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Gütgemann F, Heuvelink A, Müller A, Churin Y, Buter R, Jung A, Feberwee A, Wiegel J, Kumm F, Braun AS, Yue M, Soriano-Vargas E, Swanepoel S, Botteldoorn N, Kirchner M, Kehrenberg C. Recommendation of a standardized broth microdilution method for antimicrobial susceptibility testing of Avibacterium paragallinarum and resistance monitoring. J Clin Microbiol 2024; 62:e0101123. [PMID: 38363142 PMCID: PMC10935639 DOI: 10.1128/jcm.01011-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 12/11/2023] [Indexed: 02/17/2024] Open
Abstract
This study aimed to develop a method for standardized broth microdilution antimicrobial susceptibility testing (AST) of Avibacterium (Av.) paragallinarum, the causative agent of infectious coryza in chickens. For this, a total of 83 Av. paragallinarum isolates and strains were collected from 15 countries. To select unrelated isolates for method validation steps, macrorestriction analyses were performed with 15 Av. paragallinarum. The visible growth of Av. paragallinarum was examined in six broth media and growth curves were compiled. In Veterinary Fastidious Medium and cation-adjusted Mueller-Hinton broth (CAMHB) + 1% chicken serum + 0.0025% NADH (CAMHB + CS + NADH), visible growth of all isolates was detected and both media allowed adequate bacterial growth. Due to the better readability of Av. paragallinarum growth in microtiter plates, CAMHB + CS + NADH was chosen for AST. Repetitions of MIC testing with five epidemiologically unrelated isolates using a panel of 24 antimicrobial agents resulted in high essential MIC agreements of 96%-100% after 48-h incubation at 35 ± 2°C. Hence, the remaining 78 Av. paragallinarum were tested and demonstrated easily readable MICs with the proposed method. Differences in MICs were detected between isolates from different continents, with isolates from Africa showing lower MICs compared to isolates from America and Europe, which more often showed elevated MICs of aminoglycosides, quinolones, tetracyclines, and/or trimethoprim/sulfamethoxazole. PCR analyses of isolates used for method development revealed that isolates with elevated MICs of tetracyclines harbored the tetracycline resistance gene tet(B) but none of the other tested resistance genes were detected. Therefore, whole-genome sequencing data from 62 Av. paragallinarum were analyzed and revealed the presence of sequences showing nucleotide sequence identity to the genes aph(6)-Id, aph(3″)-Ib, blaTEM-1B, catA2, sul2, tet(B), tet(H), and mcr-like. Overall, the proposed method using CAMHB + CS + NADH for susceptibility testing with 48-h incubation time at 35 ± 2°C in ambient air was shown to be suitable for Av. paragallinarum. Due to a variety of resistance genes detected, the development of clinical breakpoints is highly recommended. IMPORTANCE Avibacterium paragallinarum is an important pathogen in veterinary medicine that causes infectious coryza in chickens. Since antibiotics are often used for treatment and resistance of the pathogen is known, targeted therapy should be given after resistance testing of the pathogen. Unfortunately, there is currently no accepted method in standards that allows susceptibility testing of this fastidious pathogen. Therefore, we have worked out a method that allows harmonized susceptibility testing of the pathogen. The method meets the requirements of the CLSI and could be used by diagnostic laboratories.
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Affiliation(s)
- Franziska Gütgemann
- Institute for Veterinary Food Science, Faculty of Veterinary Medicine, Justus Liebig University Giessen, Giessen, Germany
| | | | - Anja Müller
- Institute for Veterinary Food Science, Faculty of Veterinary Medicine, Justus Liebig University Giessen, Giessen, Germany
| | - Yury Churin
- Institute for Veterinary Food Science, Faculty of Veterinary Medicine, Justus Liebig University Giessen, Giessen, Germany
| | | | - Arne Jung
- Clinic for Poultry, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | | | | | - Franziska Kumm
- Institute for Veterinary Food Science, Faculty of Veterinary Medicine, Justus Liebig University Giessen, Giessen, Germany
| | - Ann Sophie Braun
- Institute for Veterinary Food Science, Faculty of Veterinary Medicine, Justus Liebig University Giessen, Giessen, Germany
| | - Min Yue
- Hainan Institute of Zhejiang University, Sanya, China
- Department of Veterinary Medicine, Institute of Preventive Veterinary Science, Zhejiang University College of Animal Sciences, Hangzhou, China
| | - Edgardo Soriano-Vargas
- Centro de Investigación y Estudios Avanzados en Salud Animal, Facultad de Medicina Veterinaria y Zootecnia, Universidad Autónoma del Estado de México, Toluca, Mexico
| | | | | | - Miranda Kirchner
- Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
| | - Corinna Kehrenberg
- Institute for Veterinary Food Science, Faculty of Veterinary Medicine, Justus Liebig University Giessen, Giessen, Germany
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Zhang Y, Ruff SE, Oskolkov N, Tierney BT, Ryon K, Danko D, Mason CE, Elhaik E. The microbial biodiversity at the archeological site of Tel Megiddo (Israel). Front Microbiol 2023; 14:1253371. [PMID: 37808297 PMCID: PMC10559971 DOI: 10.3389/fmicb.2023.1253371] [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: 07/11/2023] [Accepted: 08/25/2023] [Indexed: 10/10/2023] Open
Abstract
Introduction The ancient city of Tel Megiddo in the Jezreel Valley (Israel), which lasted from the Neolithic to the Iron Age, has been continuously excavated since 1903 and is now recognized as a World Heritage Site. The site features multiple ruins in various areas, including temples and stables, alongside modern constructions, and public access is allowed in designated areas. The site has been studied extensively since the last century; however, its microbiome has never been studied. We carried out the first survey of the microbiomes in Tel Megiddo. Our objectives were to study (i) the unique microbial community structure of the site, (ii) the variation in the microbial communities across areas, (iii) the similarity of the microbiomes to urban and archeological microbes, (iv) the presence and abundance of potential bio-corroding microbes, and (v) the presence and abundance of potentially pathogenic microbes. Methods We collected 40 swab samples from ten major areas and identified microbial taxa using next-generation sequencing of microbial genomes. These genomes were annotated and classified taxonomically and pathogenetically. Results We found that eight phyla, six of which exist in all ten areas, dominated the site (>99%). The relative sequence abundance of taxa varied between the ruins and the sampled materials and was assessed using all metagenomic reads mapping to a respective taxon. The site hosted unique taxa characteristic of the built environment and exhibited high similarity to the microbiome of other monuments. We identified acid-producing bacteria that may pose a risk to the site through biocorrosion and staining and thus pose a danger to the site's preservation. Differences in the microbiomes of the publicly accessible or inaccessible areas were insignificant; however, pathogens were more abundant in the former. Discussion We found that Tel Megiddo combines microbiomes of arid regions and monuments with human pathogens. The findings shed light on the microbial community structures and have relevance for bio-conservation efforts and visitor health.
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Affiliation(s)
- Yali Zhang
- Department of Biology, Lund University, Lund, Sweden
| | - S. Emil Ruff
- The Marine Biological Laboratory, Woods Hole, MA, United States
| | - Nikolay Oskolkov
- Department of Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Lund University, Lund, Sweden
| | - Braden T. Tierney
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, United States
| | - Krista Ryon
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, United States
| | - David Danko
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, United States
| | - Christopher E. Mason
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, United States
- The Feil Family Brain and Mind Research Institute (BMRI), New York, NY, United States
- The Information Society Project, Yale Law School, New Haven, CT, United States
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, United States
| | - Eran Elhaik
- Department of Biology, Lund University, Lund, Sweden
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Zhu J, Chen Y, Wu Y, Wang Y, Zhu K. Commensal bacteria contribute to the growth of multidrug-resistant Avibacterium paragallinarum in chickens. Front Microbiol 2022; 13:1010584. [PMID: 36406434 PMCID: PMC9672371 DOI: 10.3389/fmicb.2022.1010584] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 10/03/2022] [Indexed: 07/30/2024] Open
Abstract
Avibacterium paragallinarum-associated infectious coryza (IC) is an important threat in commercial poultry. Previous studies about the characteristics of A. paragallinarum are succeeded in revealing the course of IC disease, but whether and how resident microbes contribute to the infection remains unclear. To understand the role of commensal bacteria, we isolated 467 commensal bacteria, including 38 A. paragallinarum, from the respiratory tract of IC chicken. The predominant commensal isolates were Gram-positive bacteria belonging to Staphylococcus spp. [33.19%, 95% confidence interval (CI): 28.93-37.66%], Enterococcus spp. (16.49%, 95% CI: 13.23-20.17%), and Bacillus spp. (16.27%, 95% CI: 13.04-19.94%). These isolates were closely correlated with the survival of A. paragallinarum. We examined and found that commensal bacteria aggravate A. paragallinarum-associated infections because certain commensal species (28.57%, 95% CI: 15.72-44.58%) induced hemolysis and promoted the growth of A. paragallinarum in vitro. Notably, A. paragallinarum showed high resistance to routine antibiotics such as erythromycin (84.21%, 95% CI: 68.75-93.98%), tetracycline (73.68%, 95% CI: 56.90-86.60%) and carried diverse mobile resistance gene clusters. Overall, we found commensal bacteria especially Gram-positive bacteria facilitate the survival of multidrug-resistant A. paragallinarum to exacerbate infections, suggesting that novel strategies may diminish A. paragallinarum-associated infections by modulating the population dynamics of commensal bacteria.
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Affiliation(s)
- Jiajia Zhu
- National Center for Veterinary Drug Safety Evaluation, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yunsheng Chen
- National Center for Veterinary Drug Safety Evaluation, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Yifan Wu
- National Center for Veterinary Drug Safety Evaluation, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yongqiang Wang
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Kui Zhu
- National Center for Veterinary Drug Safety Evaluation, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
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