin, amoxicillin/clavulanic acid, and metronidazole, while 75% to clindamycin. F. magna isolates showed MIC values lower than species-unrelated breakpoints for cefuroxime, levofloxacin, and cefepime in 93%, 56%, and 32% of the cases, respectively. MIC values for rifampicin and doxycycline were lower than locally determined ECOFFs in 98% and 72% of the cases, respectively. In summary, we recommend the use of benzylpenicillin, amoxicillin/clavulanic acid, or metronidazole without prior AST as first-line treatment option against F. magna PJI infections. If cefuroxime, cefepime, levofloxacin, rifampicin, doxycycline, or clindamycin are used, AST is mandatory.
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Affiliation(s)
- Fabienne Walser
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Raemistrasse 100, CH-8091, Zurich, Switzerland
| | - Julia Prinz
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Raemistrasse 100, CH-8091, Zurich, Switzerland
- Department of Dermatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Stefan Rahm
- Department of Orthopedics, Balgrist University Hospital, University of Zurich, Zurich, Switzerland
| | - Patrick O Zingg
- Department of Orthopedics, Balgrist University Hospital, University of Zurich, Zurich, Switzerland
| | - Stefano Mancini
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Frank Imkamp
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Reinhard Zbinden
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Yvonne Achermann
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Raemistrasse 100, CH-8091, Zurich, Switzerland.
- Dermatology, University Hospital Zurich, University of Zurich And Department of Internfal Medicine, Hospital Zollikerberg, Zollikerberg, Switzerland.
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20
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Bächli P, Baars S, Simmler A, Zbinden R, Schulthess B. Impact of MALDI-TOF MS identification on anaerobic species and genus diversity in routine diagnostics. Anaerobe 2022; 75:102554. [DOI: 10.1016/j.anaerobe.2022.102554] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 02/08/2022] [Accepted: 03/23/2022] [Indexed: 11/30/2022]
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21
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Gao W, Li B, Ling L, Zhang L, Yu S. MALDI-TOF MS method for differentiation of methicillin-sensitive and methicillin-resistant Staphylococcus aureus using (E)-Propyl α-cyano-4-Hydroxyl cinnamylate. Talanta 2022; 244:123405. [PMID: 35349841 DOI: 10.1016/j.talanta.2022.123405] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 03/17/2022] [Accepted: 03/22/2022] [Indexed: 01/02/2023]
Abstract
Differentiating methicillin-sensitive and methicillin-resistant Staphylococcus aureus (MRSA and MSSA) is crucial for clinical diagnosis and anti-microbial treatment. Matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) is an efficient tool for identifying pathogenic microorganisms at the bacterial species level. Here, we found that MRSA and MSSA can be differentiated by MALDI-TOF MS by employing (E)-propylα-cyano-4-hydroxyl cinnamylate (CHCA-C3) as the matrix, which shows great performance for proteins/peptides, especially hydrophobic proteins. The results show that the mass spectra profile of standard MRSA (ATCC 43300) is significantly different from the profiles of standard MSSA strains (ATCC 25923 and 29213) when using CHCA-C3 as the matrix compared to traditional matrix. The mass profiles had great reproducibility and were scarcely influenced by the growth medium. Due to the enhanced discrimination ability of CHCA-C3, we collected the mass spectra of 62 clinical S. aureus strains and selected four representative peaks for principal component analysis, which showed great differentiation. Our results suggest that employing a suitable matrix could enhance the discrimination ability of antibiotic-resistant bacteria by MALDI-TOF MS.
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Affiliation(s)
- Wenjing Gao
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Bin Li
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Ling Ling
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, 315211, China.
| | - Li Zhang
- Department of Laboratory Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, 100730, China.
| | - Shaoning Yu
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, 315211, China.
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22
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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: 16] [Impact Index Per Article: 8.0] [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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23
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Palm HA, Thirumalapura NR, Boger LA, Ringler SR. An unusual outbreak of erysipelas on a goat farm in Pennsylvania. J Vet Diagn Invest 2022; 34:268-272. [PMID: 35075947 PMCID: PMC8921819 DOI: 10.1177/10406387211072831] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Erysipelothrix rhusiopathiae infection and septicemia occurred in a 5-d old Boer goat found dead on a farm in western Pennsylvania. On autopsy, there was moderate, focally extensive hemorrhage along the remnants of the urachus and umbilical arteries and the apex of the urinary bladder. Microscopic examination of immunohistochemical stained tissues revealed abundant intracellular and extracellular E. rhusiopathiae antigen-positive bacilli in all tissues stained, including lung, heart, liver, skeletal muscle, kidney, and thymus. Bacteria isolated from liver and urachus were identified as E. rhusiopathiae by MALDI-TOF mass spectrometry and further confirmed by a PCR assay. An epidemiologic investigation was conducted via an on-farm questionnaire after the owners noted a 70% mortality rate from the 2019 kidding season. The epidemiologic investigation showed that E. rhusiopathiae, an opportunistic zoonotic organism, was introduced to the farm through a breach in biosecurity and was likely perpetuated among the resident poultry species.
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Affiliation(s)
| | | | - Lore A. Boger
- Pennsylvania Veterinary Laboratory, Harrisburg, PA, USA
| | - Stephanie R. Ringler
- Stephanie R. Ringler, U.S. Department of Agriculture, Animal Plant and Health Inspection Service, Veterinary Services, 2300 Vartan Way, Suite 250, Harrisburg, PA 17110, USA.
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24
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Chang KK, Cai YH, Hsiao CH, Hsu CC, Wang YS. High-performance miniature linear time-of-flight mass spectrometry as an advantageous tool in a high mass-to-charge range. Analyst 2022; 147:4116-4123. [DOI: 10.1039/d2an00952h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A newly developed miniature MALDI-TOF mass spectrometer provides superior performance in a high m/z range.
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Affiliation(s)
- Ko-Keng Chang
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
- Department of Chemistry, National Taiwan University, Taipei 106, Taiwan
| | - Yi-Hong Cai
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
- Department of Chemistry, National Taiwan Normal University, Taipei 116, Taiwan
| | - Chih-Hao Hsiao
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Cheng-Chih Hsu
- Department of Chemistry, National Taiwan University, Taipei 106, Taiwan
| | - Yi-Sheng Wang
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
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25
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Kaiki Y, Kitagawa H, Tadera K, Taogoshi H, Ikeda M, Kano M, Harino T, Nomura T, Omori K, Shigemoto N, Takahashi S, Ohge H. Laboratory identification and clinical characteristics of Streptococcus bovis/Streptococcus equinus complex bacteremia: a retrospective, multicenter study in Hiroshima, Japan. BMC Infect Dis 2021; 21:1192. [PMID: 34836500 PMCID: PMC8626886 DOI: 10.1186/s12879-021-06880-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 11/15/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bacteremia due to the Streptococcus bovis/Streptococcus equinus complex (SBSEC) is associated with specific diseases, such as colorectal cancer and infective endocarditis. This study aimed to evaluate the clinical characteristics of SBSEC bacteremia and the accuracy of identification of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and phenotypic identification systems for SBSEC isolates. METHODS We analyzed patients with SBSEC bacteremia retrospectively between 2012 and 2019 at three hospitals in Japan. We re-identified each SBSEC isolate using sequencing superoxide dismutase (sodA) analysis, MALDI-TOF MS using the MALDI Biotyper, and phenotypic identification using the VITEK2. RESULTS During the study period, 39 patients with SBSEC bacteremia were identified. S. gallolyticus subsp. pasteurianus (SGSP, n = 29), S. gallolyticus subsp. gallolyticus (SGSG, n = 5), S. lutetiensis (SL, n = 4), and S. infantarius subsp. infantarius (n = 1) were identified using sodA sequencing analysis. Primary bacteremia (36%) was the most common cause of bacteremia, followed by infective endocarditis (26%) and biliary tract infections (23%). Colorectal cancer was associated significantly with SGSG bacteremia, while the sources of bacteremia were similar in each SBSEC subspecies. The MALDI Biotyper was significantly more accurate in identifying the SBSEC isolates at the subspecies level compared to the VITEK2 (92% vs. 67%, P = 0.010). In contrast, there were no significant differences in the rates of correct identification of the SBSEC isolates at the species level between the MALDI Biotyper and the VITEK2 (100% vs. 87%, P = 0.055). CONCLUSIONS Bacteremia with SGSG was associated with colorectal cancer, and the sources of bacteremia were similar in each SBSEC subspecies. The MALDI-TOF MS was significantly more accurate in identifying SBSEC isolates at the subspecies level than the phenotypic identification systems. The accurate identification of SBSEC isolates using the MALDI-TOF MS and phenotypic identification systems was sufficient at the species level, but it was insufficient at the subspecies level. Therefore, it may be reasonable for clinicians to perform echocardiographies and colonoscopies in all patients with SBSEC bacteremia.
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Affiliation(s)
- Yuki Kaiki
- Department of Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Hiroki Kitagawa
- Department of Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan. .,Department of Infectious Diseases, Hiroshima University Hospital, Hiroshima, Japan. .,Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, Japan.
| | - Kayoko Tadera
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, Japan.,Section of Clinical Laboratory, Division of Clinical Support, Hiroshima University Hospital, Hiroshima, Japan.,Division of Laboratory Medicine, Hiroshima University Hospital, Hiroshima, Japan
| | - Hiroyuki Taogoshi
- Department of Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan.,Department of Surgery, JA Hiroshima General Hospital, Hiroshima, Japan
| | - Mitsuyasu Ikeda
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, Japan.,Section of Clinical Research and Laboratory, JA Hiroshima General Hospital, Hiroshima, Japan
| | - Mikihiro Kano
- Department of Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan.,Department of Surgery, Hiroshima City Asa Citizens Hospital, Hiroshima, Japan
| | - Toshie Harino
- Department of Clinical Laboratory, Hiroshima City Asa Citizens Hospital, Hiroshima, Japan
| | - Toshihito Nomura
- Department of Infectious Diseases, Hiroshima University Hospital, Hiroshima, Japan
| | - Keitaro Omori
- Department of Infectious Diseases, Hiroshima University Hospital, Hiroshima, Japan
| | - Norifumi Shigemoto
- Department of Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan.,Department of Infectious Diseases, Hiroshima University Hospital, Hiroshima, Japan.,Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, Japan.,Translational Research Center, Hiroshima University, Hiroshima, Japan
| | - Shinya Takahashi
- Department of Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Hiroki Ohge
- Department of Infectious Diseases, Hiroshima University Hospital, Hiroshima, Japan.,Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, Japan
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26
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Kitagawa H, Shimizu H, Katayama K, Tadera K, Nomura T, Omori K, Shigemoto N, Takasaki T, Ohge H, Takahashi S. Postoperative mediastinitis after cardiac surgery caused by Mycoplasma hominis: a case report. Surg Case Rep 2021; 7:248. [PMID: 34812956 PMCID: PMC8611127 DOI: 10.1186/s40792-021-01326-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 11/07/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mycoplasma hominis is a human commensal bacterium of the urogenital tract, and extragenital infection caused by M. hominis has rarely been reported. The identification of M. hominis is challenging, and surgeons are generally not aware that this bacteria can cause postoperative infection. Here, we report a rare case of postoperative mediastinitis caused by M. hominis after cardiac surgery in an immunocompetent patient. CASE PRESENTATION A 54-year-old man presented with pain and purulent discharge from the wound after aortic valve replacement and patent foramen ovale closure. However, Gram staining and culture of bacteria from the purulent discharge was negative, and empiric sulbactam/ampicillin therapy was not effective. This patient developed mediastinitis and rupture of a pseudoaneurysm of the ascending aorta caused by mediastinitis, and re-operation was performed. Then, postoperative mediastinitis caused by M. hominis or Ureaplasma species was suspected and bacterial cultures targeting these pathogens were performed. M. hominis was identified from abscess and tissue obtained from the surgical site and urine. A final diagnosis of postoperative mediastinitis caused by M. hominis was determined. The patient was initially treated with levofloxacin and then with minocycline for 3 weeks. The patient's clinical condition improved; the patient was transferred to another hospital. CONCLUSION The role of M. hominis as a cause of postoperative infection might be underestimated in cardiac surgery. M. hominis should be considered when culture-negative purulent discharge is observed or there is no response to standard empiric treatment of postoperative infections.
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Affiliation(s)
- Hiroki Kitagawa
- Department of Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan. .,Department of Infectious Diseases, Hiroshima University Hospital, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan. .,Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan.
| | - Haruna Shimizu
- Department of Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan
| | - Keijiro Katayama
- Department of Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan
| | - Kayoko Tadera
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan.,Section of Infection Diseases Laboratory, Department of Clinical Support, Hiroshima University Hospital, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan.,Division of Clinical Laboratory Medicine, Hiroshima University Hospital, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan
| | - Toshihito Nomura
- Department of Infectious Diseases, Hiroshima University Hospital, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan
| | - Kietaro Omori
- Department of Infectious Diseases, Hiroshima University Hospital, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan
| | - Norifumi Shigemoto
- Department of Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan.,Department of Infectious Diseases, Hiroshima University Hospital, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan.,Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan.,Translational Research Center, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan
| | - Taiichi Takasaki
- Department of Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan
| | - Hiroki Ohge
- Department of Infectious Diseases, Hiroshima University Hospital, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan.,Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan
| | - Shinya Takahashi
- Department of Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan
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27
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Pruski P, Correia GDS, Lewis HV, Capuccini K, Inglese P, Chan D, Brown RG, Kindinger L, Lee YS, Smith A, Marchesi J, McDonald JAK, Cameron S, Alexander-Hardiman K, David AL, Stock SJ, Norman JE, Terzidou V, Teoh TG, Sykes L, Bennett PR, Takats Z, MacIntyre DA. Direct on-swab metabolic profiling of vaginal microbiome host interactions during pregnancy and preterm birth. Nat Commun 2021; 12:5967. [PMID: 34645809 PMCID: PMC8514602 DOI: 10.1038/s41467-021-26215-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 09/23/2021] [Indexed: 11/13/2022] Open
Abstract
The pregnancy vaginal microbiome contributes to risk of preterm birth, the primary cause of death in children under 5 years of age. Here we describe direct on-swab metabolic profiling by Desorption Electrospray Ionization Mass Spectrometry (DESI-MS) for sample preparation-free characterisation of the cervicovaginal metabolome in two independent pregnancy cohorts (VMET, n = 160; 455 swabs; VMET II, n = 205; 573 swabs). By integrating metataxonomics and immune profiling data from matched samples, we show that specific metabolome signatures can be used to robustly predict simultaneously both the composition of the vaginal microbiome and host inflammatory status. In these patients, vaginal microbiota instability and innate immune activation, as predicted using DESI-MS, associated with preterm birth, including in women receiving cervical cerclage for preterm birth prevention. These findings highlight direct on-swab metabolic profiling by DESI-MS as an innovative approach for preterm birth risk stratification through rapid assessment of vaginal microbiota-host dynamics.
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Affiliation(s)
- Pamela Pruski
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine Imperial College London, London, UK
| | - Gonçalo D S Correia
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine Imperial College London, London, UK
- National Phenome Centre, Imperial College London, London, UK
| | - Holly V Lewis
- March of Dimes Prematurity Research Centre at Imperial College London, London, UK
- Imperial College Parturition Research Group, Institute of Reproductive and Developmental Biology, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
- Queen Charlotte's & Chelsea Hospital, Imperial College London, London, UK
| | - Katia Capuccini
- March of Dimes Prematurity Research Centre at Imperial College London, London, UK
- Imperial College Parturition Research Group, Institute of Reproductive and Developmental Biology, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Paolo Inglese
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine Imperial College London, London, UK
- National Phenome Centre, Imperial College London, London, UK
| | - Denise Chan
- March of Dimes Prematurity Research Centre at Imperial College London, London, UK
- Imperial College Parturition Research Group, Institute of Reproductive and Developmental Biology, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
- Queen Charlotte's & Chelsea Hospital, Imperial College London, London, UK
| | - Richard G Brown
- Imperial College Parturition Research Group, Institute of Reproductive and Developmental Biology, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
- Queen Charlotte's & Chelsea Hospital, Imperial College London, London, UK
| | - Lindsay Kindinger
- Imperial College Parturition Research Group, Institute of Reproductive and Developmental Biology, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
- Elizabeth Garrett Anderson Institute for Women's Health, University College London, London, UK
| | - Yun S Lee
- March of Dimes Prematurity Research Centre at Imperial College London, London, UK
- Imperial College Parturition Research Group, Institute of Reproductive and Developmental Biology, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Ann Smith
- Faculty of Health and Applied Sciences, University West of England, Bristol, UK
| | - Julian Marchesi
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine Imperial College London, London, UK
- March of Dimes Prematurity Research Centre at Imperial College London, London, UK
| | - Julie A K McDonald
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
| | - Simon Cameron
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine Imperial College London, London, UK
- School of Biological Sciences, Institute for Global Food Security, Queen's University Belfast, Belfast, UK
| | - Kate Alexander-Hardiman
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine Imperial College London, London, UK
| | - Anna L David
- Elizabeth Garrett Anderson Institute for Women's Health, University College London, London, UK
| | - Sarah J Stock
- MRC Centre for Reproductive Health, University of Edinburgh, Edinburgh, UK
| | - Jane E Norman
- MRC Centre for Reproductive Health, University of Edinburgh, Edinburgh, UK
- Faculty of Health Sciences, University of Bristol, Bristol, UK
| | - Vasso Terzidou
- March of Dimes Prematurity Research Centre at Imperial College London, London, UK
- Imperial College Parturition Research Group, Institute of Reproductive and Developmental Biology, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
- Chelsea & Westminster Hospital, NHS Trust, London, UK
| | - T G Teoh
- St Mary's Hospital, Imperial College Healthcare NHS Trust, London, UK
| | - Lynne Sykes
- March of Dimes Prematurity Research Centre at Imperial College London, London, UK
- Imperial College Parturition Research Group, Institute of Reproductive and Developmental Biology, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
- Queen Charlotte's & Chelsea Hospital, Imperial College London, London, UK
| | - Phillip R Bennett
- March of Dimes Prematurity Research Centre at Imperial College London, London, UK
- Imperial College Parturition Research Group, Institute of Reproductive and Developmental Biology, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
- Queen Charlotte's & Chelsea Hospital, Imperial College London, London, UK
- Tommy's National Centre for Miscarriage Research, Imperial College London, London, UK
| | - Zoltan Takats
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine Imperial College London, London, UK.
- National Phenome Centre, Imperial College London, London, UK.
- March of Dimes Prematurity Research Centre at Imperial College London, London, UK.
| | - David A MacIntyre
- March of Dimes Prematurity Research Centre at Imperial College London, London, UK.
- Imperial College Parturition Research Group, Institute of Reproductive and Developmental Biology, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK.
- Tommy's National Centre for Miscarriage Research, Imperial College London, London, UK.
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28
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Reducing time in detection of Listeria monocytogenes from food by MALDI-TOF mass spectrometry. Journal of Food Science and Technology 2021; 58:4102-4109. [PMID: 34538894 DOI: 10.1007/s13197-020-04869-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 08/28/2020] [Accepted: 10/16/2020] [Indexed: 10/23/2022]
Abstract
In this study, direct detection of L. monocytogenes from liquid culture and enrichment broths containing foods was investigated by using MALDI-TOF MS. For determining the sole effect of food constituents on detection and accuracy of identification in enrichment broths, sterile foods were used before the experiments with food. L. monocytogenes could be detected in BHI broth after 24 h of incubation. Detection period was determined as 18 h for 3 × 101 cfu/mL initial bacterial count in BHI broth containing sterile food. The period extended in ONE broth containing sterile garnish, which was 24 and 30 h for 3 × 101 and 1 cfu/mL inoculum, respectively. It was found that identification times in UHT milk were longer than that of canned garnish. In the experiments performed with foods having a specific microbiota; White cheese, iceberg lettuce, parsley and watermelon were used. Although no reliable identification was obtained by using White cheese, iceberg lettuce and parsley, L. monocytogenes could be detected in 24 h in the enrichment broth containing watermelon. Detection was achieved during a single step enrichment in a reduced time of 24 h for even 1 cfu/mL initial inoculum.
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Rapid Detection of PBP2a in Staphylococci from Shortly Incubated Subcultures of Positive Blood Cultures by an Immunochromatographic Assay. Microbiol Spectr 2021; 9:e0046221. [PMID: 34319135 PMCID: PMC8552594 DOI: 10.1128/spectrum.00462-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Staphylococcus aureus, as well as coagulase-negative staphylococci (CoNS), can cause a wide range of human infections both in nosocomial and community settings. Βeta-lactams are the antibiotics of choice for the treatment of bloodstream infections (BSI) caused by these microorganisms. Resistance to virtually all β-lactams (also referred to as methicillin resistance) primarily results from the production of an alternative penicillin-binding protein (PBP2a) encoded by the mecA gene. While β-lactams are still used as first-line therapy against BSI caused by S. aureus, BSI with CoNS are usually treated with vancomycin due to the high prevalence of methicillin resistance. Rapid detection of methicillin resistance is thus critical for continuation or adjustment of the empirical therapy and therewith to improve the clinical outcome of the patients. The revised version of the immunochromatographic assay PBP2a SA culture colony test (SACCT) is a rapid, inexpensive, and easy method that enables reliable detection of PBP2a in mecA-positive staphylococcal isolates after18 to 24 h of incubation. Here, we evaluated the diagnostic performance of the SACCT using primary subcultures of spiked blood cultures after short incubation (4 to 6 h) and established a modified procedure with an equal analytical performance to that of longer-grown cultures. With the proposed method the SACCT can be employed for PBP2a detection from shortly incubated subcultures of clinically relevant staphylococcal isolates, thereby allowing more rapid and effective management of BSI caused by these organisms. IMPORTANCE Antibiotic resistance poses a major threat to health and incurs high economic costs worldwide. Rapid detection of resistance mechanisms can contribute to improving patient care and preventing the dissemination of antimicrobial resistance. Here, we describe a rapid method to detect the most important beta-lactam resistance mechanism (the plasmid-encoded alternative transpeptidase PBP2a) in staphylococcal isolates causing BSI. We show that, using a modified procedure, PBP2a can be reliably detected from primary subcultures of spiked blood cultures after short incubation (4 to 6 h) with a rapid, inexpensive, and simple immunochromatographic test (SACCT). We provide an accurate, inexpensive, and rapid method to facilitate appropriate management and control of infections in patients suffering from invasive staphylococcal infections.
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Chen XF, Hou X, Xiao M, Zhang L, Cheng JW, Zhou ML, Huang JJ, Zhang JJ, Xu YC, Hsueh PR. Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS) Analysis for the Identification of Pathogenic Microorganisms: A Review. Microorganisms 2021; 9:microorganisms9071536. [PMID: 34361971 PMCID: PMC8304613 DOI: 10.3390/microorganisms9071536] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 07/03/2021] [Accepted: 07/10/2021] [Indexed: 12/13/2022] Open
Abstract
Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been used in the field of clinical microbiology since 2010. Compared with the traditional technique of biochemical identification, MALDI-TOF MS has many advantages, including convenience, speed, accuracy, and low cost. The accuracy and speed of identification using MALDI-TOF MS have been increasing with the development of sample preparation, database enrichment, and algorithm optimization. MALDI-TOF MS has shown promising results in identifying cultured colonies and rapidly detecting samples. MALDI-TOF MS has critical research applications for the rapid detection of highly virulent and drug-resistant pathogens. Here we present a scientific review that evaluates the performance of MALDI-TOF MS in identifying clinical pathogenic microorganisms. MALDI-TOF MS is a promising tool in identifying clinical microorganisms, although some aspects still require improvement.
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Affiliation(s)
- Xin-Fei Chen
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China; (X.-F.C.); (X.H.); (M.X.); (L.Z.); (M.-L.Z.); (J.-J.H.); (J.-J.Z.)
- Graduate School, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing 100730, China
| | - Xin Hou
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China; (X.-F.C.); (X.H.); (M.X.); (L.Z.); (M.-L.Z.); (J.-J.H.); (J.-J.Z.)
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing 100730, China
| | - Meng Xiao
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China; (X.-F.C.); (X.H.); (M.X.); (L.Z.); (M.-L.Z.); (J.-J.H.); (J.-J.Z.)
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing 100730, China
| | - Li Zhang
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China; (X.-F.C.); (X.H.); (M.X.); (L.Z.); (M.-L.Z.); (J.-J.H.); (J.-J.Z.)
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing 100730, China
| | - Jing-Wei Cheng
- Center of Clinical Laboratory, Beijing Friendship Hospital, Capital Medical University, Beijing 100053, China;
| | - Meng-Lan Zhou
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China; (X.-F.C.); (X.H.); (M.X.); (L.Z.); (M.-L.Z.); (J.-J.H.); (J.-J.Z.)
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing 100730, China
| | - Jing-Jing Huang
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China; (X.-F.C.); (X.H.); (M.X.); (L.Z.); (M.-L.Z.); (J.-J.H.); (J.-J.Z.)
- Graduate School, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing 100730, China
| | - Jing-Jia Zhang
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China; (X.-F.C.); (X.H.); (M.X.); (L.Z.); (M.-L.Z.); (J.-J.H.); (J.-J.Z.)
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing 100730, China
| | - Ying-Chun Xu
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China; (X.-F.C.); (X.H.); (M.X.); (L.Z.); (M.-L.Z.); (J.-J.H.); (J.-J.Z.)
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing 100730, China
- Correspondence: (Y.-C.X.); (P.-R.H.)
| | - Po-Ren Hsueh
- Departments of Laboratory Medicine and Internal Medicine, China Medical University Hospital, School of Medicine, China Medical University, Taichung 40447, Taiwan;
- Departments of Laboratory Medicine and Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei 100, Taiwan
- Correspondence: (Y.-C.X.); (P.-R.H.)
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Bonvegna M, Grego E, Sona B, Stella MC, Nebbia P, Mannelli A, Tomassone L. Occurrence of Methicillin-Resistant Coagulase-Negative Staphylococci (MRCoNS) and Methicillin-Resistant Staphylococcus aureus (MRSA) from Pigs and Farm Environment in Northwestern Italy. Antibiotics (Basel) 2021; 10:antibiotics10060676. [PMID: 34198805 PMCID: PMC8227741 DOI: 10.3390/antibiotics10060676] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 05/27/2021] [Accepted: 06/01/2021] [Indexed: 12/23/2022] Open
Abstract
Swine farming as a source of methicillin-resistant Staphylococcus aureus (MRSA) has been well documented. Methicillin-resistant coagulase-negative staphylococci (MRCoNS) have been less studied, but their importance as pathogens is increasing. MRCoNS are indeed considered relevant nosocomial pathogens; identifying putative sources of MRCoNS is thus gaining importance to prevent human health hazards. In the present study, we investigated MRSA and MRCoNS in animals and environment in five pigsties in a high farm-density area of northwestern Italy. Farms were three intensive, one intensive with antibiotic-free finishing, and one organic. We tested nasal swabs from 195 animals and 26 environmental samples from three production phases: post-weaning, finishing and female breeders. Phenotypic tests, including MALDI-TOF MS, were used for the identification of Staphylococcus species; PCR and nucleotide sequencing confirmed resistance and bacterial species. MRCoNS were recovered in 64.5% of nasal swabs, in all farms and animal categories, while MRSA was detected only in one post-weaning sample in one farm. The lowest prevalence of MRCoNS was detected in pigs from the organic farm and in the finishing of the antibiotic-free farm. MRCoNS were mainly Staphylococcus sciuri, but we also recovered S. pasteuri, S. haemolyticus, S. cohnii, S. equorum and S. xylosus. Fifteen environmental samples were positive for MRCoNS, which were mainly S. sciuri; no MRSA was found in the farms’ environment. The analyses of the mecA gene and the PBP2-a protein highlighted the same mecA fragment in strains of S. aureus, S. sciuri and S. haemolyticus. Our results show the emergence of MRCoNS carrying the mecA gene in swine farms. Moreover, they suggest that this gene might be horizontally transferred from MRCoNS to bacterial species more relevant for human health, such as S. aureus.
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Affiliation(s)
- Miryam Bonvegna
- Department of Veterinary Sciences, University of Turin, Largo P. Braccini 2, 10095 Grugliasco, Italy; (E.G.); (M.C.S.); (P.N.); (A.M.); (L.T.)
- Correspondence:
| | - Elena Grego
- Department of Veterinary Sciences, University of Turin, Largo P. Braccini 2, 10095 Grugliasco, Italy; (E.G.); (M.C.S.); (P.N.); (A.M.); (L.T.)
| | - Bruno Sona
- Local Veterinary Service, Animal Health, ASL CN1, Via Torino, 137, 12038 Savigliano, Italy;
| | - Maria Cristina Stella
- Department of Veterinary Sciences, University of Turin, Largo P. Braccini 2, 10095 Grugliasco, Italy; (E.G.); (M.C.S.); (P.N.); (A.M.); (L.T.)
| | - Patrizia Nebbia
- Department of Veterinary Sciences, University of Turin, Largo P. Braccini 2, 10095 Grugliasco, Italy; (E.G.); (M.C.S.); (P.N.); (A.M.); (L.T.)
| | - Alessandro Mannelli
- Department of Veterinary Sciences, University of Turin, Largo P. Braccini 2, 10095 Grugliasco, Italy; (E.G.); (M.C.S.); (P.N.); (A.M.); (L.T.)
| | - Laura Tomassone
- Department of Veterinary Sciences, University of Turin, Largo P. Braccini 2, 10095 Grugliasco, Italy; (E.G.); (M.C.S.); (P.N.); (A.M.); (L.T.)
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Volokhov DV, Zagorodnyaya TA, Shen Z, Blom J, Furtak VA, Eisenberg T, Fan P, Jeong KC, Gao Y, Zhang S, Amselle M. Streptococcus vicugnae sp. nov., isolated from faeces of alpacas ( Vicugna pacos) and cattle ( Bos taurus), Streptococcus zalophi sp. nov., and Streptococcus pacificus sp. nov., isolated from respiratory tract of California sea lions ( Zalophus californianus). Int J Syst Evol Microbiol 2021; 71. [PMID: 33999792 DOI: 10.1099/ijsem.0.004826] [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: 11/18/2022] Open
Abstract
Four novel independent strains of Streptococcus spp. were isolated from faeces of alpaca (SL1232T), cattle (KCJ4950), and from respiratory tract of wild California sea lions (CSL7508T, CSL7591T). The strains were indole-, oxidase- and catalase-negative, non-spore-forming, non-motile Gram-positive cocci in short and long chains, facultative anaerobes. The 16S rRNA gene of SL1232T and KCJ4950 shared 99.40-99.60% nucleotide similarity to strains of S. equinus, S. lutetiensis, S. infantarius, and the 16S rRNA gene of CSL7508T and CSL7591T demonstrated 98.72 and 98.92% similarity, respectively, to S. marimammalium. All other known Streptococcus species had the 16S rRNA gene sequence similarities of ≤95%. The genomes were sequenced for the novel strains. Average nucleotide identity (ANI) analysis for strains SL1232T and KCJ4950, showed the highest similarity to S. equinus, S. lutetiensis, and S. infantarius with 85.21, 87.17, 88.47, 85.54, 87.47 and 88.89%, respectively, and strains CSL7508T and CSL7591T to S. marimammalium with 87.16 and 83.97%, respectively. Results of ANI were confirmed by pairwise digital DNA-DNA hybridization and phylogeny, which also revealed that the strains belong to three novel species of the genus Streptococcus. Phenotypical features of the novel species were in congruence with closely related members of the genus Streptococcus and gave negative reactions with the tested Lancefield serological groups (A-D, F and G). MALDI-TOF mass spectrometry supported identification of the species. Based on these data, we propose three novel species of the genus Streptococcus, for which the name Streptococcus vicugnae sp. nov. is proposed with the type strain SL1232T (=NCTC 14341T=DSM 110741T=CCUG 74371T), Streptococcus zalophi sp. nov. is proposed with the type strain CSL7508T (=NCTC 14410T=DSM 110742T=CCUG 74374T) and Streptococcus pacificus sp. nov. is proposed with the type strain CSL7591T (=NCTC 14455T=DSM 111148T=CCUG 74655T). The genome G+C content is 36.89, 34.85, and 35.34 % and draft genome sizes are 1906993, 1581094 and 1656080 bp for strains SL1232T, CSL7508T, and CSL7591T, respectively.
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Affiliation(s)
- Dmitriy V Volokhov
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
| | - Tatiana A Zagorodnyaya
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
| | - Zhenyu Shen
- Department of Veterinary Pathobiology, Veterinary Medical Diagnostic Laboratory, College of Veterinary Medicine, University of Missouri, 901 East Campus Loop, Columbia, MO 65211, USA
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Heinrich Buff Ring 58, 35392, Giessen, Germany
| | - Vyacheslav A Furtak
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
| | - Tobias Eisenberg
- Institute of Hygiene and Infectious Diseases of Animals, Justus-Liebig-University Giessen, Frankfurter Strasse 89-91, 35392 Giessen, Germany.,Hessian State Laboratory (LHL), Department of Veterinary Medicine, Schubertstrasse 60, 35392, Giessen, Germany
| | - Peixin Fan
- Department of Animal Sciences, Emerging Pathogens Institute, University of Florida, 2055 Mowry Road, Gainesville, FL 32611, USA
| | - Kwangcheol Casey Jeong
- Department of Animal Sciences, Emerging Pathogens Institute, University of Florida, 2055 Mowry Road, Gainesville, FL 32611, USA
| | - Yamei Gao
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
| | - Shuping Zhang
- Department of Veterinary Pathobiology, Veterinary Medical Diagnostic Laboratory, College of Veterinary Medicine, University of Missouri, 901 East Campus Loop, Columbia, MO 65211, USA
| | - Megan Amselle
- American Type Culture Collection (ATCC), 10801 University Blvd., Manassas, VA 20110, USA
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The Genotype-to-Phenotype Dilemma: How Should Laboratories Approach Discordant Susceptibility Results? J Clin Microbiol 2021; 59:JCM.00138-20. [PMID: 33441396 DOI: 10.1128/jcm.00138-20] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Traditional culture-based methods for identification and antimicrobial susceptibility testing (AST) of bacteria take 2 to 3 days on average. Syndromic molecular diagnostic panels have revolutionized clinical microbiology laboratories as they can simultaneously identify an organism and detect some of the most significant antimicrobial resistance (AMR) genes directly from positive blood culture broth or from various specimen types (e.g., whole blood, cerebrospinal fluid, and respiratory specimens). The presence or absence of an AMR marker associated with a particular organism can be used to predict the phenotypic AST results to more rapidly guide therapy. Numerous studies have shown that genotypic susceptibility predictions by syndromic panels can improve patient outcomes. However, an important limitation of AMR marker detection to predict phenotype is the potential discrepancies that may arise upon performing phenotypic AST of the recovered organism in culture. The focus of this minireview is to address how clinical laboratories should interpret rapid molecular results from commercial platforms in relation to phenotypic AST. Stepwise approaches and solutions are provided to resolve discordant results between genotypic and phenotypic susceptibility results.
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Kim E, Yang SM, Kim HY. Analysis of Cultivable Microbial Community during Kimchi Fermentation Using MALDI-TOF MS. Foods 2021; 10:foods10051068. [PMID: 34066045 PMCID: PMC8151656 DOI: 10.3390/foods10051068] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 04/28/2021] [Accepted: 05/08/2021] [Indexed: 12/31/2022] Open
Abstract
Kimchi, a traditional Korean fermented vegetable, has received considerable attention for its health-promoting effects. This study analyzes the cultivable microbial community in kimchi fermented at different temperatures using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to comprehensively understand the factors affecting the quality of kimchi. Of the 5204 strains isolated from kimchi, aligned with the in-house database, 4467 (85.8%) were correctly identified at the species level. The fermentation temperature affected the microbial community by varying the pH and acidity, which was mainly caused by temperature-dependent competition between the different lactic acid bacteria (LAB) species in kimchi. LAB, such as Levilactobacillus (Lb.) brevis and Lactiplantibacillus (Lpb.) plantarum associated with rancidity and tissue softening, proliferated faster at higher temperatures than at low temperature. In addition, LAB, such as Latilactobacillus (Lat.) sakei and Leuconostoc (Leu.) mesenteroides, which produce beneficial substances and flavor, were mainly distributed in kimchi fermented at 4 °C. This study shows as a novelty that MALDI-TOF MS is a robust and economically affordable method for investigating viable microbial communities in kimchi.
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Affiliation(s)
| | | | - Hae-Yeong Kim
- Correspondence: ; Tel.: +82-31-201-2600; Fax: +82-31-204-8116
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Horsman S, Rynhoud H, Zhou X, Soares Magalhães RJ, Gibson JS, Meler E. Environmental Recovery of Nosocomial Bacteria in a Companion Animal Shelter Before and After Infection Control Procedures. Front Vet Sci 2021; 7:608901. [PMID: 33553281 PMCID: PMC7854535 DOI: 10.3389/fvets.2020.608901] [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: 09/23/2020] [Accepted: 12/21/2020] [Indexed: 11/22/2022] Open
Abstract
While the effects of cleaning and disinfection practices on the reduction of environmental nosocomial bacteria are well-established in human and large animal veterinary hospitals, how animal movements within animal health care facilities influence environmental bacterial recovery is poorly understood. During three consecutive weeks, 155 electrostatic wipes were collected from the environment pre- and post-cleaning only or following disinfection from seven target locations within an animal shelter. All samples were cultured, and isolates were identified using a matrix-assisted laser desorption ionization-time of flight mass spectrometry. Social network analysis of animal movements during the sampling period was performed to estimate the level of connectivity of the seven target locations. The relationship between bacterial levels and connectivity estimates of the target locations were investigated using a negative binomial regression model with a random effect of sampling areas. Overall, our results indicate a significant reduction in the total bacterial contamination with disinfection when compared to cleaning only [Coefficient (Coef.) = -1.72, 95% Confidence Interval (CI) = -3.09, -0.34, P = 0.015]. Higher total bacterial contamination was significantly more likely in sampled areas with less animal movement connectivity (Coef. = -0.32, 95% CI = -0.49, -0.15, P ≤ 0.001). Pseudomonas aeruginosa and ampicillin resistant Enterobacteriaceae (Escherichia coli, Enterobacter spp. and Klebsiella spp.) were present in the animal holdings and in the shelters' veterinary clinic environment at all sampling times. Our findings demonstrate that cleaning followed by disinfection practices are effective at reducing environmental bacterial levels. Areas with less animal connectivity are more likely to have a higher bacterial contamination. These areas could represent environmental reservoirs for bacterial infection and should be targeted with effective cleaning and disinfection protocols.
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Affiliation(s)
- Sara Horsman
- School of Veterinary Science, The University of Queensland, Gatton, QLD, Australia
| | - Hester Rynhoud
- School of Veterinary Science, The University of Queensland, Gatton, QLD, Australia
| | - Xiaoyan Zhou
- School of Veterinary Science, The University of Queensland, Gatton, QLD, Australia
| | - Ricardo J. Soares Magalhães
- School of Veterinary Science, The University of Queensland, Gatton, QLD, Australia
- Children's Health and Environment Program, Child Health Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Justine S. Gibson
- School of Veterinary Science, The University of Queensland, Gatton, QLD, Australia
| | - Erika Meler
- School of Veterinary Science, The University of Queensland, Gatton, QLD, Australia
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Jussiaux F, Miot-Sertier C, Nguyen-Lopez D, Badet C, Samot J. Reliability of MALDI-TOF mass spectrometry to identify oral isolates of Streptococcus salivarius and Lactobacillus spp. Arch Oral Biol 2020; 121:104983. [PMID: 33242690 DOI: 10.1016/j.archoralbio.2020.104983] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 10/29/2020] [Accepted: 11/04/2020] [Indexed: 11/18/2022]
Abstract
OBJECTIVE The aim of this study is to evaluate the performance of MALDI-TOF mass spectrometry in identifying bacteria isolated in the oral cavity known to be of probiotic interest. DESIGN We evaluated Bruker MALDI Biotyper for the identification of 92 clinical oral isolates of probiotic interest (31 Streptococcus salivarius and 61 Lactobacillus spp.) by comparing direct colony method with on-plate formic acid extraction. Isolates were previously identified by use of biochemical methods and molecular biology. RESULTS Using the manufacturer's suggested genus and species level cutoff scores, the direct colony method identified 42 (45.7%) isolates at the genus level and 35 (38%) at the species level while the on-plate extraction method correctly identified 90 (97.8%) isolates at the genus level and 82 (89.1%) at the species level. The difference between the two methods was statistically significant at the genus and species levels (P ≤ 0.0001). After dividing the isolates into two subgroups, the analysis was repeated. The direct colony method identified correctly all isolates of Streptococcus salivarius at the species level. In contrast, the direct colony method allowed the identification of only 11 (18%) lactobacilli at the genus level and 4 (6.6%) at the species level. The on-plate extraction method was statistically (P ≤ 0.0001) more efficient since 59 (96.7%) lactobacilli were identified at the genus level and 51 (83.6%) at the species level. CONCLUSIONS MALDI Biotyper can efficiently identify Streptococcus salivarius regardless of the preparative method but on-plate extraction is superior to direct colony method for the identification of lactobacilli.
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Affiliation(s)
| | - Cécile Miot-Sertier
- Univ. Bordeaux, ISVV, EA 4577, Unité de Recherche Œnologie, USC 1366 INRAE, F-33140 Villenave d'Ornon, France
| | - Darrène Nguyen-Lopez
- Centre Hospitalier Universitaire de Bordeaux, Pôle de Médecine et Chirurgie Bucco-Dentaire, Bordeaux, France
| | - Cécile Badet
- Univ. Bordeaux, UFR des Sciences Odontologiques, Bordeaux, France; Univ. Bordeaux, ISVV, EA 4577, Unité de Recherche Œnologie, USC 1366 INRAE, F-33140 Villenave d'Ornon, France; Centre Hospitalier Universitaire de Bordeaux, Pôle de Médecine et Chirurgie Bucco-Dentaire, Bordeaux, France
| | - Johan Samot
- Univ. Bordeaux, UFR des Sciences Odontologiques, Bordeaux, France; Univ. Bordeaux, ISVV, EA 4577, Unité de Recherche Œnologie, USC 1366 INRAE, F-33140 Villenave d'Ornon, France; Centre Hospitalier Universitaire de Bordeaux, Pôle de Médecine et Chirurgie Bucco-Dentaire, Bordeaux, France.
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Tsuchida S, Umemura H, Nakayama T. Current Status of Matrix-Assisted Laser Desorption/Ionization-Time-of-Flight Mass Spectrometry (MALDI-TOF MS) in Clinical Diagnostic Microbiology. Molecules 2020; 25:molecules25204775. [PMID: 33080897 PMCID: PMC7587594 DOI: 10.3390/molecules25204775] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 10/15/2020] [Accepted: 10/15/2020] [Indexed: 12/28/2022] Open
Abstract
Mass spectrometry (MS), a core technology for proteomics and metabolomics, is currently being developed for clinical applications. The identification of microorganisms in clinical samples using matrix-assisted laser desorption/ionization–time-of-flight mass spectrometry (MALDI-TOF MS) is a representative MS-based proteomics application that is relevant to daily clinical practice. This technology has the advantages of convenience, speed, and accuracy when compared with conventional biochemical methods. MALDI-TOF MS can shorten the time used for microbial identification by about 1 day in routine workflows. Sample preparation from microbial colonies has been improved, increasing the accuracy and speed of identification. MALDI-TOF MS is also used for testing blood, cerebrospinal fluid, and urine, because it can directly identify the microorganisms in these liquid samples without prior culture or subculture. Thus, MALDI-TOF MS has the potential to improve patient prognosis and decrease the length of hospitalization and is therefore currently considered an essential tool in clinical microbiology. Furthermore, MALDI-TOF MS is currently being combined with other technologies, such as flow cytometry, to expand the scope of clinical applications.
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Sawada H, Fujikawa T, Horita H. Pseudomonas brassicae sp. nov., a pathogen causing head rot of broccoli in Japan. Int J Syst Evol Microbiol 2020; 70:5319-5329. [DOI: 10.1099/ijsem.0.004412] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Phytopathogenic bacteria, MAFF 212426, MAFF 212427T, MAFF 212428 and MAFF 212429, were isolated from head rot lesions of broccoli (Brassica oleracea L. var. italica Plenck) in Hokkaido, Japan, and subjected to polyphasic taxonomic characterization. The cells were Gram-reaction-negative, aerobic, non-spore-forming, motile with one or two polar flagella, rod-shaped and formed pale yellow colonies. Results of 16S rRNA gene sequence analysis showed that they belong to the genus
Pseudomonas
with the highest similarity to ‘Pseudomonas qingdaonensis’ JJ3T (99.86 %),
Pseudomonas laurentiana
GSL-010T (99.22 %),
Pseudomonas huaxiensis
WCHPs060044T (99.01 %),
Pseudomonas japonica
NBRC 103040T (98.87 %) and
Pseudomonas alkylphenolica
KL28T (98.73 %). The genomic DNA G+C content was 63.4 mol% and the major fatty acids (>5 % of the total fatty acids) were summed feature 3 (C16 : 1 ω7c / C16 : 1 ω6c), C16 : 0, summed feature 8 (C18 : 1 ω7c / C18 : 1 ω6c) and C17 : 0 cyclo. Multilocus sequence analysis using the partial rpoD, gyrB and rpoB gene sequences and phylogenomic analyses based on the whole genome sequences demonstrated that the strains are members of the
Pseudomonas putida
group, but form a monophyletic, robust clade separated from their closest relatives. Average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values corroborated their novel species status, with 88.39 % (ANI) and 35.8 % (dDDH) as the highest scores with ‘P. qingdaonensis’ JJ3T. The strains were differentiated from their closest relatives by phenotypic characteristics, pathogenicity on broccoli, and whole-cell MALDI-TOF mass spectrometry profiles. The phenotypic, chemotaxonomic and genotypic data showed that the strains represent a novel
Pseudomonas
species, for which the name Pseudomonas brassicae sp. nov. is proposed. The type strain is MAFF 212427T (=ICMP 23635T).
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Affiliation(s)
- Hiroyuki Sawada
- Genetic Resources Center, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Takashi Fujikawa
- Institute of Fruit Tree and Tea Science, NARO, 2-1 Fujimoto, Tsukuba, Ibaraki 305-8605, Japan
| | - Harukuni Horita
- Ornamental Plants and Vegetables Research Center, Hokkaido Research Organization, Takikawa, Hokkaido 073-0026, Japan
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Mancini S, Bodendoerfer E, Kolensnik-Goldmann N, Herren S, Röthlin K, Courvalin P, Böttger EC. Evaluation of standardized automated rapid antimicrobial susceptibility testing of Enterobacterales-containing blood cultures: a proof-of-principle study. J Antimicrob Chemother 2020; 75:3218-3229. [DOI: 10.1093/jac/dkaa336] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 07/01/2020] [Indexed: 11/14/2022] Open
Abstract
Abstract
Background
Rapid antimicrobial susceptibility testing (RAST) of bacteria causing bloodstream infections is critical for implementation of appropriate antibiotic regimens.
Objectives
We have established a procedure to prepare standardized bacterial inocula for Enterobacterales-containing clinical blood cultures and assessed antimicrobial susceptibility testing (AST) data generated with the WASPLabTM automated reading system.
Methods
A total of 258 blood cultures containing Enterobacterales were examined. Bacteria were enumerated by flow cytometry using the UF-4000 system and adjusted to an inoculum of 106 cfu/mL. Disc diffusion plates were automatically streaked, incubated for 6, 8 and 18 h and imaged using the fully automated WASPLabTM system. Growth inhibition zones were compared with those obtained with inocula prepared from primary subcultures following the EUCAST standard method. Due to time-dependent variations of the inhibition zone diameters, early AST readings were interpreted using time-adjusted tentative breakpoints and areas of technical uncertainty.
Results and conclusions
Inhibition zones obtained after 18 h incubation using an inoculum of 106 cfu/mL prepared directly from blood cultures were highly concordant with those of the EUCAST standard method based on primary subcultures, with categorical agreement (CA) of 95.8%. After 6 and 8 h incubation, 89.5% and 93.0% of the isolates produced interpretable results, respectively, with CA of >98.5% and very low numbers of clinical categorization errors for both the 6 h and 8 h readings. Overall, with the standardized and automated RAST method, consistent AST data from blood cultures containing Enterobacterales can be generated after 6–8 h of incubation and subsequently confirmed by standard reading of the same plate after 18 h.
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Affiliation(s)
- Stefano Mancini
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Schweiz
| | - Elias Bodendoerfer
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Schweiz
| | | | - Sebastian Herren
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Schweiz
| | - Kim Röthlin
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Schweiz
| | | | - Erik C Böttger
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Schweiz
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Wischer D, Schneider D, Poehlein A, Herrmann F, Oruc H, Meinhardt J, Wagner O, Ahmed R, Kharin S, Novikova N, Haag R, Daniel R, Grohmann E. Novel Antimicrobial Cellulose Fleece Inhibits Growth of Human-Derived Biofilm-Forming Staphylococci During the SIRIUS19 Simulated Space Mission. Front Microbiol 2020; 11:1626. [PMID: 32849336 PMCID: PMC7405646 DOI: 10.3389/fmicb.2020.01626] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 06/22/2020] [Indexed: 12/13/2022] Open
Abstract
Two novel antimicrobial surface coatings were assessed for their lasting antibacterial effect under simulated space conditions during the SIRIUS-19 study. Because long-term space travel can affect the human immune system, astronauts are particularly susceptible to infectious disease. Moreover, the space flight environment can alter the composition of microbial communities within the spacecraft and increase bacterial virulence and resistance to antibiotics. In addition to protecting the crew from infection by human pathogens, prevention and elimination of bacterial contamination is important to avoid corrosion and damage of the technical equipment. The antimicrobial coating AGXX® consists of micro-galvanic cells composed of silver and ruthenium which damage bacterial cells through the release of reactive oxygen species. Over the last years, several studies on the antimicrobial effect of AGXX® have demonstrated an effective inhibition of growth and even complete elimination of many pathogenic bacteria – including multiresistant microorganisms – as well as their biofilms. The second antimicrobial coating, GOX, consists of chemically modified graphene oxide. Through a positive surface charge and its flexible scaffold, GOX can multivalently bind and immobilize bacteria via electrostatic attraction. Here, AGXX® and GOX were applied to non-metallic carriers not previously tested. The antimicrobial coated materials, as well as uncoated control samples, were exposed in the SIRIUS artificial space module and analyzed at different time points during the 4-months isolation study. Survival and growth of airborne heterotrophic, aerobic bacteria on the surfaces were assessed by cultivation-based methods, employing growth conditions suitable for potential human pathogens. Human-associated, biofilm-forming Staphylococcus spp. (S. hominis, S. haemolyticus, and S. epidermidis) strongly dominated at all time points, most were resistant against erythromycin, kanamycin, and ampicillin. AGXX® coatings completely inhibited growth of these opportunistic pathogens on all tested surface materials. Particularly, AGXX®-cellulose fleece achieved a clear reduction in bacterial load able to recover post contact. GOX-cellulose fleece effectively immobilized bacteria. Sequence analysis of 16S rRNA gene amplicons revealed that the isolated Staphylococcus spp. did not dominate the overall bacterial community, accounting for only 0.1–0.4% of all sequences. Instead, molecular data revealed Lactobacillus, Comamonas, Pseudomonas, Sporosarcina, and Bacillus as the dominant genera across all samples and time points.
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Affiliation(s)
- Daniela Wischer
- Faculty of Life Sciences and Technology, Department of Microbiology, Beuth University of Applied Sciences, Berlin, Germany
| | - Dominik Schneider
- Department of Genomic and Applied Microbiology, Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology, Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany
| | - Friederike Herrmann
- Faculty of Life Sciences and Technology, Department of Microbiology, Beuth University of Applied Sciences, Berlin, Germany
| | - Harun Oruc
- Faculty of Life Sciences and Technology, Department of Microbiology, Beuth University of Applied Sciences, Berlin, Germany
| | - Junias Meinhardt
- Faculty of Life Sciences and Technology, Department of Microbiology, Beuth University of Applied Sciences, Berlin, Germany
| | - Olaf Wagner
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Rameez Ahmed
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Sergey Kharin
- Institute of Biomedical Problems (IBMP), Moscow, Russia
| | | | - Rainer Haag
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology, Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany
| | - Elisabeth Grohmann
- Faculty of Life Sciences and Technology, Department of Microbiology, Beuth University of Applied Sciences, Berlin, Germany
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Werinder A, Aspán A, Backhans A, Sjölund M, Guss B, Jacobson M. Streptococcus suis in Swedish grower pigs: occurrence, serotypes, and antimicrobial susceptibility. Acta Vet Scand 2020; 62:36. [PMID: 32580735 PMCID: PMC7315512 DOI: 10.1186/s13028-020-00533-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 06/15/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Streptococcus suis is a major cause of meningitis, arthritis, and pneumonia in pigs worldwide, and an emerging pathogen in humans. In Sweden, S. suis has previously received little attention but has in recent years become increasingly recognized as affecting the pig production. The aim of the present study was to investigate the occurrence, serotypes and antimicrobial susceptibility of S. suis in Swedish grower pigs from herds with and without reported S. suis associated disease, as well as possible associations between S. suis associated disease and selected environmental and production factors. Swab samples were taken from the tonsils of clinically healthy 8-13-week-old grower pigs from ten case herds and ten control herds. Isolates were cultured, identified using MALDI-TOF MS, and serotyped using latex agglutination. The antimicrobial susceptibility of 188 isolates was tested using broth microdilution. Production data was gathered and environmental parameters were measured on the farms. RESULTS Streptococcus suis was isolated from 95% of the sampled pigs in both the case and the control herds. Serotypes 3, 4, 5, 7, 9, 10, 11, 15, 16, and 17-34 were detected, although a majority of the isolates (81.5%) were non-typeable. There was less diversity among the serotypes isolated from the case herds than among those from the control herds; four and nine different serotypes, respectively. Isolates resistant to penicillin (3.8%) were reported for the first time in Sweden. Tetracycline resistance was common (88.4%). No association was noted between the production and the environmental factors investigated, and the carriership of S. suis. CONCLUSIONS The carriership of S. suis was found to be higher in clinically healthy Swedish pigs than previously estimated, and for the first time, the presence of Swedish isolates resistant to penicillin was reported. Many of the most commonly disease-associated serotypes, e.g. serotypes 2, 9, 3, and 7, were detected in healthy grower pigs although further studies are needed to investigate the virulence of these isolates.
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Affiliation(s)
- Anna Werinder
- Department of Clinical Sciences, Swedish University of Agricultural Sciences (SLU), Box 7054, 750 07 Uppsala, Sweden
| | - Anna Aspán
- Department of Microbiology, National Veterinary Institute (SVA), 751 89 Uppsala, Sweden
| | - Annette Backhans
- Department of Animal Health and Antimicrobial Strategies, National Veterinary Institute (SVA), 751 89 Uppsala, Sweden
| | - Marie Sjölund
- Department of Animal Health and Antimicrobial Strategies, National Veterinary Institute (SVA), 751 89 Uppsala, Sweden
| | - Bengt Guss
- Department of Biomedical Science and Veterinary Public Health, Swedish University of Agricultural Sciences (SLU), Box 7036, 750 07 Uppsala, Sweden
| | - Magdalena Jacobson
- Department of Clinical Sciences, Swedish University of Agricultural Sciences (SLU), Box 7054, 750 07 Uppsala, Sweden
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García López E, Martín-Galiano AJ. The Versatility of Opportunistic Infections Caused by Gemella Isolates Is Supported by the Carriage of Virulence Factors From Multiple Origins. Front Microbiol 2020; 11:524. [PMID: 32296407 PMCID: PMC7136413 DOI: 10.3389/fmicb.2020.00524] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 03/11/2020] [Indexed: 12/29/2022] Open
Abstract
The molecular basis of the pathogenesis of the opportunistic invasive infections caused by isolates of the Gemella genus remains largely unknown. Moreover, inconsistencies in the current species assignation were detected after genome-level comparison of 16 public Gemella isolates. A literature search detected that, between the two most pathogenic species, Gemella morbillorum causes about twice the number of cases compared to Gemella haemolysans. These two species shared their mean diseases - sepsis and endocarditis - but differed in causing other syndromes. A number of well-known virulence factors were harbored by all species, such as a manganese transport/adhesin sharing 83% identity from oral endocarditis-causing streptococci. Likewise, all Gemellae carried the genes required for incorporating phosphorylcholine into their cell walls and encoded some choline-binding proteins. In contrast, other proteins were species-specific, which may justify the known epidemiological differences. G. haemolysans, but not G. morbillorum, harbor a gene cluster potentially encoding a polysaccharidic capsule. Species-specific surface determinants also included Rib and MucBP repeats, hemoglobin-binding NEAT domains, peptidases of C5a complement factor and domains that recognize extracellular matrix molecules exposed in damaged heart valves, such as collagen and fibronectin. Surface virulence determinants were associated with several taxonomically dispersed opportunistic genera of the oral microbiota, such as Granulicatella, Parvimonas, and Streptococcus, suggesting the existence of a horizontally transferrable gene reservoir in the oral environment, likely facilitated by close proximity in biofilms and ultimately linked to endocarditis. The identification of the Gemella virulence pool should be implemented in whole genome-based protocols to rationally predict the pathogenic potential in ongoing clinical infections caused by these poorly known bacterial pathogens.
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Affiliation(s)
- Ernesto García López
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas (CSIC), Madrid, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Antonio J. Martín-Galiano
- Intrahospital Infections Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), Majadahonda, Spain
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Okcu GD, Okten HE, Yalcuk A. A hybrid process for 2,4-dichlorophenoxy acetic acid herbicidal treatment and its microbial identification by MALDI-TOF mass spectrometry. ENVIRONMENTAL TECHNOLOGY 2020; 41:764-776. [PMID: 30092741 DOI: 10.1080/09593330.2018.1510433] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 08/05/2018] [Indexed: 06/08/2023]
Abstract
The feasibility of coupling photocatalysis and a biological treatment to remove a herbicide - 2,4-dichlorophenoxy acetic acid (2,4-D) - from pure water was examined using batch experiments following three protocols: aerated (A-BR) and non-aerated biodegradation (NA-BR) alone, and intimately combined photodegradation and biodegradation (P-B). In view of a subsequent biological treatment, 15 and 180 min irradiation times were chosen in accordance with spectrophotometric and LC-MS/MS results that indicated the decrease in the COD/TOC ratio during photocatalysis. Pre-treatment led to a quick decrease in concentration of 2,4-D and COD during the biological process: a 78.79 ± 0.30% COD removal and 38.23 ± 3.12% 2,4-D elimination was measured after 5760 min in A-BR, and 80.89 ± 0.81% COD and 81.36 ± 1.37% 2,4-D removal was achieved after 2880 min in P-B. For species identification using matrix-assisted laser desorption/ionization (MALDI)-time of flight (TOF)-TOF/MS equipment, Aeromonas eucrenophila, Stenotrophomonas acidaminiphila, Ralstonia pickettii, Sphingobacterium multivorum and Acinetobacter towneri were identified with high accuracy, and they play important roles in the degradation of 2,4-D.
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Affiliation(s)
- Gamze Dogdu Okcu
- Department of Environmental Engineering, Abant Izzet Baysal University, Bolu, Turkey
| | - Hatice Eser Okten
- Department of Environmental Engineering, Izmir Institute of Technology, Urla, Izmir, Turkey
| | - Arda Yalcuk
- Department of Environmental Engineering, Abant Izzet Baysal University, Bolu, Turkey
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Wolfensberger A, Kuster SP, Marchesi M, Zbinden R, Hombach M. The effect of varying multidrug-resistence (MDR) definitions on rates of MDR gram-negative rods. Antimicrob Resist Infect Control 2019; 8:193. [PMID: 31798839 PMCID: PMC6883537 DOI: 10.1186/s13756-019-0614-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Accepted: 09/25/2019] [Indexed: 12/16/2022] Open
Abstract
Background A multitude of definitions determining multidrug resistance (MDR) of Gram-negative organisms exist worldwide. The definitions differ depending on their purpose and on the issueing country or organization. The MDR definitions of the European Centre for Disease Prevention and Control (ECDC) were primarily chosen to harmonize epidemiological surveillance. The German Commission of Hospital Hygiene and Infection Prevention (KRINKO) issued a national guideline which is mainly used to guide infection prevention and control (IPC) measures. The Swiss University Hospital Zurich (UHZ) - in absentia of national guidelines - developed its own definition for IPC purposes. In this study we aimed to determine the effects of different definitions of multidrug-resistance on rates of Gram-negative multidrug-resistant organisms (GN-MDRO). Methods MDR definitions of the ECDC, the German KRINKO and the Swiss University Hospital Zurich were applied on a dataset comprising isolates of Escherichia coli, Klebsiella pneumoniae, Enterobacter sp., Pseudomonas aeruginosa, and Acinetobacter baumannii complex. Rates of GN-MDRO were compared and the percentage of patients with a GN-MDRO was calculated. Results In total 11'407 isolates from a 35 month period were included. For Enterobacterales and P. aeruginosa, highest MDR-rates resulted from applying the 'ECDC-MDR' definition. 'ECDC-MDR' rates were up to four times higher compared to 'KRINKO-3/4MRGN' rates, and up to six times higher compared to UHZ rates. Lowest rates were observed when applying the 'KRINKO-4MRGN' definitions. Comparing the 'KRINKO-3/4MRGN' with the UHZ definitions did not show uniform trends, but yielded higher rates for E. coli and lower rates for P. aeruginosa. On the patient level, the percentages of GN-MDRO carriers were 2.1, 5.5, 6.6, and 18.2% when applying the 'KRINKO-4MRGN', 'UHZ-MDR', 'KRINKO-3/4MRGN', and the 'ECDC-MDR' definition, respectively. Conclusions Different MDR-definitions lead to considerable variation in rates of GN-MDRO. Differences arise from the number of antibiotic categories required to be resistant, the categories and drugs considered relevant, and the antibiotic panel tested. MDR definitions should be chosen carefully depending on their purpose and local resistance rates, as definitions guiding isolation precautions have direct effects on costs and patient care.
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Affiliation(s)
- Aline Wolfensberger
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital and University of Zurich, Rämistrasse 100, CH-8091 Zurich, Switzerland
| | - Stefan P. Kuster
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital and University of Zurich, Rämistrasse 100, CH-8091 Zurich, Switzerland
| | - Martina Marchesi
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Reinhard Zbinden
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Michael Hombach
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
- Present address: Roche Diagnostics International AG, Rotkreuz, Switzerland
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Rosa NM, Agnoletti F, Lollai S, Tola S. Comparison of PCR-RFLP, API® 20 Strep and MALDI-TOF MS for identification of Streptococcus spp. collected from sheep and goat milk samples. Small Rumin Res 2019. [DOI: 10.1016/j.smallrumres.2019.09.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Ling J, Wang H, Li G, Feng Z, Song Y, Wang P, Shao H, Zhou H, Chen G. A novel short-term high-lactose culture approach combined with a matrix-assisted laser desorption ionization-time of flight mass spectrometry assay for differentiating Escherichia coli and Shigella species using artificial neural networks. PLoS One 2019; 14:e0222636. [PMID: 31593573 PMCID: PMC6782097 DOI: 10.1371/journal.pone.0222636] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 09/04/2019] [Indexed: 11/29/2022] Open
Abstract
Background Escherichia coli is currently unable to be reliably differentiated from Shigella species by routine matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) analysis. In the present study, a reliable and rapid identification method was established for Escherichia coli and Shigella species based on a short-term high-lactose culture using MALDI-TOF MS and artificial neural networks (ANN). Materials and methods The Escherichia coli and Shigella species colonies, treated with (Condition 1)/without (Condition 2) a short-term culture with an in-house developed high-lactose fluid medium, were prepared for MALDI-TOF MS assays. The MS spectra were acquired in linear positive mode, with a mass range from 2000 to 12000 Da and were then compared to discover new biomarkers for identification. Finally, MS spectra data sets 1 and 2, extracted from the two conditions, were used for ANN training to investigate the benefit on bacterial classification produced by the new biomarkers. Results Twenty-seven characteristic MS peaks from the Escherichia coli and Shigella species were summarized. Seven unreported MS peaks, with m/z 2330.745, m/z 2341.299, m/z 2371.581, m/z 2401.038, m/z 3794.851, m/z 3824.839 and m/z 3852.548, were discovered in only the spectra from the E. coli strains after a short-term high-lactose culture and were identified as belonging to acid shock protein. The prediction accuracies of the ANN models, based on data set 1 and 2, were 97.71±0.16% and 74.39±0.34% (n = 5), with an extremely remarkable difference (p < 0.001), and the areas under the curve of the receiver operating characteristic curve were 0.72 and 0.99, respectively. Conclusions In summary, adding a short-term high-lactose culture approach before the analysis enabled a reliable and easy differentiation of Escherichia coli from the Shigella species using MALDI-TOF MS and ANN.
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Affiliation(s)
- Jin Ling
- Department of Biochemical Drugs and Biological Products, Shanghai Institute for Food and Drug Control, Shanghai, China
- NMPA Key Laboratory for Quality Control of Therapeutic Monoclonal Antibodies, Shanghai Institute for Food and Drug Control, Shanghai, China
- Department of Pharmacy, Zhejiang Jinhua Guangfu Hospital, Jinhua, China
| | - Hong Wang
- Department of Biochemical Drugs and Biological Products, Shanghai Institute for Food and Drug Control, Shanghai, China
- NMPA Key Laboratory for Quality Control of Therapeutic Monoclonal Antibodies, Shanghai Institute for Food and Drug Control, Shanghai, China
| | - Gaomin Li
- Department of Biochemical Drugs and Biological Products, Shanghai Institute for Food and Drug Control, Shanghai, China
- NMPA Key Laboratory for Quality Control of Therapeutic Monoclonal Antibodies, Shanghai Institute for Food and Drug Control, Shanghai, China
| | - Zhen Feng
- Department of Antibiotics and Microbiology, Shanghai Institute for Food and Drug Control, Shanghai, China
| | - Yufei Song
- Department of Gastroenterology, Lihuili Hospital of Ningbo Medical Center, Ningbo, China
| | - Peng Wang
- Shanghai Key Laboratory of Intelligent Information Processing, School of Computer Science, Fudan University, Shanghai, China
| | - Hong Shao
- Department of Biochemical Drugs and Biological Products, Shanghai Institute for Food and Drug Control, Shanghai, China
- NMPA Key Laboratory for Quality Control of Therapeutic Monoclonal Antibodies, Shanghai Institute for Food and Drug Control, Shanghai, China
| | - Hu Zhou
- Department of Analytical Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Gang Chen
- Department of Biochemical Drugs and Biological Products, Shanghai Institute for Food and Drug Control, Shanghai, China
- NMPA Key Laboratory for Quality Control of Therapeutic Monoclonal Antibodies, Shanghai Institute for Food and Drug Control, Shanghai, China
- * E-mail:
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47
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Reeve MA, Bachmann D. MALDI-TOF MS protein fingerprinting of mixed samples. Biol Methods Protoc 2019; 4:bpz013. [PMID: 32395630 PMCID: PMC7200911 DOI: 10.1093/biomethods/bpz013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 08/19/2019] [Accepted: 08/27/2019] [Indexed: 11/13/2022] Open
Abstract
Analytical techniques currently available for the characterization of mixtures of microorganisms are generally based on next-generation sequencing. Motivated to develop practical and less-expensive methods for characterizing such mixtures, we propose, as an alternative or complement, the use of matrix-assisted laser-desorption and ionization time-of-flight mass spectrometry (MALDI-TOF MS), which is capable of high-resolution discrimination between species and even between biotypes within species. Potential approaches employing this technique for such characterization are discussed along with impediments to their successful employment. As a consequence, our rationale has been to capitalize on the powerful algorithms currently available for spectral comparison. Following this rationale, the first priority is to ensure the generation of MALDI-TOF MS spectra from mixtures of microorganisms that contain manageable peak complexities and that can be handled by the existing spectral comparison algorithms, preferably with the option to archive and re-run sample preparations and to pipette replicates of these onto MALDI-TOF MS sample plates. The second priority is to ensure that database entry is comparably facile to sample preparation so that large databases of known microorganism mixture MALDI-TOF MS spectra could be readily prepared for comparison with the spectra of unknown mixtures. In this article, we address the above priorities and generate illustrative MALDI-TOF MS spectra to demonstrate the utility of this approach. In addition, we investigate methods aimed at chemically modulating the peak complexity of the obtained MALDI-TOF MS spectra.
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Affiliation(s)
- Michael A Reeve
- Department of Bioscience, CABI Bioscience, Bakeham Lane, Egham, Surrey TW20 9TY, UK
| | - Denise Bachmann
- Department of Bioscience, CABI Bioscience, Bakeham Lane, Egham, Surrey TW20 9TY, UK
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Almuzara M, V. Cárdenas KC, Barberis C, Ramirez MS, Famiglietti A, Vay C. Performance of MALDI-TOF Mass Spectrometry for the Identification of the HACEK Group and Other Fastidious Gram-Negative Rods. Open Microbiol J 2019. [DOI: 10.2174/1874285801913010125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Objective:
The aim of this study was to determine the capacity of matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) to identify 155 HACEK clinical isolates and other fastidious or infrequently isolated Gram-negative rods (e.g., Actinobacillus, Capnocytophaga, Pasteurella, Neisseria, Moraxella, Dysgonomonas, among others).
Methods:
All the isolates were identified by standard biochemical tests and MALDI-TOF MS. Two different extraction methods (direct transfer formic acid method on spot and ethanol formic acid extraction method) and different cut-offs for genus/specie level identification were used. MALDI-TOF MS identification was considered correct when the result obtained from the MS database agreed with the phenotypic identification result.
When both the methods gave discordant results, the 16S rDNA gene sequencing was considered as the gold standard identification method.
Results:
Employing the score cut-offs suggested by the manufacturer, 93.55% and 69.03% isolates were correctly identified at the genus and species level, respectively. On the contrary , employing lower cut-off scores for identification, 98.06% and 92.09% isolates were properly identified at the genus and species level respectively and no significant differences between the results obtained with two extraction methods were observed .
Conclusion:
The accurate identification of 14 genera showed the reliability of MALDI-TOF MS as an optional methodology to the routine identification methods currently used in laboratories.
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Mier A, Nestora S, Medina Rangel PX, Rossez Y, Haupt K, Tse Sum Bui B. Cytocompatibility of Molecularly Imprinted Polymers for Deodorants: Evaluation on Human Keratinocytes and Axillary-Hosted Bacteria. ACS APPLIED BIO MATERIALS 2019; 2:3439-3447. [DOI: 10.1021/acsabm.9b00388] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Alejandra Mier
- Sorbonne Universités, Université de Technologie de Compiègne (UTC), CNRS Enzyme and Cell Engineering Laboratory, Rue Roger Couttolenc, CS 60319, 60203 Compiègne Cedex, France
| | - Sofia Nestora
- Sorbonne Universités, Université de Technologie de Compiègne (UTC), CNRS Enzyme and Cell Engineering Laboratory, Rue Roger Couttolenc, CS 60319, 60203 Compiègne Cedex, France
| | - Paulina X. Medina Rangel
- Sorbonne Universités, Université de Technologie de Compiègne (UTC), CNRS Enzyme and Cell Engineering Laboratory, Rue Roger Couttolenc, CS 60319, 60203 Compiègne Cedex, France
| | - Yannick Rossez
- Sorbonne Universités, Université de Technologie de Compiègne (UTC), CNRS Enzyme and Cell Engineering Laboratory, Rue Roger Couttolenc, CS 60319, 60203 Compiègne Cedex, France
| | - Karsten Haupt
- Sorbonne Universités, Université de Technologie de Compiègne (UTC), CNRS Enzyme and Cell Engineering Laboratory, Rue Roger Couttolenc, CS 60319, 60203 Compiègne Cedex, France
| | - Bernadette Tse Sum Bui
- Sorbonne Universités, Université de Technologie de Compiègne (UTC), CNRS Enzyme and Cell Engineering Laboratory, Rue Roger Couttolenc, CS 60319, 60203 Compiègne Cedex, France
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50
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MALDI-TOF/TOF mass spectrometry for determination of yeast diversity in traditional cornelian cherry tarhana produced with different cereal/pseudocereal flours. ANN MICROBIOL 2019. [DOI: 10.1007/s13213-019-01452-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
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