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Arjun OK, Sethi M, Parida D, Dash J, Kumar Das S, Prakash T, Senapati S. Comprehensive physiological and genomic characterization of a potential probiotic strain, Lactiplantibacillus plantarum ILSF15, isolated from the gut of tribes of Odisha, India. Gene 2024; 931:148882. [PMID: 39182659 DOI: 10.1016/j.gene.2024.148882] [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: 03/18/2024] [Revised: 08/11/2024] [Accepted: 08/21/2024] [Indexed: 08/27/2024]
Abstract
Characterizing probiotic features of organisms isolated from diverse environments can lead to the discovery of novel strains with promising functional features and health attributes. The present study attempts to characterize a novel probiotic strain isolated from the gut of the tribal population of Odisha, India. Based on 16S rRNA-based phylogeny, the strain was identified as a species of the Lactiplantibacillus genus and was named Lactiplantibacillus plantarum strain ILSF15. The current investigation focuses on elucidating this strain's genetic and physiological properties associated with probiotic attributes such as biosafety risk, host adaptation/survival traits, and beneficial functional features. The novel strain was observed, in vitro, exhibiting features such as acid/bile tolerance, adhesion to the host enteric epithelial cells, cholesterol assimilation, and pathogen exclusion, indicating its ability to survive the harsh environment of the human GIT and resist the growth of harmful microorganisms. Additionally, the L. plantarum ILSF15 strain was found to harbor genes associated with the metabolism and synthesis of various bioactive molecules, including amino acids, carbohydrates, lipids, and vitamins, highlighting the organism's ability to efficiently utilize diverse resources and contribute to the host's nutrition and health. Several genes involved in host adaptation/survival strategies and host-microbe interactions were also identified from the ILSF15 genome. Moreover, L. plantarum strains, in general, were found to have an open pangenome characterized by high genetic diversity and the absence of specific lineages associated with particular habitats, signifying its versatile nature and potential applications in probiotic and functional food industries.
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Affiliation(s)
- O K Arjun
- School of Biosciences and Bioengineering, Indian Institute of Technology Mandi, Himachal Pradesh 175005, India
| | - Manisha Sethi
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha 751023, India
| | - Deepti Parida
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha 751023, India
| | - Jayalaxmi Dash
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha 751023, India
| | - Suraja Kumar Das
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha 751023, India
| | - Tulika Prakash
- School of Biosciences and Bioengineering, Indian Institute of Technology Mandi, Himachal Pradesh 175005, India.
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Jin Y, Zhou W, Ge Q, Shen P, Xiao Y. Epidemiology and clinical features of Skin and Soft Tissue Infections Caused by PVL-Positive and PVL-Negative Methicillin-Resistant Staphylococcus aureus Isolates in inpatients in China: a single-center retrospective 7-year study. Emerg Microbes Infect 2024; 13:2316809. [PMID: 38323591 PMCID: PMC10883109 DOI: 10.1080/22221751.2024.2316809] [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: 11/12/2023] [Accepted: 02/06/2024] [Indexed: 02/08/2024]
Abstract
Previous studies have mainly focused on outpatient cases of skin and soft tissue infections (SSTIs), with limited attention to inpatient occurrences. Thus, we aimed to compare the clinical parameters of inpatients with SSTIs, performed genomic characterization, and determined the subtypes of Panton-Valentine leucocidin (PVL) bacteriophages of methicillin-resistant Staphylococcus aureus (MRSA) strains isolated from these patients. We found that PVL-positive patients had shorter hospital stays (mean, 9 vs. 24 days; p < 0.001) and abscess resolution durations (mean, 8 vs. 13 days; p < 0.01). PVL-positive MRSA-induced SSTIs were more frequently associated with abscesses [36/55 (65.5%) vs. 15/124 (12.1%), p < 0.001], with 52.7% undergoing incision and drainage; over 80% of PVL-negative patients received incision, drainage, and antibiotics. In PVL-positive patients receiving empirical antibiotics, anti-staphylococcal agents such as vancomycin and linezolid were administered less frequently (32.7%, 18/55) than in PVL-negative patients (74.2%, 92/124), indicating that patients with PVL-positive SSTIs are more likely to require surgical drainage rather than antimicrobial treatment. We also found that the ST59 lineage was predominant, regardless of PVL status (41.3%, 74/179). Additionally, we investigated the linear structure of the lukSF-PV gene, revealing that major clusters were associated with specific STs, suggesting independent acquisition of PVL by different strain types and indicating that significant diversity was observed even within PVL-positive strains detected in the same facility. Overall, our study provides comprehensive insights into the clinical, genetic, and phage-related aspects of MRSA-induced SSTIs in hospitalized patients and contributes to a more profound understanding of the epidemiology and evolution of these pathogens in the Chinese population.
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Affiliation(s)
- Ye Jin
- Department of General Intensive Care Unit, the Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, People's Republic of China
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
- Key Laboratory of Early Warning and Intervention of Multiple Organ Failure, China National Ministry of Education, Hangzhou, Zhejiang, People's Republic of China
| | - Wangxiao Zhou
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
| | - Qi Ge
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
| | - Ping Shen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
| | - Yonghong Xiao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
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Shen C, Luo L, Zhou H, Xiao Y, Zeng J, Zhang L, Pu J, Zeng J, Zhang N, Jiang Y, Xu L, Chen D, Li G, Wu K, Yu H, Wang M, Guo X, Wang J, Huang B, Chen C. Emergence and ongoing outbreak of ST80 vancomycin-resistant Enterococcus faecium in Guangdong province, China from 2021 to 2023: a multicenter, time-series and genomic epidemiological study. Emerg Microbes Infect 2024; 13:2361030. [PMID: 38801248 PMCID: PMC11159589 DOI: 10.1080/22221751.2024.2361030] [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: 03/14/2024] [Accepted: 05/23/2024] [Indexed: 05/29/2024]
Abstract
BACKGROUND Surveillance systems revealed that the prevalence of vancomycin-resistant Enterococcus faecium (VREfm) has increased. We aim to investigate the epidemiological and genomic characteristics of VREfm in China. METHODS We collected 20,747 non-redundant E. faecium isolates from inpatients across 19 hospitals in six provinces between January 2018 and June 2023. VREfm was confirmed by antimicrobial susceptibility testing. The prevalence was analyzed using changepoint package in R. Genomic characteristics were explored by whole-genome sequencing. RESULTS 5.59% (1159/20,747) of E. faecium isolates were resistant to vancomycin. The prevalence of VREfm increased in Guangdong province from 5% before 2021 to 20-50% in 2023 (p < 0.0001), but not in the other five provinces. Two predominant clones before 2021, ST17 and ST78, were substituted by an emerging clone, ST80, from 2021 to 2023 (88.63%, 195/220). All ST80 VREfm from Guangdong formed a single lineage (SC11) and were genetically distant from the ST80 VREfm from other countries, suggesting a regional outbreak. All ST80 VREfm in SC11 carried a new type of plasmid harbouring a vanA cassette, which was embedded in a Tn1546-like structure flanked by IS1678 and ISL3. However, no conjugation-related gene was detected and no transconjugant was obtained in conjugation experiment, indicating that the outbreak of ST80 VREfm could be attributed to clonal transmission. CONCLUSIONS We revealed an ongoing outbreak of ST80 VREfm with a new vanA-harbouring plasmid in Guangdong, China. This clone has also been identified in other provinces and countries, foreboding a risk of wider spreading shortly. Continuous surveillance is needed to inform public health interventions.
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Affiliation(s)
- Cong Shen
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Clinical Laboratory/State Key Laboratory of Traditional Chinese Medicine Syndrome, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, People’s Republic of China
- Guangdong Provincial Key Laboratory of Research on Emergency in TCM, Guangzhou, People’s Republic of China
| | - Li Luo
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Clinical Laboratory/State Key Laboratory of Traditional Chinese Medicine Syndrome, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, People’s Republic of China
| | - Hongyun Zhou
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Clinical Laboratory/State Key Laboratory of Traditional Chinese Medicine Syndrome, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, People’s Republic of China
| | - Yinglun Xiao
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Clinical Laboratory/State Key Laboratory of Traditional Chinese Medicine Syndrome, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, People’s Republic of China
| | - Jinxiang Zeng
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Clinical Laboratory/State Key Laboratory of Traditional Chinese Medicine Syndrome, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, People’s Republic of China
| | - Liling Zhang
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Clinical Laboratory/State Key Laboratory of Traditional Chinese Medicine Syndrome, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, People’s Republic of China
| | - Jieying Pu
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Clinical Laboratory/State Key Laboratory of Traditional Chinese Medicine Syndrome, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, People’s Republic of China
- Guangdong Provincial Key Laboratory of Research on Emergency in TCM, Guangzhou, People’s Republic of China
| | - Jianming Zeng
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Clinical Laboratory/State Key Laboratory of Traditional Chinese Medicine Syndrome, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, People’s Republic of China
- Guangdong Provincial Key Laboratory of Research on Emergency in TCM, Guangzhou, People’s Republic of China
| | - Ni Zhang
- Clinical Laboratory, Guangdong Provincial People's Hospital/Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, People’s Republic of China
| | - Yueting Jiang
- Clinical Laboratory, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Lingqing Xu
- The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, People’s Republic of China
| | - Dingqiang Chen
- Clinical Laboratory, Zhujiang Hospital, Southern Medical University, Guangzhou, People’s Republic of China
| | - Gang Li
- Clinical Laboratory, General Hospital of Ningxia Medical University, Yinchuan, People’s Republic of China
| | - Kuihai Wu
- Clinical Laboratory, The First People's Hospital of Foshan, Foshan, People’s Republic of China
| | - Hua Yu
- Clinical Laboratory, Sichuan Provincial People's Hospital, Sichuan Academy of Medical Sciences, Chengdu, People’s Republic of China
| | - Min Wang
- Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, People’s Republic of China
| | - Xuemin Guo
- Clinical Laboratory, Meizhou People's Hospital, Meizhou, People’s Republic of China
| | - Juan Wang
- Clinical Laboratory, Zhongshan People's Hospital, Zhongshan, People’s Republic of China
| | - Bin Huang
- Clinical Laboratory, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Cha Chen
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Clinical Laboratory/State Key Laboratory of Traditional Chinese Medicine Syndrome, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, People’s Republic of China
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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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Nasser F, Gaudreau A, Lubega S, Zaker A, Xia X, Mer AS, D'Costa VM. Characterization of the diversity of type IV secretion system-encoding plasmids in Acinetobacter. Emerg Microbes Infect 2024; 13:2320929. [PMID: 38530969 DOI: 10.1080/22221751.2024.2320929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 02/14/2024] [Indexed: 03/28/2024]
Abstract
The multi-drug resistant pathogen Acinetobacter baumannii has gained global attention as an important clinical challenge. Owing to its ability to survive on surfaces, its capacity for horizontal gene transfer, and its resistance to front-line antibiotics, A. baumannii has established itself as a successful pathogen. Bacterial conjugation is a central mechanism for pathogen evolution. The epidemic multidrug-resistant A. baumannii ACICU harbours a plasmid encoding a Type IV Secretion System (T4SS) with homology to the E. coli F-plasmid, and plasmids with homologous gene clusters have been identified in several A. baumannii sequence types. However the genetic and host strain diversity, global distribution, and functional ability of this group of plasmids is not fully understood. Using systematic analysis, we show that pACICU2 belongs to a group of almost 120 T4SS-encoding plasmids within four different species of Acinetobacter and one strain of Klebsiella pneumoniae from human and environmental origin, and globally distributed across 20 countries spanning 4 continents. Genetic diversity was observed both outside and within the T4SS-encoding cluster, and 47% of plasmids harboured resistance determinants, with two plasmids harbouring eleven. Conjugation studies with an extensively drug-resistant (XDR) strain showed that the XDR plasmid could be successfully transferred to a more divergent A. baumanii, and transconjugants exhibited the resistance phenotype of the plasmid. Collectively, this demonstrates that these T4SS-encoding plasmids are globally distributed and more widespread among Acinetobacter than previously thought, and that they represent an important potential reservoir for future clinical concern.
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Affiliation(s)
- Farah Nasser
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada
- Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, Canada
| | - Avery Gaudreau
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada
- Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, Canada
| | - Shareefah Lubega
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada
- Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, Canada
| | - Arvin Zaker
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Canada
| | - Xuhua Xia
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Canada
- Department of Biology, University of Ottawa, Ottawa, Canada
| | - Arvind S Mer
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Canada
| | - Vanessa M D'Costa
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada
- Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, Canada
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Staudacher M, Hotz JF, Kriz R, Schefberger K, Schneider L, Spettel K, Starzengruber P, Hagemann JB, Leutzendorff A, Burgmann H, Lagler H. Differences in oxazolidinone resistance mechanisms and small colony variants emergence of Staphylococcus aureus induced in an in vitro resistance development model. Emerg Microbes Infect 2024; 13:2292077. [PMID: 38055244 PMCID: PMC10849000 DOI: 10.1080/22221751.2023.2292077] [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: 10/25/2022] [Accepted: 12/03/2023] [Indexed: 12/07/2023]
Abstract
Invasive Staphylococcus aureus infections are associated with a high burden of disease, case fatality rate and healthcare costs. Oxazolidinones such as linezolid and tedizolid are considered potential treatment choices for conditions involving methicillin resistance or penicillin allergies. Additionally, they are being investigated as potential inhibitors of toxins in toxin-mediated diseases. In this study, linezolid and tedizolid were evaluated in an in vitro resistance development model for induction of resistance in S. aureus. Whole genome sequencing was conducted to elucidate resistance mechanisms through the identification of causal mutations. After inducing resistance to both linezolid and tedizolid, several partially novel single nucleotide variants (SNVs) were detected in the rplC gene, which encodes the 50S ribosome protein L3 in S. aureus. These SNVs were found to decrease the binding affinity, potentially serving as the underlying cause for oxazolidinone resistance. Furthermore, in opposite to linezolid we were able to induce phenotypically small colony variants of S. aureus after induction of resistance with tedizolid for the first time in literature. In summary, even if different antibiotic concentrations were required and SNVs were detected, the principal capacity of S. aureus to develop resistance to oxazolidinones seems to differ between linezolid and tedizolid in-vivo but not in vitro. Stepwise induction of resistance seems to be a time and cost-effective tool for assessing resistance evolution. Inducted-resistant strains should be examined and documented for epidemiological reasons, if MICs start to rise or oxazolidinone-resistant S. aureus outbreaks become more frequent.
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Affiliation(s)
- Moritz Staudacher
- Department of Medicine I, Division of Infectious Diseases and Tropical Medicine, Medical University of Vienna, Vienna, Austria
- Department of Angiology, Medical University of Vienna, Vienna, Austria
| | - Julian Frederic Hotz
- Department of Medicine I, Division of Infectious Diseases and Tropical Medicine, Medical University of Vienna, Vienna, Austria
- Department of Neurology, Evangelic Hospital Vienna, Vienna, Austria
| | - Richard Kriz
- Department of Medicine I, Division of Infectious Diseases and Tropical Medicine, Medical University of Vienna, Vienna, Austria
| | - Katharina Schefberger
- Department of Medicine I, Division of Infectious Diseases and Tropical Medicine, Medical University of Vienna, Vienna, Austria
| | - Lisa Schneider
- Department of Medicine I, Division of Infectious Diseases and Tropical Medicine, Medical University of Vienna, Vienna, Austria
| | - Kathrin Spettel
- Department of Laboratory Medicine, Division of Clinical Microbiology, Medical University of Vienna, Vienna, Austria
| | - Peter Starzengruber
- Department of Laboratory Medicine, Division of Clinical Microbiology, Medical University of Vienna, Vienna, Austria
| | | | - Amelie Leutzendorff
- Department of Medicine I, Division of Infectious Diseases and Tropical Medicine, Medical University of Vienna, Vienna, Austria
- Department of Clinical Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Heinz Burgmann
- Department of Medicine I, Division of Infectious Diseases and Tropical Medicine, Medical University of Vienna, Vienna, Austria
| | - Heimo Lagler
- Department of Medicine I, Division of Infectious Diseases and Tropical Medicine, Medical University of Vienna, Vienna, Austria
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Zhu J, Wang J, Kang W, Zhang X, Kerdsin A, Yao H, Zheng H, Wu Z. Streptococcus suis serotype 4: a population with the potential pathogenicity in humans and pigs. Emerg Microbes Infect 2024; 13:2352435. [PMID: 38703011 PMCID: PMC11097711 DOI: 10.1080/22221751.2024.2352435] [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: 01/10/2024] [Accepted: 05/02/2024] [Indexed: 05/06/2024]
Abstract
Streptococcus suis is a major bacterial pathogen in pigs and an emerging zoonotic pathogen. Different S. suis serotypes exhibit diverse characteristics in population structure and pathogenicity. Surveillance data highlight the significance of S. suis serotype 4 (SS4) in swine streptococcusis, a pathotype causing human infections. However, except for a few epidemiologic studies, the information on SS4 remains limited. In this study, we investigated the population structure, pathogenicity, and antimicrobial characteristics of SS4 based on 126 isolates, including one from a patient with septicemia. We discovered significant diversities within this population, clustering into six minimum core genome (MCG) groups (1, 2, 3, 4, 7-2, and 7-3) and five lineages. Two main clonal complexes (CCs), CC17 and CC94, belong to MCG groups 1 and 3, respectively. Numerous important putative virulence-associated genes are present in these two MCG groups, and 35.00% (7/20) of pig isolates from CC17, CC94, and CC839 (also belonging to MCG group 3) were highly virulent (mortality rate ≥ 80%) in zebrafish and mice, similar to the human isolate ID36054. Cytotoxicity assays showed that the human and pig isolates of SS4 strains exhibit significant cytotoxicity to human cells. Antimicrobial susceptibility testing showed that 95.83% of strains isolated from our labs were classified as multidrug-resistant. Prophages were identified as the primary vehicle for antibiotic resistance genes. Our study demonstrates the public health threat posed by SS4, expanding the understanding of SS4 population structure and pathogenicity characteristics and providing valuable information for its surveillance and prevention.
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Affiliation(s)
- Jinlu Zhu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, People’s Republic of China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, People’s Republic of China
- WOAH Reference Lab for Swine Streptococcosis, Nanjing, People’s Republic of China
| | - Jianping Wang
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Weiming Kang
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Xiyan Zhang
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Anusak Kerdsin
- Faculty of Public Health, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, Thailand
| | - Huochun Yao
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, People’s Republic of China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, People’s Republic of China
- WOAH Reference Lab for Swine Streptococcosis, Nanjing, People’s Republic of China
| | - Han Zheng
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
- Department of Biochemistry and Molecular Biology, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, MOE Key Laboratory of Coal Environmental Pathogenicity and Prevention, Shanxi Medical University, Taiyuan, People’s Republic of China
| | - Zongfu Wu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, People’s Republic of China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, People’s Republic of China
- WOAH Reference Lab for Swine Streptococcosis, Nanjing, People’s Republic of China
- Guangdong Provincial Key Laboratory of Research on the Technology of Pig-breeding and Pig-disease Prevention, Guangzhou, People’s Republic of China
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Guo H, Li L, Zhang Y, Zhang Y, Song C, Wu Y, Xu J, Ruan Z, He F. Global genomic epidemiology and transmission dynamics of plasmid-borne tmexCD-toprJ-carrying Klebsiella pneumoniae in a one health context. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 953:176065. [PMID: 39244063 DOI: 10.1016/j.scitotenv.2024.176065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2024] [Revised: 09/03/2024] [Accepted: 09/04/2024] [Indexed: 09/09/2024]
Abstract
The emergence of tmexCD-toprJ, a novel plasmid-mediated resistance-nodulation-division (RND) type efflux pump gene cluster, poses a significant threat to public health by diminishing bacterial susceptibility to the last-resort antibiotics, including tigecycline. Between 2020 and 2022, 18 Klebsiella pneumoniae strains carrying the tmexCD-toprJ gene were recovered from over 30,000 human stool samples collected from patients across five hospitals in China. Phylogenetic analysis of these 18 strains revealed clonal transmission of tmexCD-toprJ-carrying K. pneumoniae among patients and hospital settings. Comparative analysis of the 18 tmexCD-toprJ-carrying plasmids showed conservation in the genetic backgrounds of tmexCD-toprJ, despite the diverse backbone structures among the plasmids. The inactive suppressor, TNfxB1, is located in front of all tmexCD1-toprJ1, while TNfxB3 is located upstream of tmexCD3-toprJ3. Conjugation experiments demonstrated the transferability of plasmids from three strains to the recipient Escherichia coli J53. Among all 237 globally distributed tmexCD-toprJ-carrying strains, the majority (92.83 %) were from China. These strains encompassed 50 sequence types, with the most prevalent being ST11 (12.66 %), ST37 (11.81 %), and ST15 (11.39 %). Samples originated from various sources: 47.26 % from human, 38.82 % from livestock, and 13.08 % from the environment. The most common tmexCD-toprJ genotype was tmexCD1-toprJ1 (86.92 %, n = 206), followed by tmexCD2-toprJ2 (8.86 %, n = 21) and tmexCD3-toprJ3 (4.22 %, n = 10). The tmexCD1-toprJ1 gene was found in livestock (44.66 %, n = 92), humans (39.81 %, n = 82), and environmental samples (15.05 %, n = 31). In contrast, tmexCD2-toprJ2 and tmexCD3-toprJ3 were only found in human samples. Additionally, tmexCD-toprJ has been detected in 79 strains of K. pneumoniae harboring carbapenem-resistance genes. Given the presence of tmexCD-toprJ across various hosts and environments, establishing a comprehensive surveillance system from a One Health perspective is particularly vital.
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Affiliation(s)
- Hao Guo
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang 310014, China
| | - Lirong Li
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang 310014, China
| | - Yingying Zhang
- Department of Blood Transfusion, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China
| | - Yawen Zhang
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang 310014, China
| | - Che Song
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou 311399, China
| | - Yuye Wu
- Department of Blood Transfusion, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China
| | - Juan Xu
- School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang 310013, China
| | - Zhi Ruan
- Department of Blood Transfusion, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China; Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Fang He
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang 310014, China.
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9
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Zheng Z, Ye L, Xu Y, Chan EWC, Chen S. Dynamics of antimicrobial resistance and genomic characteristics of foodborne Vibrio spp. in Southern China (2013-2022). JOURNAL OF HAZARDOUS MATERIALS 2024; 479:135672. [PMID: 39236546 DOI: 10.1016/j.jhazmat.2024.135672] [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: 04/21/2024] [Revised: 08/04/2024] [Accepted: 08/26/2024] [Indexed: 09/07/2024]
Abstract
Vibrio spp., known as significant marine pathogens, have become more prevalent due to global warming. Antibiotics released into the environment drive Vibrio resistance. The increasing consumption of seafood leads to more interactions between Vibrio and humans. Despite this concerning trend, there remains a lack of large-scale surveillance for Vibrio contamination across various types of food. This study isolated 4027 Vibrio strains, primarily comprising V. parahaemolyticus and V. alginolyticus, in 3581 fresh shrimp and meat products from 2013 to 2022. The Vibrio strains showed increased resistance to important antibiotics, especially β-lactams used to treat foodborne bacterial infections. Whole genome sequencing of 591 randomly chosen strains showed a strong correlation between antibiotic resistance and genotypes in Vibrio. Notably, various ESBL genes have evolved over the past 8 years, with blaVEBs being the most dominant. Additionally, carbapenemase genes, such as blaNDM-1, have become increasingly prevalent in recent years. Various mobile genetic elements, including IncQ and IncA/C plasmids, recoverable in Vibrio, facilitate the transmission of crucial β-lactamase genes. These data provide insights into the evolutionary traits of antimicrobial resistance in foodborne Vibrio strains over a decade. Policymakers should consider these findings when devising appropriate strategies to combat bacterial antimicrobial resistance and safeguard human health.
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Affiliation(s)
- Zhiwei Zheng
- State Key Lab of Chemical Biology and Drug Discovery and the Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China; Shenzhen Key Lab for Biological Safety Control, The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen, China
| | - Lianwei Ye
- State Key Lab of Chemical Biology and Drug Discovery and the Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China; Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong, China
| | - Yating Xu
- State Key Lab of Chemical Biology and Drug Discovery and the Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China; Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong, China
| | - Edward Wai-Chi Chan
- State Key Lab of Chemical Biology and Drug Discovery and the Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Sheng Chen
- State Key Lab of Chemical Biology and Drug Discovery and the Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China; Shenzhen Key Lab for Biological Safety Control, The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen, China.
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10
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Liu M, Wu J, Zhao J, Xi Y, Jin Y, Yang H, Chen S, Long J, Duan G. Global epidemiology and genetic diversity of mcr-positive Klebsiella pneumoniae: A systematic review and genomic analysis. ENVIRONMENTAL RESEARCH 2024; 259:119516. [PMID: 38950813 DOI: 10.1016/j.envres.2024.119516] [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: 04/07/2024] [Revised: 06/25/2024] [Accepted: 06/29/2024] [Indexed: 07/03/2024]
Abstract
The rapid increase of mcr-positive Klebsiella pneumoniae (K. pneumoniae) has received considerable attention and poses a major public health concern. Here, we systematically analyzed the global distribution of mcr-positive K. pneumoniae isolates based on published articles as well as publicly available genomes. Combining strain information from 78 articles and 673 K. pneumoniae genomes, a total of 1000 mcr-positive K. pneumoniae isolates were identified. We found that mcr-positive K. pneumoniae has disseminated widely worldwide, especially in Asia, with a higher diversity of sequence types (STs). These isolates were disseminated in 57 countries and were associated with 12 different hosts. Most of the isolates were found in China and were isolated from human sources. Moreover, MLST analysis showed that ST15 and ST11 accounted for the majority of mcr-positive K. pneumoniae, which deserve sustained attention in further surveillance programs. mcr-1 and mcr-9 were the dominant mcr variants in mcr-positive K. pneumoniae. Furthermore, a Genome-wide association study (GWAS) demonstrated that mcr-1- and mcr-9-producing genomes exhibited different antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), thereby indicating a distinct evolutionary path. Notably, the phylogenetic analysis suggested that certain mcr-positive K. pneumoniae genomes from various geographical areas and hosts harbored a high degree of genetic similarities (<20 SNPs), suggesting frequent cross-region and cross-host clonal transmission. Overall, our results emphasize the significance of monitoring and exploring the transmission and evolution of mcr-positive K. pneumoniae in the context of "One health".
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Affiliation(s)
- Mengyue Liu
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, Henan, China
| | - Jie Wu
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, Henan, China
| | - Jiaxue Zhao
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, Henan, China
| | - Yanyan Xi
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, Henan, China
| | - Yuefei Jin
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, Henan, China
| | - Haiyan Yang
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, Henan, China
| | - Shuaiyin Chen
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, Henan, China
| | - Jinzhao Long
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, Henan, China.
| | - Guangcai Duan
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, Henan, China
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11
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Mejía-Limones I, Andrade-Molina D, Morey-León G, Hidalgo-Olmedo JC, Chang-Asinc JG, Fernández-Cadena JC, Rojas M. Whole-genome sequencing of Klebsiella pneumoniae MDR circulating in a pediatric hospital setting: a comprehensive genome analysis of isolates from Guayaquil, Ecuador. BMC Genomics 2024; 25:928. [PMID: 39367302 DOI: 10.1186/s12864-024-10835-9] [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: 02/15/2024] [Accepted: 09/25/2024] [Indexed: 10/06/2024] Open
Abstract
BACKGROUND Klebsiella pneumoniae is the major cause of nosocomial infections worldwide and is related to a worsening increase in Multidrug-Resistant Bacteria (MDR) and virulence genes that seriously affect immunosuppressed patients, long-stay intensive care patients, elderly individuals, and children. Whole-Genome Sequencing (WGS) has resulted in a useful strategy for characterizing the genomic components of clinically important bacteria, such as K. pneumoniae, enabling them to monitor genetic changes and understand transmission, highlighting the risk of dissemination of resistance and virulence associated genes in hospitals. In this study, we report on WGS 14 clinical isolates of K. pneumoniae from a pediatric hospital biobank of Guayaquil, Ecuador. RESULTS The main findings revealed pronounced genetic heterogeneity among the isolates. Multilocus sequencing type ST45 was the predominant lineage among non-KPC isolates, whereas ST629 was found more frequently among KPC isolates. Phylogenetic analysis suggested local transmission dynamics. Comparative genomic analysis revealed a core set of 3511 conserved genes and an open pangenome in neonatal isolates. The diversity of MLSTs and capsular types, and the high genetic diversity among these isolates indicate high intraspecific variability. In terms of virulence factors, we identified genes associated with adherence, biofilm formation, immune evasion, secretion systems, multidrug efflux pump transporters, and a notably high number of genes related to iron uptake. A large number of these genes were detected in the ST45 isolate, whereas iron uptake yersiniabactin genes were found exclusively in the non-KPC isolates. We observed high resistance to commonly used antibiotics and determined that these isolates exhibited multidrug resistance including β-lactams, aminoglycosides, fluoroquinolones, quinolones, trimetropins, fosfomycin and macrolides; additionally, resistance-associated point mutations and cross-resistance genes were identified in all the isolates. We also report the first K. pneumoniae KPC-3 gene producers in Ecuador. CONCLUSIONS Our WGS results for clinical isolates highlight the importance of MDR in neonatal K. pneumoniae infections and their genetic diversity. WGS will be an imperative strategy for the surveillance of K. pneumoniae in Ecuador, and will contribute to identifying effective treatment strategies for K. pneumoniae infections in critical units in patients at stratified risk.
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Affiliation(s)
- I Mejía-Limones
- Laboratorio de Ciencias Omicas, Facultad de Ciencias de La Salud, Universidad Espíritu Santo, Samborondón, Ecuador
| | - D Andrade-Molina
- Laboratorio de Ciencias Omicas, Facultad de Ciencias de La Salud, Universidad Espíritu Santo, Samborondón, Ecuador.
| | - G Morey-León
- Laboratorio de Ciencias Omicas, Facultad de Ciencias de La Salud, Universidad Espíritu Santo, Samborondón, Ecuador
| | - J C Hidalgo-Olmedo
- Hospital de Niños Dr. Roberto Gilbert E. Junta de Beneficencia de Guayaquil, Guayaquil, Ecuador
| | - J G Chang-Asinc
- Hospital de Niños Dr. Roberto Gilbert E. Junta de Beneficencia de Guayaquil, Guayaquil, Ecuador
| | - J C Fernández-Cadena
- African Genome Center, University Mohammed VI Polytechnic (UM6P), Ben Guerir, Morocco
| | - M Rojas
- Human Genomics Corporation S.A.S., Loja, Ecuador
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12
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Romão FT, Santos ACM, Puño-Sarmiento JJ, Sperandio V, Hernandes RT, Gomes TAT. Expression of the locus of enterocyte effacement genes during the invasion process of the atypical enteropathogenic Escherichia coli 1711-4 strain of serotype O51:H40. Microbiol Spectr 2024; 12:e0030424. [PMID: 39189752 PMCID: PMC11448038 DOI: 10.1128/spectrum.00304-24] [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: 02/02/2024] [Accepted: 07/01/2024] [Indexed: 08/28/2024] Open
Abstract
Atypical enteropathogenic Escherichia coli (aEPEC) is a significant cause of diarrhea in low- and middle-income countries. Certain aEPEC strains, including the Brazilian representative strain of serotype O51:H40 called aEPEC 1711-4, can use flagella to attach to, invade, and persist in T84 and Caco-2 intestinal cells. It can also translocate from the gut to extraintestinal sites in a rat model. Although various aspects of the virulence of this strain were studied and the requirement of a type III secretion system for the efficiency of the invasion process was demonstrated, the expression of the locus of enterocyte effacement (LEE) genes during the invasion and intracellular persistence remains unclear. To address this question, the expression of flagella and the different LEE operons was evaluated during kinetic experiments of the interaction of aEPEC 1711-4 with enterocytes in vitro. The genome of the strain was also sequenced. The results showed that flagella expression remained unchanged, but the expression of eae and escJ increased during the early interaction and invasion of aEPEC 1711-4 into Caco-2 cells, and there was no change 24 h post-infection during the persistence period. The number of actin accumulation foci formed on HeLa cells also increased during the 6-h analysis. No known gene related to the invasion process was identified in the genome of aEPEC 1711-4, which was shown to belong to the global EPEC lineage 10. These findings suggest that the LEE components and the intimate adherence promoted by intimin are necessary for the invasion and persistence of aEPEC 1711-4, but the detailed mechanism needs further study.IMPORTANCEAtypical enteropathogenic Escherichia coli (aEPEC) is a major cause of diarrhea, especially in low- and middle-income countries, like Brazil. However, due to the genome heterogeneity of each clonal group, it is difficult to comprehend the pathogenicity of this strain fully. Among aEPEC strains, 1711-4 can invade eukaryotic cells in vitro, cross the gut barrier, and reach extraintestinal sites in animal models. By studying how different known aEPEC virulence factors are expressed during the invasion process, we can gain insight into the commonalities of this phenotype among other aEPEC strains. This will help in developing preventive measures to control infections caused by invasive strains. No known virulence-encoding genes linked to the invasion process were found. Nevertheless, additional studies are still necessary to evaluate the role of other factors in this phenotype.
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Affiliation(s)
- Fabiano T. Romão
- Disciplina de Microbiologia, Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
- Department of Microbiology, UT Southwestern Medical Center, Dallas, Texas, USA
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Ana C. M. Santos
- Disciplina de Microbiologia, Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Juan J. Puño-Sarmiento
- Disciplina de Microbiologia, Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Vanessa Sperandio
- Department of Microbiology, UT Southwestern Medical Center, Dallas, Texas, USA
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Rodrigo T. Hernandes
- Departamento de Ciências Químicas e Biológicas, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, São Paulo, Brazil
| | - Tânia A. T. Gomes
- Disciplina de Microbiologia, Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
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13
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Glen KA, Lamont IL. Characterization of acquired β-lactamases in Pseudomonas aeruginosa and quantification of their contributions to resistance. Microbiol Spectr 2024; 12:e0069424. [PMID: 39248479 PMCID: PMC11448201 DOI: 10.1128/spectrum.00694-24] [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: 03/15/2024] [Accepted: 07/25/2024] [Indexed: 09/10/2024] Open
Abstract
Pseudomonas aeruginosa is a highly problematic opportunistic pathogen that causes a range of different infections. Infections are commonly treated with β-lactam antibiotics, including cephalosporins, monobactams, penicillins, and carbapenems, with carbapenems regarded as antibiotics of last resort. Isolates of P. aeruginosa can contain horizontally acquired bla genes encoding β-lactamase enzymes, but the extent to which these contribute to β-lactam resistance in this species has not been systematically quantified. The overall aim of this research was to address this knowledge gap by quantifying the frequency of β-lactamase-encoding genes in P. aeruginosa and by determining the effects of β-lactamases on susceptibility of P. aeruginosa to β-lactams. Genome analysis showed that β-lactamase-encoding genes are present in 3% of P. aeruginosa but are enriched in carbapenem-resistant isolates (35%). To determine the substrate antibiotics, 10 β-lactamases were expressed from an integrative plasmid in the chromosome of P. aeruginosa reference strain PAO1. The β-lactamases reduced susceptibility to a variety of clinically used antibiotics, including carbapenems (meropenem, imipenem), penicillins (ticarcillin, piperacillin), cephalosporins (ceftazidime, cefepime), and a monobactam (aztreonam). Different enzymes acted on different β-lactams. β-lactamases encoded by the genomes of P. aeruginosa clinical isolates had similar effects to the enzymes expressed in strain PAO1. Genome engineering was used to delete β-lactamase-encoding genes from three carbapenem-resistant clinical isolates and increased susceptibility to substrate β-lactams. Our findings demonstrate that acquired β-lactamases play an important role in β-lactam resistance in P. aeruginosa, identifying substrate antibiotics for a range of enzymes and quantifying their contributions to resistance.IMPORTANCEPseudomonas aeruginosa is an extremely problematic pathogen, with isolates that are resistant to the carbapenem class of β-lactam antibiotics being in critical need of new therapies. Genes encoding β-lactamase enzymes that degrade β-lactam antibiotics can be present in P. aeruginosa, including carbapenem-resistant isolates. Here, we show that β-lactamase genes are over-represented in carbapenem-resistant isolates, indicating their key role in resistance. We also show that different β-lactamases alter susceptibility of P. aeruginosa to different β-lactam antibiotics and quantify the effects of selected enzymes on β-lactam susceptibility. This research significantly advances the understanding of the contributions of acquired β-lactamases to antibiotic resistance, including carbapenem resistance, in P. aeruginosa and by implication in other species. It has potential to expedite development of methods that use whole genome sequencing of infecting bacteria to inform antibiotic treatment, allowing more effective use of antibiotics, and facilitate the development of new antibiotics.
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Affiliation(s)
- Karl A Glen
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Iain L Lamont
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
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14
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Souza TGVD, Santana JA, Claudino MMS, Pereira ST, Xavier RGC, do Amarante VS, de Castro YG, Dorneles EMS, Aburjaile FF, de Carvalho VA, Brenig B, Silva ROS. Occurrence, genetic diversity, and antimicrobial resistance of methicillin-resistant Staphylococcus spp. in hospitalized and non-hospitalized cats in Brazil. PLoS One 2024; 19:e0309711. [PMID: 39361625 PMCID: PMC11449366 DOI: 10.1371/journal.pone.0309711] [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: 03/28/2024] [Accepted: 08/16/2024] [Indexed: 10/05/2024] Open
Abstract
Methicillin-resistant Staphylococci (MRS) cause infections at various sites and exhibit multidrug resistance. Despite their importance in veterinary medicine, only little is known about Staphylococcus spp. colonizing and infecting cats. Therefore, in this study, we aimed to isolate and identify Staphylococcus spp. colonizing hospitalized and non-hospitalized domestic cats and analyze their antimicrobial resistance profiles, genetic diversity, and risk factors associated with MRS colonization. A total of 218 oral and axillary swabs were obtained from 109 cats, including 77 non-hospitalized and 32 hospitalized cats. After plating on selective media, the isolates were identified via matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and rpoB and 16S rRNA gene sequencing. Subsequently, antimicrobial sensitivity of the strains was assessed, and they were screened for mecA gene. Methicillin-resistant S. haemolyticus (MRSH) isolates were subjected to multilocus sequence typing, whereas methicillin-resistant S. pseudintermedius (MRSP) and S. felis isolates were subjected to whole genome sequencing. S. felis was most commonly isolated from non-hospitalized cats (28.1%), whereas S. pseudintermedius and MRS were commonly isolated from hospitalized cats (25%). MRSH isolates from hospitalized animals were classified as ST3. The identified MRSP strains belonged to two well-known sequence types, ST551 and ST71. Moreover, antimicrobial use (p = 0.0001), hospitalization (p = 0.0141), and comorbidities (p = 0.002) were associated with increased MRS prevalence in cats.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Bertram Brenig
- Institute of Veterinary Medicine, University of Göttingen, Göttingen, Germany
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15
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Shidan Z, Song L, Yumin Z, Rong C, Siteng W, Meirong L, Guangjin L. First report of Streptococcus agalactiae isolated from a healthy captive sichuan golden snub-nosed monkey (Rhinopithecus roxellana) in China. Microb Pathog 2024; 195:106907. [PMID: 39218375 DOI: 10.1016/j.micpath.2024.106907] [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: 03/27/2024] [Revised: 08/19/2024] [Accepted: 08/29/2024] [Indexed: 09/04/2024]
Abstract
Streptococcus agalactiae (S. agalactiae) is an opportunistic pathogen, and to date, studies have mainly focused on S. agalactiae strains isolated from humans, dairy cows, and fish. We reported one S. agalactiae strain, named CFFB, which was isolated from a healthy Sichuan golden snub-nosed monkey. Classical bacteriological approaches, as well as, next-generation sequencing, comparative genomics, and mice challenge test were used to characterize this strain. CFFB was identified as serotype III, ST19 combination which is a common type found in human strains. Phylogenetic analysis showed that the genome of CFFB was closely related to human clinical isolates, rather far away from animal strains. In total, CFFB contained fewer virulence-associated genes and antibiotic resistance genes than human isolates that were close to CFFB in evolutionary relationships. In the mice challenge test, CFFB had a relative weak virulence that just caused death in 33 % of ICR mice at a dose of 108 CFU by intraperitoneal injection, and CFFB was reisolated from the cardiac blood of the dead mice. Meanwhile, two intact prophages (prophage 1 and 2) were identified in the CFFB genome and shared high similarities with phage Javan52 and Javan29 which from human S. agalactiae isolate Gottschalk 1002A and RBH03, respectively. Moreover, the type II-A CRISPR-Cas system was detected in the CFFB genome, and the spacers from CFFB were the same to the streptococci isolates from human. These results suggest that CFFB isolated from healthy Sichuan golden snub-nosed monkeys may have its origin in human S. agalactiae. Our results suggested some genomic similarities between the S. agalactiae colonized in Sichuan golden snub-nosed monkey and those in infected humans.
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Affiliation(s)
- Zhang Shidan
- Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Sanya, 572000, China; OIE Reference Laboratory for Swine Streptococcosis, Nanjing Agricultural University, Nanjing, 210095, China
| | - Liang Song
- OIE Reference Laboratory for Swine Streptococcosis, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhang Yumin
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai, 201100, China
| | - Chen Rong
- Nanjing Hongshan Forest Zoo, Nanjing, 210028, China
| | - Wang Siteng
- OIE Reference Laboratory for Swine Streptococcosis, Nanjing Agricultural University, Nanjing, 210095, China
| | - Li Meirong
- Nanjing Hongshan Forest Zoo, Nanjing, 210028, China.
| | - Liu Guangjin
- Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Sanya, 572000, China; OIE Reference Laboratory for Swine Streptococcosis, Nanjing Agricultural University, Nanjing, 210095, China.
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16
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Plomp N, Harmsen HJM. Description of Faecalibacterium wellingii sp. nov. and two Faecalibacterium taiwanense strains, aiding to the reclassification of Faecalibacterium species. Anaerobe 2024; 89:102881. [PMID: 38925221 DOI: 10.1016/j.anaerobe.2024.102881] [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: 04/05/2024] [Revised: 06/09/2024] [Accepted: 06/23/2024] [Indexed: 06/28/2024]
Abstract
OBJECTIVES The genus Faecalibacterium is one of the most important butyrate producers in the human intestinal tract and has been widely linked to health. Recently, several different species have been described, but still more phylogroups have been identified, suggesting that additional species may exist. Four strains HTF-FT, HTF-128, HTF-75H and HTF-76H, representing two different phylogenetic clusters, are evaluated in this study. METHODS Phylogenomic analysis was performed using whole-genome sequences and 16S rRNA gene sequences. Chemotaxonomic analysis was done based on matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Physiological and phenotypical characteristics of these strains were also determined. All characteristics of these strains were compared with other validly published species within the genus Faecalibacterium. RESULTS On a genomic level, the strains HTF-FT and HTF-128 shared an average nucleotide identity (ANI) of <95.0 % and digital DNA-DNA hybridization (dDDH) of <70.0 with other Faecalibacterium species, while between HTF-FT and HTF-128 the ANI-value was 97.18 % and the dDDH was 76.8 %. HTF-75H and HTF-76H had an ANI and dDDH value of 100 % (99.96 %) and 100 % (99.99 %) respectively. Both HTF-75H and HTF-76H were closely related to Faecalibacterium taiwanense HLW78T. 16S rRNA gene and chemotaxonomic analysis were in accordance with the genomic data, confirming that HTF-FT and HTF-128 represent a novel Faecalibacterium species and HTF-75H and HTF-76H belong to F. taiwanense. CONCLUSIONS Faecalibacterium strains HTF-FT (=DSM 117771T = NCIMB 15531T) and HTF-128 represent a novel species. The name Faecalibacterium wellingii with HTF-FT as type strain is proposed. Two novel isolates HTF-75H (=DSM 17770 = NCIMB 15530) and HTF-76H are described in this study and belong to the recently described Faecalibacterium taiwanense.
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Affiliation(s)
- Niels Plomp
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ, Groningen, the Netherlands.
| | - Hermie J M Harmsen
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ, Groningen, the Netherlands.
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17
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Thanasak J, Wongsurawat T, Jenjaroenpun P, Phumthanakorn N. Characterization of staphylococcal cassette chromosome mec in Staphylococcus haemolyticus ST3 and ST42 isolates from bovine mastitis milk: identification of novel variant in class C1 mec complex. J Antimicrob Chemother 2024; 79:2479-2483. [PMID: 39082161 DOI: 10.1093/jac/dkae242] [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: 03/06/2024] [Accepted: 06/28/2024] [Indexed: 10/02/2024] Open
Abstract
BACKGROUND Methicillin-resistant Staphylococcus haemolyticus (MRSH) is an important pathogenic agent of bovine mastitis. Among the prominent clone lineages in dairy cows are MRSH sequence types ST3 and ST42. Little information is available on the complete characterization of SCCmec elements in MRSH. OBJECTIVE In this study, two clinical isolates of MRSH ST3 and ST42 from bovine mastitis milk were selected, and their nontypable SCCmec structures were compared. METHODS Two MRSH strains, MRSH-ST3 strain M62.3 and MRSH-ST42 strain M81.1, were identified from bovine mastitis milk in Thailand in 2022. Minimum inhibitory concentration was used to screen for antimicrobial resistance susceptibility. Oxford Nanopore Technologies and Illumina sequencing were performed in combination to complete the genome. Their gene organization and structure of SCCmec types were analysed and compared with the whole sequences of other strains in the same sequence types. RESULTS Both MRSH-ST3 strain M62.3 and MRSH-ST42 strain M81.1 possessed the class C1 mec complex but lacked the ccr gene complex. Notably, MRSH-ST42 strain M81.1 contained a novel variant of C1 mec complex, which consisted of IS431-mecA-ISSha1-paaZ-upgQ-IS431, with IS431 organized in the same orientation. Apart from class C1 mec and the heavy metal-resistant cluster, the gene composition and order of the SCCmec element varied. In ST3, variations in the SCCmec type, gene content and organization were observed. CONCLUSIONS The distinct evolution of the MRSH lineage was indicated by the various SCCmec elements. The insertion of ISSha1 resulted in a unique variant of class C1 mec complex that demonstrated the important role of the insertion sequence in SCCmec diversification.
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Affiliation(s)
- Jitkamol Thanasak
- Department of Clinical Sciences and Public Health, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, Thailand
| | - Thidathip Wongsurawat
- Division of Medical Bioinformatics, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Piroon Jenjaroenpun
- Division of Medical Bioinformatics, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Nathita Phumthanakorn
- Department of Pre-clinic and Applied Animal Science, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, Thailand
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Wise MG, DeRyke CA, Alekseeva I, Siddiqui F, Young K, Motyl MR, Sahm DF. Susceptibility of Gram-negative pathogens collected in Israel to ceftolozane/tazobactam, imipenem/relebactam and comparators: SMART 2018-22. JAC Antimicrob Resist 2024; 6:dlae150. [PMID: 39291180 PMCID: PMC11406551 DOI: 10.1093/jacamr/dlae150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2024] [Accepted: 09/02/2024] [Indexed: 09/19/2024] Open
Abstract
Objectives To assess the in vitro antimicrobial activity of ceftolozane/tazobactam, imipenem/relebactam and comparator agents against clinical isolates of Gram-negative bacilli collected in Israel from 2018 to 2022. Methods Six clinical laboratories each collected up to 250 consecutive Gram-negative isolates per year from patients with bloodstream, intra-abdominal, lower respiratory tract and urinary tract infections. MICs were determined by CLSI broth microdilution and interpreted with 2024 EUCAST breakpoints. Acquired β-lactamase gene carriage was investigated for most ceftolozane/tazobactam- and imipenem/relebactam-resistant isolates. Results Among the full collection of Enterobacterales (n = 4420), 95.1% were susceptible to ceftolozane/tazobactam, including 95.3% of putative AmpC/ESBL-positive, non-carbapenem-resistant Enterobacterales (CRE) phenotype Escherichia coli and 86.6% of AmpC/ESBL-positive, non-CRE phenotype Klebsiella pneumoniae. Overall, 99.8% of non-Morganellaceae Enterobacterales (n = 3723) were imipenem/relebactam susceptible including 98% of the MDR isolates. Most Pseudomonas aeruginosa isolates (n = 1182) were inhibited by ceftolozane/tazobactam (93.9% susceptible) and imipenem/relebactam (94.7%). Imipenem/relebactam retained activity against ≥78% of cefepime-resistant, ceftazidime-resistant, and piperacillin/tazobactam-resistant P. aeruginosa, while ceftolozane/tazobactam inhibited the greatest percentage of meropenem-resistant P. aeruginosa (67.4%) among comparator β-lactam antimicrobials. Molecular characterization showed the majority of imipenem/relebactam-resistant Enterobacterales harboured a metallo-β-lactamase, while half of the ceftolozane/tazobactam-resistant Enterobacterales carried an acquired ESBL or AmpC. Most of the imipenem/relebactam- and ceftolozane/tazobactam-resistant P. aeruginosa characterized did not possess acquired β-lactamases. Conclusions Recent clinical isolates of Enterobacterales and P. aeruginosa collected in Israel were highly susceptible to ceftolozane/tazobactam and imipenem/relebactam.
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Rothrock MJ, Al Hakeem WG, Oladeinde A, Looft T, Li X, Guard JY. Salmonella Biomapping of a Commercial Broiler Hatchery. J Food Prot 2024; 87:100347. [PMID: 39151796 DOI: 10.1016/j.jfp.2024.100347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Revised: 08/09/2024] [Accepted: 08/12/2024] [Indexed: 08/19/2024]
Abstract
Poultry-associated salmonellosis results in significant costs to poultry producers and consumers. Given the vertically integrated nature of the United States poultry industry, a better understanding of Salmonella ecology throughout all levels of poultry production is essential. One nexus point is the hatchery, where eggs from multiple broiler breeder farms are incubated and hatched, with the chicks being sent to numerous farms; therefore, the hatchery represents an ideal area to understand preharvest Salmonella ecology and flow. To achieve this, a commercial broiler hatchery was biomapped, focusing on Salmonella prevalence and serotype diversity among four major sample type categories (Air, Egg, Water, Facility) across five different places in the prehatch, hatch, and posthatch areas. Following two sets of eggs from broiler breeder farms over two production days, the overall Salmonella prevalence was 26% (48/184). Of the positive samples, the highest prevalence was observed in swabs taken from the floor drains in the facility and transport truck (56%), as well as in the hatch and posthatch hatchery areas (50%). Kentucky (n = 17), Gaminara (n = 12), and Alachua (n = 11) were the dominant Salmonella serotypes, with serotypes of greatest outbreak concern from chickens (Enteritidis) representing only 6.25% (3/48) of all recovered Salmonella isolates. The posthatch transport area, including the underfloor reservoirs of the transport trucks, not only harbored Enteritidis but also the enrichment broths from these Salmonella-positive samples also possessed sequences matching the commercial live-attenuated vaccine Typhimurium strain according to CRISPR SeroSeq analyses. These findings highlight the complex diversity of commercial hatchery Salmonella populations, including identifying facility floor drains and transport trucks as potentially important critical control points for hatchery managers to focus their Salmonella mitigation efforts to reduce loads and serotypes entering live production farms.
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Affiliation(s)
- Michael J Rothrock
- USDA-ARS, US National Poultry Research Center, Egg & Poultry Production Safety Research Unit, Athens, Georgia, USA.
| | - Walid G Al Hakeem
- USDA-ARS, US National Poultry Research Center, Egg & Poultry Production Safety Research Unit, Athens, Georgia, USA; US-DOE, ORISE, USA
| | - Adelumola Oladeinde
- USDA-ARS, US National Poultry Research Center, Egg & Poultry Production Safety Research Unit, Athens, Georgia, USA
| | - Torey Looft
- USDA-ARS, National Animal Disease Center, Ames, Iowa, USA
| | - Xiang Li
- USDA-ARS, US National Poultry Research Center, Egg & Poultry Production Safety Research Unit, Athens, Georgia, USA
| | - Jean Y Guard
- USDA-ARS, US National Poultry Research Center, Egg & Poultry Production Safety Research Unit, Athens, Georgia, USA
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20
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Zhang XW, Song JJ, Zeng SH, Huang YL, Luo JJ, Guo WL, Li XY. Plasmid-mediated azithromycin resistance in non-typhoidal Salmonella recovered from human infections. J Antimicrob Chemother 2024; 79:2688-2697. [PMID: 39119898 PMCID: PMC11442001 DOI: 10.1093/jac/dkae281] [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: 12/13/2023] [Accepted: 07/11/2024] [Indexed: 08/10/2024] Open
Abstract
OBJECTIVES Mechanisms of non-typhoidal Salmonella (NTS) resistance to azithromycin have rarely been reported. Here we investigate the epidemiology and genetic features of 10 azithromycin-resistant NTS isolates. METHODS A total of 457 NTS isolates were collected from a tertiary hospital in Guangzhou. We performed antimicrobial susceptibility tests, conjugation experiments, efflux pump expression tests, whole-genome sequencing and bioinformatics analysis to conduct the study. RESULTS The results showed that 10 NTS isolates (2.8%) were resistant to azithromycin with minimum inhibitory concentration values ranging from 128 to 512 mg/L and exhibited multidrug resistance. The phylogenetic tree revealed that 5 S. London isolates (AR1-AR5) recognized at different times and departments were closely related [3-74 single-nucleotide polymorphisms (SNPs)] and 2 S. Typhimurium isolates (AR7 and AR8) were clones (<3 SNPs) at 3-month intervals. The azithromycin resistance was conferred by mph(A) gene found on different plasmids, including IncFIB, IncHI2, InFII, IncC and IncI plasmids. Among them, IncFIB, InFII and IncHI2 plasmids carried different IS26-class 1 integron (intI1) arrangement patterns that mediated multidrug resistance transmission. Conjugative IncC plasmid encoded resistance to ciprofloxacin, ceftriaxone and azithromycin. Furthermore, phylogenetic analysis demonstrated that mph(A)-positive plasmids closely related to 10 plasmids in this study were mainly discovered from NTS, Escherichia coli, Klebsiella pneumonia and Enterobacter hormaechei. The genetic environment of mph(A) in 10 NTS isolates was IS26-mph(A)-mrx(A)-mphR(A)-IS6100/IS26 that co-arranged with intI1 harbour multidrug-resistant (MDR) gene cassettes on diverse plasmids. CONCLUSIONS These findings highlighted that the dissemination of these plasmids carrying mph(A) and various intI1 MDR gene cassettes would seriously restrict the availability of essential antimicrobial agents for treating NTS infections.
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Affiliation(s)
- Xi-Wei Zhang
- Department of Clinical Laboratory, Fifth Affiliated Hospital, Southern Medical University, Guangzhou, China
| | - Jing-Jie Song
- Department of Clinical Laboratory, Fifth Affiliated Hospital, Southern Medical University, Guangzhou, China
| | - Shi-Han Zeng
- Department of Clinical Laboratory, Fifth Affiliated Hospital, Southern Medical University, Guangzhou, China
| | - Yu-Lan Huang
- Department of Clinical Laboratory, Fifth Affiliated Hospital, Southern Medical University, Guangzhou, China
| | - Jia-Jun Luo
- Department of Clinical Laboratory, Fifth Affiliated Hospital, Southern Medical University, Guangzhou, China
| | - Wei-Long Guo
- Department of Clinical Laboratory, Fifth Affiliated Hospital, Southern Medical University, Guangzhou, China
| | - Xiao-Yan Li
- Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde), No. 1 Jiazi Road, Lunjiao, Shunde District, Foshan City, Guangdong Province, China
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Yang Q, Li L, Zhao G, Cui Q, Gong X, Ying L, Yang T, Fu M, Shen Z. Characterization of a multiresistance optrA- and lsa(E)-harbouring unconventional circularizable structure in Streptococcus suis. J Antimicrob Chemother 2024; 79:2528-2533. [PMID: 39086116 DOI: 10.1093/jac/dkae250] [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: 02/22/2024] [Accepted: 06/28/2024] [Indexed: 08/02/2024] Open
Abstract
OBJECTIVES To identify novel genetic elements facilitating the horizontal transfer of the oxazolidinone/phenicol resistance gene optrA and the pleuromutilin-lincosamide-streptogramin A resistance gene lsa(E) in Streptococcus suis. METHODS The complete genomes of S. suis HB18 and two transconjugants were obtained using both the Illumina and Nanopore platforms. MICs were determined by broth microdilution. Inverse PCR was performed to identify circular forms of the novel unconventional circularizable structure (UCS), genomic island (GI) and integrative and conjugative element (ICE). Conjugation experiments assessed the transferability of optrA and lsa(E) genes in S. suis. RESULTS S. suis HB18 carried a multiresistance gene cluster optrA-lsa(E)-lnu(B)-aphA-aadE-spw. This gene cluster, flanked by intact and truncated erm(B) in the same orientation, resided on a novel ICESsuHB18. Inverse PCR revealed the existence of a novel UCS, named UCS-optrA + lsa(E), which could excise the gene cluster optrA-lsa(E)-lnu(B)-aphA-aadE-spw and one copy of erm(B) from ICESsuHB18. Two transconjugants with different characteristics were obtained. In transconjugant T-JH-GI, UCS-optrA + lsa(E) excised from ICESsuHB18 inserted into the erm(B)-positive GI, designated GISsuHB18, generating the novel GISsuHB18-1. Meanwhile, in T-JH-ICE, genetic rearrangement events occurred in ICESsuHB18 and GISsuHB18, forming the novel ICESsuHB18-1. CONCLUSIONS This is the first report demonstrating the functionally active UCS-optrA + lsa(E) excising from ICESsuHB18 and inserting into the erm(B)-positive GISsuHB18 during the conjugation process. The location of optrA and lsa(E) on a multiresistance UCS enhances its persistence and dissemination.
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Affiliation(s)
- Qin Yang
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Luxin Li
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Guanzheng Zhao
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Qingpo Cui
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Xiaowei Gong
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Luyu Ying
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Tingting Yang
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Mengjiao Fu
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Zhangqi Shen
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
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Li Q, Yang J, Wang M, Jia R, Chen S, Liu M, Zhu D, Zhao X, Wu Y, Yang Q, Huang J, Ou X, Sun D, Tian B, He Y, Wu Z, Cheng A, Zhang S. Global distribution and genomic characteristics analysis of avian-derived mcr-1-positive Escherichia coli. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 285:117109. [PMID: 39353372 DOI: 10.1016/j.ecoenv.2024.117109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2024] [Revised: 09/23/2024] [Accepted: 09/24/2024] [Indexed: 10/04/2024]
Abstract
The prevalence of avian-derived Escherichia coli (E. coli) carrying mcr-1 poses a significant threat to the development of the poultry industry and public health safety. Despite ongoing in-depth epidemiological research worldwide, a comprehensive macroscopic study based on genomics is still lacking. In response, this study collected 1104 genomic sequences of avian-derived mcr-1-positive E. coli (MCRPEC) from the NCBI public database, covering 31 countries. The majority of sequences originated from China (48.82 %), followed by the Netherlands (10.41 %). In terms of avian hosts, chicken accounted for the largest proportion (44.11 %), followed by gallus (24.09 %). Avian-derived MCRPEC also serves as a reservoir for other antibiotic resistance genes (ARGs), with 179 ARGs coexisting with mcr-1 identified. A total of 206 virulence-associated genes were also identified, revealing the pathogenic risks of MCRPEC. Pan-genome analysis revealed that avian-derived MCRPEC from different hosts, countries of origin, and serotypes exhibit minor SNP differences, indicating a high risk of cross-regional and cross-host transmission. The ST types of MCRPRC are diverse, with ST10 being the most prevalent (n=70). Spearman analysis showed a significant correlation between the number of ARGs and the insertion sequences (ISs) as well as plasmid replicon in ST10 strains. Furthermore, ST10 strains share a similar genetic basis with human-derived MCRPEC, suggesting the possibility of clonal dissemination. Pan-genome-wide association studies (pan-GWAS) indicated that the differential genes of MCRPEC from different countries and host sources are significantly different, mainly related to genes encoding type IV secretion systems and mobile genetic elements (MGEs). Plasmid mapping of showed that the prevalent plasmid types vary by country and host, with IncI2 and IncX4 being the main mcr-1-positive plasmids. Among the 12 identified mcr-1 genetic contexts with ISs, the Tn6330 transposon was the predominant carrier of mcr-1. In summary, the potential threat of avian-derived MCRPEC cannot be ignored, and long-term and comprehensive monitoring are essential.
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Affiliation(s)
- Qianlong Li
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Jing Yang
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Mingshu Wang
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the P.R.China, PR China
| | - Renyong Jia
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the P.R.China, PR China
| | - Shun Chen
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the P.R.China, PR China
| | - Mafeng Liu
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the P.R.China, PR China
| | - Dekang Zhu
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the P.R.China, PR China
| | - Xinxin Zhao
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the P.R.China, PR China
| | - Ying Wu
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the P.R.China, PR China
| | - Qiao Yang
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the P.R.China, PR China
| | - Juan Huang
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the P.R.China, PR China
| | - Xumin Ou
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the P.R.China, PR China
| | - Di Sun
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the P.R.China, PR China
| | - Bin Tian
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the P.R.China, PR China
| | - Yu He
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the P.R.China, PR China
| | - Zhen Wu
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the P.R.China, PR China
| | - Anchun Cheng
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the P.R.China, PR China.
| | - Shaqiu Zhang
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the P.R.China, PR China.
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de Almeida EL, O'Toole PW, Bassett SA. Genome sequence of the New Zealand raw milk isolate and candidate probiotic strain Lactococcus lactis FNZ339. Microbiol Resour Announc 2024:e0064824. [PMID: 39345185 DOI: 10.1128/mra.00648-24] [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: 07/03/2024] [Accepted: 08/29/2024] [Indexed: 10/01/2024] Open
Abstract
The complete genome sequence of the candidate probiotic strain Lactococcus lactis FNZ339 was determined using a hybrid genome assembly comprising data from Illumina and Oxford Nanopore Technologies sequencing platforms. The genome assembly comprised 2,673,297 bp, including the complete circular chromosome and four circular plasmids.
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Affiliation(s)
| | - Paul W O'Toole
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Shalome A Bassett
- Fonterra Research and Development Centre, Palmerston North, New Zealand
- Riddet Institute, Massey University, Palmerston North, New Zealand
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24
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de Almeida EL, O'Toole PW, Bassett SA. Genome sequence of the New Zealand cheese isolate and candidate probiotic strain Lactiplantibacillus plantarum FNZ042. Microbiol Resour Announc 2024:e0064724. [PMID: 39345104 DOI: 10.1128/mra.00647-24] [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: 06/28/2024] [Accepted: 08/29/2024] [Indexed: 10/01/2024] Open
Abstract
The complete genome sequence of the candidate probiotic strain Lactiplantibacillus plantarum FNZ042 was determined using a hybrid genome assembly comprising data from Illumina and PacBio sequencing platforms. The genome assembly comprised 3,265,637 bp, including the complete circular chromosome and three circular plasmids.
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Affiliation(s)
| | - Paul W O'Toole
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Shalome A Bassett
- Fonterra Research & Development Centre, Palmerston North, New Zealand
- Riddet Institute, Massey University, Palmerston North, New Zealand
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Naqvi M, Utheim TP, Charnock C. Whole genome sequencing and characterization of Corynebacterium isolated from the healthy and dry eye ocular surface. BMC Microbiol 2024; 24:368. [PMID: 39342108 PMCID: PMC11438203 DOI: 10.1186/s12866-024-03517-9] [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: 04/21/2024] [Accepted: 09/11/2024] [Indexed: 10/01/2024] Open
Abstract
BACKGROUND The purpose of this study was to characterize Corynebacterium isolated from the ocular surface of dry eye disease patients and healthy controls. We aimed to investigate the pathogenic potential of these isolates in relation to ocular surface health. To this end, we performed whole genome sequencing in combination with biochemical, enzymatic, and antibiotic susceptibility tests. In addition, we employed deferred growth inhibition assays to examine how Corynebacterium isolates may impact the growth of potentially competing microorganisms including the ocular pathogens Pseudomonas aeruginosa and Staphylococcus aureus, as well as other Corynebacterium present on the eye. RESULTS The 23 isolates were found to belong to 8 different species of Corynebacterium with genomes ranging from 2.12 mega base pairs in a novel Corynebacterium sp. to 2.65 mega base pairs in C. bovis. Whole genome sequencing revealed the presence of a range of antimicrobial targets present in all isolates. Pangenome analysis showed the presence of 516 core genes and that the pangenome is open. Phenotypic characterization showed variously urease, lipase, mucinase, protease and DNase activity in some isolates. Attention was particularly drawn to a potentially new or novel Corynebacterium species which had the smallest genome, and which produced a range of hydrolytic enzymes. Strikingly the isolate inhibited in vitro the growth of a range of possible pathogenic bacteria as well as other Corynebacterium isolates. The majority of Corynebacterium species included in this study did not seem to possess canonical pathogenic activity. CONCLUSIONS This study is the first reported genomic and biochemical characterization of ocular Corynebacterium. A number of potential virulence factors were identified which may have direct relevance for ocular health and contribute to the finding of our previous report on the ocular microbiome, where it was shown that DNA libraries were often dominated by members of this genus. Particularly interesting in this regard was the observation that some Corynebacterium, particularly new or novel Corynebacterium sp. can inhibit the growth of other ocular Corynebacterium as well as known pathogens of the eye.
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Affiliation(s)
- Maria Naqvi
- Department of Life Sciences and Health, Faculty of Health Sciences, Oslo Metropolitan University, Postbox 4, St. Olavs Plass, Oslo, 0130, Norway.
| | - Tor P Utheim
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway
- Department of Ophthalmology, Oslo University Hospital, Oslo, Norway
- The Norwegian Dry Eye Clinic, Ole Vigs gate 32 E, Oslo, 0366, Norway
| | - Colin Charnock
- Department of Life Sciences and Health, Faculty of Health Sciences, Oslo Metropolitan University, Postbox 4, St. Olavs Plass, Oslo, 0130, Norway
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Hongzhi Z, Wenjie C, Xiaoyu L, Yingying L, Quan X, Tianqi S, Ying Y, Ruichao L, Huanyu W. Identification of Polymyxin Resistance Gene mcr-10 from Different Food Samples in Shanghai, China. Foodborne Pathog Dis 2024. [PMID: 39330941 DOI: 10.1089/fpd.2024.0049] [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: 09/28/2024] Open
Abstract
This retrospective investigation (2019-2022) identified two plasmid-mediated mcr-10 from 6800 food samples in Shanghai, China and localized in a conjugative plasmid (pEC1918-mcr10) in Escherichia kobei from ready-to-eat food with high-level polymyxin B resistance, and a nonconjugative plasmid (pEC2001-mcr10) in E. coli from chicken. These genes were adjacent to ISEc36. This report highlights the emergence of mcr-10 from food samples in Shanghai, China. Active surveillance of vital resistance genes along food production chain should be performed.
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Affiliation(s)
- Zhang Hongzhi
- Shanghai Municipal Center for Disease Prevention and Control, Shanghai, People's Republic of China
| | - Chen Wenjie
- Shanghai Municipal Center for Disease Prevention and Control, Shanghai, People's Republic of China
| | - Lu Xiaoyu
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Disease and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, People's Republic of China
| | - Liang Yingying
- Shanghai Municipal Center for Disease Prevention and Control, Shanghai, People's Republic of China
| | - Xiao Quan
- Shanghai Municipal Center for Disease Prevention and Control, Shanghai, People's Republic of China
| | - Shi Tianqi
- Shanghai Municipal Center for Disease Prevention and Control, Shanghai, People's Republic of China
| | - Yu Ying
- Shanghai Municipal Center for Disease Prevention and Control, Shanghai, People's Republic of China
| | - Li Ruichao
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Disease and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, People's Republic of China
| | - Wu Huanyu
- Shanghai Municipal Center for Disease Prevention and Control, Shanghai, People's Republic of China
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Loncaric I, Szostak MP, Cabal-Rosel A, Grünzweil OM, Riegelnegg A, Misic D, Müller E, Feßler AT, Braun SD, Schwarz S, Monecke S, Ehricht R, Ruppitsch W, Spergser J, Lewis A, Bloom PH, Saggese MD. Molecular characterization, virulence and antimicrobial and biocidal susceptibility of selected bacteria isolated from the cloaca of nestling ospreys (Pandion haliaetus) from Mono Lake, California, USA. PLoS One 2024; 19:e0311306. [PMID: 39331631 PMCID: PMC11432900 DOI: 10.1371/journal.pone.0311306] [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: 05/28/2024] [Accepted: 09/06/2024] [Indexed: 09/29/2024] Open
Abstract
In the present study, the presence of the Enterobacterales, Staphylococcus spp., Mammaliicoccus spp., and Enterococcus spp. in cloacal samples of nestling ospreys (Pandion haliaetus), a fish-eating specialist, from Mono Lake, California, USA was examined by a multiphasic approach, including antimicrobial and biocide susceptibility testing, genotyping, and whole genome sequencing of selected isolates. The most commonly detected species was Escherichia coli, followed by Mammaliicoccus sciuri, Staphylococcus delphini, Enterococcus faecalis, Enterococcus faecium, Hafnia alvei, Klebsiella pneumoniae, Citrobacter braakii and single isolates of Edwardsiella tarda, Edwardsiella albertii, Klebsiella aerogenes, Plesiomonas shigelloides and Staphylococcus pseudintermedius. Multi-drug resistance (MDR) was observed in two E. coli isolates and in an Enterococcus faecium isolate. The MDR blaCTX-M-55-positive E. coli belonged to the pandemic clone ST58. The results of the present study suggest that nestling ospreys are exposed to MDR bacteria, possibly through the ingestion of contaminated fish. Ospreys may be good biosentinels for the presence of these microorganisms and antibiotic resistance in the local environment and the risk for other wildlife, livestock and humans.
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Affiliation(s)
- Igor Loncaric
- Institute of Microbiology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Michael P Szostak
- Institute of Microbiology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Adriana Cabal-Rosel
- Austrian Agency for Health and Food Safety (AGES), Institute of Medical Microbiology and Hygiene, Vienna, Austria
| | - Olivia M Grünzweil
- Institute of Microbiology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Alina Riegelnegg
- Institute of Microbiology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Dusan Misic
- Department of Functional Food Products Development, Faculty of Biotechnology and Food Science, Wroclaw University of Environmental and Life Sciences, Wroclaw, Poland
| | - Elke Müller
- Leibniz Institute of Photonic Technology (IPHT), Jena, Germany
- InfectoGnostics Research Campus, Jena, Germany
| | - Andrea T Feßler
- Centre of Infection Medicine, School of Veterinary Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), School of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Sascha D Braun
- Leibniz Institute of Photonic Technology (IPHT), Jena, Germany
- InfectoGnostics Research Campus, Jena, Germany
| | - Stefan Schwarz
- Centre of Infection Medicine, School of Veterinary Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), School of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Stefan Monecke
- Leibniz Institute of Photonic Technology (IPHT), Jena, Germany
- InfectoGnostics Research Campus, Jena, Germany
- Institut für Medizinische Mikrobiologie und Hygiene, Universitätsklinik Dresden, Dresden, Germany
| | - Ralf Ehricht
- Leibniz Institute of Photonic Technology (IPHT), Jena, Germany
- InfectoGnostics Research Campus, Jena, Germany
- Institute of Physical Chemistry, Friedrich Schiller University, Jena, Germany
| | - Werner Ruppitsch
- Austrian Agency for Health and Food Safety (AGES), Institute of Medical Microbiology and Hygiene, Vienna, Austria
| | - Joachim Spergser
- Institute of Microbiology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Ashli Lewis
- California State Parks, Grass Valley, CA, United States of America
| | - Peter H Bloom
- Bloom Research Inc, Santa Ana, CA, United States of America
| | - Miguel D Saggese
- College of Veterinary Medicine, Western University of Health Sciences, Pomona, CA, United States of America
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de Oliveira VF, de Britto-Costa LF, de Aragão GL, Scaccia N, Mamana AC, Côrtes MF, de Oliveira MS, de Melo Tavares B, Manuli ER, Leal FE, de Oliveira Xavier GT, Grespan RMZ, Sequeira CCR, Nunes FLS, Dropa M, Martone-Rocha S, Razzolini MTP, Sabino EC, Padoveze MC, Holmes A, Costa SF, Levin AS. Colonisation by multidrug-resistant organisms in health workers in primary care: narrow spectrum oral antimicrobials are a risk factor. Eur J Clin Microbiol Infect Dis 2024:10.1007/s10096-024-04953-1. [PMID: 39320520 DOI: 10.1007/s10096-024-04953-1] [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: 07/12/2024] [Accepted: 09/20/2024] [Indexed: 09/26/2024]
Abstract
BACKGROUND Limited information exists on carriage of multidrug-resistant organisms (MDRO) by health workers (HWs) in primary care settings. This study aims to determine the prevalence of MDRO carriage among HWs in primary care and to identify associated risk factors. METHODS A cross-sectional study was conducted across all 12 primary care units in São Caetano do Sul-SP, Brazil, from October to December 2023. Self-collected samples (nasal, oropharyngeal, and inguinal) were obtained. Environment cultures (potable water, sewage and stream water) were evaluated. Stenotrophomonas maltophilia isolates (human and environmental) were typed. RESULTS The study included 265/288 (92%) of HWs in primary care teams, mostly women with a median age of 47 years (IQR 38-57); 78% had no comorbidities. MDRO colonisation was found in 8.7% (23 HWs). The following bacteria were found: S. maltophilia (n = 9; 3.4%) in inguinal swabs; methicillin-resistant Staphylococcus aureus (n = 8; 3%) from all sites; extended-spectrum ß-lactamase-producing bacteria (n = 5; 2%) in inguinal swabs; and vancomycin-resistant enterococci in an inguinal swab (n = 1; 0.4%). Previous antibiotic use was significantly associated with MDRO colonisation (OR 2.91, 95% CI 1.19-7.09, p = 0.018), mainly narrow spectrum oral beta-lactams and macrolides. S. malthophilia was polyclonal and human and environmental isolates differed. CONCLUSION Colonisation by MRSA, VRE, and ESBL-producing bacteria was low; however, 4% were surprisingly colonized by polyclonal S. maltophilia. This pathogen may also suggest using narrow-spectrum rather than the expected broad-spectrum antimicrobials. Antibiotic use was the only risk factor found, mainly with oral narrow-spectrum drugs.
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Affiliation(s)
- Vítor Falcão de Oliveira
- Division of Infectious Diseases, Hospital das Clinicas, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil.
| | | | | | - Nazareno Scaccia
- Institute of Tropical Medicine, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Ana Carolina Mamana
- Institute of Tropical Medicine, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Marina Farrel Côrtes
- Institute of Tropical Medicine, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Maura Salaroli de Oliveira
- Division of Infectious Diseases, Hospital das Clinicas, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Bruno de Melo Tavares
- Division of Infectious Diseases, Hospital das Clinicas, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Erika Regina Manuli
- Division of Infectious Diseases, Hospital das Clinicas, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil
- Institute of Tropical Medicine, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil
- Departamento de Pesquisa Clínica E Inovação Em Saúde, Universidade Municipal de São Caetano Do Sul, Sao Paulo, Brazil
| | - Fábio Eudes Leal
- Departamento de Pesquisa Clínica E Inovação Em Saúde, Universidade Municipal de São Caetano Do Sul, Sao Paulo, Brazil
- Divisão de Pesquisa Clínica (DIPETEC), Instituto Nacional Do Câncer, Rio de Janeiro, Brazil
| | | | - Regina Maura Zetone Grespan
- Departamento de Pesquisa Clínica E Inovação Em Saúde, Universidade Municipal de São Caetano Do Sul, Sao Paulo, Brazil
| | - Cibele Cristine Remondes Sequeira
- Municipal Health Department, Primary Health System, Sao Caetano Do Sul, Sao Paulo, Brazil
- Departamento de Pesquisa Clínica E Inovação Em Saúde, Universidade Municipal de São Caetano Do Sul, Sao Paulo, Brazil
| | - Fatima L S Nunes
- Laboratory for Informatics Applications in Health, School of Arts, Humanities and Science, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Milena Dropa
- School of Public Health, Universidade de Sao Paulo, Sao Paulo, Brazil
| | | | | | - Ester Cerdeira Sabino
- Division of Infectious Diseases, Hospital das Clinicas, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil
- Institute of Tropical Medicine, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil
- Departamento de Pesquisa Clínica E Inovação Em Saúde, Universidade Municipal de São Caetano Do Sul, Sao Paulo, Brazil
| | | | - Alison Holmes
- University of Liverpool and Imperial College London, London, UK
| | - Silvia F Costa
- Division of Infectious Diseases, Hospital das Clinicas, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil
- Institute of Tropical Medicine, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Anna S Levin
- Division of Infectious Diseases, Hospital das Clinicas, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil
- Institute of Tropical Medicine, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil
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Grenier F, Baby V, Allard S, Lévesque S, Papale F, Sullivan R, Landecker HL, Higgins PG, Rodrigue S, Haraoui LP. Isolation of a blaNDM-1-positive strain in Israel predating the earliest observations from India. Microbiol Spectr 2024:e0100224. [PMID: 39320107 DOI: 10.1128/spectrum.01002-24] [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: 04/25/2024] [Accepted: 08/28/2024] [Indexed: 09/26/2024] Open
Abstract
blaNDM, the most prevalent carbapenemase among carbapenem-resistant Enterobacteriaceae, is thought to have emerged in India, as its initial detection in 2008 was linked to this country, and subsequent retrospective surveys had so far established the earliest blaNDM-positive strains to be isolated in India in 2005. Molecular dating and analyses suggest blaNDM emerged within Acinetobacter species decades prior to 2005 on a Tn125 transposon. Despite early reports of elevated rates of carbapenem-resistant Acinetobacter species in Israel starting in the 1990s, limited molecular data are available from this location. We searched for blaNDM among Acinetobacter species isolated in Israel between 2001 and 2006. One A. junii strain, Ajun-H1-3, isolated in January 2004, carried blaNDM-1 within a Tn125-like transposon on a 49-kb plasmid, pNDM-Ajun-H1-3, making Ajun-H1-3 the earliest NDM-positive isolate observed to date. The pNDM-Ajun-H1-3 plasmid matched numerous BJ01-like NDM-positive plasmids identified from 2005 onward in Acinetobacter species as well as Enterobacterales. These results indicate the need for further retrospective work on global strain archives to shed light on the conditions favoring the emergence as well as subsequent evolution and spread of blaNDM. IMPORTANCE This study presents the earliest observation of blaNDM-1, isolated in a geographical region distant from where it is believed to have originated. In doing so, this study provides novel insights into the emergence and spread of blaNDM, the most prevalent carbapenemase among carbapenem-resistant Enterobacteriaceae, and its associated mobile genetic elements. It also sheds light on the conditions that foster the evolution of antimicrobial resistance, one of the greatest public health challenges we face.
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Affiliation(s)
- Frédéric Grenier
- Department of Biology, Faculty of Science, Université de Sherbrooke, Sherbrooke, Sherbrooke, Québec, Canada
| | - Vincent Baby
- Department of Biology, Faculty of Science, Université de Sherbrooke, Sherbrooke, Sherbrooke, Québec, Canada
| | - Sarah Allard
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Canada
| | - Simon Lévesque
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Canada
- CIUSSS de l'Estrie - CHUS, Sherbrooke, Québec, Canada
| | - François Papale
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Canada
| | - Richard Sullivan
- Conflict and Health Research Group, King's College London, London, United Kingdom
| | | | - Paul G Higgins
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- German Centre for Infection Research (DZIF), partner site Cologne-Bonn, Cologne, Germany
| | - Sébastien Rodrigue
- Department of Biology, Faculty of Science, Université de Sherbrooke, Sherbrooke, Sherbrooke, Québec, Canada
| | - Louis-Patrick Haraoui
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Canada
- Centre de recherche Charles-Le Moyne, CISSS Montérégie-Centre, Longueuil, Québec, Canada
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Hossain A, Hoque MN, Bukharid MZ, Hossain MA, Sultana M. Draft genome sequence of Achromobacter aegrifaciens BAW48 isolated from arsenic-contaminated tubewell water in Bangladesh. Microbiol Resour Announc 2024:e0009724. [PMID: 39315840 DOI: 10.1128/mra.00097-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 09/06/2024] [Indexed: 09/25/2024] Open
Abstract
We report the draft genome of Achromobacter aegrifaciens strain BAW48, a bacterium with a genome size of 6,877,653 bp. This genome comprises gene clusters for arsenic conversion, such as arsenic resistance (arsHCsO), arsenite oxidation (aioBA), and arsenate reduction (arsRCDAB), along with genes for heavy metal and antibiotic resistance.
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Affiliation(s)
- Anamica Hossain
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
| | - M Nazmul Hoque
- Molecular Biology and Bioinformatics Laboratory, Department of Gynaecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | | | - M Anwar Hossain
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
- Jashore University of Science and Technology, Jashore, Bangladesh
| | - Munawar Sultana
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
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Sereme Y, Faury H, Gravrand V, Ageron E, Poyart C, Skurnik D, Mammeri H. Molecular insights into the evolutionary trajectory of a Klebsiella aerogenes clinical isolate with a complex trade-off between resistance and virulence. Antimicrob Agents Chemother 2024:e0103624. [PMID: 39315804 DOI: 10.1128/aac.01036-24] [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: 07/10/2024] [Accepted: 09/05/2024] [Indexed: 09/25/2024] Open
Abstract
The fitness cost associated with antimicrobial resistance has an important influence on evolutionary dynamics. We compared the genomes of three Klebsiella aerogenes isolates recovered from blood samples or deep abscess cultures from the same patient: the wild-type strain (CT_WT), a piperacillin-tazobactam-resistant strain (CT_PENI), and an extended-spectrum-cephalosporin (ESC)-resistant strain (CT_R). Whole-genome sequencing revealed that CT_PENI had acquired a TEM-1 β-lactamase with a mutated promoter, accounting for overproduction. CT_PENI then acquired an E240G substitution in the TEM-1 β-lactamase (resulting in TEM-207) and lost the porin-encoding ompK36 gene to give CT_R. All three strains showed the same virulence in a mouse model of intraperitoneal infection. The results of recombination and transformation assays indicated that when present separately, the TEM-207 overproduction and the ompK36 gene deletion had only small effects on susceptibility to ESCs. However, the combination of the two changes led to a much lower susceptibility to ESCs. Moreover, the levels of fitness in vitro and in vivo in a murine model of gut colonization were significantly lower after TEM-1 β-lactamase overproduction and lower still after E240G substitution and OmpK36 loss. We hypothesize that the chosen courses of antibiotics led to the stepwise emergence of a clone with resistance to penicillins and ESCs and no loss of virulence. However, acquired resistance may have a fitness cost that limits evolutionary success. Our results might explain why the overproduction of extended-spectrum β-lactamases (which should confer a high level of piperacillin-tazobactam resistance) is not observed in clinical practice and why TEM-207 has rarely been detected in clinical isolates.
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Affiliation(s)
- Youssouf Sereme
- CNRS, INSERM, Institut Necker Enfants Malades, Université Paris Cité, Paris, France
| | - Hélène Faury
- CNRS, INSERM, Institut Necker Enfants Malades, Université Paris Cité, Paris, France
- Department of Clinical Microbiology, Necker-Enfants Malades Hospital, University Paris Cité, Paris, France
| | - Victor Gravrand
- Service de Bactériologie, Hôpitaux Universitaires Paris Centre, Site Cochin, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Elisabeth Ageron
- CNRS, INSERM, Institut Necker Enfants Malades, Université Paris Cité, Paris, France
| | - Claire Poyart
- Service de Bactériologie, Hôpitaux Universitaires Paris Centre, Site Cochin, Assistance Publique Hôpitaux de Paris, Paris, France
- Institut Cochin, INSERM U1016, CNRS UMR8104, Université de Paris, Paris, France
- FHU PREMA, Paris, France
| | - David Skurnik
- CNRS, INSERM, Institut Necker Enfants Malades, Université Paris Cité, Paris, France
- Department of Clinical Microbiology, Necker-Enfants Malades Hospital, University Paris Cité, Paris, France
- FHU PREMA, Paris, France
| | - Hedi Mammeri
- CNRS, INSERM, Institut Necker Enfants Malades, Université Paris Cité, Paris, France
- Service de Bactériologie, Hôpitaux Universitaires Paris Centre, Site Cochin, Assistance Publique Hôpitaux de Paris, Paris, France
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Verkaik NJ, Wielders CCH, den Boer H, Langerak D, Vogel M, Witteveen S, de Haan A, Bos J, van Westreenen M, Notermans DW, Hendrickx APA. Antimicrobial susceptibility to last-resort antibiotics in carbapenemase-producing bacteria from Ukrainian patients. Microbiol Spectr 2024:e0114224. [PMID: 39315812 DOI: 10.1128/spectrum.01142-24] [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: 05/21/2024] [Accepted: 07/18/2024] [Indexed: 09/25/2024] Open
Abstract
Since March 2022, an increase was observed in multidrug-resistant microorganisms (MDRO), associated with the hospital transfer of Ukrainian patients. The goal was to collect phenotypic susceptibility data and assess clinical implications. Carbapenemase-producing Enterobacterales (CPE, n = 96), Pseudomonas aeruginosa (CPPA, n = 20), and carbapenem-resistant Acinetobacter baumannii-calcoaceticus (CRAB, n = 6) from Ukrainian patients were obtained from March to December 2022 from the Dutch MDRO surveillance. Antimicrobial susceptibility testing was performed using broth microdilution (BMD) when available, fosfomycin agar dilution, disk diffusion (DD) for cefiderocol, and diverse gradient strips. All isolates were sequenced with Illumina next-generation sequencing. For meropenem, aminoglycosides, ceftazidime-avibactam, ceftolozane-tazobactam, and imipenem-relebactam, susceptibility rates were low (0%-30%), due to the high number of blaNDM-positive isolates (79/122; 65%). For cefiderocol, results depended on reading with or without microcolonies, applying EUCAST or CLSI breakpoints, and whether DD or BMD was used; e.g., for Klebsiella pneumoniae, 30%-97% were susceptible. For colistin, 103/111 (93%) non-intrinsically resistant CPE/CPPA/CRAB isolates were susceptible. For most CPE, a low minimal inhibitory concentration (MIC) of <0.5 mg/L was measured for tigecycline and ceftazidime-avibactam-aztreonam. For CPPA, cefiderocol tested susceptible in 65%-100% of isolates. For CRAB, ampicillin-sulbactam MICs were ≥128 mg/L; for sulbactam-durlobactam, 1-2 mg/L. Admission in a Ukrainian hospital in the last year was a risk factor for MDRO, and majority were screening isolates (79%). There is extensive phenotypic resistance to last-resort antibiotics in MDRO from Ukrainian patients. Interpretation of cefiderocol susceptibility results depends on several variables. When treating patients recently admitted in Ukraine, suspected for Gram-negative bacterial infection, this should be taken into consideration. IMPORTANCE Since March 2022, multidrug-resistant microorganisms associated with Ukrainian patients have been detected in national surveillance systems of several European countries. We studied the phenotypic antimicrobial susceptibility to last-resort antibiotics of multidrug-resistant microorganisms from Ukrainian patients in the Netherlands and assessed clinical implications. Our research revealed that there was extensive phenotypic resistance to last-resort antibiotics. Healthcare professionals should be aware of multidrug-resistant microorganisms when treating patients recently admitted in Ukraine, suspected for Gram-negative bacterial infection.
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Affiliation(s)
- Nelianne J Verkaik
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Cornelia C H Wielders
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Hans den Boer
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Diana Langerak
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Marius Vogel
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Sandra Witteveen
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Angela de Haan
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Jeroen Bos
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Mireille van Westreenen
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Daan W Notermans
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Antoni P A Hendrickx
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
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Qian C, Hu P, Guo W, Han Y, Yu P, Zhang Y, Ma Z, Chen L, Zhou T, Cao J. Genome analysis of tigecycline-resistant Acinetobacter baumannii reveals nosocomial lineage shifts and novel resistance mechanisms. J Antimicrob Chemother 2024:dkae314. [PMID: 39287979 DOI: 10.1093/jac/dkae314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Accepted: 08/19/2024] [Indexed: 09/19/2024] Open
Abstract
OBJECTIVES To investigate the characteristics and clonal dynamics of tigecycline-resistant Acinetobacter baumannii (TRAB) isolates from a Chinese hospital from 2016 to 2021. METHODS A total of 64 TRAB isolates were screened and WGS was performed. Phylogenetic analysis and non-polymorphic mutation analysis were used to analyse their clonal dynamics and tigecycline resistance-related mutations. RT-PCR was used to analyse the expression of the resistance-nodulation cell-division (RND) efflux pump genes adeB and adeJ. Gene cloning was used to explore the effect of tet(39) variants on tigecycline resistance. RESULTS Most TRAB isolates were found to be MDR, with 95% (61/64) of the isolates showing resistance to carbapenems. These TRAB isolates were classified into three primary genetic clusters based on core-genome SNPs. The KL2 cluster persisted throughout the study period, whereas the KL7 cluster emerged in 2019 and became the dominant clone. The KL7 cluster carried more antimicrobial resistance genes than the other two clusters. The predominant tigecycline resistance mechanism of the KL2 cluster and KL7 cluster was IS insertion in adeN (82.1%, 23/28) and genetic alterations in adeS (76.2%, 16/21), respectively. Eleven novel AdeS mutations were identified associated with elevated AdeB expression and tigecycline resistance. Moreover, we characterized a plasmid-borne tet(39) variant with an Ala-36-Thr substitution that synergizes with the RND efflux pump to confer high-level tigecycline resistance. CONCLUSIONS This work provides important insights into the diverse mechanisms associated with tigecycline resistance in A. baumannii, highlighting a pressing need for further monitoring of ST2-KL7 A. baumannii in clinical settings.
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Affiliation(s)
- Changrui Qian
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Wenzhou, Zhejiang Province, China
| | - Panjie Hu
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Wenhui Guo
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Wenzhou, Zhejiang Province, China
| | - Yijia Han
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Pingting Yu
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Wenzhou, Zhejiang Province, China
| | - Yi Zhang
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Zhexiao Ma
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Lijiang Chen
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Wenzhou, Zhejiang Province, China
| | - Tieli Zhou
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Wenzhou, Zhejiang Province, China
| | - Jianming Cao
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Wenzhou, Zhejiang Province, China
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
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Contarin R, Drapeau A, François P, Madec JY, Haenni M, Dordet-Frisoni E. The interplay between mobilome and resistome in Staphylococcus aureus. mBio 2024:e0242824. [PMID: 39287446 DOI: 10.1128/mbio.02428-24] [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: 08/08/2024] [Accepted: 08/26/2024] [Indexed: 09/19/2024] Open
Abstract
Antibiotic resistance genes (ARGs) in Staphylococcus aureus can disseminate vertically through successful clones, but also horizontally through the transfer of genes conveyed by mobile genetic elements (MGEs). Even though underexplored, MGE/ARG associations in S. aureus favor the emergence of multidrug-resistant clones, which are challenging therapeutic success in both human and animal health. This study investigated the interplay between the mobilome and the resistome of more than 10,000 S. aureus genomes from human and animal origin. The analysis revealed a remarkable diversity of MGEs and ARGs, with plasmids and transposons being the main carriers of ARGs. Numerous MGE/ARG associations were identified, suggesting that MGEs play a critical role in the dissemination of resistance. A high degree of similarity was observed in MGE/ARG associations between human and animal isolates, highlighting the potential for unrestricted spread of ARGs between hosts. Our results showed that in parallel to clonal expansion, MGEs and their associated ARGs can spread across different strain types sequence types (STs), favoring the evolution of these clones and their adaptation in selective environments. The high variability of MGE/ARG associations within individual STs and their spread across several STs highlight the crucial role of MGEs in shaping the S. aureus resistome. Overall, this study provides valuable insights into the complex interplay between MGEs and ARGs in S. aureus, emphasizing the need to elucidate the mechanisms governing the epidemic success of MGEs, particularly those implicated in ARG transfer.IMPORTANCEThe research presented in this article highlights the importance of understanding the interactions between mobile genetic elements (MGEs) and antibiotic resistance genes (ARGs) carried by Staphylococcus aureus, a versatile bacterium that can be both a harmless commensal and a dangerous pathogen for humans and animals. S. aureus has a great capacity to acquire and disseminate ARGs, enabling efficient adaption to various environmental or clinical conditions. By analyzing a large data set of S. aureus genomes, we highlighted the substantial role of MGEs, particularly plasmids and transposons, in disseminating ARGs within and between S. aureus populations, bypassing host barriers. Given that multidrug-resistant S. aureus strains are classified as a high-priority pathogen by global health organizations, this knowledge is crucial for understanding the complex dynamics of transmission of antibiotic resistance in this species.
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Affiliation(s)
- Rachel Contarin
- INTHERES, Université de Toulouse, INRAE, ENVT, Toulouse, France
- Anses-Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
| | - Antoine Drapeau
- Anses-Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
| | - Pauline François
- Anses-Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
| | - Jean-Yves Madec
- Anses-Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
| | - Marisa Haenni
- Anses-Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
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Abdullahi IN, Lozano C, Latorre-Fernández J, Zarazaga M, Stegger M, Torres C. Genomic analysis of multi-drug resistant coagulase-negative staphylococci from healthy humans and animals revealed unusual mechanisms of resistance and CRISPR-Cas system. Int Microbiol 2024:10.1007/s10123-024-00577-9. [PMID: 39287832 DOI: 10.1007/s10123-024-00577-9] [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: 05/17/2024] [Revised: 07/25/2024] [Accepted: 08/07/2024] [Indexed: 09/19/2024]
Abstract
BACKGROUND Coagulase-negative staphylococci (CoNS) are evolving as major reservoirs and vectors of unusual and critical antimicrobial resistance (AMR) mechanisms. MATERIALS AND METHODS In this study, the genomic characterization of 26 multidrug-resistant (MDR)-CoNS (S. borealis, S. saprophyticus, S. sciuri, S. hominis, S. epidermidis, S. pasteuri, S. hyicus, S. simulans, S. haemolyticus, and S. arlettae) previously obtained from the nasal cavity of healthy nestling storks, humans who had no contact with animals, pigs, and pig farmers, as well as dogs and dog owners from Spain was performed. High-quality draft genomes obtained by Illumina sequencing technology were used to determine their resistome, virulome, mobile genetic elements, and CRISPR-Cas types. The relatedness of three CoNS species with publicly available genomes was assessed by core-genome single nucleotide polymorphisms (SNPs). RESULTS AMR genes to all classes of antibiotics in staphylococci were detected including unusual ones (mecC, ermT, and cfr), of which their corresponding genetic organizations were analyzed. About 96.1% of the MDR-CoNS strains harbored diverse adherence or immune evasion genes. Remarkably, one enterotoxin-C and -L-carrying S. epidermidis-ST595 strain from a nestling stork was detected. Moreover, various plasmid bound-biocide resistance genes (qacACGJ) were identified in 34.6% of the MDR-CoNS. Two genes that encode for cadmium and zinc resistance (cadD, czrC) were found, of which czrC predominated (42.3%). Complete CRISPR-Cas system was detected in 19.2% of the CoNS strains, of which cas-1, -2, and -9 predominated, especially in 75% of the S. borealis strains. The phylogenetic analysis identified clusters of related S. epidermidis lineages with those of other countries (SNP < 100). Also, highly related S. borealis isolates (SNP < 10) from pigs was confirmed for the first time in Spain. CONCLUSION These findings showed that various ecological niches harbor CoNS that presented MDR phenotypes mediated by multiple AMR genes carried by mobile genetic elements with relatively low frequency of intact CRISPR-Cas systems. Furthermore, the transmission of some CoNS species in humans and animals is strongly suggested.
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Affiliation(s)
- Idris Nasir Abdullahi
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, Logroño, Spain
- Department of Medical Laboratory Science, Faculty of Allied Health Sciences, College of Medical Sciences, Ahmadu Bello University, Zaria, Nigeria
| | - Carmen Lozano
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, Logroño, Spain
| | - Javier Latorre-Fernández
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, Logroño, Spain
| | - Myriam Zarazaga
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, Logroño, Spain
| | - Marc Stegger
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Copenhagen, Denmark
- Antimicrobial Resistance and Infectious Diseases Laboratory, Harry Butler Institute, Murdoch University, Murdoch, WA, Australia
| | - Carmen Torres
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, Logroño, Spain.
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Stein M, Brinks E, Loop J, Habermann D, Cho GS, Franz CMAP. Antibiotic resistance plasmids in Enterobacteriaceae isolated from fresh produce in northern Germany. Microbiol Spectr 2024:e0036124. [PMID: 39287384 DOI: 10.1128/spectrum.00361-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 07/25/2024] [Indexed: 09/19/2024] Open
Abstract
In this study, the genomes of 22 Enterobacteriaceae isolates from fresh produce and herbs obtained from retail markets in northern Germany were completely sequenced with MiSeq short-read and MinION long-read sequencing and assembled using a Unicycler hybrid assembly. The data showed that 17 of the strains harbored between one and five plasmids, whereas in five strains, only the circular chromosomal DNA was detected. In total, 38 plasmids were identified. The size of the plasmids detected varied between ca. 2,000 and 326,000 bp, and heavy metal resistance genes were found on seven (18.4%) of the plasmids. Eleven plasmids (28.9%) showed the presence of antibiotic resistance genes. Among large plasmids (>32,000 bp), IncF plasmids (specifically, IncFIB and IncFII) were the most abundant replicon types, while all small plasmids were Col-replicons. Six plasmids harbored unit and composite transposons carrying antibiotic resistance genes, with IS26 identified as the primary insertion sequence. Class 1 integrons carrying antibiotic resistance genes were also detected on chromosomes of two Citrobacter isolates and on four plasmids. Mob-suite analysis revealed that 36.8% of plasmids in this study were found to be conjugative, while 28.9% were identified as mobilizable. Overall, our study showed that Enterobacteriaceae from fresh produce possess antibiotic resistance genes on both chromosome and plasmid, some of which are considered to be transferable. This indicates the potential for Enterobacteriaceae from fresh produce that is usually eaten in the raw state to contribute to the transfer of resistance genes to bacteria of the human gastrointestinal system. IMPORTANCE This study showed that Enterobacteriaceae from raw vegetables carried plasmids ranging in size from 2,715 to 326,286 bp, of which about less than one-third carried antibiotic resistance genes encoding resistance toward antibiotics such as tetracyclines, aminoglycosides, fosfomycins, sulfonamides, quinolones, and β-lactam antibiotics. Some strains encoded multiple resistances, and some encoded extended-spectrum β-lactamases. The study highlights the potential of produce, which may be eaten raw, as a potential vehicle for the transfer of antibiotic-resistant bacteria.
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Affiliation(s)
- Maria Stein
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute for Nutrition and Food, Kiel, Germany
| | - Erik Brinks
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute for Nutrition and Food, Kiel, Germany
| | - Jannike Loop
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute for Nutrition and Food, Kiel, Germany
| | - Diana Habermann
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute for Nutrition and Food, Kiel, Germany
| | - Gyu-Sung Cho
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute for Nutrition and Food, Kiel, Germany
| | - Charles M A P Franz
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute for Nutrition and Food, Kiel, Germany
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Cachetas D, Vaz-Moreira I, Pereira V, Manaia CM. Towards the definition of an antibiotic resistome signature in wastewater and downstream environments. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 357:124424. [PMID: 38909773 DOI: 10.1016/j.envpol.2024.124424] [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: 03/15/2024] [Revised: 05/18/2024] [Accepted: 06/20/2024] [Indexed: 06/25/2024]
Abstract
Domestic wastewater is a significant reservoir of antibiotic resistance genes, which pose environmental and public health risks. We aimed to define an antibiotic resistome signature, represented by core genes, i.e., shared by ≥ 90% of the metagenomes of each of three conceptual environmental compartments - wastewater (influent, sludge, effluent), freshwater, and agricultural soil. The definition of resistome signatures would support the proposal of a framework for monitoring treatment efficacy and assessing the impact of treated wastewater discharge into the environment, such as freshwater and agricultural soil. Metagenomic data from 163 samples originating from wastewater (n = 81), freshwater (n = 58), and agricultural soils (n = 24) across different regions (29 countries, 5 continents), were analysed regarding antibiotic resistance diversity, based on annotation against a database that merged CARD and ResFinder databases. The relative abundance of the total antibiotic resistance genes (corresponding to the ratio between the antibiotic resistance genes and total reads number) was not statistically different between raw and treated wastewater, being significantly higher than in freshwater or agricultural soils. The latter had the significantly lowest relative abundance of antibiotic resistance genes. Genes conferring resistance to aminoglycosides, beta-lactams, and tetracyclines were among the most abundant in wastewater environments, while multidrug resistance was equally distributed across all environments. The wastewater resistome signature included 27 antibiotic resistance genes that were detected in at least 90% of the wastewater resistomes, and that were not frequent in freshwater or agricultural soil resistomes. Among these were genes responsible for resistance to tetracyclines (n = 8), macrolide-lincosamide-streptogramin B (n = 7), aminoglycosides (n = 4), beta-lactams (n = 3), multidrug (n = 2), sulphonamides (n = 2), and polypeptides (n = 1). This comprehensive assessment provides valuable insights into the dynamics of antibiotic resistance in urban wastewater systems and their potential ecological implications in diverse environmental settings. Furthermore, provides guidance for the implementation of One Health monitoring approaches.
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Affiliation(s)
- Diogo Cachetas
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua de Diogo Botelho 1327, 4169-005, Porto, Portugal
| | - Ivone Vaz-Moreira
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua de Diogo Botelho 1327, 4169-005, Porto, Portugal.
| | - Vítor Pereira
- Centre of Biological Engineering University of Minho, Braga, Portugal; LABBELS -Associate Laboratory, Braga/Guimarães, Portugal
| | - Célia M Manaia
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua de Diogo Botelho 1327, 4169-005, Porto, Portugal
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Damar Celik D, Karaynir A, Salih Dogan H, Bozdogan B, Ozbek Celik B. Characterization and genomic analysis of PA-56 Pseudomonas phage from Istanbul, Turkey: Antibacterial and antibiofilm efficacy alone and with antibiotics. Heliyon 2024; 10:e36243. [PMID: 39263065 PMCID: PMC11387251 DOI: 10.1016/j.heliyon.2024.e36243] [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: 03/26/2024] [Revised: 08/08/2024] [Accepted: 08/13/2024] [Indexed: 09/13/2024] Open
Abstract
Phages are ubiquitous in freshwater, seawater, soil, the human body, and sewage water. They are potent biopharmaceuticals against antimicrobial-resistant bacteria and offer a promising alternative for treating infectious diseases. Also, combining phages with antibiotics enhances the antibiotics' efficacy. This study focused on two Pseudomonas aeruginosa phages isolated from lake and sewage water samples and one of them selected for further investigation. Isolated phages PA-56 and PA-18 infected 92 % and 86 % of the tested 25 clinical Pseudomonas aeruginosa strains, respectively. PA-56 with strong activity was chosen for detailed characterization, antimicrobial studies, and genome analysis. Combining PA-56 with ciprofloxacin or meropenem demonstrated phage-antibiotic synergism and increased antibiofilm efficacy. Genome analysis revealed a GC ratio of 54 % and a genome size of 42.761 bp, with no virulence or antibiotic resistance genes. Notably, PA-56 harboured the toxin-antitoxin protein, MazG. Overall, this study suggests that PA-56 holds promise for future applications in industry or medicine.
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Affiliation(s)
- Damla Damar Celik
- Istanbul University Institute of Graduate Studies in Health Sciences Department of Pharmaceutical Microbiology, 34116, Beyazıt, Istanbul, Turkey
| | - Abdulkerim Karaynir
- Recombinant DNA and Recombinant Protein Research Center (REDPROM), Aydın Adnan Menderes University, Aydın, Turkey
| | - Hanife Salih Dogan
- Recombinant DNA and Recombinant Protein Research Center (REDPROM), Aydın Adnan Menderes University, Aydın, Turkey
| | - Bulent Bozdogan
- Recombinant DNA and Recombinant Protein Research Center (REDPROM), Aydın Adnan Menderes University, Aydın, Turkey
- Medical Faculty, Department of Medical Microbiology, Aydın Adnan Menderes University, Aydın, Turkey
| | - Berna Ozbek Celik
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Istanbul University, 34116, Beyazit, Istanbul, Turkey
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Dalby MJ, Kiu R, Serghiou IR, Miyazaki A, Acford-Palmer H, Tung R, Caim S, Phillips S, Kujawska M, Matsui M, Iwamoto A, Taking B, Cox SE, Hall LJ. Faecal microbiota and cytokine profiles of rural Cambodian infants linked to diet and diarrhoeal episodes. NPJ Biofilms Microbiomes 2024; 10:85. [PMID: 39277573 PMCID: PMC11401897 DOI: 10.1038/s41522-024-00562-0] [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: 01/19/2024] [Accepted: 08/28/2024] [Indexed: 09/17/2024] Open
Abstract
The gut microbiota of infants in low- to middle-income countries is underrepresented in microbiome research. This study explored the faecal microbiota composition and faecal cytokine profiles in a cohort of infants in a rural province of Cambodia and investigated the impact of sample storage conditions and infant environment on microbiota composition. Faecal samples collected at three time points from 32 infants were analysed for microbiota composition using 16S rRNA amplicon sequencing and concentrations of faecal cytokines. Faecal bacterial isolates were subjected to whole genome sequencing and genomic analysis. We compared the effects of two sample collection methods due to the challenges of faecal sample collection in a rural location. Storage of faecal samples in a DNA preservation solution preserved Bacteroides abundance. Microbiota analysis of preserved samples showed that Bifidobacterium was the most abundant genus with Bifidobacterium longum the most abundant species, with higher abundance in breast-fed infants. Most infants had detectable pathogenic taxa, with Shigella and Klebsiella more abundant in infants with recent diarrhoeal illness. Neither antibiotics nor infant growth were associated with gut microbiota composition. Genomic analysis of isolates showed gene clusters encoding the ability to digest human milk oligosaccharides in B. longum and B. breve isolates. Antibiotic-resistant genes were present in both potentially pathogenic species and in Bifidobacterium. Faecal concentrations of Interlukin-1alpha and vascular endothelial growth factor were higher in breast-fed infants. This study provides insights into an underrepresented population of rural Cambodian infants, showing pathogen exposure and breastfeeding impact gut microbiota composition and faecal immune profiles.
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Affiliation(s)
- Matthew J Dalby
- Microbes, Infection and Microbiomes, College of Medicine and Health, University of Birmingham, Birmingham, B15 2TT, UK
- Food, Microbiome & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Raymond Kiu
- Microbes, Infection and Microbiomes, College of Medicine and Health, University of Birmingham, Birmingham, B15 2TT, UK
- Food, Microbiome & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Iliana R Serghiou
- Food, Microbiome & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Asuka Miyazaki
- School of Tropical Medicine & Global Health, Nagasaki University, Nagasaki, Japan
| | - Holly Acford-Palmer
- Food, Microbiome & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Rathavy Tung
- National Maternal and Child Health Centre, Ministry of Health, Phnom Penh, Cambodia
| | - Shabhonam Caim
- Food, Microbiome & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Sarah Phillips
- Food, Microbiome & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Magdalena Kujawska
- Microbes, Infection and Microbiomes, College of Medicine and Health, University of Birmingham, Birmingham, B15 2TT, UK
- Food, Microbiome & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
- Intestinal Microbiome, School of Life Sciences, ZIEL - Institute for Food & Health, Technical University of Munich, Freising, 80333, Germany
| | - Mitsuaki Matsui
- School of Tropical Medicine & Global Health, Nagasaki University, Nagasaki, Japan
| | - Azusa Iwamoto
- Bureau of International Health Cooperation, National Centre for Global Health and Medicine, Tokyo, Japan
| | - Bunsreng Taking
- Kampong Cham Provincial Health Department, Ministry of Health, Kampong Cham, Cambodia
| | - Sharon E Cox
- School of Tropical Medicine & Global Health, Nagasaki University, Nagasaki, Japan
- London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
- Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Lindsay J Hall
- Microbes, Infection and Microbiomes, College of Medicine and Health, University of Birmingham, Birmingham, B15 2TT, UK.
- Food, Microbiome & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK.
- Intestinal Microbiome, School of Life Sciences, ZIEL - Institute for Food & Health, Technical University of Munich, Freising, 80333, Germany.
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
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Fang Y, Jin J, Peng M, Xu L, Gu L, Bao D, Zhang Q, Jin K. Genomic Characteristics of a Carbapenem-Resistant Klebsiella pneumoniae Co-Carrying bla NDM-5 and bla KPC-2 Capsular Type KL25 Recovered from a County Level Hospital in China. Infect Drug Resist 2024; 17:3979-3987. [PMID: 39296776 PMCID: PMC11410035 DOI: 10.2147/idr.s479560] [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: 06/25/2024] [Accepted: 09/11/2024] [Indexed: 09/21/2024] Open
Abstract
Background Hypervirulent carbapenem-resistant K. pneumoniae (hv-CRKP) has been spreading rapidly worldwide. Here, we investigated the genomic characteristics of ST11 K. pneumoniae isolate SM117 with capsular serotype KL25, co-carrying bla NDM-5, two copies of bla KPC-2 and multiple plasmid-borne virulence genes from a county level hospital in China. Methods Antimicrobial susceptibility of K. pneumoniae SM117 was evaluated. The Illumina NovaSeq 6000 and Oxford Nanopore MinION platforms were applied to sequence the genome and then de novo assembled. The genome sequence was annotated using the NCBI Prokaryotic Genome Annotation Pipeline and further subjected to identify the sequence type (ST), capsular type, antibiotic resistance genes, plasmid replicon types and virulence genes. The phylogenetic analysis was performed based on the core genome single nucleotide polymorphisms (cgSNPs) using CSI Phylogeny 1.4, and further visualized by Interactive Tree of Life (iTOL) V5 web server. Results The whole-genome sequence of K. pneumoniae SM117 is made up of eight contigs totaling 6,104,486 bp, contain a 5,612,620 bp single chromosome and seven plasmids. The isolate was assigned to ST11 with capsular serotype KL25, co-carrying including bla NDM-5, bla KPC-2 and multiple plasmid-borne virulence genes including rmpA2 and aerobactin genes iucABCD-iutA. The coexistence of bla KPC and bla NDM in K. pneumoniae strains exhibit a high degree of resistance to β-lactam antibiotics. The strain SM117 also carries multiple antibiotic resistance genes, making it resistant to all antibiotics except polymyxin. The closest relative of K. pneumoniae C793 was identified in 2023 from a hospital surface sample in Zhejiang, China, with just 52 SNPs difference. Conclusion This study reported the genomic characteristics of a multidrug-resistant ST11 K. pneumoniae with capsular serotype KL25, co-carrying bla NDM-5, two copies of bla KPC-2 genes and multiple plasmid-borne virulence genes in China. These findings will provide important knowledge of the antibiotic resistance mechanisms, genomic epidemiological characteristics and transmission dynamics of multidrug-resistant K. pneumoniae.
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Affiliation(s)
- Yuanzhong Fang
- Department of Clinical Laboratory, Hangzhou Linping District Women & Children Hospital, Hangzhou, Zhejiang, People's Republic of China
| | - Juan Jin
- Department of Clinical Laboratory, Hangzhou Linping District Women & Children Hospital, Hangzhou, Zhejiang, People's Republic of China
| | - Minfei Peng
- Department of Clinical Laboratory, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, 317000, People's Republic of China
| | - Lidong Xu
- Department of Clinical Laboratory, Hangzhou Linping District Women & Children Hospital, Hangzhou, Zhejiang, People's Republic of China
| | - Linyuan Gu
- Department of Clinical Laboratory, Hangzhou Linping District Women & Children Hospital, Hangzhou, Zhejiang, People's Republic of China
| | - Danni Bao
- Department of Clinical Laboratory, Sanmen People's Hospital, Sanmen Bay Branch of The First Affiliated Hospital, Zhejiang University School of Medicine, Taizhou, Zhejiang, 317100, People's Republic of China
| | - Qiuying Zhang
- Department of Clinical Laboratory, Suizhou Hospital, Hubei University of Medicine, Suizhou, Hubei, People's Republic of China
| | - Kainan Jin
- Department of Gastroenterology, Linhai First People's Hospital, Taizhou, Zhejiang, 317000, People's Republic of China
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Schadron T, van den Beld M, Mughini-Gras L, Franz E. Use of whole genome sequencing for surveillance and control of foodborne diseases: status quo and quo vadis. Front Microbiol 2024; 15:1460335. [PMID: 39345263 PMCID: PMC11427404 DOI: 10.3389/fmicb.2024.1460335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2024] [Accepted: 08/27/2024] [Indexed: 10/01/2024] Open
Abstract
Improvements in sequencing quality, availability, speed and costs results in an increased presence of genomics in infectious disease applications. Nevertheless, there are still hurdles in regard to the optimal use of WGS for public health purposes. Here, we discuss the current state ("status quo") and future directions ("quo vadis") based on literature regarding the use of genomics in surveillance, hazard characterization and source attribution of foodborne pathogens. The future directions include the application of new techniques, such as machine learning and network approaches that may overcome the current shortcomings. These include the use of fixed genomic distances in cluster delineation, disentangling similarity or lack thereof in source attribution, and difficulties ascertaining function in hazard characterization. Although, the aforementioned methods can relatively easily be applied technically, an overarching challenge is the inference and biological/epidemiological interpretation of these large amounts of high-resolution data. Understanding the context in terms of bacterial isolate and host diversity allows to assess the level of representativeness in regard to sources and isolates in the dataset, which in turn defines the level of certainty associated with defining clusters, sources and risks. This also marks the importance of metadata (clinical, epidemiological, and biological) when using genomics for public health purposes.
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Affiliation(s)
- Tristan Schadron
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Maaike van den Beld
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Lapo Mughini-Gras
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, Netherlands
| | - Eelco Franz
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
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Berwa A, Caspar Y. Easy analysis of bacterial whole-genome sequencing data for clinical microbiologists using open-source Galaxy Platform: characterization of ESBL-producing Enterobacterales from bloodstream infections. J Glob Antimicrob Resist 2024:S2213-7165(24)00167-X. [PMID: 39278463 DOI: 10.1016/j.jgar.2024.08.012] [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: 05/03/2024] [Revised: 07/30/2024] [Accepted: 08/21/2024] [Indexed: 09/18/2024] Open
Abstract
OBJECTIVES Clinical microbiologists require easy-to-use open access tools with graphical interfaces to perform bacterial whole-genome sequencing (WGS) in routine practice. This study aimed to build a bioinformatics pipeline on the open-source Galaxy platform, facilitating comprehensive and reproducible analysis of bacterial WGS data in a few steps. We then used it to characterize our local epidemiology of ESBL-producing Enterobacterales isolated from patients with bacteremia. METHODS We built a bioinformatics pipeline consisting of the following sequential tools: Fastp (input data trimming); FastQC (read quality control); SPAdes (genome assembly); Quast (quality control of genome assembly); Prokka (gene annotation); Staramr (ResFinder database) and ABRicate (CARD database) for antimicrobial resistance (AMR) gene screening and molecular strain typing. Paired-end short read WGS data from all ESBL-producing Enterobacterales strains isolated from patients with bacteremia over one year were analyzed. RESULTS The Galaxy platform does not require command line tools. The bioinformatics pipeline was constructed within one hour. It only required uploading fastq files and facilitated systematization of the de novo assembly of genomes, MLST typing, and AMR gene screening in one step. Among the 66 ESBL-producing strains analyzed, the two most frequent ESBL genes were blaCTX-M-15 (62.1 %) and blaCTX-M-27 (13.6 %). CONCLUSIONS The open-access Galaxy platform provides a graphical interface and easy-to-use tools suitable for routine use in clinical microbiology laboratories without bioinformatics specialists. We believe that this platform will facilitate fast and low-cost analysis of bacterial WGS data, especially in resource-limited settings.
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Affiliation(s)
- Aimé Berwa
- Laboratoire de Bactériologie-Hygiène Hospitalière, CHU Grenoble Alpes, Grenoble, France; Univ. Grenoble Alpes, CNRS, CHU Grenoble Alpes, CEA, IBS, 38000 Grenoble, France
| | - Yvan Caspar
- Laboratoire de Bactériologie-Hygiène Hospitalière, CHU Grenoble Alpes, Grenoble, France; Univ. Grenoble Alpes, CNRS, CHU Grenoble Alpes, CEA, IBS, 38000 Grenoble, France.
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Eskola K, Aimo-Koivisto E, Heikinheimo A, Mykkänen A, Hautajärvi T, Grönthal T. Prevalence, risk factors, and characterisation of extended-spectrum β-lactamase -producing Enterobacterales (ESBL-E) in horses entering an equine hospital and description of longitudinal excretion. BMC Vet Res 2024; 20:412. [PMID: 39272173 PMCID: PMC11396584 DOI: 10.1186/s12917-024-04260-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: 06/13/2024] [Accepted: 09/02/2024] [Indexed: 09/15/2024] Open
Abstract
BACKGROUND Extended-spectrum β-lactamase -producing Enterobacterales (ESBL-E) are important zoonotic pathogens that can cause serious clinical infections, also in horses. Preventing the spread of ESBL-E, especially in the equine hospital environment, is key to reducing the number of difficult-to-treat infections. Estimating the local prevalence of ESBL-E in horses is crucial to establish targeted infection control programs at equine hospitals. We conducted a prevalence and risk factor study in equine patients on admission to an equine teaching hospital in Finland through a rectal ESBL-E screening specimen of the horse and a questionnaire. RESULTS The prevalence of ESBL-E in admitted horses was 3% (5/161, 95% CI 1-7%); none of the tested factors remained statistically significant in multivariate analysis, although antimicrobial treatment within three months was borderline significant (p = 0.052). Extended-spectrum β-lactamase -producing Klebsiella pneumoniae ST6179:CTX-M-15 was detected in three horses using whole-genome sequencing, which in combination with patient records suggested nosocomial transmission. Escherichia coli isolates were ST1250:CTX-M-1 (n = 1), ST1079:CTX-M-1 (n = 1), and ST1245:CTX-M-14 (n = 1). Multiple virulence genes were detected in the ESBL-E isolates. In the ESBL-E positive horses enrolled in a one-year follow-up study, ESBL-E were unlikely to be isolated in rectal screening specimens after the initial positive specimen. CONCLUSIONS The prevalence of ESBL-E in horses visiting a veterinary teaching hospital in Finland is low, indicating an overall low prevalence estimate in the country's equine population. No statistically significant risk factors were identified, likely due to the low number of cases. The duration of ESBL-E carriage is likely to be very short in horses.
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Affiliation(s)
- Katarina Eskola
- Department of Equine and Small Animal Medicine, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland.
| | - Elina Aimo-Koivisto
- Department of Equine and Small Animal Medicine, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Annamari Heikinheimo
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
- Food and Feed Microbiology Unit, Finnish Food Authority, Helsinki, Finland
| | - Anna Mykkänen
- Department of Equine and Small Animal Medicine, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | | | - Thomas Grönthal
- Department of Equine and Small Animal Medicine, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland.
- Animal Health Diagnostics Unit, Finnish Food Authority, Helsinki, Finland.
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44
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Cifuentes SG, Graham J, Trueba G, Cádenas PA. Detection of mobile colistin resistance genes mcr-9.1 and mcr-10.1 in Enterobacter asburiae from Ecuadorian children. Microbiol Resour Announc 2024; 13:e0031324. [PMID: 39162443 PMCID: PMC11384748 DOI: 10.1128/mra.00313-24] [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: 03/27/2024] [Accepted: 07/10/2024] [Indexed: 08/21/2024] Open
Abstract
Colistin is one of the last-line treatments for multi-drug resistant Gram-negative bacterial infections. The emergence of mobile colistin resistance genes has driven global concern and triggered the need for surveillance. Our report reveals the identification of mcr-9.1 and mcr-10.1 in Ecuador by employing a proximity ligation technique.
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Affiliation(s)
- Sara G Cifuentes
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito USFQ, Quito, Pichincha, Ecuador
| | - Jay Graham
- Berkeley School of Public Health, University of California, Berkeley, California, USA
| | - Gabriel Trueba
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito USFQ, Quito, Pichincha, Ecuador
| | - Paúl A Cádenas
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito USFQ, Quito, Pichincha, Ecuador
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45
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Kula A, Jablonska S, Avalos L, Jensen T, Appleberry H, Putonti C. Two draft genome assemblies of Staphylococcus aureus strains isolated from a cheek swab of a healthy female participant. Microbiol Resour Announc 2024; 13:e0048824. [PMID: 39162462 PMCID: PMC11385107 DOI: 10.1128/mra.00488-24] [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: 05/10/2024] [Accepted: 07/08/2024] [Indexed: 08/21/2024] Open
Abstract
Staphylococcus aureus is an opportunistic pathogen often commensal within the nasal and oral cavities. Here we present the genomes of S. aureus O139-S and O139-NS, both isolated from the cheek swab of a healthy female participant. While found in the same sample, the two strains displayed distinct colony morphologies.
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Affiliation(s)
- Alex Kula
- Department of Biology, Loyola University Chicago, Chicago, Illinois, USA
- Bioinformatics Program, Loyola University Chicago, Chicago, Illinois, USA
| | - Sandra Jablonska
- Department of Biology, Loyola University Chicago, Chicago, Illinois, USA
- Bioinformatics Program, Loyola University Chicago, Chicago, Illinois, USA
| | - Lexi Avalos
- Department of Biology, Loyola University Chicago, Chicago, Illinois, USA
| | - Tyler Jensen
- Bioinformatics Program, Loyola University Chicago, Chicago, Illinois, USA
| | - Helen Appleberry
- Department of Biology, Loyola University Chicago, Chicago, Illinois, USA
| | - Catherine Putonti
- Department of Biology, Loyola University Chicago, Chicago, Illinois, USA
- Bioinformatics Program, Loyola University Chicago, Chicago, Illinois, USA
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46
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Kula A, Arman M, Appleberry H, Wolfe AJ, Putonti C. Draft genomes of Klebsiella aerogenes, Klebsiella huaxiensis, and Klebsiella michiganensis isolates from the urinary tract. Microbiol Resour Announc 2024; 13:e0049224. [PMID: 39162486 PMCID: PMC11385447 DOI: 10.1128/mra.00492-24] [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: 05/10/2024] [Accepted: 07/07/2024] [Indexed: 08/21/2024] Open
Abstract
Several Klebsiella spp. can be the cause of urinary tract infections. Here we present the draft genome assemblies for four urinary isolates of three Klebsiella spp.: Klebsiella aerogenes UMB7541, Klebsiella michiganensis UMB11142 and UMB11423, and Klebsiella huaxiensis UMB11391 to further explore the genetic diversity of Klebsiella in the urinary tract.
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Affiliation(s)
- Alex Kula
- Department of Biology, Loyola University Chicago, Chicago, Illinois, USA
- Bioinformatics Program, Loyola University Chicago, Chicago, Illinois, USA
| | - Muna Arman
- Department of Biology, Loyola University Chicago, Chicago, Illinois, USA
- Bioinformatics Program, Loyola University Chicago, Chicago, Illinois, USA
| | - Helen Appleberry
- Department of Biology, Loyola University Chicago, Chicago, Illinois, USA
| | - Alan J Wolfe
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, Illinois, USA
| | - Catherine Putonti
- Department of Biology, Loyola University Chicago, Chicago, Illinois, USA
- Bioinformatics Program, Loyola University Chicago, Chicago, Illinois, USA
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, Illinois, USA
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47
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Ayoub H, Kumar MS, Mehta R, Thomas P, Dhanze H, Bhilegaonkar KN, Singh V, Salih HM, Amachawadi RG. Draft genome sequences of Brucella melitensis from human and animal sources in India. Microbiol Resour Announc 2024; 13:e0009124. [PMID: 39083690 PMCID: PMC11385449 DOI: 10.1128/mra.00091-24] [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: 02/12/2024] [Accepted: 06/18/2024] [Indexed: 08/02/2024] Open
Abstract
We present the draft genome sequences of 23 Brucella melitensis isolates derived from human and animal sources across India with genome size predominantly at 3.207 M and uniform GC content (57.24%) across isolates. The accession numbers and detailed sequencing data enhance the utility of this resource for further genomic studies.
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Affiliation(s)
- Haris Ayoub
- Department of Veterinary Public Health, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - M Suman Kumar
- Department of Veterinary Public Health, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Rishabh Mehta
- Department of Veterinary Public Health, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Prasad Thomas
- Department of Bacteriology and Mycology, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Himani Dhanze
- Department of Veterinary Public Health, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - K N Bhilegaonkar
- Department of Veterinary Public Health, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Vibha Singh
- Department of Veterinary Public Health, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Harith M Salih
- Department of Clinical Sciences, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
| | - Raghavendra G Amachawadi
- Department of Clinical Sciences, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
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Li H, Oliver A, Shields RK, Kamat S, Stone G, Estabrook M. Molecular characterization of clinically isolated Pseudomonas aeruginosa with varying resistance to ceftazidime-avibactam and ceftolozane-tazobactam collected as a part of the ATLAS global surveillance program from 2020 to 2021. Antimicrob Agents Chemother 2024:e0067024. [PMID: 39254297 DOI: 10.1128/aac.00670-24] [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: 05/06/2024] [Accepted: 08/08/2024] [Indexed: 09/11/2024] Open
Abstract
Ceftazidime-avibactam (CZA) and ceftolozane-tazobactam (C/T) are important agents for treating multidrug-resistant P. aeruginosa infections. In this study, we evaluated the molecular characteristics of 300 globally collected clinical P. aeruginosa isolates non-susceptible (NS) to CZA, C/T, or both agents. Isolates were CZA-NS and C/T-NS (n = 57), CZA-susceptible (S) and C/T-NS (n = 145), or CZA-NS and C/T-S (n = 98) selected from the Antimicrobial Testing Leadership and Surveillance (ATLAS) surveillance program from 2020 to 2021. Characterization was by whole-genome sequencing. Analysis was performed to identify β-lactamase genes and mutations that impact efflux regulation, AmpC regulation, and target binding (PBP3). Of the 57 CZA-NS+C/T-NS isolates, 64.9% carried a metallo-β-lactamase (MBL), and a cumulative 84.2% carried any non-intrinsic β-lactamase [i.e., not Pseudomonas-derived cephalosporinase (PDC) or OXA-50-like]. Of the 145 CZA-S+C/T-NS isolates, 26.2% carried an extended-spectrum β-lactamase (ESBL) and no carbapenemase, 17.9% carried a serine-carbapenemase, and 42.1% were negative for non-intrinsic β-lactamases. Of 98 CZA-NS+C/T-S isolates, 34.7% carried mutations previously described as causing an upregulation of the MexAB-OprM efflux pump, while only 9.2% carried a non-intrinsic β-lactamase, and no resistance mechanism was identified in 29.6% of these isolates. MBLs were present in most isolates NS to both agents. More than half of the CZA-S+C/T-NS isolates carried serine β-lactamases. The most frequently identified resistance mechanism identified in CZA-NS+C/T-S isolates was a marker indicating the upregulation of MexAB-OprM. No mechanism was identified that is thought to support resistance to these agents in numerous isolates. This may be due in part to the fact that whole genome sequencing (WGS) cannot directly measure gene expression of chromosomal resistance mechanisms.
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Affiliation(s)
- H Li
- IHMA, Schaumburg, Illinois, USA
| | - A Oliver
- Microbiology Service, Son Espases University Hospital, IdISBa, CIBERINFEC, Palma, Illes Balears, Spain
| | - R K Shields
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | | | - G Stone
- Pfizer, Groton, Connecticut, USA
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Shashkov AS, Arbatsky NP, Senchenkova SN, Kasimova AA, Dmitrenok AS, Shneider MM, Knirel YA, Hall RM, Kenyon JJ. Characterization of the carbapenem-resistant Acinetobacter baumannii clinical reference isolate BAL062 (CC2:KL58:OCL1): resistance properties and capsular polysaccharide structure. mSystems 2024:e0094124. [PMID: 39254035 DOI: 10.1128/msystems.00941-24] [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: 07/14/2024] [Accepted: 08/19/2024] [Indexed: 09/11/2024] Open
Abstract
The carbapenem-resistant Acinetobacter baumannii isolate BAL062 is a clinical reference isolate used in several recent experimental studies. It is from a ventilator-associated pneumonia (VAP) patient in an intensive care unit at the Hospital for Tropical Diseases (HTD), Ho Chi Minh City, Vietnam in 2009. Here, BAL062 was found to belong to the B sub-lineage of global clone 2 (GC2) isolates in the previously reported outbreak (2008 and 2012) of carbapenem-resistant VAP A. baumannii at the HTD. While related sub-lineage B outbreak isolates were extensively antibiotic-resistant and carry GC2-associated genomic resistance islands, AbGRI1, AbGRI2, and AbGRI3, BAL062 has lost AbGRI3 and three aminoglycoside resistance genes, armA, aacA4, and aphA1, leading to amikacin, tobramycin and kanamycin susceptibility. The location of Tn2008VAR found in the chromosome of this sub-lineage was also corrected. Like many of the outbreak isolates, BAL062 carries the KL58 gene cluster at the capsular polysaccharide (CPS) synthesis locus and an annotation key is provided. As information about K type is important for the development of novel CPS-targeting therapies, the BAL062 K58-type CPS structure was established using NMR spectroscopy. It is most closely related to K2 and K93, sharing similar configurations and linkages between K units, and contains the rare higher monosaccharide, 5,7-diacetamido-3,5,7,9-tetradeoxy-d-glycero-l-manno-non-2-ulosonic acid (5,7-di-N-acetyl-8-epipseudaminic acid; 8ePse5Ac7Ac), the 8-epimer of Pse5Ac7Ac (5,7-di-N-acetylpseudaminic acid). Inspection of publicly available A. baumannii genomes revealed a wide distribution of the KL58 locus in geographically diverse isolates belonging to several sequence types that were recovered over two decades from clinical, animal, and environmental sources.IMPORTANCEMany published experimental studies aimed at developing a clearer understanding of the pathogenicity of carbapenem-resistant Acinetobacter baumannii strains currently causing treatment failure due to extensive antibiotic resistance are undertaken using historic, laboratory-adapted isolates. However, it is ideal if not imperative that recent clinical isolates are used in such studies. The clinical reference isolate characterized here belongs to the dominant A. baumannii GC2 clone causing extensively resistant infections and has been used in various recent studies. The correlation of resistance profiles and resistance gene data is key to identifying genes available for gene knockout and complementation analyses, and we have mapped the antibiotic resistance genes to find candidates. Novel therapies, such as bacteriophage or monoclonal antibody therapies, currently under investigation as alternatives or adjuncts to antibiotic treatment to combat difficult-to-treat CRAb infections often exhibit specificity for specific structural epitopes of the capsular polysaccharide (CPS), the outer-most polysaccharide layer. Here, we have solved the structure of the CPS type found in BAL062 and other extensively resistant isolates. As consistent gene naming and annotation are important for locus identification and interpretation of experimental studies, we also have correlated automatic annotations to the standard gene names.
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Affiliation(s)
- Alexander S Shashkov
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Nikolay P Arbatsky
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Sof'ya N Senchenkova
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Anastasiya A Kasimova
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Andrei S Dmitrenok
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Mikhail M Shneider
- M. M. Shemyakin & Y. A Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Yuriy A Knirel
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Ruth M Hall
- School of Life and Environmental Science, The University of Sydney, Sydney, Australia
| | - Johanna J Kenyon
- Centre for Immunology and Infection Control, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Australia
- School of Pharmacy and Medical Sciences, Health Group, Griffith University, Gold Coast, Australia
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50
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Wokorach G, Erima B, Alafi S, Kabatesi HO, Muhindo JT, Najjuka F, Kiyengo J, Kibuuka H, Musinguzi AK, Wabwire-Mangen F, Byarugaba DK. Draft genome sequence of Acinetobacter haemolyticus strain MUWRP1017 isolated from the pus of a female inpatient at Bwera General Hospital in Uganda. Microbiol Resour Announc 2024; 13:e0056624. [PMID: 39162454 PMCID: PMC11384747 DOI: 10.1128/mra.00566-24] [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: 05/29/2024] [Accepted: 07/18/2024] [Indexed: 08/21/2024] Open
Abstract
The bacterium Acinetobacter haemolyticus, with a genome size of 3.4 Mb, was isolated from a pus swab of a wound on the left lower limb above the ankle joint of a female patient. This strain carries the antimicrobial resistance genes cephalosporinase blaADC-25, oxallinase blaOXA-264, floR, and sul2 and other resistance and virulence genes.
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Affiliation(s)
- Godfrey Wokorach
- Makerere University Walter Reed Project, Kampala, Uganda
- Department of Biology, Faculty of Science, Muni University, Arua, Uganda
| | - Bernard Erima
- Makerere University Walter Reed Project, Kampala, Uganda
| | - Stephen Alafi
- Makerere University Walter Reed Project, Kampala, Uganda
| | | | | | | | | | - Hannah Kibuuka
- Makerere University Walter Reed Project, Kampala, Uganda
| | | | - Fred Wabwire-Mangen
- Makerere University Walter Reed Project, Kampala, Uganda
- Makerere University, Kampala, Uganda
| | - Denis K Byarugaba
- Makerere University Walter Reed Project, Kampala, Uganda
- Makerere University, Kampala, Uganda
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