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Do DT, Yang MR, Vo TNS, Le NQK, Wu YW. Unitig-centered pan-genome machine learning approach for predicting antibiotic resistance and discovering novel resistance genes in bacterial strains. Comput Struct Biotechnol J 2024; 23:1864-1876. [PMID: 38707536 PMCID: PMC11067008 DOI: 10.1016/j.csbj.2024.04.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 04/13/2024] [Accepted: 04/13/2024] [Indexed: 05/07/2024] Open
Abstract
In current genomic research, the widely used methods for predicting antimicrobial resistance (AMR) often rely on prior knowledge of known AMR genes or reference genomes. However, these methods have limitations, potentially resulting in imprecise predictions owing to incomplete coverage of AMR mechanisms and genetic variations. To overcome these limitations, we propose a pan-genome-based machine learning approach to advance our understanding of AMR gene repertoires and uncover possible feature sets for precise AMR classification. By building compacted de Brujin graphs (cDBGs) from thousands of genomes and collecting the presence/absence patterns of unique sequences (unitigs) for Pseudomonas aeruginosa, we determined that using machine learning models on unitig-centered pan-genomes showed significant promise for accurately predicting the antibiotic resistance or susceptibility of microbial strains. Applying a feature-selection-based machine learning algorithm led to satisfactory predictive performance for the training dataset (with an area under the receiver operating characteristic curve (AUC) of > 0.929) and an independent validation dataset (AUC, approximately 0.77). Furthermore, the selected unitigs revealed previously unidentified resistance genes, allowing for the expansion of the resistance gene repertoire to those that have not previously been described in the literature on antibiotic resistance. These results demonstrate that our proposed unitig-based pan-genome feature set was effective in constructing machine learning predictors that could accurately identify AMR pathogens. Gene sets extracted using this approach may offer valuable insights into expanding known AMR genes and forming new hypotheses to uncover the underlying mechanisms of bacterial AMR.
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Affiliation(s)
- Duyen Thi Do
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Ming-Ren Yang
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
- Department of Electrical Engineering, National Taiwan University of Science and Technology, Taipei, Taiwan
| | - Tran Nam Son Vo
- Department of Business Administration, College of Management, Lunghwa University of Science and Technology, Taoyuan City, Taiwan
| | - Nguyen Quoc Khanh Le
- Professional Master Program in Artificial Intelligence in Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Yu-Wei Wu
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
- Clinical Big Data Research Center, Taipei Medical University Hospital, Taipei, Taiwan
- TMU Research Center for Digestive Medicine, Taipei Medical University, Taipei, Taiwan
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Wang N, Zheng X, Leptihn S, Li Y, Cai H, Zhang P, Wu W, Yu Y, Hua X. Characteristics and phylogenetic distribution of megaplasmids and prediction of a putative chromid in Pseudomonas aeruginosa. Comput Struct Biotechnol J 2024; 23:1418-1428. [PMID: 38616963 PMCID: PMC11015739 DOI: 10.1016/j.csbj.2024.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 04/01/2024] [Accepted: 04/01/2024] [Indexed: 04/16/2024] Open
Abstract
Research on megaplasmids that contribute to the spread of antimicrobial resistance (AMR) in Pseudomonas aeruginosa strains has grown in recent years due to the now widely used technologies allowing long-read sequencing. Here, we systematically analyzed distinct and consistent genetic characteristics of megaplasmids found in P. aeruginosa. Our data provide information on their phylogenetic distribution and hypotheses tracing the potential evolutionary paths of megaplasmids. Most of the megaplasmids we found belong to the IncP-2-type, with conserved and syntenic genetic backbones carrying modules of genes associated with chemotaxis apparatus, tellurite resistance and plasmid replication, segregation, and transmission. Extensively variable regions harbor abundant AMR genes, especially those encoding β-lactamases such as VIM-2, IMP-45, and KPC variants, which are high-risk elements in nosocomial infection. IncP-2 megaplasmids act as effective vehicles transmitting AMR genes to diverse regions. One evolutionary model of the origin of megaplasmids claims that chromids can develop from megaplasmids. These chromids have been characterized as an intermediate between a megaplasmid and a chromosome, also containing core genes that can be found on the chromosome but not on the megaplasmid. Using in silico prediction, we identified the "PABCH45 unnamed replicon" as a putative chromid in P. aeruginosa, which shows a much higher similarity and closer phylogenetic relationship to chromosomes than to megaplasmids while also encoding plasmid-like partition genes. We propose that such a chromid could facilitate genome expansion, allowing for more rapid adaptations to novel ecological niches or selective conditions, in comparison to megaplasmids.
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Affiliation(s)
- Nanfei Wang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xuan Zheng
- Department of Nephrology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Sebastian Leptihn
- HMU Health and Medical University, Am Anger 64/73 – 99084, Erfurt, Germany
- Deutsches Zentrum für Infektionsforschung (DZIF) Translational Phage-Network, Inhoffenstraße 7 – 38124, Braunschweig, Germany
- University of Southern Denmark,Department of Biochemistry and Molecular Biology, Campusvej 55 – 5230, Odense, Denmark
| | - Yue Li
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Heng Cai
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Piaopiao Zhang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Wenhao Wu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yunsong Yu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaoting Hua
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
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Zagui GS, de Almeida OGG, Moreira NC, Silva NGA, Meschede MSC, Darini ALC, Andrade LN, Segura-Muñoz SI. Hospital wastewater as source of human pathogenic bacteria: A phenotypic and genomic analysis of international high-risk clone VIM-2-producing Pseudomonas aeruginosa ST235/O11. ENVIRONMENTAL RESEARCH 2024; 255:119166. [PMID: 38759772 DOI: 10.1016/j.envres.2024.119166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 05/12/2024] [Accepted: 05/15/2024] [Indexed: 05/19/2024]
Abstract
Pseudomonas aeruginosa belong to the special pathogen group capable of causing serious infections, with high mortality rates. The aim of this study was to describe the antibiotic resistance and genomic characteristics of Pseudomonas aeruginosa belonging to international high-risk clone ST235 (GPAE0131 isolate), obtained from hospital wastewater. P. aeruginosa GPAE0131 was isolated from ward tertiary hospital in Brazil and the antibiotic resistance profile was determined by the disc-diffusion method. Genomic characteristics related to antibiotic resistance and virulence factors were evaluated by genomic DNA sequencing on the Illumina MiSeq platform and bioinformatic analysis. GPAE0131 isolate showed resistance to piperacillin-tazobactam, cefepime, ceftazidime, imipenem, meropenem, ciprofloxacin, levofloxacin and tobramycin. Resistome comprehend of resistance genes to β-lactams (blaVIM-2, blaOXA-4, blaOXA-488, blaPDC-35), aminoglycosides (aph(3')-IIb, aac(6')-IIc, aac(6')-Ib9, aadA1), fosfomycin (fosA), chloramphenicol (catB7) and sulfonamides (sul1). Genome comparisons evidence insertion of blaVIM-2 and blaOXA-4 genes. GPAE0131 isolate was predicted to be pathogenic to humans and several virulence factors were found, including encoding gene for ExoU and exotoxin A. All of these features into a pathogenic international high-risk clone (ST235), classified as critical priority, stands out as public health concern due to the widespread dispersal of human pathogens through wastewater. It is suggested that mitigating measures be implemented, such as the treatment of hospital sewage and the addition of tertiary treatment, to prevent the escape of pathogens at this level into the environment.
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Affiliation(s)
- Guilherme Sgobbi Zagui
- Water Resources Research Group, Postgraduate Program in Environmental Technology, University of Ribeirão Preto, Brazil; School of Medicine, Department of Medicine, University of Ribeirão Preto, Brazil; Laboratory of Ecotoxicology and Environmental Parasitology, Ribeirão Preto College of Nursing, University of São Paulo, Brazil.
| | | | | | | | - Marina Smidt Celere Meschede
- Laboratory of Ecotoxicology and Environmental Parasitology, Ribeirão Preto College of Nursing, University of São Paulo, Brazil; Institute of Collective Health (ISCO), Federal University of Western Pará, Brazil
| | | | | | - Susana Inés Segura-Muñoz
- Laboratory of Ecotoxicology and Environmental Parasitology, Ribeirão Preto College of Nursing, University of São Paulo, Brazil
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Michels R, Papan C, Boutin S, Alhussein F, Becker SL, Nurjadi D, Last K. Clinical relevance of Staphylococcus saccharolyticus detection in human samples: a retrospective cohort study. Infection 2024:10.1007/s15010-024-02334-6. [PMID: 38963607 DOI: 10.1007/s15010-024-02334-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 06/25/2024] [Indexed: 07/05/2024]
Abstract
PURPOSE To characterize the clinical relevance of S. saccharolyticus and to identify criteria to distinguish between infection and contamination. METHODS We retrospectively investigated clinical features of patients with S. saccharolyticus detection between June 2009 and July 2021. Based on six criteria, infection was considered likely for patients with a score from 3 to 6 points, infection was considered unlikely for patients with a score from 0 to 2 points. We performed group comparison and logistic regression to identify factors than are associated with likely infection. In addition, whole genome sequencing (WGS) of 22 isolates was performed. RESULTS Of 93 patients in total, 44 were assigned to the group "infection likely" and 49 to the group "infection unlikely". Multiple regression analysis revealed "maximum body temperature during hospital stay" to have the strongest predictive effect on likely infection (adjusted odds ratio 4.40, 95% confidence interval 2.07-9.23). WGS revealed two different clades. Compared to isolates from clade A, isolates from clade B were more frequently associated with implanted medical devices (3/10 vs. 9/12, p = 0.046) and a shorter time to positivity (TTP) (4.5 vs. 3, p = 0.016). Both clades did neither differ significantly in terms of causing a likely infection (clade A 7/10 vs. clade B 5/12, p = 0.23) nor in median length of hospital stay (28 vs. 15.5 days, p = 0.083) and length of stay at the ICU (21 vs. 3.5 days, p = 0.14). CONCLUSION These findings indicate that S. saccharolyticus can cause clinically relevant infections. Differentiation between infection and contamination remains challenging.
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Affiliation(s)
- Ricarda Michels
- Center for Infectious Diseases, Institute of Medical Microbiology and Hygiene, Saarland University, Homburg, Germany
| | - Cihan Papan
- Center for Infectious Diseases, Institute of Medical Microbiology and Hygiene, Saarland University, Homburg, Germany.
- Institute for Hygiene and Public Health, University Hospital Bonn, Venusberg-Campus 1, Bonn, Germany.
| | - Sébastien Boutin
- Department of Infectious Diseases, Medical Microbiology and Hospital Hygiene, University Hospital Heidelberg, Heidelberg, Germany
- Department of Infectious Diseases and Microbiology, University of Lübeck and University Hospital Schleswig-Holstein Campus Lübeck, Lübeck, Germany
- Airway Research Center North (ARCN), German center for Lung Research (DZL), Lübeck, Germany
| | - Farah Alhussein
- Center for Infectious Diseases, Institute of Medical Microbiology and Hygiene, Saarland University, Homburg, Germany
| | - Sören L Becker
- Center for Infectious Diseases, Institute of Medical Microbiology and Hygiene, Saarland University, Homburg, Germany
| | - Dennis Nurjadi
- Department of Infectious Diseases, Medical Microbiology and Hospital Hygiene, University Hospital Heidelberg, Heidelberg, Germany
- Department of Infectious Diseases and Microbiology, University of Lübeck and University Hospital Schleswig-Holstein Campus Lübeck, Lübeck, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Lübeck, Germany
| | - Katharina Last
- Center for Infectious Diseases, Institute of Medical Microbiology and Hygiene, Saarland University, Homburg, Germany
- Institute for Hygiene and Public Health, University Hospital Bonn, Venusberg-Campus 1, Bonn, Germany
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Aldeia C, Campos-Madueno EI, Endimiani A. Genomic insights into Leminorella grimontii and its chromosomal class A GRI β-lactamase. Eur J Clin Microbiol Infect Dis 2024:10.1007/s10096-024-04888-7. [PMID: 38958811 DOI: 10.1007/s10096-024-04888-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Accepted: 06/25/2024] [Indexed: 07/04/2024]
Abstract
Leminorella grimontii strain LG-KP-E1-2-T0 was isolated from Zophobas morio larvae. It showed a susceptibility phenotype compatible with the expression of an inducible extended-spectrum β-lactamase. The presence of a chromosomal bla gene encoding for the class A GRI-1 β-lactamase was revealed by whole-genome sequencing. GRI-1 shared the highest amino acid identity with RIC-1 and OXY-type β-lactamases (76-80%). Analysis of six further publicly-available L. grimontii draft genomes deposited in NCBI revealed that blaGRI-1 was always present. Core-genome analysis indicated that LG-KP-E1-2-T0 was unique from other strains. We provided the first complete genome of L. grimontii and new insights on its chromosomal β-lactamases.
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Affiliation(s)
- Claudia Aldeia
- Institute for Infectious Diseases (IFIK), University of Bern, Friedbühlstrasse 25, Bern, CH-3001, Switzerland
| | - Edgar I Campos-Madueno
- Institute for Infectious Diseases (IFIK), University of Bern, Friedbühlstrasse 25, Bern, CH-3001, Switzerland
- Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Andrea Endimiani
- Institute for Infectious Diseases (IFIK), University of Bern, Friedbühlstrasse 25, Bern, CH-3001, Switzerland.
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Tan Y, Scornet AL, Yap MNF, Zhang D. Machine learning-based classification reveals distinct clusters of non-coding genomic allelic variations associated with Erm-mediated antibiotic resistance. mSystems 2024:e0043024. [PMID: 38953319 DOI: 10.1128/msystems.00430-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 06/05/2024] [Indexed: 07/04/2024] Open
Abstract
The erythromycin resistance RNA methyltransferase (erm) confers cross-resistance to all therapeutically important macrolides, lincosamides, and streptogramins (MLS phenotype). The expression of erm is often induced by the macrolide-mediated ribosome stalling in the upstream co-transcribed leader sequence, thereby triggering a conformational switch of the intergenic RNA hairpins to allow the translational initiation of erm. We investigated the evolutionary emergence of the upstream erm regulatory elements and the impact of allelic variation on erm expression and the MLS phenotype. Through systematic profiling of the upstream regulatory sequences across all known erm operons, we observed that specific erm subfamilies, such as ermB and ermC, have independently evolved distinct configurations of small upstream ORFs and palindromic repeats. A population-wide genomic analysis of the upstream ermB regions revealed substantial non-random allelic variation at numerous positions. Utilizing machine learning-based classification coupled with RNA structure modeling, we found that many alleles cooperatively influence the stability of alternative RNA hairpin structures formed by the palindromic repeats, which, in turn, affects the inducibility of ermB expression and MLS phenotypes. Subsequent experimental validation of 11 randomly selected variants demonstrated an impressive 91% accuracy in predicting MLS phenotypes. Furthermore, we uncovered a mixed distribution of MLS-sensitive and MLS-resistant ermB loci within the evolutionary tree, indicating repeated and independent evolution of MLS resistance. Taken together, this study not only elucidates the evolutionary processes driving the emergence and development of MLS resistance but also highlights the potential of using non-coding genomic allele data to predict antibiotic resistance phenotypes. IMPORTANCE Antibiotic resistance (AR) poses a global health threat as the efficacy of available antibiotics has rapidly eroded due to the widespread transmission of AR genes. Using Erm-dependent MLS resistance as a model, this study highlights the significance of non-coding genomic allelic variations. Through a comprehensive analysis of upstream regulatory elements within the erm family, we elucidated the evolutionary emergence and development of AR mechanisms. Leveraging population-wide machine learning (ML)-based genomic analysis, we transformed substantial non-random allelic variations into discernible clusters of elements, enabling precise prediction of MLS phenotypes from non-coding regions. These findings offer deeper insight into AR evolution and demonstrate the potential of harnessing non-coding genomic allele data for accurately predicting AR phenotypes.
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Affiliation(s)
- Yongjun Tan
- Department of Biology, College of Arts and Sciences, Saint Louis University, St. Louis, Missouri, USA
| | - Alexandre Le Scornet
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Mee-Ngan Frances Yap
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Dapeng Zhang
- Department of Biology, College of Arts and Sciences, Saint Louis University, St. Louis, Missouri, USA
- Program of Bioinformatics and Computational Biology, Saint Louis University, St. Louis, Missouri, USA
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Yao L, Cooper AL, Gill A, Koziol A, Wong A, Blais BW, Carrillo CD. Overcoming Microbial Inhibition of S. Sonnei Through the Exploitation of Genomically Predicted Antibiotic Resistance Profiles for the Development of Food Enrichment Media. J Food Prot 2024; 87:100302. [PMID: 38754553 DOI: 10.1016/j.jfp.2024.100302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 05/07/2024] [Accepted: 05/10/2024] [Indexed: 05/18/2024]
Abstract
Linking outbreaks of Shigella spp. to specific foods is challenging due to poor selectivity of current enrichment media. We have previously shown that enrichment media, tailored to the genomically-predicted antimicrobial resistance (AMR) of Shiga toxigenic E. coli strains, enhances their isolation from foods. This study investigates the application of this approach for Shigella isolation. The AMR gene profiles of 21,908 published S. sonnei genomes indicated a high prevalence of genes conferring resistance to streptomycin (aadA, aph(3″)-Ib, aph(6)-Id, 92.8%), sulfonamides (sul1, sul2, 74.8%), and/or trimethoprim (dfrA, 96.2%). Genomic analysis and antibiotic susceptibility testing conducted with a panel of 17 outbreak-associated S. sonnei strains confirmed the correlation of AMR gene detection with resistance phenotypes. Supplementation of Shigella Broth (SB) with up to 400 µg/mL of trimethoprim or sulfadiazine did not suppress the growth of sensitive strains, whereas 100 µg/mL of streptomycin increased the selectivity of this broth. All three antibiotics increased the selectivity of modified Tryptone Soya Broth (mTSB). Based on these results, supplemented media formulations were developed and assessed by measuring the relative growth of S. sonnei in cultures coinoculated with a strain of bacteriocin-producing E. coli that is inhibitory to Shigella growth. S. sonnei was not recovered from cocultures grown in SB or mTSB without antibiotics. In contrast, media supplemented with streptomycin at 50 and 100 µg/mL, trimethoprim at 25 and 50 µg/mL, and sulfadiazine at 100 µg/mL increased the relative proportion of S. sonnei in postenrichment cultures. The enhanced recovery of resistant S. sonnei strains achieved in this study indicates that, in cases where genomic data are available for clinical S. sonnei isolates, customization of selective enrichment media based on AMR gene detection could be a valuable tool for supporting the investigation of foodborne shigellosis outbreaks.
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Affiliation(s)
- Lang Yao
- Ottawa Laboratory Carling, Canadian Food Inspection Agency, Ottawa, Ontario, Canada K1A 0C6; Department of Biology, Carleton University, Ottawa, Ontario, Canada K1S 5B6.
| | - Ashley L Cooper
- Ottawa Laboratory Carling, Canadian Food Inspection Agency, Ottawa, Ontario, Canada K1A 0C6.
| | - Alex Gill
- Bureau of Microbial Hazards, Health Canada, Ottawa, Ontario, Canada.
| | - Adam Koziol
- Ottawa Laboratory Carling, Canadian Food Inspection Agency, Ottawa, Ontario, Canada K1A 0C6.
| | - Alex Wong
- Department of Biology, Carleton University, Ottawa, Ontario, Canada K1S 5B6.
| | - Burton W Blais
- Ottawa Laboratory Carling, Canadian Food Inspection Agency, Ottawa, Ontario, Canada K1A 0C6.
| | - Catherine D Carrillo
- Ottawa Laboratory Carling, Canadian Food Inspection Agency, Ottawa, Ontario, Canada K1A 0C6.
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Boutin S, Welker S, Gerigk M, Miethke T, Heeg K, Nurjadi D. Molecular surveillance of carbapenem-resistant Enterobacterales in two nearby tertiary hospitals to identify regional spread of high-risk clones in Germany, 2019-2020. J Hosp Infect 2024; 149:126-134. [PMID: 38723905 DOI: 10.1016/j.jhin.2024.04.014] [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: 01/30/2024] [Revised: 04/02/2024] [Accepted: 04/16/2024] [Indexed: 06/09/2024]
Abstract
BACKGROUND Understanding the transmission dynamics of carbapenem-resistant Enterobacterales (CRE) is critical to addressing the escalating global threat of antimicrobial resistance (AMR). Although hospital transmission of CRE has been extensively studied, information on community transmission is lacking. AIM To identify genomic clusters of CRE from two nearby institutions that may be indicative of community or inter-facility transmission. METHODS CRE isolates between January 1st, 2019 and December 31st, 2020 from two tertiary hospitals, detected in the respective routine microbiology laboratories, were collected and characterized by short-read whole-genome sequencing. FINDINGS A total of 272 CRE were collected, with Enterobacter cloacae complex (71/192, 37%) predominant in Heidelberg and Escherichia coli (19/80, 24%) in Mannheim. The most common carbapenem resistance gene, blaOXA-48, was detected in 38% of CRE from both centres. Several putative transmission clusters were found, including six clusters of E. cloacae complex, five clusters of Klebsiella pneumoniae, four clusters of Citrobacter freundii, and two clusters each of Escherichia coli and K. aerogenes. No clusters involved isolates from both study centres, except for an ST22 C. freundii cluster. Globally circulating clones were identified between the two centres for ST131 E. coli, ST66 E. hormaechei, and ST22 C. freundii. CONCLUSION This study found no widespread transmission clusters among isolates from both centres, suggesting a hospital-specific clonal structure. This suggests that CRE clusters involving both institutions may indicate emerging or circulating clones in the community, highlighting the need for intersectoral surveillance and data sharing.
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Affiliation(s)
- S Boutin
- Medical Microbiology and Hygiene, Department of Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany; Department of Infectious Diseases and Microbiology, University of Lübeck and University Hospital Schleswig Holstein Campus Lübeck, Lübeck, Germany; German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Lübeck, Germany
| | - S Welker
- Institute of Medical Microbiology and Hygiene, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - M Gerigk
- Institute of Medical Microbiology and Hygiene, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - T Miethke
- Institute of Medical Microbiology and Hygiene, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany; Mannheim Institute for Innate Immunoscience (MI3), Mannheim, Germany; Center of Experimental Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - K Heeg
- Medical Microbiology and Hygiene, Department of Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - D Nurjadi
- Medical Microbiology and Hygiene, Department of Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany; Department of Infectious Diseases and Microbiology, University of Lübeck and University Hospital Schleswig Holstein Campus Lübeck, Lübeck, Germany; German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Lübeck, Germany.
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9
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Zhao X, Qin J, Chen G, Yang C, Wei J, Li W, Jia W. Whole-genome sequencing, multilocus sequence typing, and resistance mechanism of the carbapenem-resistant Pseudomonas aeruginosa in China. Microb Pathog 2024; 192:106720. [PMID: 38815778 DOI: 10.1016/j.micpath.2024.106720] [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: 03/12/2024] [Revised: 05/14/2024] [Accepted: 05/27/2024] [Indexed: 06/01/2024]
Abstract
Pseudomonas aeruginosa is a significant pathogen responsible for severe multisite infections with high morbidity and mortality rates. This study analyzed carbapenem-resistant Pseudomonas aeruginosa (CRPA) at a tertiary hospital in Shandong, China, using whole-genome sequencing (WGS). The objective was to explore the mechanisms and molecular characteristics of carbapenem resistance. A retrospective analysis of 91 isolates from January 2022 to March 2023 was performed, which included strain identification and antimicrobial susceptibility testing. WGS was utilized to determine the genome sequences of these CRPA strains, and the species were precisely identified using average nucleotide identification (ANI), with further analysis on multilocus sequence typing and strain relatedness. Some strains were found to carry the ampD and oprD genes, while only a few harbored carbapenemase genes or related genes. Notably, all strains possessed the mexA, mexE, and mexX genes. The major lineage identified was ST244, followed by ST235. The study revealed a diverse array of carbapenem resistance mechanisms among hospital isolates, differing from previous studies in mainland China. It highlighted that carbapenem resistance is not due to a single mechanism but rather a combination of enzyme-mediated resistance, AmpC overexpression, OprD dysfunction, and efflux pump overexpression. This research provides valuable insights into the evolutionary mechanisms and molecular features of CRPA resistance in this region, aiding in the national prevention and control of CRPA, and offering references for targeting and developing new drugs.
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Affiliation(s)
- Xue Zhao
- Department of Clinical Laboratory, Weifang People's Hospital, Weifang, Shandong Province, China
| | - Jiangnan Qin
- Department of Clinical Laboratory, Weifang People's Hospital, Weifang, Shandong Province, China
| | - Guang Chen
- Department of Clinical Laboratory, Weifang People's Hospital, Weifang, Shandong Province, China
| | - Chao Yang
- The Center for Microbes, Development and Health, CAS Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
| | - Jie Wei
- Department of Clinical Laboratory, Weifang People's Hospital, Weifang, Shandong Province, China
| | - Wanxiang Li
- Department of Clinical Laboratory, Weifang People's Hospital, Weifang, Shandong Province, China
| | - Wei Jia
- Department of Clinical Laboratory, Weifang People's Hospital, Weifang, Shandong Province, China.
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Klages LJ, Kaup O, Busche T, Kalinowski J, Rückert-Reed C. Classification of a novel Serratia species, isolated from a wound swab in North Rhine-Westphalia: Proposal of Serratia sarumanii sp. nov. Syst Appl Microbiol 2024; 47:126527. [PMID: 38959748 DOI: 10.1016/j.syapm.2024.126527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 05/08/2024] [Accepted: 06/27/2024] [Indexed: 07/05/2024]
Abstract
Novel, white-pigmented, Gram-negative bacterial strains (K-M0706T, K-M0228, K-M0252, K-M0260) were isolated from clinical samples. With a similarity of up to 69.7 % to Serratia nevei S15T and up to 63.8 % to Serratia marcescens ATCC 13880T, as determined by digital DNA-DNA hybridization, the strains were assigned as novel species of the genus Serratia. The species can easily be differentiated from the red colored Serratia marcescens sensu stricto by its white phenotype. Discrimination between this strain and Serratia nevei is possible due to alpha-glucosidase activity and O/129-resistance, as shown for strain K-M0706T. The major fatty acids were determined as myristate, palmitate, cis-9,10-methylenehexadecanoate, linoleate, and (all cis-9,10)-methyleneoctadecanoate. These phenotypical and genomic data support the assignment of a novel species within the genus Serratia, named S. sarumanii due to its pathogenicity and white phenotype, with strain K-M0706T as the type strain.
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Affiliation(s)
- Levin Joe Klages
- Bielefeld University, Microbial Genomics and Biotechnology, Center for Biotechnology (CeBiTec), Bielefeld, Germany
| | - Olaf Kaup
- Bielefeld University, Medical School and University Medical Center OWL, Bielefeld Hospital, Institute of Laboratory Medicine, Microbiology and Transfusion Medicine, Bielefeld, Germany
| | - Tobias Busche
- Bielefeld University, Microbial Genomics and Biotechnology, Center for Biotechnology (CeBiTec), Bielefeld, Germany; Bielefeld University, Medical School OWL, Bielefeld, Germany
| | - Jörn Kalinowski
- Bielefeld University, Microbial Genomics and Biotechnology, Center for Biotechnology (CeBiTec), Bielefeld, Germany
| | - Christian Rückert-Reed
- Bielefeld University, Microbial Genomics and Biotechnology, Center for Biotechnology (CeBiTec), Bielefeld, Germany; Bielefeld University, Medical School OWL, Bielefeld, Germany.
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11
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Gambino M, Kushwaha SK, Wu Y, van Haastrecht P, Klein-Sousa V, Lutz VT, Bejaoui S, Jensen CMC, Bojer MS, Song W, Xiao M, Taylor NMI, Nobrega FL, Brøndsted L. Diversity and phage sensitivity to phages of porcine enterotoxigenic Escherichia coli. Appl Environ Microbiol 2024:e0080724. [PMID: 38940562 DOI: 10.1128/aem.00807-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Accepted: 06/05/2024] [Indexed: 06/29/2024] Open
Abstract
Enterotoxigenic Escherichia coli (ETEC) is a diverse and poorly characterized E. coli pathotype that causes diarrhea in humans and animals. Phages have been proposed for the veterinary biocontrol of ETEC, but effective solutions require understanding of porcine ETEC diversity that affects phage infection. Here, we sequenced and analyzed the genomes of the PHAGEBio ETEC collection, gathering 79 diverse ETEC strains isolated from European pigs with post-weaning diarrhea (PWD). We identified the virulence factors characterizing the pathotype and several antibiotic resistance genes on plasmids, while phage resistance genes and other virulence factors were mostly chromosome encoded. We experienced that ETEC strains were highly resistant to Enterobacteriaceae phage infection. It was only by enrichment of numerous diverse samples with different media and conditions, using the 41 ETEC strains of our collection as hosts, that we could isolate two lytic phages that could infect a large part of our diverse ETEC collection: vB_EcoP_ETEP21B and vB_EcoS_ETEP102. Based on genome and host range analyses, we discussed the infection strategies of the two phages and identified components of lipopolysaccharides ( LPS) as receptors for the two phages. Our detailed computational structural analysis highlights several loops and pockets in the tail fibers that may allow recognition and binding of ETEC strains, also in the presence of O-antigens. Despite the importance of receptor recognition, the diversity of the ETEC strains remains a significant challenge for isolating ETEC phages and developing sustainable phage-based products to address ETEC-induced PWD.IMPORTANCEEnterotoxigenic Escherichia coli (ETEC)-induced post-weaning diarrhea is a severe disease in piglets that leads to weight loss and potentially death, with high economic and animal welfare costs worldwide. Phage-based approaches have been proposed, but available data are insufficient to ensure efficacy. Genome analysis of an extensive collection of ETEC strains revealed that phage defense mechanisms were mostly chromosome encoded, suggesting a lower chance of spread and selection by phage exposure. The difficulty in isolating lytic phages and the molecular and structural analyses of two ETEC phages point toward a multifactorial resistance of ETEC to phage infection and the importance of extensive phage screenings specifically against clinically relevant strains. The PHAGEBio ETEC collection and these two phages are valuable tools for the scientific community to expand our knowledge on the most studied, but still enigmatic, bacterial species-E. coli.
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Affiliation(s)
- Michela Gambino
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
- Institute of Conservation, The Royal Danish Academy, Copenhagen, Denmark
| | - Simran Krishnakant Kushwaha
- School of Biological Sciences, Faculty of Environmental & Life Sciences, University of Southampton, Southampton, United Kingdom
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Rajasthan, India
| | - Yi Wu
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Rajasthan, India
| | - Pauline van Haastrecht
- School of Biological Sciences, Faculty of Environmental & Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Victor Klein-Sousa
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Veronika T Lutz
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Semeh Bejaoui
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | | | - Martin S Bojer
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | | | | | - Nicholas M I Taylor
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Franklin L Nobrega
- School of Biological Sciences, Faculty of Environmental & Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Lone Brøndsted
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
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12
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Sun RY, Fang LX, Dai JJ, Chen KC, Ke BX, Sun J, Ke CW, Wai Chi Chan E, Liu YH, Chen S, Liao XP. Antimicrobial resistance and population genomics of emerging multidrug-resistant Salmonella 4,[5],12:i:- in Guangdong, China. mSystems 2024; 9:e0116423. [PMID: 38747582 DOI: 10.1128/msystems.01164-23] [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: 11/06/2023] [Accepted: 04/09/2024] [Indexed: 06/19/2024] Open
Abstract
Salmonella 4,[5],12:i:-, a monophasic variant of Salmonella Typhimurium, has emerged as a global cause of multidrug-resistant salmonellosis and has become endemic in many developing and developed countries, especially in China. Here, we have sequenced 352 clinical isolates in Guangdong, China, during 2009-2019 and performed a large-scale collection of Salmonella 4,[5],12:i:- with whole genome sequencing (WGS) data across the globe, to better understand the population structure, antimicrobial resistance (AMR) genomic characterization, and transmission routes of Salmonella 4,[5],12:i:- across Guangdong. Salmonella 4,[5],12:i:- strains showed broad genetic diversity; Guangdong isolates were found to be widely distributed among the global lineages. Of note, we identified the formation of a novel Guangdong clade (Bayesian analysis of population structure lineage 1 [BAPS1]) genetically diversified from the global isolates and likely emerged around 1990s. BAPS1 exhibits unique genomic features, including large pan-genome, decreased ciprofloxacin susceptibility due to mutation in gyrA and carriage of plasmid-mediated quinolone resistance (PMQR) genes, and the multidrug-resistant IncHI2 plasmid. Furthermore, high genetic similarity was found between strains collected from Guangdong, Europe, and North America, indicating the association with multiple introductions from overseas. These results suggested that global dissemination and local clonal expansion simultaneously occurred in Guangdong, China, and horizontally acquired resistance to first-line and last-line antimicrobials at local level, underlying emergences of extensive drug and pan-drug resistance. Our findings have increased the knowledge of global and local epidemics of Salmonella 4,[5],12:i:- in Guangdong, China, and provided a comprehensive baseline data set essential for future molecular surveillance.IMPORTANCESalmonella 4,[5],12:i:- has been regarded as the predominant pandemic serotype causing diarrheal diseases globally, while multidrug resistance (MDR) constitutes great public health concerns. This study provided a detailed and comprehensive genome-scale analysis of this important Salmonella serovar in the past decade in Guangdong, China. Our results revealed the complexity of two distinct transmission modes, namely global transmission and local expansion, circulating in Guangdong over a decade. Using phylogeography models, the origin of Salmonella 4,[5],12:i:- was predicted from two aspects, year and country, that is, Salmonella 4,[5],12:i:- emerged in 1983, and was introduced from the UK, and subsequently differentiated into the local endemic lineage circa 1991. Additionally, based on the pan-genome analysis, it was found that the gene accumulation rate in local endemic BAPS 1 lineage was higher than in other lineages, and the horizontal transmission of MDR IncHI2 plasmid associated with high resistance played a major role, which showed the potential threat to public health.
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Affiliation(s)
- Ruan-Yang Sun
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, Guangdong, China
| | - Liang-Xing Fang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, Guangdong, China
| | - Jing-Jing Dai
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, Guangdong, China
| | - Kai-Chao Chen
- Department of Food Science and Nutrition, Faculty of Science, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China
| | - Bi-Xia Ke
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
| | - Jian Sun
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, Guangdong, China
| | - Chang-Wen Ke
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
| | - Edward Wai Chi Chan
- Department of Food Science and Nutrition, Faculty of Science, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China
| | - Ya-Hong Liu
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, Guangdong, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, China
| | - Sheng Chen
- Department of Food Science and Nutrition, Faculty of Science, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China
| | - Xiao-Ping Liao
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, Guangdong, China
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13
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Di Gregorio S, Weltman G, Fabbri C, Fernández S, Zárate S, Smayevsky J, Power P, Campos J, Llarrull LI, Mollerach M. Genetic and Phenotypic Changes Related to the Development of mec-Independent Oxacillin Non-Susceptibility in ST8 Staphylococcus aureus Recovered after Antibiotic Therapy in a Patient with Bacteremia. Antibiotics (Basel) 2024; 13:554. [PMID: 38927220 PMCID: PMC11200602 DOI: 10.3390/antibiotics13060554] [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: 04/26/2024] [Revised: 05/30/2024] [Accepted: 06/08/2024] [Indexed: 06/28/2024] Open
Abstract
The mec-independent oxacillin non-susceptible S. aureus (MIONSA) strains represent a great clinical challenge, as they are not easily detected and can lead to treatment failure. However, the responsible molecular mechanisms are still very little understood. Here, we studied four clinical ST8-MSSA-t024 isolates recovered during the course of antibiotic treatment from a patient suffering successive episodes of bacteremia. The first isolates (SAMS1, SAMS2, and SAMS3) were susceptible to cefoxitin and oxacillin. The last one (SA2) was susceptible to cefoxitin, resistant to oxacillin, lacked mec genes, and had reduced susceptibility to teicoplanin. SA2 showed higher β-lactamase activity than SAMS1. However, β-lactamase hyperproduction could not be linked to oxacillin resistance as it was not inhibited by clavulanic acid, and no genetic changes that could account for its hyperproduction were found. Importantly, we hereby report the in vivo acquisition and coexistence of different adaptive mutations in genes associated with peptidoglycan synthesis (pbp2, rodA, stp1, yjbH, and yvqF/vraT), which is possibly related with the development of oxacillin resistance and reduced susceptibility to teicoplanin in SA2. Using three-dimensional models and PBP binding assays, we demonstrated the high contribution of the SA2 PBP2 Ala450Asp mutation to the observed oxacillin resistance phenotype. Our results should be considered as a warning for physicians and microbiologists in the region, as MIONSA detection and treatment represent an important clinical challenge.
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Affiliation(s)
- Sabrina Di Gregorio
- Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autómoma de Buenos Aires 1113, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires 1113, Argentina
| | - Gabriela Weltman
- Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autómoma de Buenos Aires 1113, Argentina
| | - Carolina Fabbri
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires 1113, Argentina
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Predio CONICET Rosario, 27 de Febrero 210 bis, Rosario 2000, Argentina
| | - Silvina Fernández
- Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autómoma de Buenos Aires 1113, Argentina
| | - Soledad Zárate
- Laboratorio de Bacteriología, Micología y Parasitología, Centro de Educación Médica e Investigaciones Clínicas “Norberto Quirno” (CEMIC), Ciudad Autónoma de Buenos Aires 1431, Argentina
| | - Jorgelina Smayevsky
- Laboratorio de Bacteriología, Micología y Parasitología, Centro de Educación Médica e Investigaciones Clínicas “Norberto Quirno” (CEMIC), Ciudad Autónoma de Buenos Aires 1431, Argentina
| | - Pablo Power
- Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autómoma de Buenos Aires 1113, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires 1113, Argentina
| | - Josefina Campos
- Unidad Operativa Centro Nacional de Genómica y Bioinformática, ANLIS Dr. Carlos G. Malbrán, Ciudad Autónoma de Buenos Aires 1282, Argentina
| | - Leticia Irene Llarrull
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires 1113, Argentina
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Predio CONICET Rosario, 27 de Febrero 210 bis, Rosario 2000, Argentina
- Área Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 570, Rosario 2000, Argentina
| | - Marta Mollerach
- Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autómoma de Buenos Aires 1113, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires 1113, Argentina
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14
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Chanchaithong P, Chueahiran S, Pinpimai K, Sroithongkham P, Leelapsawas C, Indra R, Yindee J, Chuanchuen R. Chromosomal and plasmid localization of ileS2 in high-level mupirocin-resistant Staphylococcus pseudintermedius and Staphylococcus aureus isolated from canine and feline origins. J Antimicrob Chemother 2024:dkae172. [PMID: 38863334 DOI: 10.1093/jac/dkae172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 05/11/2024] [Indexed: 06/13/2024] Open
Abstract
OBJECTIVES To characterize the mobile genetic elements and genetic localization of ileS2 in high-level mupirocin-resistant (Hi-MupR) methicillin-resistant Staphylococcus pseudintermedius (MRSP) and MRSA isolates recovered from canine and feline clinical samples. METHODS The identification of bacterial species and presence of mecA and ileS2 genes in MRSP and MRSA isolates were performed using MALDI-TOF MS and PCR, respectively. Antimicrobial resistance (AMR) phenotypes were determined by broth microdilution assays. The genome characteristics, ileS2-containing elements and staphylococcal cassette chromosome mec (SCCmec) were illustrated using complete circular genomes obtained from hybrid assembly of Illumina short-reads and Oxford Nanopore Technologies long-reads. These were analysed through phylogenetic and bioinformatics approaches. RESULTS A total of 18 MRSP clinical isolates and four MRSA clinical isolates exhibited the Hi-MupR phenotype and carried multiple AMR genes, including mecA and ileS2 genes. MRSP ST182-SCCmec V (n = 6) and ST282-ΨSCCmec57395-t10 (n = 4) contained the ileS2 transposable unit associated with IS257 on the chromosome. Three MRSA ST398-SCCmec V-t034/t4652 isolates carried ∼42 kb pSK41-like ileS2 plasmids, whereas similar ileS2 plasmids lacking tra genes were found in MRSP ST282-ΨSCCmec57395-t72/t21 isolates. Furthermore, a new group of ileS2 plasmids, carried by MRSP ST45-ΨSCCmec57395, ST433-ΨSCCmecKW21-t05 and ST2165-SCCmec IV-t06, and by one MRSA ST398-SCCmec V-t034 strain, shared the plasmid backbone with the cfr/fexA-carrying plasmid pM084526_1 in MRSA ST398. CONCLUSIONS This study provides the first evidence of ileS2 integration into the S. pseudintermedius chromosome, which is a rare occurrence in staphylococcal species, and plasmids played a pivotal role in dissemination of ileS2 in both staphylococcal species.
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Affiliation(s)
- Pattrarat Chanchaithong
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
- Research Unit in Microbial Food Safety and Antimicrobial Resistance, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Surawit Chueahiran
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Komkiew Pinpimai
- Aquatic Resources Research Institute, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Parinya Sroithongkham
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Chavin Leelapsawas
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Rusmin Indra
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Jitrapa Yindee
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Rungtip Chuanchuen
- Research Unit in Microbial Food Safety and Antimicrobial Resistance, Chulalongkorn University, Bangkok, 10330, Thailand
- Department of Veterinary Public Health, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
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15
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Garzon A, Basbas C, Schlesener C, Silva-Del-Rio N, Karle BM, Lima FS, Weimer BC, Pereira RV. WGS of intrauterine E. coli from cows with early postpartum uterine infection reveals a non-uterine specific genotype and virulence factors. mBio 2024; 15:e0102724. [PMID: 38742889 DOI: 10.1128/mbio.01027-24] [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: 04/08/2024] [Accepted: 04/09/2024] [Indexed: 05/16/2024] Open
Abstract
Escherichia coli has been attributed to playing a major role in a cascade of events that affect the prevalence and severity of uterine disease in cattle. The objectives of this project were to (i) define the association between the prevalence of specific antimicrobial resistance and virulence factor genes in E. coli with the clinical status related to uterine infection, (ii) identify the genetic relationship between E. coli isolates from cows with diarrhea, with mastitis, and with and without metritis, and (iii) determine the association between the phenotypic and genotypic antimicrobial resistance identified on the E. coli isolated from postpartum cattle. Bacterial isolates (n = 148) were obtained from a larger cross-sectional study. Cows were categorized into one of three clinical groups before enrollment: metritis, cows with purulent discharge, and control cows. For genomic comparison, public genomes (n = 130) from cows with diarrhea, mastitis, and metritis were included in a genome-wide association study, to evaluate differences between the drug classes or the virulence factor category among clinical groups. A distinct E. coli genotype associated with metritis could not be identified. Instead, a high genetic diversity among the isolates from uterine sources was present. A virulence factor previously associated with metritis (fimH) using PCR was not associated with metritis. There was moderate accuracy for whole-genome sequencing to predict phenotypic resistance, which varied depending on the antimicrobial tested. Findings from this study contradict the traditional pathotype classification and the unique intrauterine E. coli genotype associated with metritis in dairy cows.IMPORTANCEMetritis is a common infectious disease in dairy cattle and the second most common reason for treating a cow with antimicrobials. The pathophysiology of the disease is complex and is not completely understood. Specific endometrial pathogenic Escherichia coli have been reported to be adapted to the endometrium and sometimes lead to uterine disease. Unfortunately, the specific genomic details of the endometrial-adapted isolates have not been investigated using enough genomes to represent the genomic diversity of this organism to identify specific virulence genes that are consistently associated with disease development and severity. Results from this study provide key microbial ecological advances by elucidating and challenging accepted concepts for the role of Intrauterine E. coli in metritis in dairy cattle, especially contradicting the existence of a unique intrauterine E. coli genotype associated with metritis in dairy cows, which was not found in our study.
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Affiliation(s)
- Adriana Garzon
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, California, USA
| | - Carl Basbas
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, California, USA
| | - Cory Schlesener
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, California, USA
- Department of Population Health and Reproduction, 100K Pathogen Genome Project, School of Veterinary Medicine, University of California, Davis, California, USA
| | - Noelia Silva-Del-Rio
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, California, USA
- Veterinary Medicine Teaching and Research Center, School of Veterinary Medicine, University of California, Tulare, California, USA
| | - Betsy M Karle
- Cooperative Extension, Division of Agriculture and Natural Resources, University of California, Orland, California, USA
| | - Fabio S Lima
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, California, USA
| | - Bart C Weimer
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, California, USA
- Department of Population Health and Reproduction, 100K Pathogen Genome Project, School of Veterinary Medicine, University of California, Davis, California, USA
| | - Richard V Pereira
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, California, USA
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16
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Sahni RD, V A, Suji T, V AS, Jayanth ST. Complete genome sequence of Yokenella regensburgei isolated from a patient with urinary tract infection in India. Microbiol Resour Announc 2024; 13:e0116223. [PMID: 38682779 DOI: 10.1128/mra.01162-23] [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: 12/04/2023] [Accepted: 04/14/2024] [Indexed: 05/01/2024] Open
Abstract
Yokenella regensburgei, an environmental organism, is an emerging pathogen in patients chiefly with immune suppression. We report the draft genome of Y. regensburgei, strain UU2206353, isolated from the urinary tract of an immunocompetent individual. The assembled genome consisted of 4,669,536 bp distributed over 20 contigs with 4,283 protein-coding genes.
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Affiliation(s)
- Rani Diana Sahni
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Aravind V
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Thangamani Suji
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Annie Sheeba V
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
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17
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Madden DE, Baird T, Bell SC, McCarthy KL, Price EP, Sarovich DS. Keeping up with the pathogens: improved antimicrobial resistance detection and prediction from Pseudomonas aeruginosa genomes. Genome Med 2024; 16:78. [PMID: 38849863 PMCID: PMC11157771 DOI: 10.1186/s13073-024-01346-z] [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: 10/29/2023] [Accepted: 05/20/2024] [Indexed: 06/09/2024] Open
Abstract
BACKGROUND Antimicrobial resistance (AMR) is an intensifying threat that requires urgent mitigation to avoid a post-antibiotic era. Pseudomonas aeruginosa represents one of the greatest AMR concerns due to increasing multi- and pan-drug resistance rates. Shotgun sequencing is gaining traction for in silico AMR profiling due to its unambiguity and transferability; however, accurate and comprehensive AMR prediction from P. aeruginosa genomes remains an unsolved problem. METHODS We first curated the most comprehensive database yet of known P. aeruginosa AMR variants. Next, we performed comparative genomics and microbial genome-wide association study analysis across a Global isolate Dataset (n = 1877) with paired antimicrobial phenotype and genomic data to identify novel AMR variants. Finally, the performance of our P. aeruginosa AMR database, implemented in our AMR detection and prediction tool, ARDaP, was compared with three previously published in silico AMR gene detection or phenotype prediction tools-abritAMR, AMRFinderPlus, ResFinder-across both the Global Dataset and an analysis-naïve Validation Dataset (n = 102). RESULTS Our AMR database comprises 3639 mobile AMR genes and 728 chromosomal variants, including 75 previously unreported chromosomal AMR variants, 10 variants associated with unusual antimicrobial susceptibility, and 281 chromosomal variants that we show are unlikely to confer AMR. Our pipeline achieved a genotype-phenotype balanced accuracy (bACC) of 85% and 81% across 10 clinically relevant antibiotics when tested against the Global and Validation Datasets, respectively, vs. just 56% and 54% with abritAMR, 58% and 54% with AMRFinderPlus, and 60% and 53% with ResFinder. ARDaP's superior performance was predominantly due to the inclusion of chromosomal AMR variants, which are generally not identified with most AMR identification tools. CONCLUSIONS Our ARDaP software and associated AMR variant database provides an accurate tool for predicting AMR phenotypes in P. aeruginosa, far surpassing the performance of current tools. Implementation of ARDaP for routine AMR prediction from P. aeruginosa genomes and metagenomes will improve AMR identification, addressing a critical facet in combatting this treatment-refractory pathogen. However, knowledge gaps remain in our understanding of the P. aeruginosa resistome, particularly the basis of colistin AMR.
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Affiliation(s)
- Danielle E Madden
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, QLD, Australia
- Sunshine Coast Health Institute, Birtinya, Queensland, Australia
| | - Timothy Baird
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, QLD, Australia
- Sunshine Coast Health Institute, Birtinya, Queensland, Australia
- Respiratory Department, Sunshine Coast University Hospital, Birtinya, Queensland, Australia
| | - Scott C Bell
- Adult Cystic Fibrosis Centre, The Prince Charles Hospital, Chermside, Queensland, Australia
- Children's Health Research Centre, Faculty of Medicine, The University of Queensland, South Brisbane, Queensland, Australia
| | - Kate L McCarthy
- University of Queensland Medical School, Herston, QLD, Australia
- Royal Brisbane and Women's Hospital, Herston, Queensland, Australia
| | - Erin P Price
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, QLD, Australia
- Sunshine Coast Health Institute, Birtinya, Queensland, Australia
| | - Derek S Sarovich
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, QLD, Australia.
- Sunshine Coast Health Institute, Birtinya, Queensland, Australia.
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18
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Soto KD, Alcalde-Rico M, Ugalde JA, Olivares-Pacheco J, Quiroz V, Brito B, Rivas LM, Munita JM, García PC, Wozniak A. Ceftazidime/avibactam resistance is associated with PER-3-producing ST309 lineage in Chilean clinical isolates of non-carbapenemase producing Pseudomonas aeruginosa. Front Cell Infect Microbiol 2024; 14:1410834. [PMID: 38903939 PMCID: PMC11188487 DOI: 10.3389/fcimb.2024.1410834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 05/13/2024] [Indexed: 06/22/2024] Open
Abstract
Introduction Ceftazidime/avibactam (CZA) is indicated against multidrug-resistant Pseudomonas aeruginosa, particularly those that are carbapenem resistant. CZA resistance in P. aeruginosa producing PER, a class A extended-spectrum β-lactamase, has been well documented in vitro. However, data regarding clinical isolates are scarce. Our aim was to analyze the contribution of PER to CZA resistance in non-carbapenemase-producing P. aeruginosa clinical isolates that were ceftazidime and/or carbapenem non-susceptible. Methods Antimicrobial susceptibility was determined through agar dilution and broth microdilution, while bla PER gene was screened through PCR. All PER-positive isolates and five PER-negative isolates were analyzed through Whole Genome Sequencing. The mutational resistome associated to CZA resistance was determined through sequence analysis of genes coding for PBPs 1b, 3 and 4, MexAB-OprM regulators MexZ, MexR, NalC and NalD, AmpC regulators AmpD and AmpR, and OprD porin. Loss of bla PER-3 gene was induced in a PER-positive isolate by successive passages at 43°C without antibiotics. Results Twenty-six of 287 isolates studied (9.1%) were CZA-resistant. Thirteen of 26 CZA-resistant isolates (50%) carried bla PER. One isolate carried bla PER but was CZA-susceptible. PER-producing isolates had significantly higher MICs for CZA, amikacin, gentamicin, ceftazidime, meropenem and ciprofloxacin than non-PER-producing isolates. All PER-producing isolates were ST309 and their bla PER-3 gene was associated to ISCR1, an insertion sequence known to mobilize adjacent DNA. PER-negative isolates were classified as ST41, ST235 (two isolates), ST395 and ST253. PER-negative isolates carried genes for narrow-spectrum β-lactamases and the mutational resistome showed that all isolates had one major alteration in at least one of the genes analyzed. Loss of bla PER-3 gene restored susceptibility to CZA, ceftolozane/tazobactam and other β-lactamsin the in vitro evolved isolate. Discussion PER-3-producing ST309 P. aeruginosa is a successful multidrug-resistant clone with blaPER-3 gene implicated in resistance to CZA and other β-lactams.
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Affiliation(s)
- Katherine D. Soto
- Laboratory of Microbiology, Department of Clinical Laboratories; Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Manuel Alcalde-Rico
- Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina, Universidad del Desarrollo. Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago, Chile
- Grupo de Resistencia Antimicrobiana en Bacterias Patógenas y Ambientales (GRABPA), Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen Macarena, Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Sevilla, Sevilla, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Juan A. Ugalde
- Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina, Universidad del Desarrollo. Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago, Chile
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Jorge Olivares-Pacheco
- Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina, Universidad del Desarrollo. Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago, Chile
- Grupo de Resistencia Antimicrobiana en Bacterias Patógenas y Ambientales (GRABPA), Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Valeria Quiroz
- Laboratory of Microbiology, Department of Clinical Laboratories; Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
- Genomics and Resistant Microbes Group (GeRM), Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
| | - Bárbara Brito
- Australian Institute for Microbiology and Infection, Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia
| | - Lina M. Rivas
- Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina, Universidad del Desarrollo. Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago, Chile
- Genomics and Resistant Microbes Group (GeRM), Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
| | - José M. Munita
- Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina, Universidad del Desarrollo. Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago, Chile
- Genomics and Resistant Microbes Group (GeRM), Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
| | - Patricia C. García
- Laboratory of Microbiology, Department of Clinical Laboratories; Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
- Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina, Universidad del Desarrollo. Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago, Chile
- Clinical Laboratories Network, Red de Salud UC-CHRISTUS, Santiago, Chile
| | - Aniela Wozniak
- Laboratory of Microbiology, Department of Clinical Laboratories; Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
- Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina, Universidad del Desarrollo. Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago, Chile
- Clinical Laboratories Network, Red de Salud UC-CHRISTUS, Santiago, Chile
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Barta L, Prieto BD, Stöger A, Polzer D, Schmoll F, Sattler T, Ruppitsch W. Complete genome of a multiresistant Pasteurella multocida isolated from a diseased Austrian bovine calf. Microbiol Resour Announc 2024:e0021224. [PMID: 38832799 DOI: 10.1128/mra.00212-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 05/09/2024] [Indexed: 06/05/2024] Open
Abstract
Pasteurella multocida (P. multocida) plays an important role in bovine respiratory diseases. Here we describe the complete genome of a multiresistant P. multocida. The strain was isolated from the lung of a diseased, 4-month old, male Fleckvieh calf with a clinical history of bronchopneumonia in Upper Austria.
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Affiliation(s)
- Leonard Barta
- Institute for Veterinary Investigations Mödling, Austrian Agency for Health and Food Safety, Mödling, Austria
| | - Beatriz Daza Prieto
- Institute of Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety, Vienna, Austria
| | - Anna Stöger
- Institute of Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety, Vienna, Austria
| | - Daniel Polzer
- Institute for Veterinary Investigations Mödling, Austrian Agency for Health and Food Safety, Mödling, Austria
| | - Friedrich Schmoll
- Institute for Veterinary Investigations Mödling, Austrian Agency for Health and Food Safety, Mödling, Austria
| | - Tatjana Sattler
- Institute for Veterinary Investigations Mödling, Austrian Agency for Health and Food Safety, Mödling, Austria
- University of Leipzig, Clinic for Ruminants and Swine, Leipzig, Germany
| | - Werner Ruppitsch
- Institute of Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety, Vienna, Austria
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
- Faculty of Food Technology, Food Safety and Ecology, University of Donja Gorica, Podgorica, Montenegro
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20
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Parzygnat JL, Crespo R, Koci MD, Dunn RR, Harden L, Fosnaught M, Thakur S. Widespread prevalence of plasmid-mediated blaCTX-M type extended-spectrum beta-lactamase Escherichia coli in backyard broiler production systems in the United States. PLoS One 2024; 19:e0304599. [PMID: 38829840 PMCID: PMC11146730 DOI: 10.1371/journal.pone.0304599] [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: 01/18/2024] [Accepted: 05/14/2024] [Indexed: 06/05/2024] Open
Abstract
Extended-spectrum beta-lactamase (ESBL) Escherichia coli (E. coli) is an emerging pathogen of high concern given its resistance to extended-spectrum cephalosporins. Broiler chicken, which is the number one consumed meat in the United States and worldwide, can be a reservoir of ESBL E. coli. Backyard poultry ownership is on the rise in the United States, yet there is little research investigating prevalence of ESBL E. coli in this setting. This study aims to identify the prevalence and antimicrobial resistance profiles (phenotypically and genotypically) of ESBL E. coli in some backyard and commercial broiler farms in the U.S. For this study ten backyard and ten commercial farms were visited at three time-points across flock production. Fecal (n = 10), litter/compost (n = 5), soil (n = 5), and swabs of feeders and waterers (n = 6) were collected at each visit and processed for E. coli. Assessment of ESBL phenotype was determined through using disk diffusion with 3rd generation cephalosporins, cefotaxime and ceftazidime, and that with clavulanic acid. Broth microdilution and whole genome sequencing were used to investigate both phenotypic and genotypic resistance profiles, respectively. ESBL E. coli was more prevalent in backyard farms with 12.95% of samples testing positive whereas 0.77% of commercial farm samples were positive. All isolates contained a blaCTX-M gene, the dominant variant being blaCTX-M-1, and its presence was entirely due to plasmids. Our study confirms concerns of growing resistance to fourth generation cephalosporin, cefepime, as roughly half (51.4%) of all isolates were found to be susceptible dose-dependent and few were resistant. Resistance to non-beta lactams, gentamicin and ciprofloxacin, was also detected in our samples. Our study identifies prevalence of blaCTX-M type ESBL E. coli in U.S. backyard broiler farms, emphasizing the need for interventions for food and production safety.
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Affiliation(s)
- Jessica L. Parzygnat
- Department of Population Health and Pathobiology, North Carolina State University College of Veterinary Medicine, Raleigh, NC, United States of America
| | - Rocio Crespo
- Department of Population Health and Pathobiology, North Carolina State University College of Veterinary Medicine, Raleigh, NC, United States of America
| | - Matthew D. Koci
- Prestage Department of Poultry Science, North Carolina State University, Raleigh, NC, United States of America
| | - Robert R. Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, United States of America
| | - Lyndy Harden
- Department of Population Health and Pathobiology, North Carolina State University College of Veterinary Medicine, Raleigh, NC, United States of America
| | - Mary Fosnaught
- Prestage Department of Poultry Science, North Carolina State University, Raleigh, NC, United States of America
| | - Siddhartha Thakur
- Department of Population Health and Pathobiology, North Carolina State University College of Veterinary Medicine, Raleigh, NC, United States of America
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21
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Hinić V, Seth-Smith HMB, Stammler S, Egli A. Rapid detection of plasmid-mediated AmpC-producers by eazyplex® SuperBug AmpC assay compared to whole-genome sequencing. J Microbiol Methods 2024; 221:106938. [PMID: 38642781 DOI: 10.1016/j.mimet.2024.106938] [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: 08/28/2023] [Revised: 01/11/2024] [Accepted: 04/18/2024] [Indexed: 04/22/2024]
Abstract
Current methods for plasmid-mediated AmpC β-lactamase (pAmpC) detection in routine microbiological laboratories are based on various phenotypic tests. Eazyplex®SuperBug AmpC assay is a molecular assay based on isothermal amplification for rapid detection of the most common pAmpC types from bacterial culture: CMY-2 group, DHA, ACC and MOX. Our aim was to evaluate the diagnostic performance of this assay. The assay was evaluated on 64 clinical isolates of Enterobacterales without chromosomal inducible AmpC, and with phenotypically confirmed AmpC production. The results were confirmed, and isolates further characterized by whole-genome sequencing (WGS). eazyplex®SuperBug AmpC assay correctly detected the two most common pAmpC types CMY-2 group (16/16) and DHA (19/19). Detection of ACC and MOX could not be evaluated on our set of isolates since there was only one isolate harbouring ACC and none with MOX. pAmpC encoding genes could be detected in only eight of 36 investigated Escherichia coli isolates. The remaining 28 E. coli isolates harboured previously described mutations in the blaEC promoter, leading to the overexpression of chromosomally encoded E. coli specific AmpC β-lactamase. All results were 100% concordant with the results of WGS. eazyplex®SuperBug AmpC assay enabled rapid and reliable detection of pAmpC-encoding genes in Enterobacterales like Klebsiella spp. and Proteus spp. and the distinction between plasmid-mediated and chromosomally encoded AmpC in E. coli.
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Affiliation(s)
- Vladimira Hinić
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland; Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.
| | - Helena M B Seth-Smith
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland; Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland; Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Sabrina Stammler
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
| | - Adrian Egli
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland; Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland; Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
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22
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Pustam A, Jayaraman J, Ramsubhag A. Whole genome sequencing reveals complex resistome features of Klebsiella pneumoniae isolated from patients at major hospitals in Trinidad, West Indies. J Glob Antimicrob Resist 2024; 37:141-149. [PMID: 38608934 DOI: 10.1016/j.jgar.2024.03.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 02/17/2024] [Accepted: 03/26/2024] [Indexed: 04/14/2024] Open
Abstract
OBJECTIVES Antibiotic-resistant Klebsiella pneumoniae is a human pathogen of major global concern due to its ability to cause multiple severe diseases that are often difficult to treat therapeutically. This study aimed to investigate the resistome of local clinical K. pneumoniae isolates. METHODS Herein, we used a whole genome sequencing approach and bioinformatics tools to reconstruct the resistome of 10 clinical K. pneumoniae isolates and one clinical isolate of the closely related Klebsiella quasipneumoniae obtained from patients from three major hospitals in Trinidad, West Indies. RESULTS The results of the study revealed the presence of a complex antibiotic-resistant armoury among the local isolates with multiple resistance mechanisms involving (i) inactivation of antibiotics, (ii) efflux pumps, (iii) antibiotic target alteration, protection, and replacement against antibiotics, and (iv) altered porin protein that reduced the permeability to antibiotics. Several resistance genes such as blaCTX-M-15, blaTEM-1B, blaSHV-28, blaKPC-2, oqxA, sul1, tetD, aac(6')-Ib-cr5, aph(6)-Id, and fosA6, which are known to confer resistance to antibiotics used to treat K. pneumoniae infections. In most cases, the resistance genes were flanked by mobile elements, including insertion sequences and transposons, which facilitate the spread of these genetic features among related organisms. CONCLUSION This is the first comprehensive study to thoroughly investigate the resistome of clinical K. pneumoniae isolates and K. quasipneumoniae from Trinidad, West Indies. These findings suggest that monitoring K. pneumoniae and its genome-wide antibiotic resistance features in clinical strains would be of critical importance for guiding antibiotic stewardship programs and improving regional disease management systems for this pathogen.
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Affiliation(s)
- Aarti Pustam
- Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Jayaraj Jayaraman
- Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Adesh Ramsubhag
- Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies, St. Augustine, Trinidad and Tobago.
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23
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Díaz-Torres O, Los Cobos EOVD, Kreft JU, Loge FJ, Díaz-Vázquez D, Mahlknecht J, Gradilla-Hernández MS, Senés-Guerrero C. A metagenomic study of antibiotic resistance genes in a hypereutrophic subtropical lake contaminated by anthropogenic sources. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 927:172216. [PMID: 38583614 DOI: 10.1016/j.scitotenv.2024.172216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 03/18/2024] [Accepted: 04/02/2024] [Indexed: 04/09/2024]
Abstract
Antibiotic resistance genes (ARGs) are a major threat to human and environmental health. This study investigated the occurrence and distribution of ARGs in Lake Cajititlán, a hypereutrophic subtropical lake in Mexico contaminated by anthropogenic sources (urban wastewater and runoff from crop and livestock production). ARGs (a total of 475 genes) were detected in 22 bacterial genera, with Pseudomonas (144 genes), Stenotrophomonas (88 genes), Mycobacterium (54 genes), and Rhodococcus (27 genes) displaying the highest frequencies of ARGs. Among these, Pseudomonas aeruginosa and Stenotrophomonas maltophilia showed the highest number of ARGs. The results revealed a diverse array of ARGs, including resistance to macrolides (11.55 %), aminoglycosides (8.22 %), glycopeptides (6.22 %), tetracyclines (4 %), sulfonamides (4 %), carbapenems (1.11 %), phenicols (0.88 %), fluoroquinolones (0.44 %), and lincosamides (0.22 %). The most frequently observed ARGs were associated with multidrug resistance (63.33 %), with MexF (42 genes), MexW (36 genes), smeD (31 genes), mtrA (25 genes), and KHM-1 (22 genes) being the most common. Lake Cajititlán is a recreational area for swimming, fishing, and boating, while also supporting irrigation for agriculture and potentially acting as a drinking water source for some communities. This raises concerns about the potential for exposure to antibiotic-resistant bacteria through these activities. The presence of ARGs in Lake Cajititlán poses a significant threat to both human and environmental health. Developing strategies to mitigate the risks of antibiotic resistance, including improving wastewater treatment, and promoting strategic antibiotic use and disposal, is crucial. This study represents a significant advancement in the understanding of antibiotic resistance dynamics in a hypereutrophic subtropical lake in a developing country, providing valuable insights for the scientific community and policymakers.
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Affiliation(s)
- Osiris Díaz-Torres
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Laboratorio de Sostenibilidad y Cambio Climático, Av. General Ramon Corona 2514, Nuevo México, Zapopan, CP, 45138 Jalisco, México.
| | - Eric Oswaldo Valencia-de Los Cobos
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Laboratorio de Sostenibilidad y Cambio Climático, Av. General Ramon Corona 2514, Nuevo México, Zapopan, CP, 45138 Jalisco, México
| | - Jan-Ulrich Kreft
- Institute of Microbiology and Infection & School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Frank J Loge
- Department of Civil and Environmental Engineering, University of California Davis, One Shields Avenue, Davis, CA 95616, USA; Tecnologico de Monterrey, Escuela de Ingeniería y Ciencias, Ave. Eugenio Sada 2501 Sur, Monterrey, N.L. 64849, Mexico
| | - Diego Díaz-Vázquez
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Laboratorio de Sostenibilidad y Cambio Climático, Av. General Ramon Corona 2514, Nuevo México, Zapopan, CP, 45138 Jalisco, México
| | - Jürgen Mahlknecht
- Tecnologico de Monterrey, Escuela de Ingeniería y Ciencias, Ave. Eugenio Sada 2501 Sur, Monterrey, N.L. 64849, Mexico
| | - Misael Sebastián Gradilla-Hernández
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Laboratorio de Sostenibilidad y Cambio Climático, Av. General Ramon Corona 2514, Nuevo México, Zapopan, CP, 45138 Jalisco, México.
| | - Carolina Senés-Guerrero
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Laboratorio de Sostenibilidad y Cambio Climático, Av. General Ramon Corona 2514, Nuevo México, Zapopan, CP, 45138 Jalisco, México.
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24
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Choudhary BK, Choudhary M, Barbuddhe SB, Shanker A. Partial genomic characterization of Chromobacterium piscinae from India reveals multi drug resistance. Braz J Microbiol 2024; 55:1557-1567. [PMID: 38374322 PMCID: PMC11153472 DOI: 10.1007/s42770-024-01288-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 02/10/2024] [Indexed: 02/21/2024] Open
Abstract
Species of genus Chromobacterium have been isolated from diverse geographical settings, which exhibits significant metabolic flexibility as well as biotechnological and pathogenic properties. This study describes the isolation, characterization, draft assembly, and detailed sequence analysis of Chromobacterium piscinae strain W1B-CG-NIBSM isolated from water samples from multi use community pond. The organism was characterized by biochemical tests, Matrix Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry (MALDI TOF-MS) and partial genome sequencing. The partial genomic data of Chromobacterium pisciane isolate W1B NIBSM strain was submitted to GenBank with Bio project number PRJNA803347 and accession no CP092474. An integrated genome analysis of Chromobacterium piscinae has been accomplished with PATRIC which indicates good quality genome. DNA sequencing using the illumina HiSeq 4000 system generated total length of 4,155,481 bp with 63 contig with G + C content is 62.69%. This partial genome contains 4,126 protein-coding sequences (CDS), 27 repeats region and 78 transfer RNA (tRNA) genes as well as 3 ribosomal RNA (rRNA) genes. The genomic annotation of Chromobacterium W1B depicts 2,925 proteins with functional assignments and 1201 hypothetical proteins. A repertoire of specialty genes implicated in antibiotic resistance (45 genes), drug target (6 genes), Transporter (3 genes) and virulence factor (10 genes). The genomic analysis reveals the adaptability, displays metabolic varied pathways and shows specific structural complex and various virulence factors which makes this strain multi drug resistant. The isolate was found to be highly resistant to β-lactam antibiotics whereas it showed sensitivity towards aminoglycosides and fluoroquinolone antibiotics. Hence, the recovery of Chromobacterium piscinae from community pond evidenced for uncertain hidden source of public health hazard. To the best of authors knowledge this is first report of isolation and genomic description of C. piscinae from India.
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Affiliation(s)
- Binod Kumar Choudhary
- Indian Council of Agricultural Research-National Institute of Biotic Stress Management, Baronda, Raipur, 493 225, Chhattisgarh, India.
| | - Mamta Choudhary
- Indian Council of Agricultural Research-National Institute of Biotic Stress Management, Baronda, Raipur, 493 225, Chhattisgarh, India
| | | | - Asheesh Shanker
- Department of Bioinformatics, Central University of South Bihar, Gaya, Bihar, 824236, India
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25
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Pham DN, Li M. Comparative resistomics analysis of multidrug-resistant Chryseobacteria. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13288. [PMID: 38923192 PMCID: PMC11194056 DOI: 10.1111/1758-2229.13288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Accepted: 05/03/2024] [Indexed: 06/28/2024]
Abstract
Chryseobacteria consists of important human pathogens that can cause a myriad of nosocomial infections. We isolated four multidrug-resistant Chryseobacterium bacteria from activated sludge collected at domestic wastewater treatment facilities in the New York Metropolitan area. Their genomes were sequenced with Nanopore technology and used for a comprehensive resistomics comparison with 211 Chryseobacterium genomes available in the public databases. A majority of Chryseobacteria harbor 3 or more antibiotic resistance genes (ARGs) with the potential to confer resistance to at least two types of commonly prescribed antimicrobials. The most abundant ARGs, including β-lactam class A (blaCGA-1 and blaCIA) and class B (blaCGB-1 and blaIND) and aminoglycoside (ranA and ranB), are considered potentially intrinsic in Chryseobacteria. Notably, we reported a new resistance cluster consisting of a chloramphenicol acetyltransferase gene catB11, a tetracycline resistance gene tetX, and two mobile genetic elements (MGEs), IS91 family transposase and XerD recombinase. Both catB11 and tetX are statistically enriched in clinical isolates as compared to those with environmental origins. In addition, two other ARGs encoding aminoglycoside adenylyltransferase (aadS) and the small multidrug resistance pump (abeS), respectively, are found co-located with MGEs encoding recombinases (e.g., RecA and XerD) or transposases, suggesting their high transmissibility among Chryseobacteria and across the Bacteroidota phylum, particularly those with high pathogenicity. High resistance to different classes of β-lactam, as well as other commonly used antimicrobials (i.e., kanamycin, gentamicin, and chloramphenicol), was confirmed and assessed using our isolates to determine their minimum inhibitory concentrations. Collectively, though the majority of ARGs in Chryseobacteria are intrinsic, the discovery of a new resistance cluster and the co-existence of several ARGs and MGEs corroborate interspecies and intergenera transfer, which may accelerate their dissemination in clinical environments and complicate efforts to combat bacterial infections.
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Affiliation(s)
- Dung Ngoc Pham
- Department of Chemistry and Environmental ScienceNew Jersey Institute of TechnologyNewarkNew JerseyUSA
| | - Mengyan Li
- Department of Chemistry and Environmental ScienceNew Jersey Institute of TechnologyNewarkNew JerseyUSA
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Axell-House DB, Ashley PA, Egge SL, Tran TT, Pedroza C, Zhang M, Dinh AQ, Simar SR, Sahasrabhojane PV, Miller WR, Shelburne SA, Hanson BM, Arias CA. Clinical Features and Genomic Epidemiology of Bloodstream Infections due to Enterococcal Species Other Than Enterococcus faecalis or E. faecium in Patients With Cancer. Open Forum Infect Dis 2024; 11:ofae288. [PMID: 38835498 PMCID: PMC11148474 DOI: 10.1093/ofid/ofae288] [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: 02/02/2024] [Accepted: 05/15/2024] [Indexed: 06/06/2024] Open
Abstract
Background Non-Enterococcus faecium, non-E. faecalis (NFF) enterococci are a heterogeneous group of clinically pathogenic enterococci that include species with intrinsic low-level vancomycin resistance. Patients with cancer are at increased risk for bacteremia with NFF enterococci, but their clinical and molecular epidemiology have not been extensively described. Methods We conducted a retrospective review of all patients (n = 70) with NFF bacteremia from 2016 to 2022 at a major cancer center. The main outcomes assessed were 30-day mortality, microbiological failure (positive blood cultures for ≥4 days), and recurrence of bacteremia (positive blood culture <14 days after clearance). Whole-genome sequencing was performed on all available NFF (n = 65). Results Patients with hematological malignancies made up 56% of the cohort (77% had leukemia). The majority of solid malignancies (87%) were gastrointestinal in origin. The majority of infections (83%) originated from an intra-abdominal source. The most common NFF species were E. gallinarum (50%) and E. casseliflavus (30%). Most (61%) patients received combination therapy. Bacteremia recurred in 4.3% of patients, there was a 30-day mortality of 23%, and 4.3% had microbiological failure. E. gallinarum and E. casseliflavus isolates were genetically diverse with no spatiotemporal clustering to suggest a single strain. Frequencies of ampicillin resistance (4.3%) and daptomycin resistance (1.9%) were low. Patients with hematologic malignancy had infections with NFF enterococci that harbored more resistance genes than patients with solid malignancy (P = .005). Conclusions NFF bacteremia is caused by a heterogeneous population of isolates and is associated with significant mortality. Hematological malignancy is an important risk factor for infection with NFF resistant to multiple antibiotics.
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Affiliation(s)
- Dierdre B Axell-House
- Division of Infectious Diseases, Department of Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Center for Infectious Diseases, Houston Methodist Research Institute, Houston, Texas, USA
- Department of Medicine, Weill Cornell Medical College, New York City, New York, USA
| | - Patrycja A Ashley
- Division of Infectious Diseases, Department of Medicine, Houston Methodist Hospital, Houston, Texas, USA
| | - Stephanie L Egge
- Division of Infectious Diseases, Department of Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Center for Infectious Diseases, Houston Methodist Research Institute, Houston, Texas, USA
| | - Truc T Tran
- Center for Infectious Diseases, Houston Methodist Research Institute, Houston, Texas, USA
| | - Claudia Pedroza
- Center for Clinical Research and Evidence-Based Medicine, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Meng Zhang
- Center for Clinical Research and Evidence-Based Medicine, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - An Q Dinh
- Center for Infectious Diseases, Houston Methodist Research Institute, Houston, Texas, USA
- Center for Infectious Diseases, School of Public Health, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Shelby R Simar
- Center for Infectious Diseases, School of Public Health, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Pranoti V Sahasrabhojane
- Department of Infectious Diseases, Infection Control, and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - William R Miller
- Division of Infectious Diseases, Department of Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Center for Infectious Diseases, Houston Methodist Research Institute, Houston, Texas, USA
- Department of Medicine, Weill Cornell Medical College, New York City, New York, USA
| | - Samuel A Shelburne
- Department of Infectious Diseases, Infection Control, and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Blake M Hanson
- Center for Infectious Diseases, School of Public Health, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Cesar A Arias
- Division of Infectious Diseases, Department of Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Center for Infectious Diseases, Houston Methodist Research Institute, Houston, Texas, USA
- Department of Medicine, Weill Cornell Medical College, New York City, New York, USA
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Bedane TD, Megersa B, Abunna F, Waktole H, Woldemariyam FT, Tekle M, Shimelis E, Gutema FD. Occurrence, molecular characterization, and antimicrobial susceptibility of sorbitol non-fermenting Escherichia coli in lake water, fish and humans in central Oromia, Ethiopia. Sci Rep 2024; 14:12461. [PMID: 38816376 PMCID: PMC11139919 DOI: 10.1038/s41598-024-61810-z] [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: 10/31/2023] [Accepted: 05/09/2024] [Indexed: 06/01/2024] Open
Abstract
Contaminated lake water and fish can be sources of bacterial pathogens of public health concern, including pathogenic E. coli. Within Ethiopia, specifically, Central Oromia, raw fish consumption is a common practice. Although there are few reports on occurrence of E. coli O157 in fish destined for human consumption and children under five years, information on the transmission pathways of E. coli O157 and other sorbitol non-fermenting (SN-F) E. coli from water-to-fish-to-human, and their virulence factors and antimicrobial resistant determinants along the fish supply chain is lacking. The study aimed to investigate the occurrence, molecular characteristics, and antimicrobial susceptibility of E. coli O157 and other SN-F E. coli strains in fish, lake water and humans in central Oromia, Ethiopia. A total of 750 samples (450 fish samples, 150 water samples, 150 human stool samples) were collected from five lakes and three health facilities. The samples were processed following the standard protocol recommended by European Food Safety Authority and Kirby-Bauer disc diffusion method for detection of the bacteria, and antimicrobial susceptibility tests, respectively. Molecular characterization of presumptive isolates was performed using Whole-Genome Sequencing (WGS) for serotyping, determination of virulence factors, antimicrobial resistance traits, and genetic linkage of the isolates. Overall, 3.9% (29/750) of the samples had SN-F E. coli; of which 6.7% (n = 10), 1.8% (n = 8) and 7.3% (n = 11) were retrieved from water, fish, and diarrheic human patients, respectively. The WGS confirmed that all the isolates were SN-F non-O157: H7 E. coli strains. We reported two new E. coli strains with unknown O-antigen from fish and human samples. All the strains have multiple virulence factors and one or more genes encoding for them. Genetic relatedness was observed among strains from the same sources (water, fish, and humans). Most isolates were resistant to ampicillin (100%), tetracycline (100%), cefotaxime (100%), ceftazidime (100%), meropenem (100%), nalidixic acid (93.1%) and sulfamethoxazole/trimethoprim (79.3%). Majority of the strains were resistant to chloramphenicol (58.6%) and ciprofloxacin (48.3%), while small fraction showed resistance to azithromycin (3.45%). Isolates had an overall MDR profile of 87.5%. Majority, (62.1%; n = 18) of the strains had acquired MDR traits. Genes encoding for mutational resistance and Extended-spectrum beta-lactamases (ESBL) were also detected. In conclusion, our study revealed the occurrence of virulent and MDR SN-F E. coli strains in water, fish, and humans. Although no genetic relatedness was observed among strains from various sources, the genomic clustering among strains from the same sources strongly suggests the potential risk of transmission along the supply chain at the human-fish-environment interface if strict hygienic fish production is not in place. Further robust genetic study of the new strains with unknown O-antigens, and the epidemiology of SN-F E. coli is required to elucidate the molecular profile and public health implications of the pathogens.
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Affiliation(s)
- Tesfaye D Bedane
- Department of Microbiology, Immunology and Veterinary Public Health, Addis Ababa University, P.O. Box 34, Bishoftu, Oromia, Ethiopia.
- Department of Veterinary Science, Salale University, P.O. Box 245, Fiche, Oromia, Ethiopia.
| | - Bekele Megersa
- Department of Microbiology, Immunology and Veterinary Public Health, Addis Ababa University, P.O. Box 34, Bishoftu, Oromia, Ethiopia
| | - Fufa Abunna
- Department of Microbiology, Immunology and Veterinary Public Health, Addis Ababa University, P.O. Box 34, Bishoftu, Oromia, Ethiopia
| | - Hika Waktole
- Department of Microbiology, Immunology and Veterinary Public Health, Addis Ababa University, P.O. Box 34, Bishoftu, Oromia, Ethiopia
| | | | - Muluken Tekle
- Department of Microbiology, Immunology and Veterinary Public Health, Addis Ababa University, P.O. Box 34, Bishoftu, Oromia, Ethiopia
| | - Ephrem Shimelis
- Department of Microbiology, Immunology and Veterinary Public Health, Addis Ababa University, P.O. Box 34, Bishoftu, Oromia, Ethiopia
| | - Fanta D Gutema
- Department of Microbiology, Immunology and Veterinary Public Health, Addis Ababa University, P.O. Box 34, Bishoftu, Oromia, Ethiopia
- Department of Occupational and Environmental Health, University of Iowa, Iowa City, IA, 52246, USA
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28
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Manoil D, Parga A, Bostanci N, Belibasakis GN. Microbial diagnostics in periodontal diseases. Periodontol 2000 2024. [PMID: 38797888 DOI: 10.1111/prd.12571] [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: 02/06/2024] [Revised: 03/27/2024] [Accepted: 04/15/2024] [Indexed: 05/29/2024]
Abstract
Microbial analytical methods have been instrumental in elucidating the complex microbial etiology of periodontal diseases, by shaping our understanding of subgingival community dynamics. Certain pathobionts can orchestrate the establishment of dysbiotic communities that can subvert the host immune system, triggering inflammation and tissue destruction. Yet, diagnosis and management of periodontal conditions still rely on clinical and radiographic examinations, overlooking the well-established microbial etiology. This review summarizes the chronological emergence of periodontal etiological models and the co-evolution with technological advances in microbial detection. We additionally review the microbial analytical approaches currently accessible to clinicians, highlighting their value in broadening the periodontal assessment. The epidemiological importance of obtaining culture-based antimicrobial susceptibility profiles of periodontal taxa for antibiotic resistance surveillance is also underscored, together with clinically relevant analytical approaches to guide antibiotherapy choices, when necessary. Furthermore, the importance of 16S-based community and shotgun metagenomic profiling is discussed in outlining dysbiotic microbial signatures. Because dysbiosis precedes periodontal damage, biomarker identification offers early diagnostic possibilities to forestall disease relapses during maintenance. Altogether, this review highlights the underutilized potential of clinical microbiology in periodontology, spotlighting the clinical areas most conductive to its diagnostic implementation for enhancing prevention, treatment predictability, and addressing global antibiotic resistance.
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Affiliation(s)
- Daniel Manoil
- Division of Cariology and Endodontics, University Clinics of Dental Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Division of Oral Health and Periodontology, Department of Dental Medicine, Karolinska Institutet, Huddinge, Stockholm, Sweden
| | - Ana Parga
- Division of Cariology and Endodontics, University Clinics of Dental Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Department of Microbiology and Parasitology, CIBUS-Faculty of Biology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Nagihan Bostanci
- Division of Oral Health and Periodontology, Department of Dental Medicine, Karolinska Institutet, Huddinge, Stockholm, Sweden
| | - Georgios N Belibasakis
- Division of Oral Health and Periodontology, Department of Dental Medicine, Karolinska Institutet, Huddinge, Stockholm, Sweden
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29
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Toorop MMA, Hoogendijk IV, Dogterom-Ballering HCM, Boers SA, Kraakman MEM, van Prehn J, Wessels E, Bekker V, Veldkamp KE. Implications of ad-hoc molecular typing for infection control measures in a multi-cluster, multi-phenotypic Serratia marcescens outbreak in a neonatal intensive care unit. J Hosp Infect 2024; 150:26-33. [PMID: 38782059 DOI: 10.1016/j.jhin.2024.05.004] [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: 03/05/2024] [Revised: 05/01/2024] [Accepted: 05/06/2024] [Indexed: 05/25/2024]
Abstract
BACKGROUND Serratia marcescens is known to cause outbreaks in neonatal intensive care units (NICUs). Traditionally epidemiological data, antimicrobial resistance patterns and epidemiological typing have been used to guide infection prevention methods. Whole-genome sequencing (WGS) applications such as core-genome multi-locus sequence typing (cgMLST) applied during an outbreak would potentially yield more information. AIM To use cgMLST to acquire detailed information on the source and spread of bacteria, enabling more efficient control measures during an S. marcescens outbreak at a NICU. METHODS Neonates admitted to the NICU of the Leiden University Medical Center (LUMC) during an outbreak between September 2023 and January 2024, with S. marcescens being cultured, were included. Environmental samples were taken to search for a common source, antibiotic susceptibility testing was performed, and antimicrobial resistance genes were analysed. FINDINGS S. marcescens strains from 17 of the 20 positive patients were available for molecular typing. The cgMLST scheme revealed five different complex types consisting of four separate clusters. Multiple clusters made an unidentified persistent environmental source as cause of the outbreak less likely, leading to a quick downscaling of infection prevention measures. Differences were shown in aminoglycoside resistance patterns of isolates within the same complex types and patients. CONCLUSION The use of ad-hoc cgMLST provided timely data for rational decision-making during an S. marcescens outbreak at the NICU. Antibiotic phenotyping alone was found not to be suitable for studying clonal spread during this outbreak with S. marcescens.
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Affiliation(s)
- M M A Toorop
- Leiden University Center for Infectious Diseases (LU-CID) Medical Microbiology and Infection Control, Leiden University Medical Center, Leiden, The Netherlands
| | - I V Hoogendijk
- Leiden University Center for Infectious Diseases (LU-CID) Medical Microbiology and Infection Control, Leiden University Medical Center, Leiden, The Netherlands
| | - H C M Dogterom-Ballering
- Leiden University Center for Infectious Diseases (LU-CID) Medical Microbiology and Infection Control, Leiden University Medical Center, Leiden, The Netherlands
| | - S A Boers
- Leiden University Center for Infectious Diseases (LU-CID) Medical Microbiology and Infection Control, Leiden University Medical Center, Leiden, The Netherlands
| | - M E M Kraakman
- Leiden University Center for Infectious Diseases (LU-CID) Medical Microbiology and Infection Control, Leiden University Medical Center, Leiden, The Netherlands
| | - J van Prehn
- Leiden University Center for Infectious Diseases (LU-CID) Medical Microbiology and Infection Control, Leiden University Medical Center, Leiden, The Netherlands
| | - E Wessels
- Leiden University Center for Infectious Diseases (LU-CID) Medical Microbiology and Infection Control, Leiden University Medical Center, Leiden, The Netherlands
| | - V Bekker
- Division of Neonatology, Department of Pediatrics, Willem Alexander Children's Hospital - Leiden University Medical Center, Leiden, The Netherlands
| | - K E Veldkamp
- Leiden University Center for Infectious Diseases (LU-CID) Medical Microbiology and Infection Control, Leiden University Medical Center, Leiden, The Netherlands.
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Franklin AM, Weller DL, Durso LM, Bagley M, Davis BC, Frye JG, Grim CJ, Ibekwe AM, Jahne MA, Keely SP, Kraft AL, McConn BR, Mitchell RM, Ottesen AR, Sharma M, Strain EA, Tadesse DA, Tate H, Wells JE, Williams CF, Cook KL, Kabera C, McDermott PF, Garland JL. A one health approach for monitoring antimicrobial resistance: developing a national freshwater pilot effort. FRONTIERS IN WATER 2024; 6:10.3389/frwa.2024.1359109. [PMID: 38855419 PMCID: PMC11157689 DOI: 10.3389/frwa.2024.1359109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Antimicrobial resistance (AMR) is a world-wide public health threat that is projected to lead to 10 million annual deaths globally by 2050. The AMR public health issue has led to the development of action plans to combat AMR, including improved antimicrobial stewardship, development of new antimicrobials, and advanced monitoring. The National Antimicrobial Resistance Monitoring System (NARMS) led by the United States (U.S) Food and Drug Administration along with the U.S. Centers for Disease Control and U.S. Department of Agriculture has monitored antimicrobial resistant bacteria in retail meats, humans, and food animals since the mid 1990's. NARMS is currently exploring an integrated One Health monitoring model recognizing that human, animal, plant, and environmental systems are linked to public health. Since 2020, the U.S. Environmental Protection Agency has led an interagency NARMS environmental working group (EWG) to implement a surface water AMR monitoring program (SWAM) at watershed and national scales. The NARMS EWG divided the development of the environmental monitoring effort into five areas: (i) defining objectives and questions, (ii) designing study/sampling design, (iii) selecting AMR indicators, (iv) establishing analytical methods, and (v) developing data management/analytics/metadata plans. For each of these areas, the consensus among the scientific community and literature was reviewed and carefully considered prior to the development of this environmental monitoring program. The data produced from the SWAM effort will help develop robust surface water monitoring programs with the goal of assessing public health risks associated with AMR pathogens in surface water (e.g., recreational water exposures), provide a comprehensive picture of how resistant strains are related spatially and temporally within a watershed, and help assess how anthropogenic drivers and intervention strategies impact the transmission of AMR within human, animal, and environmental systems.
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Affiliation(s)
- Alison M. Franklin
- United States (U.S.) Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, United States
| | - Daniel L. Weller
- U.S. Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Lisa M. Durso
- U.S. Department of Agriculture, Agricultural Research Service (USDA, ARS), Agroecosystem Management Research, Lincoln, NE, United States
| | - Mark Bagley
- United States (U.S.) Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, United States
| | - Benjamin C. Davis
- United States (U.S.) Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, United States
| | - Jonathan G. Frye
- USDA ARS, U.S. National Poultry Research Center, Poultry Microbiological Safety and Processing Research Unit, Athens, GA, United States
| | - Christopher J. Grim
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, United States
| | - Abasiofiok M. Ibekwe
- USDA, ARS, Agricultural Water Efficiency and Salinity Research Unit, Riverside, CA, United States
| | - Michael A. Jahne
- United States (U.S.) Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, United States
| | - Scott P. Keely
- United States (U.S.) Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, United States
| | - Autumn L. Kraft
- Oak Ridge Institute for Science and Education, USDA, ARS, Beltsville, MD, United States
| | - Betty R. McConn
- Oak Ridge Institute for Science and Education, USDA, ARS, Beltsville, MD, United States
| | - Richard M. Mitchell
- Environmental Protection Agency, Office of Water, Washington, DC, United States
| | - Andrea R. Ottesen
- Center for Veterinary Medicine, National Antimicrobial Resistance Monitoring System (NARMS), U.S. Food and Drug Administration, Laurel, MD, United States
| | - Manan Sharma
- USDA, ARS Environmental Microbial and Food Safety Laboratory, Beltsville, MD, United States
| | - Errol A. Strain
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, United States
| | - Daniel A. Tadesse
- Center for Veterinary Medicine, National Antimicrobial Resistance Monitoring System (NARMS), U.S. Food and Drug Administration, Laurel, MD, United States
| | - Heather Tate
- Center for Veterinary Medicine, National Antimicrobial Resistance Monitoring System (NARMS), U.S. Food and Drug Administration, Laurel, MD, United States
| | - Jim E. Wells
- USDA, ARS, U.S. Meat Animal Research Center, Meat Safety and Quality, Clay Center, NE, United States
| | - Clinton F. Williams
- USDA, ARS, US Arid-Land Agricultural Research Center, Maricopa, AZ, United States
| | - Kim L. Cook
- USDA, ARS Nutrition, Food Safety and Quality National Program Staff, Beltsville, MD, United States
| | - Claudine Kabera
- Center for Veterinary Medicine, National Antimicrobial Resistance Monitoring System (NARMS), U.S. Food and Drug Administration, Laurel, MD, United States
| | - Patrick F. McDermott
- Center for Veterinary Medicine, National Antimicrobial Resistance Monitoring System (NARMS), U.S. Food and Drug Administration, Laurel, MD, United States
| | - Jay L. Garland
- United States (U.S.) Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, United States
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Irby I, Broddrick JT. Microbial adaptation to spaceflight is correlated with bacteriophage-encoded functions. Nat Commun 2024; 15:3474. [PMID: 38750067 PMCID: PMC11096397 DOI: 10.1038/s41467-023-42104-w] [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: 02/25/2023] [Accepted: 09/27/2023] [Indexed: 05/18/2024] Open
Abstract
Evidence from the International Space Station suggests microbial populations are rapidly adapting to the spacecraft environment; however, the mechanism of this adaptation is not understood. Bacteriophages are prolific mediators of bacterial adaptation on Earth. Here we survey 245 genomes sequenced from bacterial strains isolated on the International Space Station for dormant (lysogenic) bacteriophages. Our analysis indicates phage-associated genes are significantly different between spaceflight strains and their terrestrial counterparts. In addition, we identify 283 complete prophages, those that could initiate bacterial lysis and infect additional hosts, of which 21% are novel. These prophage regions encode functions that correlate with increased persistence in extreme environments, such as spaceflight, to include antimicrobial resistance and virulence, DNA damage repair, and dormancy. Our results correlate microbial adaptation in spaceflight to bacteriophage-encoded functions that may impact human health in spaceflight.
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Affiliation(s)
- Iris Irby
- Space Biosciences Research Branch, NASA Ames Research Center, Moffett Field, CA, USA
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Jared T Broddrick
- Space Biosciences Research Branch, NASA Ames Research Center, Moffett Field, CA, USA.
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Pei Y, Shum MHH, Liao Y, Leung VW, Gong YN, Smith DK, Yin X, Guan Y, Luo R, Zhang T, Lam TTY. ARGNet: using deep neural networks for robust identification and classification of antibiotic resistance genes from sequences. MICROBIOME 2024; 12:84. [PMID: 38725076 PMCID: PMC11080312 DOI: 10.1186/s40168-024-01805-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 04/02/2024] [Indexed: 05/12/2024]
Abstract
BACKGROUND Emergence of antibiotic resistance in bacteria is an important threat to global health. Antibiotic resistance genes (ARGs) are some of the key components to define bacterial resistance and their spread in different environments. Identification of ARGs, particularly from high-throughput sequencing data of the specimens, is the state-of-the-art method for comprehensively monitoring their spread and evolution. Current computational methods to identify ARGs mainly rely on alignment-based sequence similarities with known ARGs. Such approaches are limited by choice of reference databases and may potentially miss novel ARGs. The similarity thresholds are usually simple and could not accommodate variations across different gene families and regions. It is also difficult to scale up when sequence data are increasing. RESULTS In this study, we developed ARGNet, a deep neural network that incorporates an unsupervised learning autoencoder model to identify ARGs and a multiclass classification convolutional neural network to classify ARGs that do not depend on sequence alignment. This approach enables a more efficient discovery of both known and novel ARGs. ARGNet accepts both amino acid and nucleotide sequences of variable lengths, from partial (30-50 aa; 100-150 nt) sequences to full-length protein or genes, allowing its application in both target sequencing and metagenomic sequencing. Our performance evaluation showed that ARGNet outperformed other deep learning models including DeepARG and HMD-ARG in most of the application scenarios especially quasi-negative test and the analysis of prediction consistency with phylogenetic tree. ARGNet has a reduced inference runtime by up to 57% relative to DeepARG. CONCLUSIONS ARGNet is flexible, efficient, and accurate at predicting a broad range of ARGs from the sequencing data. ARGNet is freely available at https://github.com/id-bioinfo/ARGNet , with an online service provided at https://ARGNet.hku.hk . Video Abstract.
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Grants
- T21-705/20-N Hong Kong Research Grants Council's Theme-based Research Scheme
- T21-705/20-N Hong Kong Research Grants Council's Theme-based Research Scheme
- T21-705/20-N Hong Kong Research Grants Council's Theme-based Research Scheme
- T21-705/20-N Hong Kong Research Grants Council's Theme-based Research Scheme
- T21-705/20-N Hong Kong Research Grants Council's Theme-based Research Scheme
- T21-705/20-N Hong Kong Research Grants Council's Theme-based Research Scheme
- 2019B121205009, HZQB-KCZYZ-2021014, 200109155890863, 190830095586328 and 190824215544727 Innovation and Technology Commission's InnoHK funding (D24H), and the Government of Guangdong Province
- 2019B121205009, HZQB-KCZYZ-2021014, 200109155890863, 190830095586328 and 190824215544727 Innovation and Technology Commission's InnoHK funding (D24H), and the Government of Guangdong Province
- 2019B121205009, HZQB-KCZYZ-2021014, 200109155890863, 190830095586328 and 190824215544727 Innovation and Technology Commission's InnoHK funding (D24H), and the Government of Guangdong Province
- 2019B121205009, HZQB-KCZYZ-2021014, 200109155890863, 190830095586328 and 190824215544727 Innovation and Technology Commission's InnoHK funding (D24H), and the Government of Guangdong Province
- 2019B121205009, HZQB-KCZYZ-2021014, 200109155890863, 190830095586328 and 190824215544727 Innovation and Technology Commission's InnoHK funding (D24H), and the Government of Guangdong Province
- 2019B121205009, HZQB-KCZYZ-2021014, 200109155890863, 190830095586328 and 190824215544727 Innovation and Technology Commission's InnoHK funding (D24H), and the Government of Guangdong Province
- 2019B121205009, HZQB-KCZYZ-2021014, 200109155890863, 190830095586328 and 190824215544727 Innovation and Technology Commission's InnoHK funding (D24H), and the Government of Guangdong Province
- 2019B121205009, HZQB-KCZYZ-2021014, 200109155890863, 190830095586328 and 190824215544727 Innovation and Technology Commission's InnoHK funding (D24H), and the Government of Guangdong Province
- 31922087 National Natural Science Foundation of China's Excellent Young Scientists Fund (Hong Kong and Macau)
- Hong Kong Research Grants Council’s Theme-based Research Scheme
- Innovation and Technology Commission’s InnoHK funding (D24H), and the Government of Guangdong Province
- National Natural Science Foundation of China’s Excellent Young Scientists Fund (Hong Kong and Macau)
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Affiliation(s)
- Yao Pei
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Joint Institute of Virology (Shantou University and The University of Hong Kong), Guangdong-Hongkong Joint Laboratory of Emerging Infectious Diseases, Shantou University, Shantou, Guangdong, 515063, China
- Laboratory of Data Discovery for Health (D²4H), Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China
- Advanced Pathogen Research Institute, Futian District, Shenzhen City, Guangdong, 518045, China
| | - Marcus Ho-Hin Shum
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Joint Institute of Virology (Shantou University and The University of Hong Kong), Guangdong-Hongkong Joint Laboratory of Emerging Infectious Diseases, Shantou University, Shantou, Guangdong, 515063, China
- Laboratory of Data Discovery for Health (D²4H), Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China
- Advanced Pathogen Research Institute, Futian District, Shenzhen City, Guangdong, 518045, China
| | - Yunshi Liao
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Joint Institute of Virology (Shantou University and The University of Hong Kong), Guangdong-Hongkong Joint Laboratory of Emerging Infectious Diseases, Shantou University, Shantou, Guangdong, 515063, China
- Advanced Pathogen Research Institute, Futian District, Shenzhen City, Guangdong, 518045, China
- Centre for Immunology & Infection (C2i), Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China
| | - Vivian W Leung
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Joint Institute of Virology (Shantou University and The University of Hong Kong), Guangdong-Hongkong Joint Laboratory of Emerging Infectious Diseases, Shantou University, Shantou, Guangdong, 515063, China
- Laboratory of Data Discovery for Health (D²4H), Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China
- Advanced Pathogen Research Institute, Futian District, Shenzhen City, Guangdong, 518045, China
| | - Yu-Nong Gong
- Division of Biotechnology, Research Center of Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- International Master Degree Program for Molecular Medicine in Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
| | - David K Smith
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Laboratory of Data Discovery for Health (D²4H), Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China
| | - Xiaole Yin
- Department of Civil Engineering, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Yi Guan
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Joint Institute of Virology (Shantou University and The University of Hong Kong), Guangdong-Hongkong Joint Laboratory of Emerging Infectious Diseases, Shantou University, Shantou, Guangdong, 515063, China
- Laboratory of Data Discovery for Health (D²4H), Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China
- Advanced Pathogen Research Institute, Futian District, Shenzhen City, Guangdong, 518045, China
| | - Ruibang Luo
- Department of Computer Science, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Tong Zhang
- Department of Civil Engineering, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Tommy Tsan-Yuk Lam
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
- Joint Institute of Virology (Shantou University and The University of Hong Kong), Guangdong-Hongkong Joint Laboratory of Emerging Infectious Diseases, Shantou University, Shantou, Guangdong, 515063, China.
- Laboratory of Data Discovery for Health (D²4H), Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China.
- Advanced Pathogen Research Institute, Futian District, Shenzhen City, Guangdong, 518045, China.
- Centre for Immunology & Infection (C2i), Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China.
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Herman EK, Lacoste SR, Freeman CN, Otto SJG, McCarthy EL, Links MG, Stothard P, Waldner CL. Bacterial enrichment prior to third-generation metagenomic sequencing improves detection of BRD pathogens and genetic determinants of antimicrobial resistance in feedlot cattle. Front Microbiol 2024; 15:1386319. [PMID: 38779502 PMCID: PMC11110911 DOI: 10.3389/fmicb.2024.1386319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 04/08/2024] [Indexed: 05/25/2024] Open
Abstract
Introduction Bovine respiratory disease (BRD) is one of the most important animal health problems in the beef industry. While bacterial culture and antimicrobial susceptibility testing have been used for diagnostic testing, the common practice of examining one isolate per species does not fully reflect the bacterial population in the sample. In contrast, a recent study with metagenomic sequencing of nasal swabs from feedlot cattle is promising in terms of bacterial pathogen identification and detection of antimicrobial resistance genes (ARGs). However, the sensitivity of metagenomic sequencing was impeded by the high proportion of host biomass in the nasal swab samples. Methods This pilot study employed a non-selective bacterial enrichment step before nucleic acid extraction to increase the relative proportion of bacterial DNA for sequencing. Results Non-selective bacterial enrichment increased the proportion of bacteria relative to host sequence data, allowing increased detection of BRD pathogens compared with unenriched samples. This process also allowed for enhanced detection of ARGs with species-level resolution, including detection of ARGs for bacterial species of interest that were not targeted for culture and susceptibility testing. The long-read sequencing approach enabled ARG detection on individual bacterial reads without the need for assembly. Metagenomics following non-selective bacterial enrichment resulted in substantial agreement for four of six comparisons with culture for respiratory bacteria and substantial or better correlation with qPCR. Comparison between isolate susceptibility results and detection of ARGs was best for macrolide ARGs in Mannheimia haemolytica reads but was also substantial for sulfonamide ARGs within M. haemolytica and Pasteurella multocida reads and tetracycline ARGs in Histophilus somni reads. Discussion By increasing the proportion of bacterial DNA relative to host DNA through non-selective enrichment, we demonstrated a corresponding increase in the proportion of sequencing data identifying BRD-associated pathogens and ARGs in deep nasopharyngeal swabs from feedlot cattle using long-read metagenomic sequencing. This method shows promise as a detection strategy for BRD pathogens and ARGs and strikes a balance between processing time, input costs, and generation of on-target data. This approach could serve as a valuable tool to inform antimicrobial management for BRD and support antimicrobial stewardship.
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Affiliation(s)
- Emily K. Herman
- Department of Agricultural, Food, and Nutritional Science, Faculty of Agricultural, Life, and Environmental Sciences, University of Alberta, Edmonton, AB, Canada
| | - Stacey R. Lacoste
- Department of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Claire N. Freeman
- Department of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Simon J. G. Otto
- HEAT-AMR (Human-Environment-Animal Transdisciplinary AMR) Research Group, School of Public Health, University of Alberta, Edmonton, AB, Canada
- Healthy Environments Thematic Area Lead, Centre for Healthy Communities, School of Public Health, University of Alberta, Edmonton, AB, Canada
| | - E. Luke McCarthy
- Department of Animal and Poultry Science, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK, Canada
| | - Matthew G. Links
- Department of Animal and Poultry Science, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK, Canada
- Department of Computer Science, College of Arts and Science, University of Saskatchewan, Saskatoon, SK, Canada
| | - Paul Stothard
- Department of Agricultural, Food, and Nutritional Science, Faculty of Agricultural, Life, and Environmental Sciences, University of Alberta, Edmonton, AB, Canada
| | - Cheryl L. Waldner
- Department of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
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Mancuso CP, Baker JS, Qu E, Tripp AD, Balogun IO, Lieberman TD. Intraspecies warfare restricts strain coexistence in human skin microbiomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.07.592803. [PMID: 38765968 PMCID: PMC11100718 DOI: 10.1101/2024.05.07.592803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Determining why only a fraction of encountered or applied bacterial strains engraft in a given person's microbiome is crucial for understanding and engineering these communities1. Previous work has established that metabolism can determine colonization success in vivo2-4, but relevance of bacterial warfare in preventing engraftment has been less explored. Here, we demonstrate that intraspecies warfare presents a significant barrier to strain transmission in the skin microbiome by profiling 14,884 pairwise interactions between Staphylococcus epidermidis cultured from eighteen human subjects from six families. We find that intraspecies antagonisms are abundant; these interactions are mechanistically diverse, independent of the relatedness between strains, and consistent with rapid evolution via horizontal gene transfer. Ability to antagonize more strains is associated with reaching a higher fraction of the on-person S. epidermidis community. Moreover, antagonisms are significantly depleted among strains residing on the same person relative to random assemblages. Two notable exceptions, in which bacteria evolved to become sensitive to antimicrobials found on the same host, are explained by mutations that provide phage resistance, contextualizing the importance of warfare among other lethal selective pressures. Taken together, our results emphasize that accounting for intraspecies bacterial warfare is essential to the design of long-lasting probiotic therapeutics.
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Affiliation(s)
- Christopher P. Mancuso
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology; Cambridge, MA 02142, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology; Cambridge, MA 02142, USA
| | - Jacob S. Baker
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology; Cambridge, MA 02142, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology; Cambridge, MA 02142, USA
| | - Evan Qu
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology; Cambridge, MA 02142, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology; Cambridge, MA 02142, USA
| | - A. Delphine Tripp
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology; Cambridge, MA 02142, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology; Cambridge, MA 02142, USA
- Department of Systems Biology, Harvard University; Cambridge, MA 02138, USA
| | - Ishaq O. Balogun
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology; Cambridge, MA 02142, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology; Cambridge, MA 02142, USA
| | - Tami D. Lieberman
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology; Cambridge, MA 02142, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology; Cambridge, MA 02142, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- Ragon Institute of MGH, MIT, and Harvard; Cambridge, MA 02142, USA
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35
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Halema AA, El-Beltagi HS, Al-Dossary O, Alsubaie B, Henawy AR, Rezk AA, Almutairi HH, Mohamed AA, Elarabi NI, Abdelhadi AA. Omics technology draws a comprehensive heavy metal resistance strategy in bacteria. World J Microbiol Biotechnol 2024; 40:193. [PMID: 38709343 DOI: 10.1007/s11274-024-04005-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 04/24/2024] [Indexed: 05/07/2024]
Abstract
The rapid industrial revolution significantly increased heavy metal pollution, becoming a major global environmental concern. This pollution is considered as one of the most harmful and toxic threats to all environmental components (air, soil, water, animals, and plants until reaching to human). Therefore, scientists try to find a promising and eco-friendly technique to solve this problem i.e., bacterial bioremediation. Various heavy metal resistance mechanisms were reported. Omics technologies can significantly improve our understanding of heavy metal resistant bacteria and their communities. They are a potent tool for investigating the adaptation processes of microbes in severe conditions. These omics methods provide unique benefits for investigating metabolic alterations, microbial diversity, and mechanisms of resistance of individual strains or communities to harsh conditions. Starting with genome sequencing which provides us with complete and comprehensive insight into the resistance mechanism of heavy metal resistant bacteria. Moreover, genome sequencing facilitates the opportunities to identify specific metal resistance genes, operons, and regulatory elements in the genomes of individual bacteria, understand the genetic mechanisms and variations responsible for heavy metal resistance within and between bacterial species in addition to the transcriptome, proteome that obtain the real expressed genes. Moreover, at the community level, metagenome, meta transcriptome and meta proteome participate in understanding the microbial interactive network potentially novel metabolic pathways, enzymes and gene species can all be found using these methods. This review presents the state of the art and anticipated developments in the use of omics technologies in the investigation of microbes used for heavy metal bioremediation.
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Affiliation(s)
- Asmaa A Halema
- Genetics Department, Faculty of Agriculture, Cairo University, Giza, 12613, Egypt
| | - Hossam S El-Beltagi
- Agricultural Biotechnology Department, College of Agriculture and Food Sciences, King Faisal University, Al-Ahsa, 31982, Saudi Arabia.
- Biochemistry Department, Faculty of Agriculture, Cairo University, Giza, 12613, Egypt.
| | - Othman Al-Dossary
- Agricultural Biotechnology Department, College of Agriculture and Food Sciences, King Faisal University, Al-Ahsa, 31982, Saudi Arabia
| | - Bader Alsubaie
- Agricultural Biotechnology Department, College of Agriculture and Food Sciences, King Faisal University, Al-Ahsa, 31982, Saudi Arabia
| | - Ahmed R Henawy
- Microbiology Department, Faculty of Agriculture, Cairo University, Giza, 12613, Egypt
| | - Adel A Rezk
- Agricultural Biotechnology Department, College of Agriculture and Food Sciences, King Faisal University, Al-Ahsa, 31982, Saudi Arabia
- Plant Virology Department, Plant Pathology Research Institute, Agriculture Research Center, Giza, 12619, Egypt
| | - Hayfa Habes Almutairi
- Chemistry Department, College of Science, King Faisal University, Al-Ahsa, 31982, Saudi Arabia
| | - Amal A Mohamed
- Chemistry Dept, Al-Leith University College, Umm Al-Qura University, P.O. Box 6725- 21955, Makkah, Saudi Arabia
| | - Nagwa I Elarabi
- Genetics Department, Faculty of Agriculture, Cairo University, Giza, 12613, Egypt
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Rizk AM, Elsayed MM, Abd El Tawab AA, Elhofy FI, Soliman EA, Kozytska T, Brangsch H, Sprague LD, Neubauer H, Wareth G. Phenotypic and genotypic characterization of resistance and virulence in Pseudomonas aeruginosa isolated from poultry farms in Egypt using whole genome sequencing. Vet Microbiol 2024; 292:110063. [PMID: 38554598 DOI: 10.1016/j.vetmic.2024.110063] [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: 01/30/2024] [Revised: 03/18/2024] [Accepted: 03/19/2024] [Indexed: 04/01/2024]
Abstract
Pseudomonas aeruginosa (P. aeruginosa) is an ESKAPE pathogen that can quickly develop resistance to most antibiotics. This bacterium is a zoonotic pathogen that can be found in humans, animals, foods, and environmental samples, making it a One-Health concern. P. aeruginosa threatens the poultry industry in Egypt, leading to significant economic losses. However, the investigation of this bacterium using NGS technology is nearly non-existent in Egypt. In this study, 38 isolates obtained from broiler farms of the Delta region were phenotypically investigated, and their genomes were characterized using whole genome sequencing (WGS). The study found that 100% of the isolates were resistant to fosfomycin and harbored the fosA gene. They were also resistant to trimethoprim/sulfamethoxazole, although only one isolate harbored the sul1 gene. Non-susceptibility (resistant, susceptible with increased dose) of colistin was observed in all isolates. WGS analysis revealed a high level of diversity between isolates, and MLST analysis allocated the 38 P. aeruginosa isolates into 11 distinct sequence types. The most predominant sequence type was ST267, found in 13 isolates, followed by ST1395 in 8 isolates. The isolates were susceptible to almost all tested antibiotics carrying only few different antimicrobial resistance (AMR) genes. Various AMR genes that confer resistance mainly to ß-lactam, aminoglycoside, sulfonamide, and phenicol compounds were identified. Additionally, several virulence associated genes were found without any significant differences in number and distribution among isolates. The majority of the virulence genes was identified in almost all isolates. The fact that P. aeruginosa, which harbors several AMR and virulence-associated factors, is present in poultry farms is alarming and threatens public health. The misuse of antimicrobial compounds in poultry farms plays a significant role in resistance development. Thus, increasing awareness and implementing strict veterinary regulations to guide the use of veterinary antibiotics is required to reduce health and environmental risks. Further studies from a One-Health perspective using WGS are necessary to trace the potential transmission routes of resistance between animals and humans and clarify resistance mechanisms.
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Affiliation(s)
- Amira M Rizk
- Department of Bacteriology, Immunology, and Mycology, Faculty of Veterinary Medicine, Benha University, Toukh 13736, Moshtohor, Egypt
| | - Marwa M Elsayed
- Department of Bacteriology, Immunology, and Mycology, Faculty of Veterinary Medicine, Benha University, Toukh 13736, Moshtohor, Egypt
| | - Ashraf A Abd El Tawab
- Department of Bacteriology, Immunology, and Mycology, Faculty of Veterinary Medicine, Benha University, Toukh 13736, Moshtohor, Egypt
| | - Fatma I Elhofy
- Department of Bacteriology, Immunology, and Mycology, Faculty of Veterinary Medicine, Benha University, Toukh 13736, Moshtohor, Egypt
| | - Enas A Soliman
- Department of Bacteriology, Immunology, and Mycology, Faculty of Veterinary Medicine, Benha University, Toukh 13736, Moshtohor, Egypt
| | - Tamara Kozytska
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena 07743, Germany
| | - Hanka Brangsch
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena 07743, Germany
| | - Lisa D Sprague
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena 07743, Germany
| | - Heinrich Neubauer
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena 07743, Germany
| | - Gamal Wareth
- Department of Bacteriology, Immunology, and Mycology, Faculty of Veterinary Medicine, Benha University, Toukh 13736, Moshtohor, Egypt; Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena 07743, Germany; Institute of Infectious Diseases and Infection Control, Jena University Hospital, Jena 07747, Germany.
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37
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Eckstrand CD, Torrevillas BK, Wolking RM, Francis M, Goodman LB, Ceric O, Alexander TL, Snekvik KR, Burbick CR. Genomic characterization of antimicrobial resistance in 61 aquatic bacterial isolates. J Vet Diagn Invest 2024; 36:393-399. [PMID: 38566327 PMCID: PMC11110781 DOI: 10.1177/10406387241241042] [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] [Indexed: 04/04/2024] Open
Abstract
Antimicrobial resistance (AMR) in pathogens important to aquatic animal health is of increasing concern but vastly understudied. Antimicrobial therapy is used to both treat and prevent bacterial disease in fish and is critical for a viable aquaculture industry and for maintenance of wild fish populations. Unfortunately, phenotypic antimicrobial susceptibility testing is technically difficult for bacteria recovered from aquatic animal hosts resulting in challenges in resistance monitoring using traditional methods. Whole-genome sequencing provides an appealing methodology for investigation of putative resistance. As part of the ongoing efforts of the FDA CVM Vet-LIRN to monitor AMR, source laboratories cultured and preliminarily identified pathogenic bacteria isolated from various fish species collected in 2019 from across the United States. Sixty-one bacterial isolates were evaluated using whole-genome sequencing. We present here the assembled draft genomes, AMR genes, predicted resistance phenotypes, and virulence factors of the 61 isolates and discuss concurrence of the identifications made by source laboratories using matrix-assisted laser desorption/time-of-flight mass spectrometry.
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Affiliation(s)
- Chrissy D. Eckstrand
- Washington Animal Disease Diagnostic Laboratory, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
| | - Brandi K. Torrevillas
- Washington Animal Disease Diagnostic Laboratory, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
| | - Rebecca M. Wolking
- Washington Animal Disease Diagnostic Laboratory, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
| | - Marla Francis
- Washington Animal Disease Diagnostic Laboratory, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
| | - Laura B. Goodman
- Baker Institute for Animal Health, Cornell University, Ithaca, NY, USA
| | - Olgica Ceric
- Veterinary Laboratory Investigation and Response Network (Vet-LIRN), Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, MD, USA
| | - Trevor L. Alexander
- Washington Animal Disease Diagnostic Laboratory, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
| | - Kevin R. Snekvik
- Washington Animal Disease Diagnostic Laboratory, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
| | - Claire R. Burbick
- Washington Animal Disease Diagnostic Laboratory, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
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38
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O’Grady K, Hong S, Putsathit P, George N, Hemphill C, Huntington PG, Korman TM, Kotsanas D, Lahra M, McDougall R, McGlinchey A, Levy A, Moore CV, Nimmo G, Prendergast L, Robson J, Speers DJ, Waring L, Wehrhahn MC, Weldhagen GF, Wilson RM, Riley TV, Knight DR. Defining the phylogenetics and resistome of the major Clostridioides difficile ribotypes circulating in Australia. Microb Genom 2024; 10:001232. [PMID: 38717815 PMCID: PMC11165652 DOI: 10.1099/mgen.0.001232] [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: 01/29/2024] [Accepted: 03/27/2024] [Indexed: 06/13/2024] Open
Abstract
Clostridioides difficile infection (CDI) remains a significant public health threat globally. New interventions to treat CDI rely on an understanding of the evolution and epidemiology of circulating strains. Here we provide longitudinal genomic data on strain diversity, transmission dynamics and antimicrobial resistance (AMR) of C. difficile ribotypes (RTs) 014/020 (n=169), 002 (n=77) and 056 (n=36), the three most prominent C. difficile strains causing CDI in Australia. Genome scrutiny showed that AMR was uncommon in these lineages, with resistance-conferring alleles present in only 15/169 RT014/020 strains (8.9 %), 1/36 RT056 strains (2.78 %) and none of 77 RT002 strains. Notably, ~90 % of strains were resistant to MLSB agents in vitro, but only ~5.9 % harboured known resistance alleles, highlighting an incongruence between AMR genotype and phenotype. Core genome analyses revealed all three RTs contained genetically heterogeneous strain populations with limited evidence of clonal transmission between CDI cases. The average number of pairwise core genome SNP (cgSNP) differences within each RT group ranged from 23.3 (RT056, ST34, n=36) to 115.6 (RT002, ST8, n=77) and 315.9 (RT014/020, STs 2, 13, 14, 49, n=169). Just 19 clonal groups (encompassing 40 isolates), defined as isolates differing by ≤2 cgSNPs, were identified across all three RTs (RT014/020, n=14; RT002, n=3; RT056, n=2). Of these clonal groups, 63 % (12/19) comprised isolates from the same Australian State and 37 % (7/19) comprised isolates from different States. The low number of plausible transmission events found for these major RTs (and previously documented populations in animal and environmental sources/reservoirs) points to widespread and persistent community sources of diverse C. difficile strains as opposed to ongoing nationwide healthcare outbreaks dominated by a single clone. Together, these data provide new insights into the evolution of major lineages causing CDI in Australia and highlight the urgent need for enhanced surveillance, and for public health interventions to move beyond the healthcare setting and into a One Health paradigm to effectively combat this complex pathogen.
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Affiliation(s)
- Keeley O’Grady
- Centre for Biosecurity and One Health, Harry Butler Institute, Murdoch University, Murdoch, Western Australia, Australia
| | - Stacey Hong
- Communicable Disease Control Directorate, WA Department of Health, East Perth, Western Australia, Australia
| | - Papanin Putsathit
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
| | - Narelle George
- Pathology Queensland, Royal Brisbane and Women’s Hospital, Herston, Queensland, Australia
| | | | - Peter G. Huntington
- Department of Microbiology, NSW Health Pathology, Royal North Shore Hospital, St Leonards, New South Wales, Australia
| | - Tony M. Korman
- Monash University, Monash Health, Clayton, Victoria, Australia
| | - Despina Kotsanas
- Monash Infectious Diseases, Monash Health, Monash Medical Centre, Clayton, Victoria, Australia
| | - Monica Lahra
- Department of Microbiology, The Prince of Wales Hospital, Randwick, New South Wales, Australia
| | | | | | - Avram Levy
- Department of Microbiology, PathWest Laboratory Medicine WA, Nedlands, Western Australia, Australia
| | - Casey V. Moore
- Microbiology and Infectious Diseases Laboratories, SA Pathology, Adelaide, South Australia, Australia
| | - Graeme Nimmo
- Pathology Queensland, Royal Brisbane and Women’s Hospital, Herston, Queensland, Australia
| | | | - Jennifer Robson
- Sullivan Nicolaides Pathology, Taringa, Queensland, Australia
| | - David J. Speers
- Department of Microbiology, PathWest Laboratory Medicine WA, Nedlands, Western Australia, Australia
- School of Medicine, The University of Western Australia, Nedlands, Western Australia, Australia
| | | | | | - Gerhard F. Weldhagen
- Microbiology and Infectious Diseases Laboratories, SA Pathology, Adelaide, South Australia, Australia
| | - Richard M. Wilson
- Australian Clinical Labs, Microbiology Department, Wayville, South Australia, Australia
| | - Thomas V. Riley
- Centre for Biosecurity and One Health, Harry Butler Institute, Murdoch University, Murdoch, Western Australia, Australia
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
- Department of Microbiology, PathWest Laboratory Medicine WA, Nedlands, Western Australia, Australia
- School of Biomedical Sciences, The University of Western Australia, Nedlands, Western Australia, Australia
| | - Daniel R. Knight
- Department of Microbiology, PathWest Laboratory Medicine WA, Nedlands, Western Australia, Australia
- School of Biomedical Sciences, The University of Western Australia, Nedlands, Western Australia, Australia
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39
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Algarni S, Gudeta DD, Han J, Nayak R, Foley SL. Genotypic analyses of IncHI2 plasmids from enteric bacteria. Sci Rep 2024; 14:9802. [PMID: 38684834 PMCID: PMC11058233 DOI: 10.1038/s41598-024-59870-2] [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: 11/22/2023] [Accepted: 04/15/2024] [Indexed: 05/02/2024] Open
Abstract
Incompatibility (Inc) HI2 plasmids are large (typically > 200 kb), transmissible plasmids that encode antimicrobial resistance (AMR), heavy metal resistance (HMR) and disinfectants/biocide resistance (DBR). To better understand the distribution and diversity of resistance-encoding genes among IncHI2 plasmids, computational approaches were used to evaluate resistance and transfer-associated genes among the plasmids. Complete IncHI2 plasmid (N = 667) sequences were extracted from GenBank and analyzed using AMRFinderPlus, IntegronFinder and Plasmid Transfer Factor database. The most common IncHI2-carrying genera included Enterobacter (N = 209), Escherichia (N = 208), and Salmonella (N = 204). Resistance genes distribution was diverse, with plasmids from Escherichia and Salmonella showing general similarity in comparison to Enterobacter and other taxa, which grouped together. Plasmids from Enterobacter and other taxa had a higher prevalence of multiple mercury resistance genes and arsenic resistance gene, arsC, compared to Escherichia and Salmonella. For sulfonamide resistance, sul1 was more common among Enterobacter and other taxa, compared to sul2 and sul3 for Escherichia and Salmonella. Similar gene diversity trends were also observed for tetracyclines, quinolones, β-lactams, and colistin. Over 99% of plasmids carried at least 25 IncHI2-associated conjugal transfer genes. These findings highlight the diversity and dissemination potential for resistance across different enteric bacteria and value of computational-based approaches for the resistance-gene assessment.
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Affiliation(s)
- Suad Algarni
- Division of Microbiology, National Center for Toxicological Research, Food and Drug Administration, 3900 NCTR Rd, Jefferson, AR, 72079, USA.
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, 72701, USA.
| | - Dereje D Gudeta
- Division of Microbiology, National Center for Toxicological Research, Food and Drug Administration, 3900 NCTR Rd, Jefferson, AR, 72079, USA
| | - Jing Han
- Division of Microbiology, National Center for Toxicological Research, Food and Drug Administration, 3900 NCTR Rd, Jefferson, AR, 72079, USA
| | - Rajesh Nayak
- Office of Regulatory Compliance and Risk Management, National Center for Toxicological Research, Food and Drug Administration, 3900 NCTR Rd, Jefferson, AR, 72079, USA
| | - Steven L Foley
- Division of Microbiology, National Center for Toxicological Research, Food and Drug Administration, 3900 NCTR Rd, Jefferson, AR, 72079, USA.
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, 72701, USA.
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Ma J, Xu R, Li W, Liu M, Ding X. Whole-genome sequencing of clinical isolates of Citrobacter Europaeus in China carrying bla OXA-48 and bla NDM-1. Ann Clin Microbiol Antimicrob 2024; 23:38. [PMID: 38685062 PMCID: PMC11059591 DOI: 10.1186/s12941-024-00699-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 04/22/2024] [Indexed: 05/02/2024] Open
Abstract
OBJECTIVE To analyze the clinical infection characteristics and genetic environments of resistance genes in carbapenem-resistant Citrobacter europaeus using whole-genome sequencing. METHODS The susceptibility of two clinical isolates of C. europaeus (WF0003 and WF1643) to 24 antimicrobial agents was assessed using the BD Phoenix™ M50 System and Kirby-Bauer (K-B) disk-diffusion method. Whole-genome sequencing was performed on the Illumina and Nanopore platforms, and ABRicate software was used to predict resistance and virulence genes of carbapenem-resistant C. europaeus. The characteristics of plasmids carrying carbapenem-resistance genes and their genetic environments were analyzed. Single nucleotide polymorphisms were used to construct a phylogenetic tree to analyze the homology of these two C. europaeus strains with ten strains of C. europaeus in the NCBI database. RESULTS The two strains of carbapenem-resistant C. europaeus are resistant to various antimicrobial agents, particularly carbapenems and β-lactams. WF0003 carries blaNDM- 1, which is located on an IncX3 plasmid that has high homology to the pNDM-HN380 plasmid. blaNDM- 1 is located on a truncated Tn125. It differs from Tn125 by the insertion of IS5 in the upstream ISAba125 and the deletion of the downstream ISAba125, which is replaced by IS26. WF1643 carries blaOXA- 48 in a Tn1999 transposon on the IncL/M plasmid, carrying only that single drug resistance gene. Homology analysis of these two strains of C. europaeus with ten C. europaeus strains in the NCBI database revealed that the 12 strains can be classified into three clades, with both WF0003 and WF1643 in the B clade. CONCLUSION To the best of our knowledge, this is the first study to report an IncX3 plasmid carrying blaNDM- 1 in C. europaeus in China. C. europaeus strains harboring carbapenem-resistance genes are concerning in relation to the spread of antimicrobial resistance, and the presence of carbapenem-resistance genes in C. europaeus should be continuously monitored.
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Affiliation(s)
- Jie Ma
- Department of Clinical Laboratory, Weifang People's Hospital, Weifang, Shandong, China
| | - Ranran Xu
- Department of Clinical Laboratory, The First Affiliated Hospital of Weifang Medical University, Weifang Medical University, Weifang, Shandong, China
| | - Wanxiang Li
- Department of Clinical Laboratory, Weifang People's Hospital, Weifang, Shandong, China
| | - Mi Liu
- Department of Clinical Laboratory, Weifang People's Hospital, Weifang, Shandong, China
| | - Xiaomei Ding
- Department of Clinical Laboratory, Weifang People's Hospital, Weifang, Shandong, China.
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Nitz AA, Johnson DL, Lupiyaningdyah P, Meinzer MA, Ramsey JS, Robinson CM, Valencia Amores CS, Pickett BE. Secondary analysis of Staphylococcus aureus whole genomes reveals diverse antimicrobial resistance profiles. MICROPUBLICATION BIOLOGY 2024; 2024:10.17912/micropub.biology.000903. [PMID: 38741934 PMCID: PMC11089388 DOI: 10.17912/micropub.biology.000903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 04/16/2024] [Accepted: 04/25/2024] [Indexed: 05/16/2024]
Abstract
Antimicrobial resistance (AMR) in microorganisms is an ongoing threat to human health across the globe. To better characterize the AMR profiles of six strains of Staphylococcus aureus , we performed a secondary analysis that consisted of the following steps: 1) download fastq files from the Sequence Read Archive, 2) perform a de novo genome assembly from the sequencing reads, 3) annotate the assembled contigs, 4) predict the presence of antimicrobial resistance genes. We predicted the presence of 75 unique genes that conferred resistance against 22 unique antimicrobial compounds.
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Affiliation(s)
- Alyssa A Nitz
- Brigham Young University, Provo, Utah, United States
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Markova J, Langova D, Babak V, Kostovova I. Ovine and Caprine Strains of Corynebacterium pseudotuberculosis on Czech Farms-A Comparative Study. Microorganisms 2024; 12:875. [PMID: 38792705 PMCID: PMC11123211 DOI: 10.3390/microorganisms12050875] [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: 04/01/2024] [Revised: 04/19/2024] [Accepted: 04/23/2024] [Indexed: 05/26/2024] Open
Abstract
Caseous lymphadenitis (CLA) is a worldwide disease of small ruminants caused by Corynebacterium pseudotuberculosis, a facultative intracellular pathogen that is able to survive and multiply in certain white blood cells of the host. In this study, 33 strains of C. pseudotuberculosis were isolated from sheep and goats suffering from CLA on nine farms in the Czech Republic. All these strains were tested for their antibiotic susceptibility, ability to form a biofilm and resistance to the effects of commonly used disinfectant agents. To better understand the virulence of C. pseudotuberculosis, the genomes of strains were sequenced and comparative genomic analysis was performed with another 123 genomes of the same species, including ovis and equi biovars, downloaded from the NCBI. The genetic determinants for the virulence factors responsible for adherence and virulence factors specialized for iron uptake and exotoxin phospholipase D were revealed in every analyzed genome. Carbohydrate-Active Enzymes were compared, revealing the presence of genetic determinants encoding exo-α-sialidase (GH33) and the CP40 protein in most of the analyzed genomes. Thirty-three Czech strains of C. pseudotuberculosis were identified as the biovar ovis on the basis of comparative genome analysis. All the compared genomes of the biovar ovis strains were highly similar regardless of their country of origin or host, reflecting their clonal behavior.
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Affiliation(s)
- Jirina Markova
- Department of Microbiology and Antimicrobial Resistance, Veterinary Research Institute, 62100 Brno, Czech Republic; (D.L.); (V.B.); (I.K.)
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Lu K, Wang X, Zhou Y, Zhu Q. Genomic characterization and probiotic potential assessment of an exopolysaccharide-producing strain Pediococcus pentosaceus LL-07 isolated from fermented meat. BMC Microbiol 2024; 24:142. [PMID: 38664612 PMCID: PMC11044368 DOI: 10.1186/s12866-024-03304-6] [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: 01/16/2024] [Accepted: 04/12/2024] [Indexed: 04/29/2024] Open
Abstract
BACKGROUND The genomic information available for Pediococcus pentosaceus is primarily derived from fermented fruits and vegetables, with less information available from fermented meat. P. pentosaceus LL-07, a strain isolated from fermented meat, has the capability of producing exopolysaccharides (EPS). To assess the probiotic attributes of P. pentosaceus LL-07, we conducted whole-genome sequencing (WGS) using the PacBio SequelIIe and Illumina MiSeq platforms, followed by in vitro experiments to explore its probiotic potential. RESULTS The genome size of P. pentosaceus LL-07 is 1,782,685 bp, comprising a circular chromosome and a circular plasmid. Our investigation revealed the absence of a CRISPR/Cas system. Sugar fermentation experiments demonstrated the characteristics of carbohydrate metabolism. P. pentosaceus LL-07 contains an EPS synthesis gene cluster consisting of 13 genes, which is different from the currently known gene cluster structure. NO genes associated with hemolysis or toxin synthesis were detected. Additionally, eighty-six genes related to antibiotic resistance were identified but not present in the prophage, transposon or plasmid. In vitro experiments demonstrated that P. pentosaceus LL-07 was comparable to the reference strain P. pentosaceus ATCC25745 in terms of tolerance to artificial digestive juice and bile, autoaggregation and antioxidation, and provided corresponding genomic evidence. CONCLUSION This study confirmed the safety and probiotic properties of P. pentosaceus LL-07 via complete genome and phenotype analysis, supporting its characterization as a potential probiotic candidate.
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Affiliation(s)
- Kuan Lu
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guizhou Province, Guiyang, 550025, China
- Guizhou Province Key Laboratory of Agricultural and Animal Products Storage and Processing, School of Liquor and Food Engineering, Guizhou University, Guizhou, Guiyang, 550025, China
| | - Xueya Wang
- Chili Pepper Research Institute, Guizhou Provincial Academy of Agricultural Sciences, Guizhou, Guiyang, 550006, China
| | - Ying Zhou
- Guizhou Province Key Laboratory of Agricultural and Animal Products Storage and Processing, School of Liquor and Food Engineering, Guizhou University, Guizhou, Guiyang, 550025, China
| | - Qiujin Zhu
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guizhou Province, Guiyang, 550025, China.
- Guizhou Province Key Laboratory of Agricultural and Animal Products Storage and Processing, School of Liquor and Food Engineering, Guizhou University, Guizhou, Guiyang, 550025, China.
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Omar KM, Kitundu GL, Jimoh AO, Namikelwa DN, Lisso FM, Babajide AA, Olufemi SE, Awe OI. Investigating antimicrobial resistance genes in Kenya, Uganda and Tanzania cattle using metagenomics. PeerJ 2024; 12:e17181. [PMID: 38666081 PMCID: PMC11044882 DOI: 10.7717/peerj.17181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 03/11/2024] [Indexed: 04/28/2024] Open
Abstract
Antimicrobial resistance (AMR) is a growing problem in African cattle production systems, posing a threat to human and animal health and the associated economic value chain. However, there is a poor understanding of the resistomes in small-holder cattle breeds in East African countries. This study aims to examine the distribution of antimicrobial resistance genes (ARGs) in Kenya, Tanzania, and Uganda cattle using a metagenomics approach. We used the SqueezeMeta-Abricate (assembly-based) pipeline to detect ARGs and benchmarked this approach using the Centifuge-AMRplusplus (read-based) pipeline to evaluate its efficiency. Our findings reveal a significant number of ARGs of critical medical and economic importance in all three countries, including resistance to drugs of last resort such as carbapenems, suggesting the presence of highly virulent and antibiotic-resistant bacterial pathogens (ESKAPE) circulating in East Africa. Shared ARGs such as aph(6)-id (aminoglycoside phosphotransferase), tet (tetracycline resistance gene), sul2 (sulfonamide resistance gene) and cfxA_gen (betalactamase gene) were detected. Assembly-based methods revealed fewer ARGs compared to read-based methods, indicating the sensitivity and specificity of read-based methods in resistome characterization. Our findings call for further surveillance to estimate the intensity of the antibiotic resistance problem and wider resistome classification. Effective management of livestock and antibiotic consumption is crucial in minimizing antimicrobial resistance and maximizing productivity, making these findings relevant to stakeholders, agriculturists, and veterinarians in East Africa and Africa at large.
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Affiliation(s)
- Kauthar M. Omar
- Department of Biochemistry and Biotechnology, School of Pure and Applied Sciences, Pwani University, Kilifi, Kenya
| | - George L. Kitundu
- Department of Biochemistry and Biotechnology, School of Pure and Applied Sciences, Pwani University, Kilifi, Kenya
| | - Adijat O. Jimoh
- Division of Immunology, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Genetics, Genomics and Bioinformatics Department, National Biotechnology Development Agency, Abuja, Nigeria
| | - Dorcus N. Namikelwa
- Department of Data Management, Modelling and Geo-Information Unit, International Centre of Insect Physiology and Ecology, Nairobi, Kenya
| | - Felix M. Lisso
- Department of Biochemistry and Biotechnology, School of Pure and Applied Sciences, Pwani University, Kilifi, Kenya
| | - Abiola A. Babajide
- South African National Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa
| | - Seun E. Olufemi
- Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Nigeria
| | - Olaitan I. Awe
- African Society for Bioinformatics and Computational Biology, Cape Town, South Africa
- Department of Computer Science, University of Ibadan, Ibadan, Oyo State, Nigeria
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Parzygnat JL, Crespo R, Fosnaught M, Muyyarrikkandy M, Hull D, Harden L, Thakur S. Megaplasmid Dissemination in Multidrug-Resistant Salmonella Serotypes from Backyard and Commercial Broiler Production Systems in the Southeastern United States. Foodborne Pathog Dis 2024. [PMID: 38635963 DOI: 10.1089/fpd.2023.0181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2024] Open
Abstract
Over the past decade, there has been a rise in U.S. backyard poultry ownership, raising concern for residential area antimicrobial-resistant (AMR) Salmonella contamination. This study aims to lay the groundwork to better understand the persistence of AMR Salmonella in residential broiler production systems and make comparisons with commercial systems. Ten backyard and 10 commercial farms were sampled at three time points across bird production. Both fecal (n = 10) and environmental (soil, n = 5, litter/compost, n = 5, feeder, and waterer swabs, n = 6) samples were collected at each visit on days 10, 31, and 52 of production for backyard farms and days 10, 24, and 38 of production for commercial farms. AMR Salmonella was characterized phenotypically by broth microdilution and genotypically by whole-genome sequencing. Overall, Salmonella was more prevalent in commercial farm samples (52.31%) over backyard farms (19.10%). Kentucky (sequence type (ST) 152) was the most common serotype found in both backyard and commercial farms. Multidrug-resistant (MDR, resistance to ≥3 or more antimicrobial classes) isolates were found in both production systems, while ciprofloxacin- and nalidixic acid-resistant and intermediate isolates were more prevalent in commercial (33%) than backyard samples (1%). Plasmids that have been associated with MDR were found in Kentucky and Infantis isolates, particularly IncFIB(K)_1_Kpn3 megaplasmid (Infantis). Our study emphasizes the need to understand the selection pressures in disseminating megaplasmids in MDR Salmonella in distinct broiler production systems.
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Affiliation(s)
- Jessica L Parzygnat
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
| | - Rocio Crespo
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
| | - Mary Fosnaught
- Prestage Department of Poultry Science, North Carolina State University, Raleigh, North Carolina, USA
| | - Muhammed Muyyarrikkandy
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brooking, South Dakota, USA
| | - Dawn Hull
- Bacterial Diseases Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Lyndy Harden
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
| | - Siddhartha Thakur
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
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Kondo S, Phornsiricharoenphant W, Na-rachasima L, Phokhaphan P, Ruangchai W, Palittapongarnpim P, Apisarnthanarak A. Genomic characterization of extended-spectrum β-lactamase-producing Enterobacterales isolated from abdominal surgical patients. Epidemiol Infect 2024; 152:e70. [PMID: 38606647 PMCID: PMC11077598 DOI: 10.1017/s0950268824000578] [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: 03/11/2024] [Revised: 04/24/2024] [Accepted: 03/18/2024] [Indexed: 04/13/2024] Open
Abstract
Rectal swabs of 104 patients who underwent abdominal surgery were screened for ESBL producers. Sequence types (STs) and resistance genes were identified by whole-genome sequencing of 46 isolates from 17 patients. All but seven isolates were assigned to recognized STs. While 18 ESBL-producing E. coli (EPEC) strains were of unique STs, ESBL-producing K. pneumoniae (EPKP) strains were mainly ST14 or ST15. Eight patients harboured strains of the same ST before and after abdominal surgery. The most prevalent resistant genes in E. coli were blaEC (69.57%), blaCTX-M (65.22%), and blaTEM (36.95%), while blaSHV was present in only K. pneumoniae (41.30%). Overall, genes encoding β-lactamases of classes A (blaCTX-M, blaTEM, blaZ), C (blaSHV, blaMIR, and blaDHA), and D (blaOXA) were identified, the most prevalent variants being blaCTX-M-15, blaTEM-1B, blaSHV-28, and blaOXA-1. Interestingly, blaCMY-2, the most common pAmpC β-lactamase genes reported worldwide, and mobile colistin resistance genes, mcr-10-1, were also identified. The presence of blaCMY-2 and mcr-10-1 is concerning as they may constitute a potentially high risk of pan-resistant post-surgical infections. It is imperative that healthcare professionals monitor intra-abdominal surgical site infections rigorously to prevent transmission of faecal ESBL carriage in high-risk patients.
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Affiliation(s)
- Sumalee Kondo
- Faculty of Medicine, Thammasat University, Pathum Thani, Thailand
| | - Worawich Phornsiricharoenphant
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Lalita Na-rachasima
- Graduate School, Faculty of Medicine, Thammasat University, Pathum Thani, Thailand
| | - Pimonwan Phokhaphan
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Wuthiwat Ruangchai
- Pornchai Matangkasombut Center for Microbial Genomics, Mahidol University, Bangkok, Thailand
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Ramnarine SDBJ, Jayaraman J, Ramsubhag A. Crucifer Lesion-Associated Xanthomonas Strains Show Multi-Resistance to Heavy Metals and Antibiotics. Curr Microbiol 2024; 81:136. [PMID: 38598029 DOI: 10.1007/s00284-024-03646-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 02/20/2024] [Indexed: 04/11/2024]
Abstract
Copper resistance in phytopathogens is a major challenge to crop production globally and is known to be driven by excessive use of copper-based pesticides. However, recent studies have shown co-selection of multiple heavy metal and antibiotic resistance genes in bacteria exposed to heavy metal and xenobiotics, which may impact the epidemiology of plant, animal, and human diseases. In this study, multi-resistance to heavy metals and antibiotics were evaluated in local Xanthomonas campestris pv. campestris (Xcc) and co-isolated Xanthomonas melonis (Xmel) strains from infected crucifer plants in Trinidad. Resistance to cobalt, cadmium, zinc, copper, and arsenic (V) was observed in both Xanthomonas species up to 25 mM. Heavy metal resistance (HMR) genes were found on a small plasmid-derived locus with ~ 90% similarity to a Stenotrophomonas spp. chromosomal locus and a X. perforans pLH3.1 plasmid. The co-occurrence of mobile elements in these regions implies their organization on a composite transposon-like structure. HMR genes in Xcc strains showed the lowest similarity to references, and the cus and ars operons appear to be unique among Xanthomonads. Overall, the similarity of HMR genes to Stenotrophomonas sp. chromosomal genomes suggest their origin in this genus or a related organism and subsequent spread through lateral gene transfer events. Further resistome characterization revealed the presence of small multidrug resistance (SMR), multidrug resistance (MDR) efflux pumps, and bla (Xcc) genes for broad biocide resistance in both species. Concurrently, resistance to antibiotics (streptomycin, kanamycin, tetracycline, chloramphenicol, and ampicillin) up to 1000 µg/mL was confirmed.
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Affiliation(s)
- Stephen D B Jr Ramnarine
- Department of Life Sciences, Faculty of Science and Technology, The University of The West Indies, St. Augustine, Trinidad and Tobago
| | - Jayaraj Jayaraman
- Department of Life Sciences, Faculty of Science and Technology, The University of The West Indies, St. Augustine, Trinidad and Tobago
| | - Adesh Ramsubhag
- Department of Life Sciences, Faculty of Science and Technology, The University of The West Indies, St. Augustine, Trinidad and Tobago.
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Miliotis G, Sengupta P, Hameed A, Chuvochina M, McDonagh F, Simpson AC, Parker CW, Singh NK, Rekha PD, Morris D, Raman K, Kyrpides NC, Hugenholtz P, Venkateswaran K. Novel spore-forming species exhibiting intrinsic resistance to third- and fourth-generation cephalosporins and description of Tigheibacillus jepli gen. nov., sp. nov. mBio 2024; 15:e0018124. [PMID: 38477597 PMCID: PMC11005411 DOI: 10.1128/mbio.00181-24] [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: 01/24/2024] [Accepted: 01/29/2024] [Indexed: 03/14/2024] Open
Abstract
A comprehensive microbial surveillance was conducted at NASA's Mars 2020 spacecraft assembly facility (SAF), where whole-genome sequencing (WGS) of 110 bacterial strains was performed. One isolate, designated 179-BFC-A-HST, exhibited less than 80% average nucleotide identity (ANI) to known species, suggesting a novel organism. This strain demonstrated high-level resistance [minimum inhibitory concentration (MIC) >256 mg/L] to third-generation cephalosporins, including ceftazidime, cefpodoxime, combination ceftazidime/avibactam, and the fourth-generation cephalosporin cefepime. The results of a comparative genomic analysis revealed that 179-BFC-A-HST is most closely related to Virgibacillus halophilus 5B73CT, sharing an ANI of 78.7% and a digital DNA-DNA hybridization (dDDH) value of 23.5%, while their 16S rRNA gene sequences shared 97.7% nucleotide identity. Based on these results and the recent recognition that the genus Virgibacillus is polyphyletic, strain 179-BFC-A-HST is proposed as a novel species of a novel genus, Tigheibacillus jepli gen. nov., sp. nov (type strain 179-BFC-A-HST = DSM 115946T = NRRL B-65666T), and its closest neighbor, V. halophilus, is proposed to be reassigned to this genus as Tigheibacillus halophilus comb. nov. (type strain 5B73CT = DSM 21623T = JCM 21758T = KCTC 13935T). It was also necessary to reclassify its second closest neighbor Virgibacillus soli, as a member of a novel genus Paracerasibacillus, reflecting its phylogenetic position relative to the genus Cerasibacillus, for which we propose Paracerasibacillus soli comb. nov. (type strain CC-YMP-6T = DSM 22952T = CCM 7714T). Within Amphibacillaceae (n = 64), P. soli exhibited 11 antibiotic resistance genes (ARG), while T. jepli encoded for 3, lacking any known β-lactamases, suggesting resistance from variant penicillin-binding proteins, disrupting cephalosporin efficacy. P. soli was highly resistant to azithromycin (MIC >64 mg/L) yet susceptible to cephalosporins and penicillins. IMPORTANCE The significance of this research extends to understanding microbial survival and adaptation in oligotrophic environments, such as those found in SAF. Whole-genome sequencing of several strains isolated from Mars 2020 mission assembly cleanroom facilities, including the discovery of the novel species Tigheibacillus jepli, highlights the resilience and antimicrobial resistance (AMR) in clinically relevant antibiotic classes of microbes in nutrient-scarce settings. The study also redefines the taxonomic classifications within the Amphibacillaceae family, aligning genetic identities with phylogenetic data. Investigating ARG and virulence factors (VF) across these strains illuminates the microbial capability for resistance under resource-limited conditions while emphasizing the role of human-associated VF in microbial survival, informing sterilization practices and microbial management in similar oligotrophic settings beyond spacecraft assembly cleanrooms such as pharmaceutical and medical industry cleanrooms.
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Affiliation(s)
- Georgios Miliotis
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland
- Centre for One Health, Ryan Institute, University of Galway, Galway, Ireland
| | - Pratyay Sengupta
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu, India
- Center for Integrative Biology and Systems mEdicine (IBSE), Indian Institute of Technology Madras, Chennai, Tamil Nadu, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), Indian Institute of Technology Madras, Chennai, Tamil Nadu, India
| | - Asif Hameed
- Division of Microbiology and Biotechnology, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka, India
| | - Maria Chuvochina
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, Brisbane, Australia
| | - Francesca McDonagh
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland
| | - Anna C. Simpson
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Ceth W. Parker
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Nitin K. Singh
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Punchappady D. Rekha
- Division of Microbiology and Biotechnology, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka, India
| | - Dearbháile Morris
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland
- Centre for One Health, Ryan Institute, University of Galway, Galway, Ireland
| | - Karthik Raman
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu, India
- Center for Integrative Biology and Systems mEdicine (IBSE), Indian Institute of Technology Madras, Chennai, Tamil Nadu, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), Indian Institute of Technology Madras, Chennai, Tamil Nadu, India
| | - Nikos C. Kyrpides
- US Department of Energy Joint Genome Institute, Berkeley, California, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Philip Hugenholtz
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, Brisbane, Australia
| | - Kasthuri Venkateswaran
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
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49
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Mahmud B, Vargas RC, Sukhum KV, Patel S, Liao J, Hall LR, Kesaraju A, Le T, Kitchner T, Kronholm E, Koshalek K, Bendixsen CG, VanWormer JJ, Shukla SK, Dantas G. Longitudinal dynamics of farmer and livestock nasal and faecal microbiomes and resistomes. Nat Microbiol 2024; 9:1007-1020. [PMID: 38570675 DOI: 10.1038/s41564-024-01639-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 02/14/2024] [Indexed: 04/05/2024]
Abstract
Globally, half a billion people are employed in animal agriculture and are directly exposed to the associated microorganisms. However, the extent to which such exposures affect resident human microbiomes is unclear. Here we conducted a longitudinal profiling of the nasal and faecal microbiomes of 66 dairy farmers and 166 dairy cows over a year-long period. We compare farmer microbiomes to those of 60 age-, sex- and ZIP code-matched people with no occupational exposures to farm animals (non-farmers). We show that farming is associated with microbiomes containing livestock-associated microbes; this is most apparent in the nasal bacterial community, with farmers harbouring a richer and more diverse nasal community than non-farmers. Similarly, in the gut microbial communities, we identify more shared microbial lineages between cows and farmers from the same farms. Additionally, we find that shared microbes are associated with antibiotic resistance genes. Overall, our study demonstrates the interconnectedness of human and animal microbiomes.
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Affiliation(s)
- Bejan Mahmud
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Rhiannon C Vargas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Kimberley V Sukhum
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Sanket Patel
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - James Liao
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Lindsey R Hall
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Akhil Kesaraju
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Thao Le
- Integrated Research Development Laboratory, Marshfield Clinic Research Institute, Marshfield, WI, USA
| | - Terrie Kitchner
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, WI, USA
| | - Erik Kronholm
- Center for Clinical Epidemiology & Population Health, Marshfield Clinic Research Institute, Marshfield, WI, USA
| | - Kyle Koshalek
- National Farm Medicine Center, Marshfield Clinic Research Institute, Marshfield, WI, USA
| | - Casper G Bendixsen
- National Farm Medicine Center, Marshfield Clinic Research Institute, Marshfield, WI, USA
| | - Jeffrey J VanWormer
- Center for Clinical Epidemiology & Population Health, Marshfield Clinic Research Institute, Marshfield, WI, USA
| | - Sanjay K Shukla
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, WI, USA.
- Computational Informatics in Biology and Medicine program, University of Wisconsin-Madison, Madison, WI, USA.
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, USA.
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA.
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St Louis, MO, USA.
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA.
- Department of Biomedical Engineering, Washington University in St Louis, St Louis, MO, USA.
- Department of Pediatrics, Washington University School of Medicine, St Louis, MO, USA.
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50
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Jung H, Pitout JDD, Matsumura Y, Strydom KA, Kingsburgh C, Ehlers MM, Kock MM. Genomic epidemiology and molecular characteristics of bla NDM-1-positive carbapenem-resistant Pseudomonas aeruginosa belonging to international high-risk clone ST773 in the Gauteng region, South Africa. Eur J Clin Microbiol Infect Dis 2024; 43:627-640. [PMID: 38265603 DOI: 10.1007/s10096-024-04763-5] [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: 10/12/2023] [Accepted: 01/12/2024] [Indexed: 01/25/2024]
Abstract
PURPOSE The emergence of carbapenem-resistant P. aeruginosa (CRPA) harbouring acquired carbapenemase genes (blaVIM, blaIMP and blaNDM) has become a global public health threat. Three CRPA isolates included in the study had an extensively drug-resistant phenotype with susceptibility to colistin only and were positive for the blaNDM-1 gene. The current study aimed to investigate the genomic epidemiology and molecular characteristics of the blaNDM-1-positive CRPA isolates collected from the Gauteng region, South Africa. METHODS Short read whole genome sequencing (WGS) was performed to determine sequence types (STs), genetic relatedness, resistome, virulome and the genetic environment of the blaNDM-1 gene. RESULTS The WGS and phylogenetic analyses revealed that the study isolates belonged to an international high-risk clone ST773 and belonged to the same clade with eight blaNDM-1-positive ST773 isolates from Hungary, India, Nigeria, South Korea and USA. The study isolates harboured a wide repertoire of intrinsic and acquired antibiotic resistance genes (ARGs) related with mobile genetic elements, porins and efflux pumps, as well as virulence factor genes. The clade-specific ARGs (blaNDM-1, floR2/cmlA9, rmtB4, tetG) were found in a putative integrative and conjugative element (ICE) region similar to ICE6660-like. CONCLUSION As ICE carrying the blaNDM-1 gene can easily spread to other P. aeruginosa isolates and other Gram-negative bacteria, the findings in this study highlight the need for appropriate management strategies and active surveillance of CRPA isolates in the Gauteng region, South Africa.
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Affiliation(s)
- Hyunsul Jung
- Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa
| | - Johann D D Pitout
- Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa
- Division of Microbiology, Alberta Public Laboratories, Cummings School of Medicine, University of Calgary, Calgary, Canada
| | - Yasufumi Matsumura
- Department of Clinical Laboratory Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Kathy-Anne Strydom
- Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa
- Ampath National Reference Laboratory, Centurion, South Africa
| | - Chanel Kingsburgh
- Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa
- Ampath National Reference Laboratory, Centurion, South Africa
| | - Marthie M Ehlers
- Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa
- Department of Medical Microbiology, Tshwane Academic Division, National Health Laboratory Service (NHLS), Pretoria, South Africa
| | - Marleen M Kock
- Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa.
- Department of Medical Microbiology, Tshwane Academic Division, National Health Laboratory Service (NHLS), Pretoria, South Africa.
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