1
|
Jin C, Jia C, Hu W, Xu H, Shen Y, Yue M. Predicting antimicrobial resistance in E. coli with discriminative position fused deep learning classifier. Comput Struct Biotechnol J 2024; 23:559-565. [PMID: 38274998 PMCID: PMC10809114 DOI: 10.1016/j.csbj.2023.12.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/26/2023] [Accepted: 12/26/2023] [Indexed: 01/27/2024] Open
Abstract
Escherichia coli (E. coli) has become a particular concern due to the increasing incidence of antimicrobial resistance (AMR) observed worldwide. Using machine learning (ML) to predict E. coli AMR is a more efficient method than traditional laboratory testing. However, further improvement in the predictive performance of existing models remains challenging. In this study, we collected 1937 high-quality whole genome sequencing (WGS) data from public databases with an antimicrobial resistance phenotype and modified the existing workflow by adding an attention mechanism to enable the modified workflow to focus more on core single nucleotide polymorphisms (SNPs) that may significantly lead to the development of AMR in E. coli. While comparing the model performance before and after adding the attention mechanism, we also performed a cross-comparison among the published models using random forest (RF), support vector machine (SVM), logistic regression (LR), and convolutional neural network (CNN). Our study demonstrates that the discriminative positional colors of Chaos Game Representation (CGR) images can selectively influence and highlight genome regions without prior knowledge, enhancing prediction accuracy. Furthermore, we developed an online tool (https://github.com/tjiaa/E.coli-ML/tree/main) for assisting clinicians in the rapid prediction of the AMR phenotype of E. coli and accelerating clinical decision-making.
Collapse
Affiliation(s)
- Canghong Jin
- School of Computer and Computing Science, Hangzhou City University, Hangzhou 310015, China
| | - Chenghao Jia
- Institute of Preventive Veterinary Sciences and Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou 310058, China
| | - Wenkang Hu
- School of Computer and Computing Science, Hangzhou City University, Hangzhou 310015, China
- College of Computer Science and Technology, Zhejiang University, Hangzhou 310027, China
| | - Haidong Xu
- School of Computer and Computing Science, Hangzhou City University, Hangzhou 310015, China
| | - Yanyi Shen
- School of Computer and Computing Science, Hangzhou City University, Hangzhou 310015, China
| | - Min Yue
- Institute of Preventive Veterinary Sciences and Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou 310058, China
- Hainan Institute of Zhejiang University, Sanya 572000, China
- Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou 310058, China
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
| |
Collapse
|
2
|
Zou Q, Wu Y, Zhang S, Li S, Li S, Su Y, Zhang L, Li Q, Zou H, Zhang X, Wang T, Liang S, Yang J, Li C. Escherichia coli and HPV16 coinfection may contribute to the development of cervical cancer. Virulence 2024; 15:2319962. [PMID: 38380669 PMCID: PMC10883084 DOI: 10.1080/21505594.2024.2319962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 02/09/2024] [Indexed: 02/22/2024] Open
Abstract
Persistent human papillomavirus HPV infection is a necessary but insufficient condition for cervical cancer. Microorganisms are crucial environmental factors in cancers susceptibility and progression, recently attracting considerable attention. This study aimed to determine the infection status and relationship between high-risk HPV (HR-HPV) and lower genital tract infectious pathogens in cervical cancer and its precursors. From a retrospective and a prospective cohort analysis, Escherichia coli (E. coli) dominated the pathogens isolated from cervical discharges, and an isolation rate uptrend has been shown recently. HPV16 and E. coli's coinfection rate gradually increased with the severity of cervical intraepithelial neoplasia. The adhesion and invasion abilities of the isolated E. coli to HPV16-positive SiHa cells were evaluated in vitro. The TCGA database and cervical tissues samples analysis showed that IL-10 was upregulated in cervical cancer. IL-10 expression levels increased in tissue samples with the severity of cervical cancer and its precursors with HPV16 and E. coli coinfection. Although no significant changes in IL-10 production were observed in the co-culture supernatant, we hypothesized that Treg immune cells in the tumour microenvironment might be responsible for the local IL-10 upregulation, according to our data showing Foxp3 upregulation and an upward trend with the cervical intraepithelial neoplasia grading to cancer and tumours with E. coli and HPV16 coinfection. Our data provide insights into the possible role of E. coli in cervical cancer progression and suggest that the application of HPV and E. coli screening programs may be an effective strategy to relieve the burden of cervical cancer and its precursor lesions.
Collapse
Affiliation(s)
- Qin Zou
- Department of Clinical Laboratory, Women and Children's Hospital of Chongqing Medical University, Chongqing Health Center for Women and Children, Chongqing, China
| | - Yingying Wu
- Department of Clinical Laboratory, Women and Children's Hospital of Chongqing Medical University, Chongqing Health Center for Women and Children, Chongqing, China
| | - ShuaiShuai Zhang
- Department of Clinical Laboratory, Chongqing University Three Gorges Hospital, Chongqing, China
| | - Shu Li
- Department of Clinical Laboratory, Women and Children's Hospital of Chongqing Medical University, Chongqing Health Center for Women and Children, Chongqing, China
| | - Siyue Li
- Department of Clinical Laboratory, Women and Children's Hospital of Chongqing Medical University, Chongqing Health Center for Women and Children, Chongqing, China
| | - Yan Su
- Department of Clinical Laboratory, Women and Children's Hospital of Chongqing Medical University, Chongqing Health Center for Women and Children, Chongqing, China
| | - Lei Zhang
- Department of Clinical Laboratory, Women and Children's Hospital of Chongqing Medical University, Chongqing Health Center for Women and Children, Chongqing, China
| | - Qian Li
- Department of Clinical Laboratory, Women and Children's Hospital of Chongqing Medical University, Chongqing Health Center for Women and Children, Chongqing, China
| | - Hua Zou
- Department of Clinical Laboratory, Women and Children's Hospital of Chongqing Medical University, Chongqing Health Center for Women and Children, Chongqing, China
| | - Xinyuan Zhang
- Department of Clinical Laboratory, Women and Children's Hospital of Chongqing Medical University, Chongqing Health Center for Women and Children, Chongqing, China
| | - Teng Wang
- Department of Hematology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Shuang Liang
- Department of Pathology, Women and Children's Hospital of Chongqing Medical University, Chongqing Health Center for Women and Children, Chongqing, China
| | - Jun Yang
- Department of Obstetrics and Gynecology, Women and Children's Hospital of Chongqing Medical University, Chongqing Health Center for Women and Children, Chongqing, China
| | - Chunli Li
- Department of Clinical Laboratory, Women and Children's Hospital of Chongqing Medical University, Chongqing Health Center for Women and Children, Chongqing, China
| |
Collapse
|
3
|
Chen F, Fang H, Zhao J, Jiang P, Dong H, Zhao Y, Wang H, Zhang T, Zhang D. Multivariate modular metabolic engineering and medium optimization for vitamin B 12 production by Escherichia coli. Synth Syst Biotechnol 2024; 9:453-461. [PMID: 38634001 PMCID: PMC11021867 DOI: 10.1016/j.synbio.2024.03.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 03/24/2024] [Accepted: 03/29/2024] [Indexed: 04/19/2024] Open
Abstract
Vitamin B12 is a complex compound synthesized by microorganisms. The industrial production of vitamin B12 relies on specific microbial fermentation processes. E. coli has been utilized as a host for the de novo biosynthesis of vitamin B12, incorporating approximately 30 heterologous genes. However, a metabolic imbalance in the intricate pathway significantly limits vitamin B12 production. In this study, we employed multivariate modular metabolic engineering to enhance vitamin B12 production in E. coli by manipulating two modules comprising a total of 10 genes within the vitamin B12 biosynthetic pathway. These two modules were integrated into the chromosome of a chassis cell, regulated by T7, J23119, and J23106 promoters to achieve combinatorial pathway optimization. The highest vitamin B12 titer was attained by engineering the two modules controlled by J23119 and T7 promoters. The inclusion of yeast powder to the fermentation medium increased the vitamin B12 titer to 1.52 mg/L. This enhancement was attributed to the effect of yeast powder on elevating the oxygen transfer rate and augmenting the strain's isopropyl-β-d-1-thiogalactopyranoside (IPTG) tolerance. Ultimately, vitamin B12 titer of 2.89 mg/L was achieved through scaled-up fermentation in a 5-liter fermenter. The strategies reported herein will expedite the development of industry-scale vitamin B12 production utilizing E. coli.
Collapse
Affiliation(s)
- Feitao Chen
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Huan Fang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- University of Chinese Academy of Science, Beijing, 100049, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
| | - Jianghua Zhao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- University of Chinese Academy of Science, Beijing, 100049, China
| | - Pingtao Jiang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Huina Dong
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- University of Chinese Academy of Science, Beijing, 100049, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
| | - Ying Zhao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Huiying Wang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Tongcun Zhang
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Dawei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- University of Chinese Academy of Science, Beijing, 100049, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
| |
Collapse
|
4
|
Mostajabodavati S, Mousavizadegan M, Hosseini M, Mohammadimasoudi M, Mohammadi J. Machine learning-assisted liquid crystal-based aptasensor for the specific detection of whole-cell Escherichia coli in water and food. Food Chem 2024; 448:139113. [PMID: 38552467 DOI: 10.1016/j.foodchem.2024.139113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 04/24/2024]
Abstract
We have developed a rapid, facile liquid crystal (LC)-based aptasensor for E. coli detection in water and juice samples. A textile grid-anchored LC platform was used with specific aptamers adsorbed via a cationic surfactant, cetyltrimethylammonium bromide (CTAB), on the LC surface. The presence of E. coli dissociates the aptamers from CTAB and restores the dark signal induced by the surfactant. Using polarized microscopy, the images of the LCs in the presence of various concentrations of E. coli were captured and analyzed using image analysis and machine learning (ML). The artificial neural networks (ANN) and extreme gradient boosting (XGBoost) rendered the best results for water samples (R2 = 0.986 and RMSE = 0.209) and juice samples (R2 = 0.976 and RMSE = 0.262), respectively. The platform was able to detect E. coli with a detection limit (LOD) of 6 CFU mL-1.
Collapse
Affiliation(s)
- Saba Mostajabodavati
- Nanobiosensors Lab, Department of Life Science Engineering, Faculty of New Sciences and Technologies, University of Tehran, Tehran 1439817435, Iran
| | - Maryam Mousavizadegan
- Nanobiosensors Lab, Department of Life Science Engineering, Faculty of New Sciences and Technologies, University of Tehran, Tehran 1439817435, Iran
| | - Morteza Hosseini
- Nanobiosensors Lab, Department of Life Science Engineering, Faculty of New Sciences and Technologies, University of Tehran, Tehran 1439817435, Iran; Department of Pharmaceutical Biomaterials, Medical Biomaterials Research Center, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran.
| | - Mohammad Mohammadimasoudi
- Nano-bio-photonics Laboratory, Faculty of New Sciences and Technologies, University of Tehran, Tehran 1439817435, Iran
| | - Javad Mohammadi
- Department of Life Science Engineering, Faculty of New Sciences and Technologies, University of Tehran, Tehran 1439817435, Iran
| |
Collapse
|
5
|
Brown TW, Murphy JL, Akers P, Patrick M, Hill V, Mattioli M, Tsige Y, Adow A, Abdirashid M, Mohamed MN, Githiri D, Handzel T. An environmental evaluation of urine-diverting dry toilets in Hiloweyn Camp, Dollo Ado, Ethiopia. Sci Total Environ 2024; 926:171838. [PMID: 38518820 DOI: 10.1016/j.scitotenv.2024.171838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 03/24/2024]
Abstract
Safe and hygienic management of human waste is essential in humanitarian settings. Urine-diverting dry toilets (UDDTs) can enable this management in some humanitarian emergency settings. A seeded, longitudinal environmental study was conducted in Hiloweyn refugee camp, Dollo Ado, Ethiopia, to measure Escherichia coli and Ascaris suum ova inactivation within closed UDDT vaults and to document environmental conditions (temperature, moisture content, and pH) that could influence inactivation. Hiloweyn camp represented an optimal location for a desiccation-based sanitation technology such as the UDDT. E. coli and Ascaris ova inactivation was observed in UDDTs under warm, dry, alkaline conditions at 6, 9, and 12 months of storage; UDDTs with samples containing <1000 E. coli/g total solids increased from 30 % to 95 % over 12 months, and a >2.8-log10 reduction in Ascaris ova viability was observed after 6 months. Additional laboratory-based studies were conducted to provide insights into the field study findings and study the impact of hydrated lime on E. coli and Ascaris ova inactivation. Results suggest that adding hydrated lime to elevate pH > 12 may increase inactivation and decrease storage time. Overall, UDDTs could contribute to the safe and hygienic management of human waste in comparable warm and dry humanitarian settings.
Collapse
Affiliation(s)
- Travis W Brown
- Emergency Response and Recovery Branch, Division of Global Health Protection, Centers for Disease Control and Prevention, Atlanta, GA, USA; Waterborne Disease Prevention Branch, Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA.
| | - Jennifer L Murphy
- Waterborne Disease Prevention Branch, Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Patricia Akers
- Waterborne Disease Prevention Branch, Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Molly Patrick
- Emergency Response and Recovery Branch, Division of Global Health Protection, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Vincent Hill
- Waterborne Disease Prevention Branch, Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Mia Mattioli
- Waterborne Disease Prevention Branch, Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Yegerem Tsige
- United Nations High Commissioner for Refugees, Switzerland
| | | | | | | | - David Githiri
- United Nations High Commissioner for Refugees, Switzerland
| | - Thomas Handzel
- Emergency Response and Recovery Branch, Division of Global Health Protection, Centers for Disease Control and Prevention, Atlanta, GA, USA
| |
Collapse
|
6
|
Ncir S, Haenni M, Châtre P, Drapeau A, François P, Chaouch C, Souguir M, Azaiez S, Madec JY, Mansour W. Occurrence and persistence of multidrug-resistant Enterobacterales isolated from urban, industrial and surface water in Monastir, Tunisia. Sci Total Environ 2024; 926:171562. [PMID: 38460700 DOI: 10.1016/j.scitotenv.2024.171562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 03/02/2024] [Accepted: 03/05/2024] [Indexed: 03/11/2024]
Abstract
The One Health approach of antimicrobial resistance highlighted the role of the aquatic environment as a reservoir and dissemination source of resistance genes and resistant bacteria, especially due to anthropogenic activities. Resistance to extended-spectrum cephalosporins (ESC) conferred by extended-spectrum beta-lactamases (ESBLs) in E. coli has been proposed as the major marker of the AMR burden in cross-sectoral approaches. In this study, we investigated wastewater, surface water and seawater that are subjected to official water quality monitoring in Monastir, Tunisia. While all but one sample were declared compliant according to the official tests, ESC-resistant bacteria were detected in 31 (19.1 %) samples. Thirty-nine isolates, coming from urban, industrial and surface water in Monastir, were collected and characterized using antibiograms and whole-genome sequencing. These isolates were identified as 27 Escherichia coli (69.3 %) belonging to 13 STs, 10 Klebsiella pneumoniae (25.6 %) belonging to six STs, and two Citrobacter freundii (5.1 %). We observed the persistence and dissemination of clones over time and in different sampling sites, and no typically human-associated pathogens could be identified apart from one ST131. All isolates presented a blaCTX-M gene - blaCTX-M-15 (n = 22) and blaCTX-M-55 (n = 8) being the most frequent variants - which were identified on plasmids (n = 20) or on the chromosome (n = 19). In conclusion, we observed ESC resistance in rather ubiquitous bacteria that are capable of surviving in the water environment. This suggests that including the total coliform count and the ESBL count as determined by bacterial growth on selective plates in the official monitoring would greatly improve water quality control in Tunisia.
Collapse
Affiliation(s)
- Sana Ncir
- Université de Sousse, Faculté de Médecine Ibn Al Jazzar Sousse, Laboratoire de Recherche Biophysique Métabolique et Pharmacologie Appliquée, LR12ES02, Tunisie; ANSES - Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
| | - Marisa Haenni
- ANSES - Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
| | - Pierre Châtre
- 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
| | - Cherifa Chaouch
- Laboratory of Transmissible Diseases and Biologically Active Substances LR99ES27, Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
| | - Meriem Souguir
- Université de Sousse, Faculté de Médecine Ibn Al Jazzar Sousse, Laboratoire de Recherche Biophysique Métabolique et Pharmacologie Appliquée, LR12ES02, Tunisie; ANSES - Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
| | - Sana Azaiez
- Université de Sousse, Faculté de Médecine Ibn Al Jazzar Sousse, Laboratoire de Recherche Biophysique Métabolique et Pharmacologie Appliquée, LR12ES02, Tunisie
| | - Jean-Yves Madec
- ANSES - Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
| | - Wejdene Mansour
- Université de Sousse, Faculté de Médecine Ibn Al Jazzar Sousse, Laboratoire de Recherche Biophysique Métabolique et Pharmacologie Appliquée, LR12ES02, Tunisie.
| |
Collapse
|
7
|
Sánchez-Cano A, López-Calderón C, Cardona-Cabrera T, Green AJ, Höfle U. Connectivity at the human-wildlife interface: starling movements relate to carriage of E. coli. Sci Total Environ 2024; 926:171899. [PMID: 38527537 DOI: 10.1016/j.scitotenv.2024.171899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 03/27/2024]
Abstract
Synanthropic bird species in human, poultry or livestock environments can increase the spread of pathogens and antibiotic-resistant bacteria between wild and domestic animals. We present the first telemetry-based spatial networks for a small songbird. We quantified landscape connectivity exerted by spotless starling movements, and aimed to determine if connectivity patterns were related to carriage of potential pathogens. We captured 28 starlings on a partridge farm in 2020 and tested them for Avian influenza virus, West Nile virus WNV, Avian orthoavulavirus 1, Coronavirus, Salmonella spp. and Escherichia coli. We did not detect any viruses or Salmonella, but one individual had antibodies against WNV or cross-reacting Flaviviruses. We found E. coli in 61 % (17 of 28) of starlings, 76 % (13 of 17) of which were resistant to gentamicin, 12 % (2 of 17) to cefotaxime/enrofloxacin and 6 % (1 of 17) were phenotypic extended spectrum beta-lactamase (ESBL) carriers. We GPS-tracked 17 starlings and constructed spatial networks showing how their movements (i.e. links) connect different farms with nearby urban and natural habitats (i.e. nodes with different attributes). Using E. coli carriage as a proxy for acquisition/dispersal of bacteria, we found differences across spatial networks constructed for E. coli positive (n = 7) and E. coli negative (n = 9) starlings. We used Exponential Random Graph Models to reveal significant differences between networks. In particular, an urban roost was more connected to other sites by movements of E. coli positive than by movements of E. coli negative starlings. Furthermore, an open pine forest used mainly for roosting was more connected to other sites by movements of E. coli negative than by movements of E. coli positive starlings. Using E. coli as a proxy for a potential pathogen carried by starlings, we reveal the pathways of spread that starlings could provide between farms, urban and natural habitats.
Collapse
Affiliation(s)
- Alberto Sánchez-Cano
- SaBio Research Group, Institute for Game and Wildlife Research IREC (CSIC-UCLM-JCCM), Ciudad Real, Spain.
| | - Cosme López-Calderón
- Department of Conservation Biology and Global Change, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain; Grupo de Investigación en Conservación, Biodiversidad y Cambio Global, Universidad de Extremadura, Badajoz, Spain
| | - Teresa Cardona-Cabrera
- SaBio Research Group, Institute for Game and Wildlife Research IREC (CSIC-UCLM-JCCM), Ciudad Real, Spain
| | - Andy J Green
- Department of Conservation Biology and Global Change, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain
| | - Ursula Höfle
- SaBio Research Group, Institute for Game and Wildlife Research IREC (CSIC-UCLM-JCCM), Ciudad Real, Spain.
| |
Collapse
|
8
|
Yang X, Xia S, Hao L, Tian D, Wang L, Chen R. Deciphering the behavior and potential mechanism of biochar at different pyrolysis temperatures to alleviate membrane biofouling. Sci Total Environ 2024; 924:171638. [PMID: 38485027 DOI: 10.1016/j.scitotenv.2024.171638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 03/04/2024] [Accepted: 03/09/2024] [Indexed: 03/19/2024]
Abstract
Biofouling limits applications of membrane technology in wastewater treatment, but dosing additives to membrane tanks is an effective method to alleviate biofouling. In this study, biochar derived from corncob and pyrolyzed at 300, 500, and 700°C was dosed to determine the underlying anti-biofouling mechanism. The effects of the biochar on the membrane properties and foulant behavior were systematically investigated. The results showed that biochar delayed the occurrence of the fouling transition (0.5-3.0 h), and decreased the flux decline rate, thus achieving a higher water flux (3.1-3.7 times of the control group). Biochar altered membrane surface properties, and increased the membrane surface charge, roughness, and hydrophilicity, which all contributed to higher membrane permeability. Moreover, adding biochar reduced the number of foulants in the fouling layer, particularly protein substances. The flux model fit and the XDLVO theory further revealed the mitigating effect of biochar on membrane biofouling. At the initial intermediate-blocking stage, the effect of biochar on membrane fouling was determined by its properties, and adsorption capacity to the foulants, BC500 presented the best mitigation performance. At the later cake-filtration stage, the role of biochar in membrane fouling was strongly associated with protein content in the fouling layer, and the minimum rate of flux decline occurred in BC300. This study promotes the understanding and development of biochar to alleviate membrane biofouling.
Collapse
Affiliation(s)
- Xiaohuan Yang
- Key Lab of Environmental Engineering, Shaanxi Province, Xi'an University of Architecture and Technology, No.13 Yanta Road, Xi'an 710055, Shaanxi Province, PR China
| | - Silian Xia
- Key Lab of Environmental Engineering, Shaanxi Province, Xi'an University of Architecture and Technology, No.13 Yanta Road, Xi'an 710055, Shaanxi Province, PR China
| | - Litu Hao
- Key Lab of Environmental Engineering, Shaanxi Province, Xi'an University of Architecture and Technology, No.13 Yanta Road, Xi'an 710055, Shaanxi Province, PR China
| | - Duanyun Tian
- Key Lab of Environmental Engineering, Shaanxi Province, Xi'an University of Architecture and Technology, No.13 Yanta Road, Xi'an 710055, Shaanxi Province, PR China
| | - Lianxu Wang
- Key Lab of Environmental Engineering, Shaanxi Province, Xi'an University of Architecture and Technology, No.13 Yanta Road, Xi'an 710055, Shaanxi Province, PR China
| | - Rong Chen
- Key Lab of Environmental Engineering, Shaanxi Province, Xi'an University of Architecture and Technology, No.13 Yanta Road, Xi'an 710055, Shaanxi Province, PR China; International S&T Cooperation Center for Urban Alternative Water Resources Development, Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, No.13 Yanta Road, Xi'an 710055, PR China.
| |
Collapse
|
9
|
Kong Y, Deering AJ, Nemali K. Minimizing Escherichia coli O157:H7 contamination in indoor farming: effects of cultivar type and ultra-violet light quality. J Sci Food Agric 2024; 104:4218-4225. [PMID: 38294189 DOI: 10.1002/jsfa.13303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 10/31/2023] [Accepted: 01/07/2024] [Indexed: 02/01/2024]
Abstract
BACKGROUND Bacterial contamination of produce is a concern in indoor farming due to close plant spacing, recycling irrigation, warm temperatures, and high relative humidity during production. Cultivars that inherently resist contamination and photo-sanitization using ultraviolet (UV) radiation during the production phase can reduce bacterial contamination. However, there is limited information to support their use in indoor farming. RESULTS Lettuce (Lactuca sativa) cultivars with varying plant architectures grown in a custom-built indoor farm exhibited differences in E. coli O157:H7 survival after inoculation. The survival of E. coli O157:H7 was lowest in the leaf cultivar (open architecture) and highest in the romaine and oakleaf cultivars (compact architecture). Of the different UV wavelengths that were tested (UV-A, UV-A + B, UV-A + C), UV A + C at an intensity of 54.5 μmol m-2 s-1 (with 3.5 μmol m-2 s-1 of UV-C), provided for 15 min every day, was found to be most efficacious in reducing the E. coli O157:H7 survival on romaine lettuce with no negative effects on plant growth and quality. CONCLUSION Contamination of E. coli O157:H7 on lettuce plants can be reduced and the food safety levels in indoor farms can be increased by selecting cultivars with an open leaf architecture coupled with photo-sanitization using low and frequent exposure to UV A + C radiation. © 2024 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
Collapse
Affiliation(s)
- Yuyao Kong
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, USA
| | - Amanda J Deering
- Department of Food Science, Purdue University, West Lafayette, IN, USA
| | - Krishna Nemali
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, USA
| |
Collapse
|
10
|
Gager C, Flores-Mireles AL. Blunted blades: new CRISPR-derived technologies to dissect microbial multi-drug resistance and biofilm formation. mSphere 2024; 9:e0064223. [PMID: 38511958 DOI: 10.1128/msphere.00642-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2024] Open
Abstract
The spread of multi-drug-resistant (MDR) pathogens has rapidly outpaced the development of effective treatments. Diverse resistance mechanisms further limit the effectiveness of our best treatments, including multi-drug regimens and last line-of-defense antimicrobials. Biofilm formation is a powerful component of microbial pathogenesis, providing a scaffold for efficient colonization and shielding against anti-microbials, which further complicates drug resistance studies. Early genetic knockout tools didn't allow the study of essential genes, but clustered regularly interspaced palindromic repeat inference (CRISPRi) technologies have overcome this challenge via genetic silencing. These tools rapidly evolved to meet new demands and exploit native CRISPR systems. Modern tools range from the creation of massive CRISPRi libraries to tunable modulation of gene expression with CRISPR activation (CRISPRa). This review discusses the rapid expansion of CRISPRi/a-based technologies, their use in investigating MDR and biofilm formation, and how this drives further development of a potent tool to comprehensively examine multi-drug resistance.
Collapse
Affiliation(s)
- Christopher Gager
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA
| | - Ana L Flores-Mireles
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA
- W. M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, Indiana, USA
| |
Collapse
|
11
|
Wang Y, Xu F, Yuan C, Zhang Y, Ren J, Yue H, Ma T, Song Q. Comparison of immune effects of porcine circovirus type 2d (PCV2d) capsid protein expressed by Escherichia coli and baculovirus-insect cells. Vaccine 2024; 42:2848-2857. [PMID: 38514351 DOI: 10.1016/j.vaccine.2024.03.048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 03/23/2024]
Abstract
Porcine circovirus type 2 (PCV2) is an important pathogen harmful to global pig production, which causes immunosuppression and serious economic losses. PCV2 capsid (Cap) protein expressed by E. coli or baculovirus-insect cells are often used in preparation of PCV2 subunit vaccines, but the latter is expensive to produce. It is therefore crucial to comparison of the immune effects of Cap protein expressed by the above two expression systems for reducing the production cost and guaranteeing PCV2 vaccine quality. In this study, the PCV2d-Cap protein lacking nuclear localization signal (NLS), designated as E. coli-Cap and Bac-Cap, was expressed by E. coli and baculovirus-Spodoptera frugiperda Sf9 (Bac-Sf9) cells, respectively. The expressed Cap proteins could self-assemble into virus-like particles (VLPs), but the Bac-Cap-assembled VLPs were more regular. The two system-expressed Cap proteins induced similar specific IgG responses in mice, but the neutralizing antibody levels of Bac-Cap-immunized mice was higher than those of E. coli-Cap. After PCV2 challenge, IL-10 in Bac-Cap immunized mice decreased significantly than that in E. coli-Cap. The lesions and PCV2 antigen positive cells in tissues of mice immunized with E. coli-Cap and Bac-Cap were significantly reduced, and Bac-Cap appeared mild lesions and fewer PCV2 antigen-positive cells compared with E. coli-Cap immunized mice. The study indicated that Cap proteins expressed by E. coli and Bac-Sf9 cells could induce specific protective immunity, but the latter induced more effective immunity, which provides valuable information for the research and development of PCV2 vaccine.
Collapse
Affiliation(s)
- Yawen Wang
- College of Veterinary Medicine & Hebei Veterinary Biotechnology Innovation Center, Hebei Agricultural University, Baoding 071001, China
| | - Fan Xu
- College of Veterinary Medicine & Hebei Veterinary Biotechnology Innovation Center, Hebei Agricultural University, Baoding 071001, China
| | - Chen Yuan
- College of Veterinary Medicine & Hebei Veterinary Biotechnology Innovation Center, Hebei Agricultural University, Baoding 071001, China
| | - Yanan Zhang
- College of Veterinary Medicine & Hebei Veterinary Biotechnology Innovation Center, Hebei Agricultural University, Baoding 071001, China
| | - Jing Ren
- College of Veterinary Medicine & Hebei Veterinary Biotechnology Innovation Center, Hebei Agricultural University, Baoding 071001, China
| | - Huaining Yue
- College of Veterinary Medicine & Hebei Veterinary Biotechnology Innovation Center, Hebei Agricultural University, Baoding 071001, China
| | - Tiantian Ma
- College of Veterinary Medicine & Hebei Veterinary Biotechnology Innovation Center, Hebei Agricultural University, Baoding 071001, China
| | - Qinye Song
- College of Veterinary Medicine & Hebei Veterinary Biotechnology Innovation Center, Hebei Agricultural University, Baoding 071001, China.
| |
Collapse
|
12
|
Thiermann R, Sandler M, Ahir G, Sauls JT, Schroeder J, Brown S, Le Treut G, Si F, Li D, Wang JD, Jun S. Tools and methods for high-throughput single-cell imaging with the mother machine. eLife 2024; 12:RP88463. [PMID: 38634855 PMCID: PMC11026091 DOI: 10.7554/elife.88463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2024] Open
Abstract
Despite much progress, image processing remains a significant bottleneck for high-throughput analysis of microscopy data. One popular platform for single-cell time-lapse imaging is the mother machine, which enables long-term tracking of microbial cells under precisely controlled growth conditions. While several mother machine image analysis pipelines have been developed in the past several years, adoption by a non-expert audience remains a challenge. To fill this gap, we implemented our own software, MM3, as a plugin for the multidimensional image viewer napari. napari-MM3 is a complete and modular image analysis pipeline for mother machine data, which takes advantage of the high-level interactivity of napari. Here, we give an overview of napari-MM3 and test it against several well-designed and widely used image analysis pipelines, including BACMMAN and DeLTA. Researchers often analyze mother machine data with custom scripts using varied image analysis methods, but a quantitative comparison of the output of different pipelines has been lacking. To this end, we show that key single-cell physiological parameter correlations and distributions are robust to the choice of analysis method. However, we also find that small changes in thresholding parameters can systematically alter parameters extracted from single-cell imaging experiments. Moreover, we explicitly show that in deep learning-based segmentation, 'what you put is what you get' (WYPIWYG) - that is, pixel-level variation in training data for cell segmentation can propagate to the model output and bias spatial and temporal measurements. Finally, while the primary purpose of this work is to introduce the image analysis software that we have developed over the last decade in our lab, we also provide information for those who want to implement mother machine-based high-throughput imaging and analysis methods in their research.
Collapse
Affiliation(s)
- Ryan Thiermann
- Department of Physics, University of California, San DiegoLa JollaUnited States
| | - Michael Sandler
- Department of Physics, University of California, San DiegoLa JollaUnited States
| | - Gursharan Ahir
- Department of Physics, University of California, San DiegoLa JollaUnited States
| | - John T Sauls
- Department of Physics, University of California, San DiegoLa JollaUnited States
| | - Jeremy Schroeder
- Department of Biological Chemistry, University of Michigan Medical SchoolAnn ArborUnited States
| | - Steven Brown
- Department of Physics, University of California, San DiegoLa JollaUnited States
| | | | - Fangwei Si
- Department of Physics, Carnegie Mellon UniversityPittsburghUnited States
| | - Dongyang Li
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - Jue D Wang
- Department of Bacteriology, University of Wisconsin–MadisonMadisonUnited States
| | - Suckjoon Jun
- Department of Physics, University of California, San DiegoLa JollaUnited States
| |
Collapse
|
13
|
Nhu NTK, Phan MD, Hancock SJ, Peters KM, Alvarez-Fraga L, Forde BM, Andersen SB, Miliya T, Harris PNA, Beatson SA, Schlebusch S, Bergh H, Turner P, Brauner A, Westerlund-Wikström B, Irwin AD, Schembri MA. High-risk Escherichia coli clones that cause neonatal meningitis and association with recrudescent infection. eLife 2024; 12:RP91853. [PMID: 38622998 PMCID: PMC11021048 DOI: 10.7554/elife.91853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2024] Open
Abstract
Neonatal meningitis is a devastating disease associated with high mortality and neurological sequelae. Escherichia coli is the second most common cause of neonatal meningitis in full-term infants (herein NMEC) and the most common cause of meningitis in preterm neonates. Here, we investigated the genomic relatedness of a collection of 58 NMEC isolates spanning 1974-2020 and isolated from seven different geographic regions. We show NMEC are comprised of diverse sequence types (STs), with ST95 (34.5%) and ST1193 (15.5%) the most common. No single virulence gene profile was conserved in all isolates; however, genes encoding fimbrial adhesins, iron acquisition systems, the K1 capsule, and O antigen types O18, O75, and O2 were most prevalent. Antibiotic resistance genes occurred infrequently in our collection. We also monitored the infection dynamics in three patients that suffered recrudescent invasive infection caused by the original infecting isolate despite appropriate antibiotic treatment based on antibiogram profile and resistance genotype. These patients exhibited severe gut dysbiosis. In one patient, the causative NMEC isolate was also detected in the fecal flora at the time of the second infection episode and after treatment. Thus, although antibiotics are the standard of care for NMEC treatment, our data suggest that failure to eliminate the causative NMEC that resides intestinally can lead to the existence of a refractory reservoir that may seed recrudescent infection.
Collapse
Affiliation(s)
- Nguyen Thi Khanh Nhu
- Institute for Molecular Bioscience (IMB), The University of QueenslandBrisbaneAustralia
- School of Chemistry and Molecular Biosciences, The University of QueenslandBrisbaneAustralia
- Australian Infectious Diseases Research Centre, The University of QueenslandBrisbaneAustralia
| | - Minh-Duy Phan
- Institute for Molecular Bioscience (IMB), The University of QueenslandBrisbaneAustralia
- School of Chemistry and Molecular Biosciences, The University of QueenslandBrisbaneAustralia
- Australian Infectious Diseases Research Centre, The University of QueenslandBrisbaneAustralia
| | - Steven J Hancock
- School of Chemistry and Molecular Biosciences, The University of QueenslandBrisbaneAustralia
- Australian Infectious Diseases Research Centre, The University of QueenslandBrisbaneAustralia
| | - Kate M Peters
- Institute for Molecular Bioscience (IMB), The University of QueenslandBrisbaneAustralia
- School of Chemistry and Molecular Biosciences, The University of QueenslandBrisbaneAustralia
- Australian Infectious Diseases Research Centre, The University of QueenslandBrisbaneAustralia
| | - Laura Alvarez-Fraga
- School of Chemistry and Molecular Biosciences, The University of QueenslandBrisbaneAustralia
- Australian Infectious Diseases Research Centre, The University of QueenslandBrisbaneAustralia
| | - Brian M Forde
- Australian Infectious Diseases Research Centre, The University of QueenslandBrisbaneAustralia
- University of Queensland Centre for Clinical Research, The University of QueenslandBrisbaneAustralia
| | - Stacey B Andersen
- Genome Innovation Hub, The University of QueenslandBrisbaneAustralia
| | - Thyl Miliya
- Cambodia Oxford Medical Research Unit, Angkor Hospital for ChildrenSiem ReapCambodia
| | - Patrick NA Harris
- University of Queensland Centre for Clinical Research, The University of QueenslandBrisbaneAustralia
- Pathology Queensland, Queensland HealthBrisbaneAustralia
| | - Scott A Beatson
- School of Chemistry and Molecular Biosciences, The University of QueenslandBrisbaneAustralia
- Australian Infectious Diseases Research Centre, The University of QueenslandBrisbaneAustralia
| | - Sanmarie Schlebusch
- University of Queensland Centre for Clinical Research, The University of QueenslandBrisbaneAustralia
- Pathology Queensland, Queensland HealthBrisbaneAustralia
- Q-PHIRE Genomics and Public Health Microbiology, Forensic and Scientific Services, Coopers PlainsBrisbaneAustralia
| | - Haakon Bergh
- Pathology Queensland, Queensland HealthBrisbaneAustralia
| | - Paul Turner
- Cambodia Oxford Medical Research Unit, Angkor Hospital for ChildrenSiem ReapCambodia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
| | - Annelie Brauner
- Department of Microbiology, Tumor and Cell Biology, Division of Clinical Microbiology, Karolinska Institutet and Karolinska University HospitalStockholmSweden
| | | | - Adam D Irwin
- Australian Infectious Diseases Research Centre, The University of QueenslandBrisbaneAustralia
- University of Queensland Centre for Clinical Research, The University of QueenslandBrisbaneAustralia
- Infection Management Prevention Service, Queensland Children's HospitalBrisbaneAustralia
| | - Mark A Schembri
- Institute for Molecular Bioscience (IMB), The University of QueenslandBrisbaneAustralia
- School of Chemistry and Molecular Biosciences, The University of QueenslandBrisbaneAustralia
- Australian Infectious Diseases Research Centre, The University of QueenslandBrisbaneAustralia
| |
Collapse
|
14
|
Funck D, Sinn M, Forlani G, Hartig JS. Guanidine production by plant homoarginine-6-hydroxylases. eLife 2024; 12:RP91458. [PMID: 38619227 PMCID: PMC11018352 DOI: 10.7554/elife.91458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2024] Open
Abstract
Metabolism and biological functions of the nitrogen-rich compound guanidine have long been neglected. The discovery of four classes of guanidine-sensing riboswitches and two pathways for guanidine degradation in bacteria hint at widespread sources of unconjugated guanidine in nature. So far, only three enzymes from a narrow range of bacteria and fungi have been shown to produce guanidine, with the ethylene-forming enzyme (EFE) as the most prominent example. Here, we show that a related class of Fe2+- and 2-oxoglutarate-dependent dioxygenases (2-ODD-C23) highly conserved among plants and algae catalyze the hydroxylation of homoarginine at the C6-position. Spontaneous decay of 6-hydroxyhomoarginine yields guanidine and 2-aminoadipate-6-semialdehyde. The latter can be reduced to pipecolate by pyrroline-5-carboxylate reductase but more likely is oxidized to aminoadipate by aldehyde dehydrogenase ALDH7B in vivo. Arabidopsis has three 2-ODD-C23 isoforms, among which Din11 is unusual because it also accepted arginine as substrate, which was not the case for the other 2-ODD-C23 isoforms from Arabidopsis or other plants. In contrast to EFE, none of the three Arabidopsis enzymes produced ethylene. Guanidine contents were typically between 10 and 20 nmol*(g fresh weight)-1 in Arabidopsis but increased to 100 or 300 nmol*(g fresh weight)-1 after homoarginine feeding or treatment with Din11-inducing methyljasmonate, respectively. In 2-ODD-C23 triple mutants, the guanidine content was strongly reduced, whereas it increased in overexpression plants. We discuss the implications of the finding of widespread guanidine-producing enzymes in photosynthetic eukaryotes as a so far underestimated branch of the bio-geochemical nitrogen cycle and propose possible functions of natural guanidine production.
Collapse
Affiliation(s)
- Dietmar Funck
- Department of Chemistry, University of KonstanzKonstanzGermany
| | - Malte Sinn
- Department of Chemistry, University of KonstanzKonstanzGermany
| | - Giuseppe Forlani
- Department of Life Science and Biotechnology, University of FerraraFerraraItaly
| | - Jörg S Hartig
- Department of Chemistry, University of KonstanzKonstanzGermany
| |
Collapse
|
15
|
Bachoon DS, Redhead ASZ, Mead AJ. Mitochondrial DNA marker: A PCR approach for tracking rat (Rattus rattus and Rattus norvegicus) fecal pollution in surface water systems. Sci Total Environ 2024; 921:171164. [PMID: 38402984 DOI: 10.1016/j.scitotenv.2024.171164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 02/19/2024] [Accepted: 02/19/2024] [Indexed: 02/27/2024]
Abstract
Rats act as reservoirs for a wide range of zoonotic pathogens and can negatively impact human health. In this study, we developed a novel dye base mitochondrial DNA (mtDNA) PCR-assay (RatMt) specifically targeting a 180 bp fragment of the NADH dehydrogenase subunit 2 gene for detecting fecal pollution from two species of rats (Rattus rattus and Rattus norvegicus) in environmental samples. Estimation of Escherichia coli concentrations in Rattus norvegicus fecal pellets suggested that there were approximately 2.24 × 10 4 ± 4.86 × 103 MPN/g of fecal pellet. The RatMt PCR assay was robust, had a detection limit of rat feces in water of 0.274 ± 0.14 mg/100 mL and was 100 % specific for detecting Rattus rattus and Rattus norvegicus fecal mtDNA. Fecal Indicator Bacteria (FIB) along an urbanized gradient in Pensacola-Bay was assessed by the IDEXX Colilert™ - 18 and indicated that the majority of the fifteen sampling sites in the Pensacola-Bay area had E. coli concentrations >410 MPN/100 mL. Rattus rattus and Rattus norvegicus mtDNA were detected in all the urban marine sites, three of the urban freshwater sampling areas, and three of the forested sampling sites. The RatMt PCR assay is a useful tool for rapidly detecting Rattus rattus and Rattus norvegicus fecal pollution in environmental samples.
Collapse
Affiliation(s)
- Dave S Bachoon
- Department of Biological and Environmental Sciences, Georgia College & State University, Campus Box 81, Milledgeville, GA 31061-0490, USA.
| | - Aaden S Z Redhead
- Department of Biological and Environmental Sciences, Georgia College & State University, Campus Box 81, Milledgeville, GA 31061-0490, USA
| | - Alfred J Mead
- Department of Biological and Environmental Sciences, Georgia College & State University, Campus Box 81, Milledgeville, GA 31061-0490, USA
| |
Collapse
|
16
|
Mzyece CC, Glendell M, Gagkas Z, Quilliam RS, Jones I, Pagaling E, Akoumianaki I, Newman C, Oliver DM. Eliciting expert judgements to underpin our understanding of faecal indicator organism loss from septic tank systems. Sci Total Environ 2024; 921:171074. [PMID: 38378059 DOI: 10.1016/j.scitotenv.2024.171074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 02/05/2024] [Accepted: 02/16/2024] [Indexed: 02/22/2024]
Abstract
Septic tank systems (STS) in rural catchments represent a potential source of microbial pollution to watercourses; however, data concerning the risk of faecal indicator organism (FIO) export from STS to surface waters are scarce. In the absence of empirical data, elicitation of expert judgements can provide an alternative approach to aid understanding of FIO pollution risk from STS. Our study employed a structured elicitation process using the Sheffield Elicitation Framework to obtain expert judgements on the proportion of FIOs likely to be delivered from STS to watercourses, based on 36 scenarios combining: (i) septic tank effluent movement risk, driven by soil hydro-morphological characteristics; (ii) distance of septic tank to watercourse; and (iii) degree of slope. Experts used the tertile method to elicit a range of values representing their beliefs of the proportion of FIOs likely to be delivered to a watercourse for each scenario. The experts judged that 93 % of FIOs would likely be delivered from an STS to a watercourse under the highest risk scenario that combined (i) very high STS effluent movement risk, (ii) STS distance to watercourse <10 m, and (iii) a location on a steep slope with gradient >25 %. Under the lowest risk scenario, the proportion of FIOs reaching a watercourse would likely reduce to 5 %. Expert confidence was high for scenarios that represented extremes of risk, while uncertainty increased for scenarios depicting intermediate risk conditions. The behavioural aggregation process employed to obtain a consensus among the experts proved to be useful for highlighting both areas of strong consensus and high uncertainty. The latter therefore represent priorities for future empirical research to further improve our understanding of potential pollution risk from septic tanks and in turn enable better assessments of potential threats to water quality in rural catchments throughout the world where decentralised wastewater systems are common.
Collapse
Affiliation(s)
- Chisha Chongo Mzyece
- Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, Scotland, United Kingdom of Great Britain and Northern Ireland.
| | - Miriam Glendell
- Environmental and Biochemical Sciences Group, The James Hutton Institute, Craigiebuckler, Aberdeen AB15 8QH, Scotland, United Kingdom of Great Britain and Northern Ireland
| | - Zisis Gagkas
- Environmental and Biochemical Sciences Group, The James Hutton Institute, Craigiebuckler, Aberdeen AB15 8QH, Scotland, United Kingdom of Great Britain and Northern Ireland
| | - Richard S Quilliam
- Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, Scotland, United Kingdom of Great Britain and Northern Ireland
| | - Ian Jones
- Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, Scotland, United Kingdom of Great Britain and Northern Ireland
| | - Eulyn Pagaling
- Environmental and Biochemical Sciences Group, The James Hutton Institute, Craigiebuckler, Aberdeen AB15 8QH, Scotland, United Kingdom of Great Britain and Northern Ireland
| | - Ioanna Akoumianaki
- Environmental and Biochemical Sciences Group, The James Hutton Institute, Craigiebuckler, Aberdeen AB15 8QH, Scotland, United Kingdom of Great Britain and Northern Ireland
| | - Claire Newman
- Environmental and Biochemical Sciences Group, The James Hutton Institute, Craigiebuckler, Aberdeen AB15 8QH, Scotland, United Kingdom of Great Britain and Northern Ireland
| | - David M Oliver
- Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, Scotland, United Kingdom of Great Britain and Northern Ireland
| |
Collapse
|
17
|
Saenkham-Huntsinger P, Ritter M, Donati GL, Mitchell AM, Subashchandrabose S. The inner membrane protein YhiM links copper and CpxAR envelope stress responses in uropathogenic E. coli. mBio 2024; 15:e0352223. [PMID: 38470052 PMCID: PMC11005409 DOI: 10.1128/mbio.03522-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 02/13/2024] [Indexed: 03/13/2024] Open
Abstract
Urinary tract infection (UTI) is a ubiquitous infectious condition, and uropathogenic Escherichia coli (UPEC) is the predominant causative agent of UTI. Copper (Cu) is implicated in innate immunity, including against UPEC. Cu is a trace element utilized as a co-factor, but excess Cu is toxic due to mismetalation of non-cognate proteins. E. coli precisely regulates Cu homeostasis via efflux systems. However, Cu import mechanisms into the bacterial cell are not clear. We hypothesized that Cu import defective mutants would exhibit increased resistance to Cu. This hypothesis was tested in a forward genetic screen with transposon (Tn5) insertion mutants in UPEC strain CFT073, and we identified 32 unique Cu-resistant mutants. Transposon and defined mutants lacking yhiM, which encodes a hypothetical inner membrane protein, were more resistant to Cu than parental strain. Loss of YhiM led to decreased cellular Cu content and increased expression of copA, encoding a Cu efflux pump. The CpxAR envelope stress response system was activated in the ΔyhiM mutant as indicated by increased expression of cpxP. Transcription of yhiM was regulated by CueR and CpxR, and the CpxAR system was essential for increased Cu resistance in the ΔyhiM mutant. Importantly, activation of CpxAR system in the ΔyhiM mutant was independent of NlpE, a known activator of this system. YhiM was required for optimal fitness of UPEC in a mouse model of UTI. Our findings demonstrate that YhiM is a critical mediator of Cu homeostasis and links bacterial adaptation to Cu stress with the CpxAR-dependent envelope stress response in UPEC.IMPORTANCEUPEC is a common bacterial infection. Bacterial pathogens are exposed to host-derived Cu during infection, including UTI. Here, we describe detection of genes involved in Cu homeostasis in UPEC. A UPEC mutant lacking YhiM, a membrane protein, exhibited dramatic increase in resistance to Cu. Our study demonstrates YhiM as a nexus between Cu stress and the CpxAR-dependent envelope stress response system. Importantly, our findings establish NlpE-independent activation of CpxAR system during Cu stress in UPEC. Collectively, YhiM emerges as a critical mediator of Cu homeostasis in UPEC and highlights the interlinked nature of bacterial adaptation to survival during Cu and envelope stress.
Collapse
Affiliation(s)
- Panatda Saenkham-Huntsinger
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - Matthew Ritter
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - George L. Donati
- Department of Chemistry, Wake Forest University, Winston-Salem, North Carolina, USA
| | - Angela M. Mitchell
- Department of Biology, College of Science, Texas A&M University, College Station, Texas, USA
| | - Sargurunathan Subashchandrabose
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| |
Collapse
|
18
|
Tadesse T, Alemayehu H, Medhin G, Akalu A, Eguale T. Antibiogram of Escherichia coli Isolated from Dairy Cattle and in-Contact Humans in Selected Areas of Central Ethiopia. Vet Med (Auckl) 2024; 15:117-127. [PMID: 38617107 PMCID: PMC11016264 DOI: 10.2147/vmrr.s456247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 04/03/2024] [Indexed: 04/16/2024]
Abstract
Background Antimicrobial resistance (AMR) is a global threat to public and animal health. Escherichia coli is considered an indicator organism for monitoring AMR among gram-negative Enterobacteriaceae in humans and animals. The current study aims to assess the antibiogram profile of E. coli isolated from dairy cattle and in-contact humans in central Ethiopia and to identify risk factors associated with multidrug resistance (MDR). Methods A cross-sectional study was conducted in which 58 farms were recruited from selected districts of central Ethiopia. E. coli was isolated using standard bacteriological techniques. A total of 200 representative isolates (140 from cattle and 60 from humans in contact) were randomly selected and tested for susceptibility to a panel of 13 antimicrobials using the Kirby-Bauer disc diffusion assay. Results The highest rate of resistance was observed for sulfamethoxazole+trimethoprim (58.6%, 82/140) and amoxicillin+clavulanic acid (70.0%, 42/60) among E. coli isolates from cattle and hmans, respectively. In contrast, resistance rates in isolates from in contact humans with the cattle were 30%, 33.3%, and 66.7%, respectively. Resistance to tetracycline (p=0.02), streptomycin (p=0.03), and sulfamethoxazole+trimethoprim (p=0.007) was significantly high in E. coli isolated from cattle on commercial dairy farms than in those isolated from cattle on smallholder farms. There was no significant difference (p>0.05) in the rate of resistance between E. coli isolated from in contact humans with smallholder and commercial dairy farms. Antimicrobial use for treatment purpose (p=0.04) and non-compliance with the drug withdrawal period (p=0.03) were significantly associated with the farm-level occurrence of MDR. Conclusion A high rate of resistance was detected in E. coli isolated from the feces of dairy cattle and in-contact humans. This necessitates an effective intervention through a one-health approach and further molecular studies are required to establish source attribution.
Collapse
Affiliation(s)
- Tekalign Tadesse
- Department of Veterinary Science, Mattu University, Mattu, Ethiopia
| | - Haile Alemayehu
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Girmay Medhin
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Aberaw Akalu
- Food, Medicine and Healthcare Administration and Control, Addis Ababa, Ethiopia
| | - Tadesse Eguale
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
- The Ohio State University, Global One Health LLC, Addis Ababa, Ethiopia
| |
Collapse
|
19
|
Royer C, Patin NV, Jesser KJ, Peña-Gonzalez A, Hatt JK, Trueba G, Levy K, Konstantinidis KT. Comparison of metagenomic and traditional methods for diagnosis of E. coli enteric infections. mBio 2024; 15:e0342223. [PMID: 38488359 PMCID: PMC11005377 DOI: 10.1128/mbio.03422-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 02/23/2024] [Indexed: 04/11/2024] Open
Abstract
Diarrheagenic Escherichia coli, collectively known as DEC, is a leading cause of diarrhea, particularly in children in low- and middle-income countries. Diagnosing infections caused by different DEC pathotypes traditionally relies on the cultivation and identification of virulence genes, a resource-intensive and error-prone process. Here, we compared culture-based DEC identification with shotgun metagenomic sequencing of whole stool using 35 randomly drawn samples from a cohort of diarrhea-afflicted patients. Metagenomic sequencing detected the cultured isolates in 97% of samples, revealing, overall, reliable detection by this approach. Genome binning yielded high-quality E. coli metagenome-assembled genomes (MAGs) for 13 samples, and we observed that the MAG did not carry the diagnostic DEC virulence genes of the corresponding isolate in 60% of these samples. Specifically, two distinct scenarios were observed: diffusely adherent E. coli (DAEC) isolates without corresponding DAEC MAGs appeared to be relatively rare members of the microbiome, which was further corroborated by quantitative PCR (qPCR), and thus unlikely to represent the etiological agent in 3 of the 13 samples (~23%). In contrast, ETEC virulence genes were located on plasmids and largely escaped binning in associated MAGs despite being prevalent in the sample (5/13 samples or ~38%), revealing limitations of the metagenomic approach. These results provide important insights for diagnosing DEC infections and demonstrate how metagenomic methods can complement isolation efforts and PCR for pathogen identification and population abundance. IMPORTANCE Diagnosing enteric infections based on traditional methods involving isolation and PCR can be erroneous due to isolation and other biases, e.g., the most abundant pathogen may not be recovered on isolation media. By employing shotgun metagenomics together with traditional methods on the same stool samples, we show that mixed infections caused by multiple pathogens are much more frequent than traditional methods indicate in the case of acute diarrhea. Further, in at least 8.5% of the total samples examined, the metagenomic approach reliably identified a different pathogen than the traditional approach. Therefore, our results provide a methodology to complement existing methods for enteric infection diagnostics with cutting-edge, culture-independent metagenomic techniques, and highlight the strengths and limitations of each approach.
Collapse
Affiliation(s)
- C. Royer
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - N. V. Patin
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - K. J. Jesser
- Department of Environmental and Occupational Health, University of Washington, Seattle, Washington, USA
| | - A. Peña-Gonzalez
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotà, Colombia
| | - J. K. Hatt
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - G. Trueba
- Institute of Microbiology, Universidad San Francisco de Quito, Quito, Ecuador
| | - K. Levy
- Department of Environmental and Occupational Health, University of Washington, Seattle, Washington, USA
| | - K. T. Konstantinidis
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| |
Collapse
|
20
|
Bohl V, Hollmann NM, Melzer T, Katikaridis P, Meins L, Simon B, Flemming D, Sinning I, Hennig J, Mogk A. The Listeria monocytogenes persistence factor ClpL is a potent stand-alone disaggregase. eLife 2024; 12:RP92746. [PMID: 38598269 PMCID: PMC11006417 DOI: 10.7554/elife.92746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024] Open
Abstract
Heat stress can cause cell death by triggering the aggregation of essential proteins. In bacteria, aggregated proteins are rescued by the canonical Hsp70/AAA+ (ClpB) bi-chaperone disaggregase. Man-made, severe stress conditions applied during, e.g., food processing represent a novel threat for bacteria by exceeding the capacity of the Hsp70/ClpB system. Here, we report on the potent autonomous AAA+ disaggregase ClpL from Listeria monocytogenes that provides enhanced heat resistance to the food-borne pathogen enabling persistence in adverse environments. ClpL shows increased thermal stability and enhanced disaggregation power compared to Hsp70/ClpB, enabling it to withstand severe heat stress and to solubilize tight aggregates. ClpL binds to protein aggregates via aromatic residues present in its N-terminal domain (NTD) that adopts a partially folded and dynamic conformation. Target specificity is achieved by simultaneous interactions of multiple NTDs with the aggregate surface. ClpL shows remarkable structural plasticity by forming diverse higher assembly states through interacting ClpL rings. NTDs become largely sequestered upon ClpL ring interactions. Stabilizing ring assemblies by engineered disulfide bonds strongly reduces disaggregation activity, suggesting that they represent storage states.
Collapse
Affiliation(s)
- Valentin Bohl
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH AllianceHeidelbergGermany
| | - Nele Merret Hollmann
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL) HeidelbergHeidelbergGermany
| | - Tobias Melzer
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH AllianceHeidelbergGermany
| | - Panagiotis Katikaridis
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH AllianceHeidelbergGermany
| | - Lena Meins
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH AllianceHeidelbergGermany
| | - Bernd Simon
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL) HeidelbergHeidelbergGermany
| | - Dirk Flemming
- Heidelberg University Biochemistry Center (BZH)HeidelbergGermany
| | - Irmgard Sinning
- Heidelberg University Biochemistry Center (BZH)HeidelbergGermany
| | - Janosch Hennig
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL) HeidelbergHeidelbergGermany
- Chair of Biochemistry IV, Biophysical Chemistry, University of BayreuthBayreuthGermany
| | - Axel Mogk
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH AllianceHeidelbergGermany
| |
Collapse
|
21
|
Miner MV, Rauch I. Why put yourself on a pedestal? The pathogenic role of the A/E pedestal. Infect Immun 2024:e0048923. [PMID: 38591884 DOI: 10.1128/iai.00489-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/10/2024] Open
Abstract
Certain Escherichia coli (E. coli) strains are attaching and effacing (A/E) lesion pathogens that primarily infect intestinal epithelial cells. They cause actin restructuring and polymerization within the host cell to create an actin-rich protrusion below the site of adherence, termed the pedestal. Although there is clarity on the pathways initiating pedestal formation, the underlying purpose(s) of the pedestal remains ambiguous. The conservation of pedestal-forming activity across multiple pathogens and redundancy in formation pathways indicate a pathogenic advantage. However, few decisive conclusions have been drawn, given that the results vary between model systems. Some research argues that the pedestal increases the colonization capability of the bacterium. These studies utilize A/E pathogens specifically deficient in pedestal formation to evaluate adhesion and intestinal colonization following infection. There have been many proposed mechanisms for the colonization benefit conferred by the pedestal. One suggested benefit is that the pedestal allows for direct cytosolic anchoring through incorporation of the established host cortical actin, causing a stable link between the pathogen and cell structure. The pedestal may confer enhanced motility, as enteropathogenic E. coli (EPEC) and enterohemorrhagic E. coli (EHEC) are better able to migrate on the surface of host cells and infect neighboring cells in the presence of the pedestal. Additionally, some research suggests that the pedestal improves effector delivery. This review will investigate the purpose of pedestal formation using evidence from recent literature and will critically evaluate the methodology and model systems. Most importantly, we will contextualize the proposed functions to reconcile potential synergistic effects.
Collapse
Affiliation(s)
- M V Miner
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, Oregon, USA
| | - I Rauch
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, Oregon, USA
| |
Collapse
|
22
|
Chen L, Umar Z. The complete genome sequencing of Escherichia coli isolated from a patient who visited Pediatrics People's Hospital of Pingguo, China. Microbiol Resour Announc 2024:e0002024. [PMID: 38591919 DOI: 10.1128/mra.00020-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 03/29/2024] [Indexed: 04/10/2024] Open
Abstract
In this article, we present a comprehensive analysis of the genome sequence of Escherichia coli isolate ACESH02881hy, which has a 5,071,463-bp genome size. The strain was isolated from patient who visited the Pediatrics People's Hospital of Pingguo, China, 2021.
Collapse
Affiliation(s)
- Lifeng Chen
- Department of Clinical Engineering and Materials Supplies, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Zeeshan Umar
- Marshall Laboratory of Biomedical Engineering, School of Medicine, Shenhzen University, Shenzhen , China
| |
Collapse
|
23
|
Paladini J, Maier A, Habazettl JM, Hertel I, Sonti R, Grzesiek S. The molecular basis of Abelson kinase regulation by its αI-helix. eLife 2024; 12:RP92324. [PMID: 38588001 PMCID: PMC11001296 DOI: 10.7554/elife.92324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/10/2024] Open
Abstract
Abelson tyrosine kinase (Abl) is regulated by the arrangement of its regulatory core, consisting sequentially of the SH3, SH2, and kinase (KD) domains, where an assembled or disassembled core corresponds to low or high kinase activity, respectively. It was recently established that binding of type II ATP site inhibitors, such as imatinib, generates a force from the KD N-lobe onto the SH3 domain and in consequence disassembles the core. Here, we demonstrate that the C-terminal αI-helix exerts an additional force toward the SH2 domain, which correlates both with kinase activity and type II inhibitor-induced disassembly. The αI-helix mutation E528K, which is responsible for the ABL1 malformation syndrome, strongly activates Abl by breaking a salt bridge with the KD C-lobe and thereby increasing the force onto the SH2 domain. In contrast, the allosteric inhibitor asciminib strongly reduces Abl's activity by fixating the αI-helix and reducing the force onto the SH2 domain. These observations are explained by a simple mechanical model of Abl activation involving forces from the KD N-lobe and the αI-helix onto the KD/SH2SH3 interface.
Collapse
Affiliation(s)
- Johannes Paladini
- Structural Biology and Biophysics, Biozentrum, University of BaselBaselSwitzerland
| | - Annalena Maier
- Structural Biology and Biophysics, Biozentrum, University of BaselBaselSwitzerland
| | | | - Ines Hertel
- Structural Biology and Biophysics, Biozentrum, University of BaselBaselSwitzerland
| | - Rajesh Sonti
- Structural Biology and Biophysics, Biozentrum, University of BaselBaselSwitzerland
| | - Stephan Grzesiek
- Structural Biology and Biophysics, Biozentrum, University of BaselBaselSwitzerland
| |
Collapse
|
24
|
Wu X, Chen R, Liang P, Zha J. Identification of Escherichia coli multidrug resistance transporters involved in anthocyanin biosynthesis. Front Microbiol 2024; 15:1357794. [PMID: 38646631 PMCID: PMC11026601 DOI: 10.3389/fmicb.2024.1357794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 03/25/2024] [Indexed: 04/23/2024] Open
Abstract
The anthocyanin compound cyanidin 3-O-glucoside (C3G) is a natural pigment widely used in food and nutraceutical industries. Its microbial synthesis by E. coli is a promising alternative to the traditional extraction methods. However, part of the synthesized C3G accumulates in the cytoplasm, thus potentially causing growth inhibition and product degradation. Therefore, it is necessary to enhance C3G secretion via exploration of native transporters facilitating C3G export. In this study, we report the screening and verification of native multidrug resistance transporters from 40 candidates in E. coli that can improve the extracellular C3G production when using catechin as the substrate. Overexpression of single transporter genes including fsr, yebQ, ynfM, mdlAB, and emrKY were found to increase C3G production by 0.5- to 4.8-fold. Genetic studies indicated that mdlAB and emrKY are vital transporters in the secretion of C3G. Our study reveals a set of new multidrug resistance transporters for the improvement of microbial biosynthesis of C3G and other anthocyanins.
Collapse
Affiliation(s)
- Xia Wu
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi’an, China
- Xi’an Key Laboratory of Antiviral and Antimicrobial-Resistant Bacteria Therapeutics Research, Xi’an, China
| | - Rongxia Chen
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi’an, China
| | - Ping Liang
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi’an, China
| | - Jian Zha
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi’an, China
- Xi’an Key Laboratory of Antiviral and Antimicrobial-Resistant Bacteria Therapeutics Research, Xi’an, China
| |
Collapse
|
25
|
Khattak SU, Iqbal Z, Ahmad J, Shi Y, Rehman IU. Purification of andibenin and a chromanone analogue from rhizospheric Aspergillus flavus and soil-borne Penicillium notatum exhibiting cytotoxic and antibacterial properties. Mycologia 2024:1-15. [PMID: 38573188 DOI: 10.1080/00275514.2024.2324620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 02/25/2024] [Indexed: 04/05/2024]
Abstract
The discovery of bioactive compounds from fungal natural sources holds immense potential for the development of novel therapeutics. The present study investigates the extracts of soil-borne Penicillium notatum and rhizosphere-inhabiting Aspergillus flavus for their antibacterial, antifungal, and cytotoxic potential. Additionally, two compounds were purified using chromatographic and spectroscopic techniques. The results demonstrated that the ethyl acetate fraction of A. flavus exhibited prominent cytotoxic activity against Artemia salina, whereas the ethyl acetate fraction of P. notatum displayed promising antibacterial potential. At dose concentrations of 10, 100, and 1000 µg mL-1, the ethyl acetate fraction of A. flavus showed mortality percentages of 7.6%, 66.4%, and 90%, respectively. The ethyl acetate fraction of P. notatum extract exhibited significant antibacterial activity, forming inhibition zones measuring 41, 38, 34, 34, and 30 mm against B. subtilis, S. flexneri, E. coli, K. pneumoniae, and S. aureus, respectively, at 1000 µg mL-1. At this concentration, inhibition zones of 28, 27, and 15 mm were recorded for P. vulgaris, S. typhi, and X. oryzae. Using bioassay-guided approach, one compound each was purified from the fungal extracts. The initial purification involved mass spectroscopic analysis, followed by structural elucidation using 500 MHz nuclear magnetic resonance (NMR) spectroscopy. Compound 1, derived from A. flavus, was identified as ethyl 2-hydroxy-5,6-dimethyl-4-oxocyclohex-2-ene-1-carboxylate, with a mass of 212, whereas compound 2, isolated from P. notatum, was identified as 3-amino-2-(cyclopenta-2,4-dien-1-ylamino)-8-methoxy-4H-chromen-4-one, with an exact mass of 270. Based on bioassay results, compound 1 was subjected to brine shrimp lethality assay and compound 2 was tested for its antibacterial potential. Compound 1 exhibited 30% lethality against brine shrimp larvae at a concentration of 100 µg mL-1, whereas at 1000 µg mL-1 the mortality increased to 70%. Compound 2 displayed notable antibacterial potential, forming inhibition zones of 30, 24, 19, and 12 mm against S. aureus, E. coli, B. subtilis, and S. flexneri, respectively. In comparison, the standard antibiotic tetracycline produced inhibition zones of 18, 18, 15, and 10 mm against the respective bacterial strains at the same concentration.
Collapse
Affiliation(s)
- Saeed Ullah Khattak
- Center of Biotechnology and Microbiology, University of Peshawar, University Road, Rahat Abad, Peshawar, Khyber Pakhtunkhwa 25120, Pakistan
| | - Zafar Iqbal
- Department of Agricultural Chemistry, The University of Agriculture Peshawar, Peshawar, Khyber Pakhtunkhwa, Pakistan
| | - Jamshaid Ahmad
- Center of Biotechnology and Microbiology, University of Peshawar, University Road, Rahat Abad, Peshawar, Khyber Pakhtunkhwa 25120, Pakistan
| | - Yanbin Shi
- School of Pharmacy, Lanzhou University, 2VW8+9FQ, Donggang W Road, Cheng Guan Qu, Lan Zhou Shi, Gan Su Sheng 730000, China
| | - Irshad Ur Rehman
- Center of Biotechnology and Microbiology, University of Peshawar, University Road, Rahat Abad, Peshawar, Khyber Pakhtunkhwa 25120, Pakistan
| |
Collapse
|
26
|
Wang WS, Lin-Chao S. Hfq-Antisense RNA I Binding Regulates RNase E-Dependent RNA Stability and ColE1 Plasmid Copy Number. Int J Mol Sci 2024; 25:3955. [PMID: 38612765 PMCID: PMC11012335 DOI: 10.3390/ijms25073955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 03/27/2024] [Accepted: 03/31/2024] [Indexed: 04/14/2024] Open
Abstract
The mechanisms and consequences of gene regulation by Hfq on trans-encoded small RNAs (sRNAs) have been well studied and documented. Recent employment of Genomic SELEX to search for Hfq-binding motifs has indicated that Hfq might frequently regulate gene expression controlled by cis-antisense RNAs. Here, we use the classic ColE1 plasmid antisense RNA-based regulation model (i.e., RNA I) to study the role of Hfq in controlling antisense regulatory functions. We show that Hfq exhibits a high binding affinity for RNA I and that binding limits RNase E cleavage, thereby stabilizing RNA I and reducing the plasmid copy number. Full-length RNA I displays a binding affinity for Hfq in the sub-micromolar range. In vivo overexpression of Hfq prolongs RNA I stability and reduces the ColE1 plasmid copy number, whereas deletion of hfq reduces RNA I stability and increases the plasmid copy number. RNA I predominantly binds to the proximal face of Hfq and exhibits competitive ability against a chromosome-borne proximal face-bound sRNA (DsrA) for Hfq binding. Through its strong promoter and high gene dosage features, plasmid-encoded antisense RNA I results in high RNA I expression, so it may antagonize the effects of trans-encoded RNAs in controlling target gene expression.
Collapse
Affiliation(s)
- Wei-Syuan Wang
- Molecular and Cell Biology, Taiwan International Graduate Program, Academia Sinica and Graduate Institute of Life Science, National Defense Medical Center, Taipei 11490, Taiwan
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei 10002, Taiwan
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Sue Lin-Chao
- Molecular and Cell Biology, Taiwan International Graduate Program, Academia Sinica and Graduate Institute of Life Science, National Defense Medical Center, Taipei 11490, Taiwan
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei 10002, Taiwan
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| |
Collapse
|
27
|
Moreira da Silva J, Menezes J, Fernandes L, Santos Costa S, Amaral A, Pomba C. Carbapenemase-producing Enterobacterales strains causing infections in companion animals-Portugal. Microbiol Spectr 2024; 12:e0341623. [PMID: 38446073 DOI: 10.1128/spectrum.03416-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 02/15/2024] [Indexed: 03/07/2024] Open
Abstract
An increase in Klebsiella pneumoniae carbapenem-resistant human nosocomial strains is occurring in Europe, namely with the blaOXA-48-like and blaKPC-like genes. We determined the prevalence of carbapenemase-producing Enterobacterales clinical strains in companion animals in Portugal and characterized their mobile genetic elements. Susceptibility data of a consecutive collection of 977 Enterobacterales clinical strains from a Portuguese private veterinary diagnostic laboratory were evaluated (January-December 2020). Additional phenotypical and genotypical assays were performed in a subset of 261 strains with a resistant phenotype. Whole-genome sequencing was performed for carbapenemase-producing strains. The frequency of carbapenemase-producing Enterobacterales clinical strains in companion animals in Portugal was 0.51% (n = 5/977). Thus, five strains were characterized: (i) one OXA-181-producing K. pneumoniae ST273, (ii) two KPC-3-producing K. pneumoniae ST147; (iii) one KPC-3-producing K. pneumoniae ST392; and (iv) one OXA-48-producing E. coli ST127. The blaKPC-3 gene was located on transposon Tn4401d on IncFIA type plasmid for the K. pneumoniae ST147 strains and on a IncN-type plasmid for the K. pneumoniae ST392 strain, while blaOXA-181 gene was located on an IncX3 plasmid. All de novo assembled plasmids and plasmid-encoded transposons harboring carbapenemase genes were homologous to those previously described in the human healthcare. No plasmid replicons were detected on the OXA-48-producing E. coli ST127. The dissemination of carbapenem resistance is occurring horizontally via plasmid spreading from the human high burden carbapenem resistance setting to the companion animal sector. Furthermore, companion animals may act as reservoirs of carbapenem resistance. Implementation of carbapenemase detection methods in routine clinical veterinary microbiology is urgently needed. IMPORTANCE This is the first study on the prevalence of carbapenemase-producing Enterobacterales (CPE) clinical strains from companion animals in Portugal. Despite the generally low prevalence of CPE in companion animals, it is imperative for veterinary diagnostic laboratories to employ diagnostic methods for carbapenemase detection. The resemblance found in the mobile genetic elements transporting carbapenemase genes between veterinary medicine and human medicine implies a potential circulation within a One Health framework.
Collapse
Affiliation(s)
- Joana Moreira da Silva
- CIISA-Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
- AL4AnimalS-Associate Laboratory for Animal and Veterinary Sciences, Vila Real, Portugal
| | - Juliana Menezes
- CIISA-Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
- AL4AnimalS-Associate Laboratory for Animal and Veterinary Sciences, Vila Real, Portugal
| | - Laura Fernandes
- CIISA-Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
- AL4AnimalS-Associate Laboratory for Animal and Veterinary Sciences, Vila Real, Portugal
| | - Sofia Santos Costa
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL, Lisbon, Portugal
| | - Andreia Amaral
- CIISA-Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
- AL4AnimalS-Associate Laboratory for Animal and Veterinary Sciences, Vila Real, Portugal
| | - Constança Pomba
- CIISA-Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
- AL4AnimalS-Associate Laboratory for Animal and Veterinary Sciences, Vila Real, Portugal
- Genevet, Veterinary Molecular Diagnostic Laboratory, Carnaxide, Portugal
| |
Collapse
|
28
|
Beterams A, Püning C, Wyink B, Grosse-Kleimann J, Gölz G, Schönknecht A, Alter T, Reich F. Status quo: Levels of Campylobacter spp. and hygiene indicators in German slaughterhouses for broiler and turkey. Int J Food Microbiol 2024; 414:110610. [PMID: 38330527 DOI: 10.1016/j.ijfoodmicro.2024.110610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 12/22/2023] [Accepted: 01/29/2024] [Indexed: 02/10/2024]
Abstract
Poultry is a common reservoir for Campylobacter and a main source for human campylobacteriosis. With broiler being the predominant poultry for food production, most food safety related research is conducted for this species, for turkey, few studies are available. Although animals are typically colonized at the farm level, the slaughtering process is considered an important factor in re- and cross-contamination. We examined the development of Campylobacter, E. coli and total colony counts (TCC) after several processing steps in three broiler and one turkey slaughterhouses. Whole carcass rinsing and neck skin sampling was applied for broilers resulting in 486 samples in total, while 126 neck skin samples were collected for turkeys. A decrease in the loads of the different bacterial groups along the broiler slaughtering process was observed. Campylobacter mean counts dropped from 4.5 ± 1.7 log10 CFU/ml after killing to 1.6 ± 0.4 log10 CFU/ml after chilling. However, an increase in Campylobacter counts was evident after evisceration before the values again decreased by the final processing step. Although the Campylobacter prevalence in the turkey samples showed a similar development, the bacterial loads were much lower with 1.7 ± 0.3 log10 CFU/g after killing and 1.7 ± 0.4 log10 CFU/g after chilling compared to those of broilers. The loads of E. coli and total colony count of turkey were higher after killing, were reduced by scalding and remained stable until after chilling. This study highlights trends during the slaughtering process in reducing the levels of Campylobacter, E. coli, and total colony counts for broiler and turkey carcasses, from the initial step to after chilling. These results contribute to our understanding of microbial dynamics during meat processing.
Collapse
Affiliation(s)
- A Beterams
- German Federal Institute for Risk Assessment, Max-Dohrn-Strasse 8-10, D-10589 Berlin, Germany
| | - C Püning
- Institute of Food Safety and Food Hygiene, Center for Veterinary Public Health, Freie Universität Berlin, Königsweg 69, 14163 Berlin, Germany
| | - B Wyink
- Frankenförder Forschungsgesellschaft, Potsdamer Straße 18a, 14943 Luckenwalde, Germany
| | - J Grosse-Kleimann
- Department of Biometry, Epidemiology and Information Processing, University of Veterinary Medicine Hannover, Bünteweg 2, 30559 Hannover, Germany
| | - G Gölz
- Institute of Food Safety and Food Hygiene, Center for Veterinary Public Health, Freie Universität Berlin, Königsweg 69, 14163 Berlin, Germany
| | - A Schönknecht
- Institute of Food Safety and Food Hygiene, Center for Veterinary Public Health, Freie Universität Berlin, Königsweg 69, 14163 Berlin, Germany
| | - T Alter
- Institute of Food Safety and Food Hygiene, Center for Veterinary Public Health, Freie Universität Berlin, Königsweg 69, 14163 Berlin, Germany
| | - F Reich
- German Federal Institute for Risk Assessment, Max-Dohrn-Strasse 8-10, D-10589 Berlin, Germany.
| |
Collapse
|
29
|
Wada K, Tsuboi I, Takahashi S, Yasuda M, Miyazaki J, Kobayashi K, Matsumoto M, Hayami H, Yamamoto S, Kiyota H, Sato J, Matsumoto T, Hasegawa N, Kobayashi I, Masumori N, Kimura T, Yamada H, Matsumoto K, Ishikawa K, Fujimoto K, Shigemura K, Sadahira T, Ito K, Yokoyama T, Izumitani M, Sumii T, Hosobe T, Hikosaka K, Kawahara M, Sato T, Ito S, Masue N, Sakurai T, Kokura K, Kadena H, Morikawa T, Minamidate Y, Yoh M, Hashimoto J, Maruyama T, Yoshioka M, Takashima K, Kawai S, Nishi S, Matsumoto T, Hirayama H, Okusa H, Uno S, Inoue Y, Kurimura Y, Shirane T, Takaoka E, Tojo T, Arakawa S, Hamasuna R, Tomioka A, Iihara K, Ishitoya S, Maeda H, Terado M. Third nationwide surveillance of bacterial pathogens in patients with acute uncomplicated cystitis conducted by the Japanese surveillance committee during 2020 and 2021: Antimicrobial susceptibility of Escherichia coli, Klebsiella pneumoniae, and Staphylococcus saprophyticus. J Infect Chemother 2024; 30:277-285. [PMID: 38242285 DOI: 10.1016/j.jiac.2024.01.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/09/2024] [Accepted: 01/16/2024] [Indexed: 01/21/2024]
Abstract
The Japanese surveillance committee conducted a third nationwide surveillance of antimicrobial susceptibility of acute uncomplicated cystitis at 55 facilities throughout Japan between April 2020 and September 2021. In this surveillance, we investigated the susceptibility of Escherichia coli (E. coli), Klebsiella pneumoniae (K. pneumoniae), and Staphylococcus saprophyticus (S. saprophyticus) for various antimicrobial agents by isolating and culturing bacteria from urine samples. In total, 823 strains were isolated from 848 patients and 569 strains of target bacteria, including E. coli (n = 529, 92.9 %), K. pneumoniae (n = 28, 4.9 %), and S. saprophyticus (n = 12, 2.2 %) were isolated. The minimum inhibitory concentrations of 18 antibacterial agents were determined according to the Clinical and Laboratory Standards Institute manual. In premenopausal patients, there were 31 (10.5 %) and 20 (6.8 %) fluoroquinolone (FQ)-resistant E. coli and extended-spectrum β-lactamase (ESBL)-producing E. coli, respectively. On the other hand, in postmenopausal patients, there were 75 (32.1 %) and 36 (15.4 %) FQ-resistant E. coli and ESBL-producing E. coli, respectively. The rate of FQ-resistant E. coli and ESBL-producing E. coli in post-menopausal women was higher than that for our previous nationwide surveillance (20.7 % and 32.1 %: p = 0.0004, 10.0 % and 15.4 %; p = 0.0259). For pre-menopausal women, there was no significant difference in the rate of FQ-resistant E. coli and ESBL-producing E. coli between this and previous reports, but the frequency of FQ-resistant E. coli and ESBL-producing E. coli exhibited a gradual increase. For appropriate antimicrobial agent selection and usage, it is essential for clinicians to be aware of the high rate of these antimicrobial-resistant bacteria in acute uncomplicated cystitis in Japan.
Collapse
Affiliation(s)
- Koichiro Wada
- Department of Urology, Shimane University Faculty of Medicine, Shimane, Japan; The Urogenital Sub-committee and the Surveillance Committee of Japanese Society of Chemotherapy (JSC), The Japanese Association for Infectious Diseases (JAID) and the Japanese Society for Clinical Microbiology (JSCM), Tokyo, Japan.
| | - Ichiro Tsuboi
- Department of Urology, Shimane University Faculty of Medicine, Shimane, Japan
| | - Satoshi Takahashi
- The Urogenital Sub-committee and the Surveillance Committee of Japanese Society of Chemotherapy (JSC), The Japanese Association for Infectious Diseases (JAID) and the Japanese Society for Clinical Microbiology (JSCM), Tokyo, Japan; Department of Infection Control and Laboratory Medicine, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Mitsuru Yasuda
- The Urogenital Sub-committee and the Surveillance Committee of Japanese Society of Chemotherapy (JSC), The Japanese Association for Infectious Diseases (JAID) and the Japanese Society for Clinical Microbiology (JSCM), Tokyo, Japan; Department of Infection Control and Laboratory Medicine, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Jun Miyazaki
- The Urogenital Sub-committee and the Surveillance Committee of Japanese Society of Chemotherapy (JSC), The Japanese Association for Infectious Diseases (JAID) and the Japanese Society for Clinical Microbiology (JSCM), Tokyo, Japan; Department of Urology, International University of Health and Welfare Ichikawa Hospital, Chiba, Japan; Department of Urology, International University of Health and Welfare Narita Hospital, Chiba, Japan
| | - Kanao Kobayashi
- The Urogenital Sub-committee and the Surveillance Committee of Japanese Society of Chemotherapy (JSC), The Japanese Association for Infectious Diseases (JAID) and the Japanese Society for Clinical Microbiology (JSCM), Tokyo, Japan; Department of Urology, Chugoku Rosai Hospital, Hiroshima, Japan
| | - Masahiro Matsumoto
- The Urogenital Sub-committee and the Surveillance Committee of Japanese Society of Chemotherapy (JSC), The Japanese Association for Infectious Diseases (JAID) and the Japanese Society for Clinical Microbiology (JSCM), Tokyo, Japan; Department of Urology, University of Occupational and Environmental Health, Kitakyushu, Japan
| | - Hiroshi Hayami
- The Urogenital Sub-committee and the Surveillance Committee of Japanese Society of Chemotherapy (JSC), The Japanese Association for Infectious Diseases (JAID) and the Japanese Society for Clinical Microbiology (JSCM), Tokyo, Japan; Blood Purification Center, Kagoshima University Hospital, Kagoshima, Japan
| | - Shingo Yamamoto
- The Surveillance Committee of JSC, JAID and JSCM, Tokyo, Japan; Department of Urology, Hyogo College of Medicine, Hyogo, Japan
| | - Hiroshi Kiyota
- The Surveillance Committee of JSC, JAID and JSCM, Tokyo, Japan; Department of Urology, School of Medicine, The Jikei University Katsushika Medical Center, Tokyo, Japan; Iguchi Nephrourology and Internal Medicine Clinic Shinkoiwa, Tokyo, Japan
| | - Junko Sato
- The Surveillance Committee of JSC, JAID and JSCM, Tokyo, Japan
| | | | - Naoki Hasegawa
- The Surveillance Committee of JSC, JAID and JSCM, Tokyo, Japan
| | - Intetsu Kobayashi
- Department of Infection Control and Prevention, Toho University Faculty of Nursing, Tokyo, Japan
| | - Naoya Masumori
- Department of Urology, School of Medicine, Sapporo Medical University, Sapporo, Japan
| | - Takahiro Kimura
- Department of Urology, The Jikei University School of Medicine, Tokyo, Japan
| | - Hiroki Yamada
- Department of Urology, School of Medicine, The Jikei University Katsushika Medical Center, Tokyo, Japan
| | - Kazumasa Matsumoto
- Department of Urology, Kitasato University School of Medicine, Kanagawa, Japan
| | - Kiyohito Ishikawa
- Department of Urology, School of Medicine, Fujita Health University, Aichi, Japan
| | | | | | - Takuya Sadahira
- Department of Urology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Kenji Ito
- Ito Urology Clinic, Kitakyushu, Japan
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Shohei Nishi
- Nishi Urology and Dermatology Clinic, Kitakyushu, Japan
| | | | | | - Hiroshi Okusa
- Ookusa Urology & Internal Medicine Clinic, Kanagawa, Japan
| | | | | | | | | | - Eiichiro Takaoka
- Department of Urology, International University of Health and Welfare Hospital, Tochigi, Japan
| | - Takanori Tojo
- Department of Urology, Tomei Atsugi Hospital, Kanagawa, Japan
| | - Soichi Arakawa
- Department of Urology, Sanda City Hospital, Hyogo, Japan
| | | | - Atsushi Tomioka
- Department of Urology, Saiseikai Chuwa Hospital, Nara, Japan
| | - Kiyotaka Iihara
- Department of Urology, Fukuoka Shin Mizumaki Hospital, Fukuoka, Japan
| | - Satoshi Ishitoya
- Department of Urology, Japanese Red Cross Otsu Hospital, Shiga, Japan
| | | | | |
Collapse
|
30
|
Hosseini F, Habibi Najafi MB, Rasool Oromiehie A, Nasiri Mahalati M, Yavarmanesh M. Study on synergistic effects of curcumin and bixin against foodborne pathogens. Food Sci Nutr 2024; 12:2426-2435. [PMID: 38628195 PMCID: PMC11016438 DOI: 10.1002/fsn3.3926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 11/13/2023] [Accepted: 12/15/2023] [Indexed: 04/19/2024] Open
Abstract
Various studies have shown that natural colorants, in addition to their coloring attributes, have valuable biological effects such as antioxidant, anti-inflammation, and anticarcinogenic properties. Moreover, their use as a food colorant can restrict the potential disadvantages of synthetic additives and turn foods into functional products. In this study, in vitro antimicrobial activities of two natural colorants of bixin and curcumin against some important foodborne pathogens: Staphylococcus aureus (S. aureus), Listeria innocua (L. innocua), and Escherichia coli (E. coli) were investigated by disk diffusion method. Minimum inhibitory concentration and minimum bactericidal concentration values were determined by agar dilution and broth microdilution methods. The synergistic activity of the colorants against selected microorganisms was assayed by the checkerboard microdilution method. The results showed that the inhibitory effects of bixin against S. aureus were more pronounced than E. coli and L. innocua. The lowest concentration of curcumin (0.6 mg/mL) in the disk diffusion method was not inhibited by any tested bacteria. However, it was effective at the higher concentrations against three microorganisms, but its diameter of inhibition zones was lower than gentamicin in all concentrations. Synergetic effects were observed by curcumin and bixin combination against S. aureus (FICI ≤ 0.5), but they act as an antagonist against E. coli and L. innocua. The results of the synergy test were confirmed by the isobologram curves.
Collapse
Affiliation(s)
- Fereshteh Hosseini
- Department of Food Additives, Food Science & Technology Research InstituteIranian Academic Center for Education, Culture & Research (ACECR)Khorasan Razavi BranchIran
| | | | | | - Mehdi Nasiri Mahalati
- Department of Agronomy, Faculty of AgricultureFerdowsi University of MashhadMashhadIran
| | - Masoud Yavarmanesh
- Department of Food Science and Technology, Faculty of AgricultureFerdowsi University of MashhadMashhadIran
| |
Collapse
|
31
|
Zabolotskii AI, Riabkova NS. A new look at the fluorescent protein-based approach for identifying optimal coding sequence for recombinant protein expression in E. coli. Biotechnol J 2024; 19:e2300343. [PMID: 38622786 DOI: 10.1002/biot.202300343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 03/06/2024] [Accepted: 03/20/2024] [Indexed: 04/17/2024]
Abstract
Due to the degeneracy of the genetic code, most amino acids are encoded by several codons. The choice among synonymous codons at the N-terminus of genes has a profound effect on protein expression in Escherichia coli. This is often explained by the different contributions of synonymous codons to mRNA secondary structure formation. Strong secondary structures at the 5'-end of mRNA interfere with ribosome binding and affect the process of translation initiation. In silico optimization of the gene 5'-end can significantly increase the level of protein expression; however, this method is not always effective due to the uncertainty of the exact mechanism by which synonymous substitutions affect expression; thus, it may produce nonoptimal variants as well as miss some of the best producers. In this paper, an alternative approach is proposed based on screening a partially randomized library of expression constructs comprising hundreds of selected synonymous variants. The effect of such substitutions was evaluated using the gene of interest fused to the reporter gene of the fluorescent protein with subsequent screening for the most promising candidates according to the reporter's signal intensity. The power of the approach is demonstrated by a significant increase in the prokaryotic expression of three proteins: canine cystatin C, human BCL2-associated athanogene 3 and human cardiac troponin I. This simple approach was suggested which may provide an efficient, easy, and inexpensive optimization method for poorly expressed proteins in bacteria.
Collapse
|
32
|
Jamal RB, Bay Gosewinkel U, Ferapontova EE. Electrocatalytic aptasensor for bacterial detection exploiting ferricyanide reduction by methylene blue on mixed PEG/aptamer monolayers. Bioelectrochemistry 2024; 156:108620. [PMID: 38006817 DOI: 10.1016/j.bioelechem.2023.108620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 11/19/2023] [Accepted: 11/20/2023] [Indexed: 11/27/2023]
Abstract
Pathogen-triggered infections are the most severe global threat to human health, and to provide their timely treatment and prevention, robust methods for rapid and reliable identification of pathogenic microorganisms are required. Here, we have developed a fast and inexpensive electrocatalytic aptamer assay enabling specific and ultrasensitive detection of E. coli. E. coli, a biomarker of environmental contamination and infections, was captured on the mixed aptamer/thiolated PEG self-assembled monolayers formed on electrochemically pre-treated gold screen-printed electrodes (SPE). Signals from aptamer - E. coli binding were amplified by electrocatalytic reduction of ferricyanide mediated by methylene blue (MB) adsorbed on bacterial and aptamer surfaces. PEG operated as an antifouling agent and inhibited direct (not MB-mediated) discharge of ferricyanide. The assay allowed from 10 to 1000 CFU mL-1E. coli detection in 30 min, with no interference from B. subtilis, in buffer and artificial urine samples. This electrocatalytic approach is fast, specific, sensitive, and can be used directly in in-field and point-of-care applications for analysis of bacteria in human environment.
Collapse
Affiliation(s)
- Rimsha B Jamal
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
| | - Ulrich Bay Gosewinkel
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, DK-4000 Roskilde, Denmark
| | - Elena E Ferapontova
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark.
| |
Collapse
|
33
|
Bashir A, Khan SR, Aqib AI, Shafique L, Ataya FS. Multifunctional integration of tungsten oxide (WO 3) coating: A versatile approach for enhanced performance of antibiotics against single mixed bacterial infections. Microb Pathog 2024; 189:106571. [PMID: 38341107 DOI: 10.1016/j.micpath.2024.106571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/25/2024] [Accepted: 02/07/2024] [Indexed: 02/12/2024]
Abstract
Nanomaterials containing tungsten (TNMs), characterized by diverse nanostructures had been extensively used in biomedical sector. Despite numerous reports focusing on TNM applications in specific biomedical areas, there is a noticeable absence of comprehensive studies that focused on detailed characterization of nanomaterials along with their biological applications. The present work described the structural, morphological, and antimicrobial properties of tungsten oxide (WO3) nanoparticles coated by antibiotics (nanobiotics), and their application on single and mixed bacterial culture. The nanobiotics included in this study were WO3 coated with ampicillin (W+A), WO3 coated with penicillin (P+W), and WO3 coated with ciprofloxacin (C+W). Techniques such as X-ray diffraction (XRD), scanning electron microscopy (SEM), X-ray spectroscopy (EDX), Fourier transforms infrared spectroscopy (FTIR), Rrman spectroscopy, and UV-visible spectroscopy were used to characterize synthesized nanoparticles. The minimum inhibitory concentration of C+W nanobiotic against S. aureus, E. coli, and mixed culture (S. aureus +E. coli) was lower than that of P+W and A+W. The impact of incubation period showed significant differences for each of nanobiotic against S. aureus, E. coli, and mixed culture. However, there were also non-significant differences among incubation periods for antibacterial activity of nanobiotics. It was pertinent to note that percentage variation in susceptibility of S. aureus with respect to mixed culture remained higher as compared to E. coli, indicating it stronger candidate imposing resistance. This paper thus suggested the strategy of coating of antibiotics with with WO3 nanoparticles as an ideal combination for resistance modulation against single and mixed culture bacteria.
Collapse
Affiliation(s)
- Arslan Bashir
- Department of Chemistry, University of Agriculture, Faisalabad, 38000, Pakistan
| | - Shanza Rauf Khan
- Department of Chemistry, University of Agriculture, Faisalabad, 38000, Pakistan
| | - Amjad Islam Aqib
- Department of Medicine, Cholistan University of Veterinary and Animal Sciences, Bahawalpur, 63100, Pakistan.
| | - Laiba Shafique
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gulf University, Guangxi, 535011, China
| | - Farid S Ataya
- Department of Biochemistry, College of Science, King Saud University, PO Box 2455, Riyadh, 11451, Saudi Arabia
| |
Collapse
|
34
|
Jaiswal A, Khan A, Yogi A, Singh S, Pal AK, Soni R, Tripathi P, Lal JA, Tripathi V. Isolation and molecular characterization of multidrug‑resistant Escherichia coli from chicken meat. 3 Biotech 2024; 14:107. [PMID: 38476645 PMCID: PMC10925582 DOI: 10.1007/s13205-024-03950-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 01/28/2024] [Indexed: 03/14/2024] Open
Abstract
Antibiotics in animal farms play a significant role in the proliferation and spread of antibiotic-resistant genes (ARGs) and antibiotic-resistant bacteria (ARB). The dissemination of antibiotic resistance from animal facilities to the nearby environment has become an emerging concern. The present study was focused on the isolation and molecular identification of Escherichia coli (E. coli) isolates from broiler chicken meat and further access their antibiotic-resistant profile against different antibiotics. Broiler chicken meat samples were collected from 44 retail poultry slaughter shops in Prayagraj district, Uttar Pradesh, India. Standard bacteriological protocols were followed to first isolate the E. coli, and molecular characterization was performed with genus-specific PCR. Phenotypic and genotypic antibiotic-resistant profiles of all confirmed 154 E. coli isolates were screened against 09 antibiotics using the disc diffusion and PCR-based method for selected resistance genes. In antibiotic sensitivity testing, the isolates have shown maximum resistance potential against tetracycline (78%), ciprofloxacin (57.8%), trimethoprim (54.00%) and erythromycin (49.35%). E. coli bacterial isolates have shown relative resistant to amoxicillin-clavulanic acid (43.00%) and against ampicillin (44.15%). Notably, 64.28% E. coli bacteria were found to be multidrug resistant. The results of PCR assays exposed that tetA and blaTEM genes were the most abundant genes harboured by 83 (84.0%) and 82 (82.0%) out of all 99 targeted E. coli isolates, followed by 48.0% for AmpC (CITM) gene and cmlA (23.00%) for chloramphenicol resistance. It is notable that most of the isolates collected from chicken meat samples were multidrug resistant (> 3 antibiotics), with more than 80% of them carrying tetracycline (tetA) and beta-lactam gene (blaTEM). This study highlights the high risk associated with poultry products due to MDR-E. coli and promote the limited use of antibiotics in poultry farms. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-024-03950-7.
Collapse
Affiliation(s)
- Anugya Jaiswal
- Department of Molecular and Cellular Engineering, Jacob Institute of Biotechnology and Bioengineering, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj, India
| | - Aquib Khan
- Department of Molecular and Cellular Engineering, Jacob Institute of Biotechnology and Bioengineering, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj, India
| | - Akanksha Yogi
- Department of Molecular and Cellular Engineering, Jacob Institute of Biotechnology and Bioengineering, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj, India
| | - Sweta Singh
- Department of Molecular and Cellular Engineering, Jacob Institute of Biotechnology and Bioengineering, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj, India
| | - Arun Kumar Pal
- Department of Molecular and Cellular Engineering, Jacob Institute of Biotechnology and Bioengineering, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj, India
| | - Ramendra Soni
- Department of Molecular and Cellular Engineering, Jacob Institute of Biotechnology and Bioengineering, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj, India
| | - Pooja Tripathi
- Center of Computational Biology and Bioinformatics, Jacob Institute of Biotechnology and Bioengineering, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj, India
| | - Jonathan A Lal
- Department of Molecular and Cellular Engineering, Jacob Institute of Biotechnology and Bioengineering, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj, India
| | - Vijay Tripathi
- Department of Molecular and Cellular Engineering, Jacob Institute of Biotechnology and Bioengineering, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj, India
- Department of Microbiology, Graphic Era Deemed to be University, Clement Town, Dehradun, India
| |
Collapse
|
35
|
Mohammed AF, Othman SA, Abou-Ghadir OF, Kotb AA, Mostafa YA, El-Mokhtar MA, Abdu-Allah HHM. Design, synthesis, biological evaluation and docking study of some new aryl and heteroaryl thiomannosides as FimH antagonists. Bioorg Chem 2024; 145:107258. [PMID: 38447463 DOI: 10.1016/j.bioorg.2024.107258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 02/29/2024] [Accepted: 03/01/2024] [Indexed: 03/08/2024]
Abstract
FimH is a mannose-recognizing lectin that is expressed by Escherichia coli guiding its ability to adhere and infect cells. It is involved in pathogenesis of urinary tract infections and Chron's disease. Several X-ray structure-guided ligand design studies were extensively utilized in the discovery and optimization of small molecule aryl mannoside FimH antagonists. These antagonists retain key specific interactions of the mannose scaffolds with the FimH carbohydrate recognition domains. Thiomannosides are attractive and stable scaffolds, and this work reports the synthesis of some of their new aryl and heteroaryl derivatives as FimH antagonists. FimH-competitive binding assays as well as biofilm inhibition of the new compounds (24-32) were determined in comparison with the reference n-heptyl α-d-mannopyranoside (HM). The affinity among these compounds was found to be governed by the structure of the aryl and heteroarylf aglycones. Two compounds 31 and 32 revealed higher activity than HM. Molecular docking and total hydrophobic to topological polar surface area ratio calculations attributed to explain the obtained biological results. Finally, the SAR study suggested that introducing an aryl or heteroaryl aglycone of sufficient hydrophobicity and of proper orientation within the tyrosine binding site considerably enhance binding affinity. The potent and synthetically feasible FimH antagonists described herein hold potential as leads for the development of sensors for detection of E. coli and treatment of its diseases.
Collapse
Affiliation(s)
- Anber F Mohammed
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Assiut University, Assiut 71526, Egypt
| | - Shimaa A Othman
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Assiut University, Assiut 71526, Egypt
| | - Ola F Abou-Ghadir
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Assiut University, Assiut 71526, Egypt
| | - Ahmed A Kotb
- Department of Microbiology and Immunology, Faculty of Pharmacy, Assiut University, Assiut, 71526, Egypt
| | - Yaser A Mostafa
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Assiut University, Assiut 71526, Egypt
| | - Mohamed A El-Mokhtar
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Assiut University, Assiut 71515, Egypt
| | - Hajjaj H M Abdu-Allah
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Assiut University, Assiut 71526, Egypt.
| |
Collapse
|
36
|
Gharaibeh MH, Al Sheyab SY, Malkawi IM, Al Qudsi FR. Phenotypic and genotypic characterization of Escherichia coli isolated from the chicken liver in relation to slaughterhouse conditions. Heliyon 2024; 10:e27759. [PMID: 38515697 PMCID: PMC10955320 DOI: 10.1016/j.heliyon.2024.e27759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 03/04/2024] [Accepted: 03/06/2024] [Indexed: 03/23/2024] Open
Abstract
Avian pathogenic Escherichia coli (APEC) has been identified as a sub-group of extraintestinal pathogenic E. coli (ExPEC). Recent studies indicate APEC as a potential foodborne zoonotic pathogen and a source or reservoir of human extraintestinal infections. The slaughtering and processing of poultry in low-income countries such as Jordan occurs in two distinct ways: in informal facilities known as Natafat and in formal slaughterhouses. This study compared E. coli phenotypes and genotypes according to slaughtering conditions (formal slaughterhouses vs. informal slaughter facilities). Therefore, liver samples (n = 242) were collected from formal (n = 121) and informal slaughter facilities (n = 121). Results revealed a high prevalence (94.2%) of E. coli among all isolates, with 59 (17 formal and 42 informal) isolates considered avian pathogenic E. coli (APEC) based on the virulence-associated genes. The prevalence of resistance among isolates was relatively high, reaching up to 99% against penicillin and 97% against nalidixic acid. However, the prevalence of resistance was the lowest (1.3%) against both meropenem and imipenem. Based on the MIC test findings, colistin resistance was 46.9% (107/228). The mcr -1 gene prevalence was 51.4% (55/107), of which 17.1 % were from formal plants (6/36) and 68.1% from informal facilities (49/72). Interestingly, only one isolate (0.9%) expressed mcr-10. Escherichia coli O157:H7 and associated virulence genes were found more in informal (n = 15 genes) than in formal slaughterhouses (n = 8). Phylogroups B1, C, and A were the most frequent in 228 E. coli isolates, while G, B2, and clade were the least frequent. In conclusion, these findings highlight the importance of implementing biosecurity measures in slaughterhouses to reduce antibiotic-resistant E. coli spread. Furthermore, this study provides valuable insights into the effects of wet market (Natafat) slaughter conditions on increasing bacterial resistance and virulence.
Collapse
Affiliation(s)
- Mohammad H. Gharaibeh
- Department of Basic Veterinary Medical Science, Faculty of Veterinary Medicine, Jordan University of Science and Technology, P. O. Box 3030, Irbid, 22110, Jordan
| | - Sahba Y. Al Sheyab
- Department of Basic Veterinary Medical Science, Faculty of Veterinary Medicine, Jordan University of Science and Technology, P. O. Box 3030, Irbid, 22110, Jordan
| | - Ismail M. Malkawi
- Department of Basic Veterinary Medical Science, Faculty of Veterinary Medicine, Jordan University of Science and Technology, P. O. Box 3030, Irbid, 22110, Jordan
| | - Farah R. Al Qudsi
- Department of Nutrition and Food Technology, Jordan University of Science and Technology, Irbid, 21121, Jordan
| |
Collapse
|
37
|
DeLira-Bustillos N, Angulo-Zamudio UA, Leon-Sicairos N, Flores-Villaseñor H, Velazquez-Roman J, Tapia-Pastrana G, Martínez-Villa FA, Velázquez-Cruz R, Salmerón J, Canizales-Quinteros S, Canizalez-Roman A. Distribution and virulence of Escherichia coli harboring cyclomodulins and supplementary virulence genes isolates from clinical and environmental samples. Microb Pathog 2024; 190:106634. [PMID: 38556104 DOI: 10.1016/j.micpath.2024.106634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 03/25/2024] [Accepted: 03/27/2024] [Indexed: 04/02/2024]
Abstract
This study aimed to determine the prevalence of cyclomodulins (cdt, cnf, pks and cif) in Escherichia coli (E. coli) isolated from clinical and environmental samples, the presence of supplementary virulence genes (SVG), antibiotic resistance, and in vitro cytotoxicity. 413 E. coli were isolated from clinical (stool from obese subjects, normal weight subjects, children with diarrhea, and children without diarrhea; and urine from pregnant and non-pregnant women with urinary tract infections) and environmental (water and different foods) samples. PCR was performed to identify E. coli pathotypes, the four cyclomodulins, and 18 SVG; virulence score, cytotoxic assay, and antibiotic resistance assay were performed. Fifteen percent of E. coli were positive for cyclomodulins and were found in all isolation sources; however, in children with diarrhea, they were more frequent. The most frequent cyclomodulin was cdt. More DEC strains harbor cyclomodulins than non-DEC, and cyclomodulins were most frequent among aEPEC pathotype. SVG ehaC was associated with cyclomodulin-positive strains. Cyclomodulin-positive E. coli had a higher virulence score but no significant cytotoxic activity. They were slightly more resistant to antibiotics. In conclusion, cyclomodulins-positive E. coli was widely distributed in humans, food, and the environment, and they were associated with SVG ehaC, suggesting that these genes may play a role in the pathogenesis of the cyclomodulins. However, more research is needed.
Collapse
Affiliation(s)
- Nora DeLira-Bustillos
- Programa de Doctorado, Posgrado Integral en Biotecnología, FCQB, UAS, 80030, Culiacan Sinaloa, Mexico
| | | | - Nidia Leon-Sicairos
- School of Medicine, Autonomous University of Sinaloa, 80019, Culiacan Sinaloa, Mexico; Pediatric Hospital of Sinaloa, 80200, Culiacan Sinaloa, Mexico
| | - Hector Flores-Villaseñor
- School of Medicine, Autonomous University of Sinaloa, 80019, Culiacan Sinaloa, Mexico; The Sinaloa State Public Health Laboratory, Secretariat of Health, 80058, Culiacan Sinaloa, Mexico
| | - Jorge Velazquez-Roman
- School of Medicine, Autonomous University of Sinaloa, 80019, Culiacan Sinaloa, Mexico
| | - Gabriela Tapia-Pastrana
- Laboratorio de Investigación Biomédica, Hospital Regional de Alta Especialidad de Oaxaca, Oaxaca, 71256, Mexico
| | | | - Rafael Velázquez-Cruz
- Laboratorio de Genómica del Metabolismo Óseo, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, 14610, Mexico
| | - Jorge Salmerón
- Centro de Investigación en Políticas, Población y Salud de la Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Mexico City, 04510, Mexico
| | | | - Adrian Canizalez-Roman
- School of Medicine, Autonomous University of Sinaloa, 80019, Culiacan Sinaloa, Mexico; The Women's Hospital, Secretariat of Health, 80020, Culiacan Sinaloa, Mexico.
| |
Collapse
|
38
|
Karapetian M, Alimbarashvili E, Vishnepolsky B, Gabrielian A, Rosenthal A, Hurt DE, Tartakovsky M, Mchedlishvili M, Arsenadze D, Pirtskhalava M, Zaalishvili G. Evaluation of the synergistic potential and mechanisms of action for de novo designed cationic antimicrobial peptides. Heliyon 2024; 10:e27852. [PMID: 38560672 PMCID: PMC10979160 DOI: 10.1016/j.heliyon.2024.e27852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 03/01/2024] [Accepted: 03/07/2024] [Indexed: 04/04/2024] Open
Abstract
Antimicrobial peptides (AMPs) have emerged as promising candidates in combating antimicrobial resistance - a growing issue in healthcare. However, to develop AMPs into effective therapeutics, a thorough analysis and extensive investigations are essential. In this study, we employed an in silico approach to design cationic AMPs de novo, followed by their experimental testing. The antibacterial potential of de novo designed cationic AMPs, along with their synergistic properties in combination with conventional antibiotics was examined. Furthermore, the effects of bacterial inoculum density and metabolic state on the antibacterial activity of AMPs were evaluated. Finally, the impact of several potent AMPs on E. coli cell envelope and genomic DNA integrity was determined. Collectively, this comprehensive analysis provides insights into the unique characteristics of cationic AMPs.
Collapse
Affiliation(s)
- Margarita Karapetian
- Laboratory of Chromatin Biology, Institute of Cellular and Molecular Biology, Agricultural University of Georgia, 240 David Aghmashenebeli Alley, 0159, Tbilisi, Georgia
| | - Evgenia Alimbarashvili
- Laboratory of Chromatin Biology, Institute of Cellular and Molecular Biology, Agricultural University of Georgia, 240 David Aghmashenebeli Alley, 0159, Tbilisi, Georgia
- Ivane Beritashvili Center of Experimental Biomedicine, 0160, Tbilisi, Georgia
| | - Boris Vishnepolsky
- Ivane Beritashvili Center of Experimental Biomedicine, 0160, Tbilisi, Georgia
| | - Andrei Gabrielian
- Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Alex Rosenthal
- Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Darrell E. Hurt
- Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Michael Tartakovsky
- Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Mariam Mchedlishvili
- Laboratory of Chromatin Biology, Institute of Cellular and Molecular Biology, Agricultural University of Georgia, 240 David Aghmashenebeli Alley, 0159, Tbilisi, Georgia
| | - Davit Arsenadze
- Laboratory of Chromatin Biology, Institute of Cellular and Molecular Biology, Agricultural University of Georgia, 240 David Aghmashenebeli Alley, 0159, Tbilisi, Georgia
| | - Malak Pirtskhalava
- Ivane Beritashvili Center of Experimental Biomedicine, 0160, Tbilisi, Georgia
| | - Giorgi Zaalishvili
- Laboratory of Chromatin Biology, Institute of Cellular and Molecular Biology, Agricultural University of Georgia, 240 David Aghmashenebeli Alley, 0159, Tbilisi, Georgia
- Ivane Beritashvili Center of Experimental Biomedicine, 0160, Tbilisi, Georgia
| |
Collapse
|
39
|
Castillo-Corujo A, Uchida Y, Saaranen MJ, Ruddock LW. Escherichia coli Cytoplasmic Expression of Disulfide-Bonded Proteins: Side-by-Side Comparison Between Two Competing Strategies. J Microbiol Biotechnol 2024; 34:1-10. [PMID: 38563095 DOI: 10.4014/jmb.2311.11025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 04/04/2024]
Abstract
The production of disulfide bond-containing recombinant proteins in Escherichia coli has traditionally been done by either refolding from inclusion bodies or by targeting the protein to the periplasm. However, both approaches have limitations and were developed to allow the production of proteins with disulfide bonds in the cytoplasm of E. coli: i) engineered strains with deletions in the disulfide reduction pathways, e.g. SHuffle, and ii) the co-expression of oxidative folding catalysts, e.g. CyDisCo. However, to our knowledge, the effectiveness of these strategies has not been properly evaluated. Here, we systematically compare the purified yields of 14 different proteins of interest (POI) that contain disulfide bonds in their native state when expressed in both systems. We also compared the effects of different background strains, commonly used promoters, and two media types: defined and rich autoinduction. In rich autoinduction media, POI which can be produced in a soluble (non-native) state without a system for disulfide bond formation were produced in higher purified yields from SHuffle, whereas all other proteins were produced in higher purified yields using CyDisCo. In chemically defined media, purified yields were at least 10x higher in all cases using CyDisCo. In addition, the quality of the three POI tested was superior when produced using CyDisCo.
Collapse
Affiliation(s)
- Angel Castillo-Corujo
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu FI-90014, Finland
| | - Yuko Uchida
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu FI-90014, Finland
| | - Mirva J Saaranen
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu FI-90014, Finland
| | - Lloyd W Ruddock
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu FI-90014, Finland
| |
Collapse
|
40
|
Anderson JW, Vaisar D, Jones DN, Pegram LM, Vigers GP, Chen H, Moffat JG, Ahn NG. Conformation selection by ATP-competitive inhibitors and allosteric communication in ERK2. eLife 2024; 12:RP91507. [PMID: 38537148 PMCID: PMC10972564 DOI: 10.7554/elife.91507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024] Open
Abstract
Activation of the extracellular signal-regulated kinase-2 (ERK2) by phosphorylation has been shown to involve changes in protein dynamics, as determined by hydrogen-deuterium exchange mass spectrometry (HDX-MS) and NMR relaxation dispersion measurements. These can be described by a global exchange between two conformational states of the active kinase, named 'L' and 'R,' where R is associated with a catalytically productive ATP-binding mode. An ATP-competitive ERK1/2 inhibitor, Vertex-11e, has properties of conformation selection for the R-state, revealing movements of the activation loop that are allosterically coupled to the kinase active site. However, the features of inhibitors important for R-state selection are unknown. Here, we survey a panel of ATP-competitive ERK inhibitors using HDX-MS and NMR and identify 14 new molecules with properties of R-state selection. They reveal effects propagated to distal regions in the P+1 and helix αF segments surrounding the activation loop, as well as helix αL16. Crystal structures of inhibitor complexes with ERK2 reveal systematic shifts in the Gly loop and helix αC, mediated by a Tyr-Tyr ring stacking interaction and the conserved Lys-Glu salt bridge. The findings suggest a model for the R-state involving small movements in the N-lobe that promote compactness within the kinase active site and alter mobility surrounding the activation loop. Such properties of conformation selection might be exploited to modulate the protein docking interface used by ERK substrates and effectors.
Collapse
Affiliation(s)
- Jake W Anderson
- Department of Biochemistry, University of ColoradoBoulderUnited States
| | - David Vaisar
- Department of Biochemistry, University of ColoradoBoulderUnited States
| | - David N Jones
- Department of Pharmacology, University of Colorado Anschutz Medical CenterBoulderUnited States
| | - Laurel M Pegram
- Department of Biochemistry, University of ColoradoBoulderUnited States
| | | | - Huifen Chen
- Genentech, Inc.South San FranciscoUnited States
| | | | - Natalie G Ahn
- Department of Biochemistry, University of ColoradoBoulderUnited States
| |
Collapse
|
41
|
Chareyre S, Li X, Anjuwon-Foster BR, Updegrove TB, Clifford S, Brogan AP, Su Y, Zhang L, Chen J, Shroff H, Ramamurthi KS. Cell division machinery drives cell-specific gene activation during differentiation in Bacillus subtilis. Proc Natl Acad Sci U S A 2024; 121:e2400584121. [PMID: 38502707 PMCID: PMC10990147 DOI: 10.1073/pnas.2400584121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 02/22/2024] [Indexed: 03/21/2024] Open
Abstract
When faced with starvation, the bacterium Bacillus subtilis transforms itself into a dormant cell type called a "spore". Sporulation initiates with an asymmetric division event, which requires the relocation of the core divisome components FtsA and FtsZ, after which the sigma factor σF is exclusively activated in the smaller daughter cell. Compartment-specific activation of σF requires the SpoIIE phosphatase, which displays a biased localization on one side of the asymmetric division septum and associates with the structural protein DivIVA, but the mechanism by which this preferential localization is achieved is unclear. Here, we isolated a variant of DivIVA that indiscriminately activates σF in both daughter cells due to promiscuous localization of SpoIIE, which was corrected by overproduction of FtsA and FtsZ. We propose that the core components of the redeployed cell division machinery drive the asymmetric localization of DivIVA and SpoIIE to trigger the initiation of the sporulation program.
Collapse
Affiliation(s)
- Sylvia Chareyre
- Laboratory of Molecular Biology, National Cancer Institute, NIH, Bethesda, MD20892
| | - Xuesong Li
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, NIH, Bethesda, MD20892
- HHMI, Ashburn, VA20147
| | | | - Taylor B. Updegrove
- Laboratory of Molecular Biology, National Cancer Institute, NIH, Bethesda, MD20892
| | - Sarah Clifford
- Laboratory of Molecular Biology, National Cancer Institute, NIH, Bethesda, MD20892
| | - Anna P. Brogan
- Laboratory of Molecular Biology, National Cancer Institute, NIH, Bethesda, MD20892
| | - Yijun Su
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, NIH, Bethesda, MD20892
- HHMI, Ashburn, VA20147
| | - Lixia Zhang
- Advanced Imaging and Microscopy Resource, NIH, Bethesda, MD20892
| | - Jiji Chen
- Advanced Imaging and Microscopy Resource, NIH, Bethesda, MD20892
| | - Hari Shroff
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, NIH, Bethesda, MD20892
- HHMI, Ashburn, VA20147
| | | |
Collapse
|
42
|
Yu L, Gao Y, He Y, Liu Y, Shen J, Liang H, Gong R, Duan H, Price NPJ, Song X, Deng Z, Chen W. Developing the E. coli platform for efficient production of UMP-derived chemicals. Metab Eng 2024; 83:61-74. [PMID: 38522576 DOI: 10.1016/j.ymben.2024.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 03/10/2024] [Accepted: 03/21/2024] [Indexed: 03/26/2024]
Abstract
5-Methyluridine (5-MU) is a prominent intermediate for industrial synthesis of several antiviral-drugs, however, its availability over the past decades has overwhelmingly relied on chemical and enzymatic strategies. Here, we have realized efficient production of 5-MU in E. coli, for the first time, via a designer artificial pathway consisting of a two-enzyme cascade (UMP 5-methylase and phosphatase). More importantly, we have engineered the E. coli cell factory to boost 5-MU production by systematic evaluation of multiple strategies, and as a proof of concept, we have further developed an antibiotic-free fermentation strategy to realize 5-MU production (10.71 g/L) in E. coli MB229 (a ΔthyA strain). Remarkably, we have also established a versatile and robust platform with exploitation of the engineered E. coli for efficient production of diversified UMP-derived chemicals. This study paves the way for future engineering of E. coli as a synthetic biology platform for acceleratively accessing UMP-derived chemical diversities.
Collapse
Affiliation(s)
- Le Yu
- Department of Anesthesiology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China; Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Yaojie Gao
- Department of Anesthesiology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China; Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Yuanyuan He
- Department of Anesthesiology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China; Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Yang Liu
- Department of Anesthesiology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China; Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Jianning Shen
- Department of Anesthesiology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China; Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Han Liang
- Department of Anesthesiology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China; Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Rong Gong
- Department of Anesthesiology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China; Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - He Duan
- Department of Anesthesiology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China; Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Neil P J Price
- US Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research, Peoria, IL, USA
| | - Xuemin Song
- Department of Anesthesiology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Zixin Deng
- Department of Anesthesiology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China; TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430071, China; Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Wenqing Chen
- Department of Anesthesiology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China; TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430071, China; Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China.
| |
Collapse
|
43
|
Aydamo AA, Robele Gari S, Mereta ST. Seasonal Variations in Household Water Use, Microbiological Water Quality, and Challenges to the Provision of Adequate Drinking Water: A Case of Peri-urban and Informal Settlements of Hosanna Town, Southern Ethiopia. Environ Health Insights 2024; 18:11786302241238940. [PMID: 38525297 PMCID: PMC10958793 DOI: 10.1177/11786302241238940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 02/26/2024] [Indexed: 03/26/2024]
Abstract
Several studies have been conducted on household water use and microbial water quality globally. However, studies that considered seasonal variability of household water use and microbial water quality were limited. Therefore, this study investigated the seasonal variability of household water use, microbiological water quality, and challenges to the provision of adequate water in the peri-urban and informal settlements of Hosanna town, Southern Ethiopia. A longitudinal study was conducted on 288 households. The data was gathered using a pretested structured questionnaire, laboratory-analysis, interviews, storage-container inventories, focus group discussions, key-informant interviews, and an observational checklist. The data was analyzed using stepwise-multiple linear regression, bivariate and multivariable logistic regression, thematic-analysis, t-tests, and non-parametric-tests. Households were visited for 7 consecutive days during the dry and rainy seasons to account for changes in daily and seasonal variation of water use. 440 stored water and 12 source samples were analyzed for E. coli presence during dry and rainy seasons. The prevalence of stored water contamination with E. coli was 43.2% and 34.5% during the dry and rainy seasons, respectively. The per capita water consumption was 19.4 and 20.3 l during the dry and rainy seasons, respectively. Piped water on-premises, small family size, volume, and number of water storage containers were significant predictors of per capita water consumption in both seasons. Piped water off-premises, storing water for more than 3 days, uncovered, and wide-mouthed water storage containers were significantly associated with the presence of E. coli in water in both seasons. Seasonal variability of household water use and microbiological water quality was statistically significant, which is a significant public health concern and needs intervention to enhance water quantity and quality to mitigate the risk of waterborne diseases. Findings also suggest seasonal monitoring of the safety of drinking water to ensure that the water is safe and healthy.
Collapse
Affiliation(s)
- Abiot Abera Aydamo
- Ethiopian Institute of Water Resources (EiWR), Addis Ababa University, Addis Ababa, Ethiopia
- Department of Environmental Sciences, Wachemo University, Hosanna, Ethiopia
| | - Sirak Robele Gari
- Ethiopian Institute of Water Resources (EiWR), Addis Ababa University, Addis Ababa, Ethiopia
| | - Seid Tiku Mereta
- Department of Environmental Health and Technology, Jimma University, Jimma, Ethiopia
| |
Collapse
|
44
|
Nguyet LTY, Ounjai P, Ngamwongsatit N, Kaeoket K. The immune response of pregnant sow after vaccination with crude fimbriae (F4) extracts vaccine and immunoprotection of nursery pig against pathogenic E. coli (F4 +ETEC). Acta Trop 2024; 254:107173. [PMID: 38503364 DOI: 10.1016/j.actatropica.2024.107173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 02/22/2024] [Accepted: 03/05/2024] [Indexed: 03/21/2024]
Abstract
BACKGROUND Neonatal and post-weaning diarrhea is a concern disease caused by enterotoxigenic Escherichia coli fimbriae F4 (F4+ETEC) in pig farms. Diarrhea outbreaks are often severe and costly due to the high prevalence and spread of the disease within the same herd. Autogenous Vaccine is one of strategic solution in protecting pig against F4+ETEC infection in particular pig farm. In present study, we conducted two trials of vaccination with crude F4 fimbriae extract vaccine in pregnant sow and nursery pigs. METHODS In experiment 1 (20 sows; non-vaccinated control, n=10), we vaccinated pregnant sows (n=10) twice at 4 wk and 2 wk before farrowing and evaluated impact of vaccination on maternal immunity. The sow serum and colostrum were collected before vaccination, 2 and 4 weeks after vaccination, 6 hours after farrowing, respectively, and the piglet's serum from both groups (2 piglet/sow, 10 piglets from each group) were also collected on 3 days old to measure F4 specific IgG, F4 specific IgA using in house ELISA kit. In experiment 2, to optimize doses and dosage of candidate vaccine in piglets, 18 piglets (3 piglets/group) were allocated into five immunized groups and one control group (unimmunized group), we immunized piglets twice at 4 and 6 weeks old with difference doses (i.e., 0, 50, 100, 150, 200 µg), and for a dose 150 µg, we immunized with two dosages at 1 ml and 2 ml. Piglets were challenged with a 3 ml dose of 3 × 109 CFU/ml bacterial culture of enterotoxigenic Escherichia coli (F4+ETEC) in order to evaluate the efficacy of vaccine. After challenging, the clinical sign of the piglets was daily observed and the rectal swab was performed every day for investigation of the fecal shedding of Escherichia coli (F4+ETEC) by using PCR technique. Serum were collected before, 2 and 4 weeks after vaccination and 1 week after challenge to measure F4 specific IgG, F4 specific IgA using in house ELISA kit and cytokines levels (i.e., IL-1 beta, IL-6, IL-8 and TNF alpha) before and 1 week after challenge using commercial ELISA kit. RESULTS The levels of antibody results showed that in experiment 1, the anti-F4 antibody levels both F4 specific IgG and F4 specific IgA in serum and colostrum of vaccinated sow increased significantly after vaccination. The piglets of immunized sows have antibody level both F4 specific IgG and F4 specific IgA in their serum higher than those piglets of unimmunized sows significantly (p < 0.01). In experiment 2, irrespective of different doses and dosage, there is no difference in term of F4 specific IgG and F4 specific IgA levels among immunized groups. However, all of vaccinated piglets showed F4 specific IgG and F4 specific IgA levels higher and the elimination of Escherichia coli (F4+ETEC) in feces post challenge faster (< 3 days) than unvaccinated group (> 5 days). For cytokines levels, a higher level of IL-1 beta, IL-6, IL-8 and TNF alpha at 1 week after challenge in vaccinated groups was found when compared with the levels in non-vaccinated group. CONCLUSIONS Our results suggest that crude F4 fimbriae extract autogenous vaccine is a candidate vaccine for protecting piglets against diarrhea disease caused by enterotoxigenic Escherichia coli (F4+ETEC) and vaccination the pregnant sow twice before farrowing is one of strategies to provide maternal derived antibody to the newborn piglets for against enterotoxigenic Escherichia coli (F4+ETEC) during early life.
Collapse
Affiliation(s)
- Luong Thi Yen Nguyet
- Department of Clinical Sciences and Public Health, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, 73170, Thailand
| | - Puey Ounjai
- Department of Biology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Natharin Ngamwongsatit
- Department of Clinical Sciences and Public Health, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, 73170, Thailand; Laboratory of Bacteria, Veterinary Diagnostic Center, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, 73170, Thailand
| | - Kampon Kaeoket
- Department of Clinical Sciences and Public Health, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, 73170, Thailand.
| |
Collapse
|
45
|
Wu X, Ren J, Wang J, Koffas MAG, Zha J. A major facilitator superfamily transporter MdtH in Escherichia coli is involved in anthocyanin biosynthesis and secretion. Appl Environ Microbiol 2024; 90:e0207923. [PMID: 38349148 PMCID: PMC10952383 DOI: 10.1128/aem.02079-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 01/16/2024] [Indexed: 03/21/2024] Open
Abstract
Anthocyanin cyanidin 3-O-glucoside (C3G) is a natural pigment widely used in food and nutraceutical industries. Its microbial synthesis in Escherichia coli is a promising and efficient way toward large-scale production. The current production titer is low partly due to the accumulation of C3G inside the producing microbes; thus, it is important to explore native transporters responsible for anthocyanin secretion. Currently, there has been only one native E. coli transporter identified with C3G-transporting capability, and its overexpression has a very limited effect on the promotion of extracellular C3G production. In this study, we report the identification and verification of an efficient intrinsic C3G efflux transporter MdtH in E. coli through transcriptomic analysis and genetic/biochemical studies. MdtH could bind C3G with high affinity, and its overexpression increased the extracellular C3G biosynthesis in E. coli by 110%. Our study provides a new regulation target for microbial biosynthesis of C3G and other anthocyanins. IMPORTANCE Cyanidin 3-O-glucoside (C3G) is a natural colorant with health-promoting activities and is, hence, widely used in food, cosmetic, and nutraceutical industries. Its market supply is currently dependent on extraction from plants. As an alternative, C3G can be produced by the microbe Escherichia coli in a green and sustainable way. However, a large portion of this compound is retained inside the cell of E. coli, thus complicating the purification process and limiting the high-level production. We have identified and verified an efficient native transporter named MdtH in E. coli that can export C3G to the cultivation medium. Overexpression of MdtH could improve extracellular C3G production by 110% without modifications of the metabolic pathway genes or enzymes. This study reveals a new regulation target for C3G production in bacteria and provides guidance to the microbial biosynthesis of related compounds.
Collapse
Affiliation(s)
- Xia Wu
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi’an, Shaanxi, China
| | - Juan Ren
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi’an, Shaanxi, China
| | - Jing Wang
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi’an, Shaanxi, China
| | - Mattheos A. G. Koffas
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, USA
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York, USA
| | - Jian Zha
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi’an, Shaanxi, China
| |
Collapse
|
46
|
Keith M, Park de la Torriente A, Chalka A, Vallejo-Trujillo A, McAteer SP, Paterson GK, Low AS, Gally DL. Predictive phage therapy for Escherichia coli urinary tract infections: Cocktail selection for therapy based on machine learning models. Proc Natl Acad Sci U S A 2024; 121:e2313574121. [PMID: 38478693 PMCID: PMC10962980 DOI: 10.1073/pnas.2313574121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 02/04/2024] [Indexed: 03/27/2024] Open
Abstract
This study supports the development of predictive bacteriophage (phage) therapy: the concept of phage cocktail selection to treat a bacterial infection based on machine learning (ML) models. For this purpose, ML models were trained on thousands of measured interactions between a panel of phage and sequenced bacterial isolates. The concept was applied to Escherichia coli associated with urinary tract infections. This is an important common infection in humans and companion animals from which multidrug-resistant (MDR) bloodstream infections can originate. The global threat of MDR infection has reinvigorated international efforts into alternatives to antibiotics including phage therapy. E. coli exhibit extensive genome-level variation due to horizontal gene transfer via phage and plasmids. Associated with this, phage selection for E. coli is difficult as individual isolates can exhibit considerable variation in phage susceptibility due to differences in factors important to phage infection including phage receptor profiles and resistance mechanisms. The activity of 31 phage was measured on 314 isolates with growth curves in artificial urine. Random Forest models were built for each phage from bacterial genome features, and the more generalist phage, acting on over 20% of the bacterial population, exhibited F1 scores of >0.6 and could be used to predict phage cocktails effective against previously untested strains. The study demonstrates the potential of predictive ML models which integrate bacterial genomics with phage activity datasets allowing their use on data derived from direct sequencing of clinical samples to inform rapid and effective phage therapy.
Collapse
Affiliation(s)
- Marianne Keith
- The Roslin Institute, Division of Bacteriology, University of Edinburgh, EdinburghEH25 9RG, United Kingdom
| | - Alba Park de la Torriente
- The Roslin Institute, Division of Bacteriology, University of Edinburgh, EdinburghEH25 9RG, United Kingdom
| | - Antonia Chalka
- The Roslin Institute, Division of Bacteriology, University of Edinburgh, EdinburghEH25 9RG, United Kingdom
| | - Adriana Vallejo-Trujillo
- The Roslin Institute, Division of Bacteriology, University of Edinburgh, EdinburghEH25 9RG, United Kingdom
| | - Sean P. McAteer
- The Roslin Institute, Division of Bacteriology, University of Edinburgh, EdinburghEH25 9RG, United Kingdom
| | - Gavin K. Paterson
- The Roslin Institute, Division of Bacteriology, University of Edinburgh, EdinburghEH25 9RG, United Kingdom
- Royal (Dick) School of Veterinary Studies, Easter Bush Pathology, University of Edinburgh, EdinburghEH25 9RG, United Kingdom
| | - Alison S. Low
- The Roslin Institute, Division of Bacteriology, University of Edinburgh, EdinburghEH25 9RG, United Kingdom
| | - David L. Gally
- The Roslin Institute, Division of Bacteriology, University of Edinburgh, EdinburghEH25 9RG, United Kingdom
| |
Collapse
|
47
|
Gensler CA, Hempstead SC, Keelara S, Fedorka-Cray PJ, Urie NJ, Wiedenheft AM, Stuart K, Marshall KL, Jacob ME. Antimicrobial Resistance Characteristics of Fecal Escherichia coli and Enterococcus Species in U.S. Goats: 2019 National Animal Health Monitoring System Enteric Study. Foodborne Pathog Dis 2024. [PMID: 38502797 DOI: 10.1089/fpd.2023.0089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024] Open
Abstract
Escherichia coli and Enterococcus species are normal bacteria of the gastrointestinal tract and serve as indicator organisms for the epidemiology and emergence of antimicrobial resistance in their hosts and the environment. Some E. coli serovars, including E. coli O157:H7, are important human pathogens, although reservoir species such as goats remain asymptomatic. We describe the prevalence and antimicrobial resistance of generic E. coli, E. coli O157:H7, and Enterococcus species collected from a national surveillance study of goat feces as part of the National Animal Health Monitoring System (NAHMS) Goat 2019 study. Fecal samples were collected from 4918 goats on 332 operations across the United States. Expectedly, a high prevalence of E. coli (98.7%, 4850/4915) and Enterococcus species (94.8%, 4662/4918) was found. E. coli O157:H7 prevalence was low (0.2%; 10/4918). E. coli isolates, up to three per operation, were evaluated for antimicrobial susceptibility and 84.7% (571/674) were pansusceptible. Multidrug resistance (MDR; ≥3 classes) was uncommon among E. coli, occurring in 8.2% of isolates (55/674). Resistance toward seven antimicrobial classes was observed in a single isolate. Resistance to tetracycline alone (13.6%, 92/674) or to tetracycline, streptomycin, and sulfisoxazole (7.0% 47/674) was the most common pattern. All E. coli O157:H7 isolates were pansusceptible. Enterococcus isolates, up to four per operation, were prioritized by public health importance, including Enterococcus faecium and Enterococcus faecalis and evaluated. Resistance to lincomycin (93.8%, 1232/1313) was most common, with MDR detected in 29.5% (388/1313) of isolates. The combination of ciprofloxacin, lincomycin, and quinupristin resistance (27.1%, 105/388) was the most common pattern detected. Distribution and characteristics of antimicrobial resistance in E. coli and Enterococcus in the U.S. goat population from this study can inform stewardship considerations and public health efforts surrounding goats and their products.
Collapse
Affiliation(s)
- Catherine A Gensler
- Department of Agricultural and Human Sciences, College of Agriculture and Life Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Stephanie C Hempstead
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
| | - Shivaramu Keelara
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
| | - Paula J Fedorka-Cray
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
| | - Natalie J Urie
- National Animal Health Monitoring System, Veterinary Services, Animal and Plant Health Inspection Service, United States Department of Agriculture, Fort Collins, Colorado, USA
| | - Alyson M Wiedenheft
- National Animal Health Monitoring System, Veterinary Services, Animal and Plant Health Inspection Service, United States Department of Agriculture, Fort Collins, Colorado, USA
- Department of Clinical Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Keira Stuart
- National Veterinary Services Laboratories, Veterinary Services, Animal and Plant Health Inspection Service, United States Department of Agriculture, Ames, Iowa, USA
| | - Katherine L Marshall
- National Animal Health Monitoring System, Veterinary Services, Animal and Plant Health Inspection Service, United States Department of Agriculture, Fort Collins, Colorado, USA
| | - Megan E Jacob
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
| |
Collapse
|
48
|
Xu H, Tan C, Li C, Li J, Han Y, Tang Y, Lei C, Wang H. ESBL- Escherichia coli extracellular vesicles mediate bacterial resistance to β-lactam and mediate horizontal transfer of bla CTX-M-55. Int J Antimicrob Agents 2024; 63:107145. [PMID: 38494146 DOI: 10.1016/j.ijantimicag.2024.107145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 02/08/2024] [Accepted: 03/11/2024] [Indexed: 03/19/2024]
Abstract
OBJECTIVES Extracellular vesicles (EVs) have become the focus of research as an emerging method of horizontal gene transfer. In recent years, studies on the association between EVs and the spread of bacterial resistance have emerged, but there is a lack of research on the role of EVs secreted by extended-spectrum β-lactamase (ESBL)-producing Escherichia coli in the spread of β-lactam resistance. Therefore, the aim of this study was to investigate the role of EVs in the transmission of β-lactam resistance. METHODS In this study, the role of EVs in the transmission of β-lactam resistance in E. coli was evaluated by the EVs-mediated bacterial resistance to β-lactam antibiotics test and the EVs-mediated blaCTX-M-55 transfer experiments using EVs secreted by ESBL-E. coli. RESULTS The results showed that ESBL-EVs were protective against β-lactam antibiotic-susceptible bacteria, and this protective effect was dependent on the integrity of the EVs and showed dose- and time-dependent effects. At the same time, ESBL-EVs can also mediate the horizontal transmission of blaCTX-M-55, and EVs-mediated gene transfer is selective, preferring to transfer in more closely related species. CONCLUSIONS In this study, we demonstrated the important role of EVs in the transmission of β-lactam resistance in chicken ESBL-E. coli, and evaluated the risk of EVs-mediated horizontal gene transfer, which provided a theoretical basis for elucidating the mechanism of EVs-mediated resistance transmission.
Collapse
Affiliation(s)
- Heting Xu
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu 610022, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610022, China
| | - Chang Tan
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu 610022, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610022, China
| | - Chao Li
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu 610022, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610022, China; Kunming National High-level Biosafety Research Center for Non-human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650023, China.
| | - Jinpeng Li
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu 610022, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610022, China
| | - Yun Han
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu 610022, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610022, China
| | - Yizhi Tang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu 610022, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610022, China
| | - Changwei Lei
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu 610022, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610022, China
| | - Hongning Wang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu 610022, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610022, China.
| |
Collapse
|
49
|
Menezes KV, Duarte CEDS, Moreira MG, Moreno TDJC, Pereira VJDS, Ucella-Filho JGM, Otenio MH, Ignacchiti MDC, Resende JA. Enterobacteria in anaerobic digestion of dairy cattle wastewater: Assessing virulence and resistance for one health security. Water Res 2024; 252:121192. [PMID: 38309066 DOI: 10.1016/j.watres.2024.121192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 12/26/2023] [Accepted: 01/23/2024] [Indexed: 02/05/2024]
Abstract
Samples from a dairy cattle waste-fed anaerobic digester were collected across seasons to assess sanitary safety for biofertilizer use. Isolated enterobacteria (suggestive of Escherichia coli) were tested for susceptibility to biocides, antimicrobials, and biofilm-forming capability. Results revealed a decrease in total bacteria, coliforms, and enterobacteria in biofertilizer compared to the effluent. Among 488 isolates, 98.12 % exhibited high biofilm formation. Biofertilizer isolates exhibited a similar biofilm formation capability as effluent isolates in summer, but greater propensity in winter. Resistance to biocides and antimicrobials varied, with tetracycline resistance reaching 19 %. Of the isolates, 25 were multidrug-resistant (MDR), with 64 % resistant to three drugs. Positive correlations were observed between MDR and increased biofilm formation capacity in both samples, while there was negative correlation between MDR and increased biocide resistance. A higher number of MDR bacteria were found in biofertilizer compared to the effluent, revealing the persistence of E. coli resistance, posing challenges to food safety and public health.
Collapse
Affiliation(s)
- Kássia Vidal Menezes
- Graduate Program in Veterinary Sciences, Center for Agricultural Sciences and Engineering - CCAE, Federal University of Espírito Santo - UFES, Alto Universitário, no number, Guararema, Alegre, ES 29500-000, Brazil
| | | | - Myleny Goularte Moreira
- Department of Pharmacy and Nutrition, Federal University of Espírito Santo - UFES, Alegre, ES 29500-000, Brazil
| | | | - Vitor José da Silva Pereira
- Department of Pharmacy and Nutrition, Federal University of Espírito Santo - UFES, Alegre, ES 29500-000, Brazil
| | - João Gilberto Meza Ucella-Filho
- Department of Forestry and Wood Sciences, Federal University of Espírito Santo - UFES, Jerônimo Monteiro, ES 29550-000, Brazil
| | | | | | - Juliana Alves Resende
- Graduate Program in Veterinary Sciences, Center for Agricultural Sciences and Engineering - CCAE, Federal University of Espírito Santo - UFES, Alto Universitário, no number, Guararema, Alegre, ES 29500-000, Brazil; Department of Pharmacy and Nutrition, Federal University of Espírito Santo - UFES, Alegre, ES 29500-000, Brazil.
| |
Collapse
|
50
|
Hoque MN, Faisal GM, Jerin S, Moyna Z, Islam MA, Talukder AK, Alam MS, Das ZC, Isalm T, Hossain MA, Rahman ANMA. Unveiling distinct genetic features in multidrug-resistant Escherichia coli isolated from mammary tissue and gut of mastitis induced mice. Heliyon 2024; 10:e26723. [PMID: 38434354 PMCID: PMC10904246 DOI: 10.1016/j.heliyon.2024.e26723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 02/08/2024] [Accepted: 02/19/2024] [Indexed: 03/05/2024] Open
Abstract
Escherichia coli is one of the major pathogens causing mastitis in lactating mammals. We hypothesized that E. coli from the gut and mammary glands may have similar genomic characteristics in the causation of mastitis. To test this hypothesis, we used whole genome sequencing to analyze two multidrug resistant E. coli strains isolated from mammary tissue (G2M6U) and fecal sample (G6M1F) of experimentally induced mastitis mice. Both strains showed resistance to multiple (>7) antibiotics such as oxacillin, aztreonam, nalidixic acid, streptomycin, gentamicin, cefoxitin, ampicillin, tetracycline, azithromycin and nitrofurantoin. The genome of E. coli G2M6U had 59 antimicrobial resistance genes (ARGs) and 159 virulence factor genes (VFGs), while the E. coli G6M1F genome possessed 77 ARGs and 178 VFGs. Both strains were found to be genetically related to many E. coli strains causing mastitis and enteric diseases originating from different hosts and regions. The G6M1F had several unique ARGs (e.g., QnrS1, sul2, tetA, tetR, emrK, blaTEM-1/105, and aph(6)-Id, aph(3″)-Ib) conferring resistance to certain antibiotics, whereas G2M6U had a unique heat-stable enterotoxin gene (astA) and 7192 single nucleotide polymorphisms. Furthermore, there were 43 and 111 unique genes identified in G2M6U and G6M1F genomes, respectively. These results indicate distinct differences in the genomic characteristics of E. coli strain G2M6U and G6M1F that might have important implications in the pathophysiology of mammalian mastitis, and treatment strategies for mastitis in dairy animals.
Collapse
Affiliation(s)
- M. Nazmul Hoque
- Molecular Biology and Bioinformatics Laboratory, Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, 1706, Bangladesh
| | - Golam Mahbub Faisal
- Molecular Biology and Bioinformatics Laboratory, Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, 1706, Bangladesh
| | - Shobnom Jerin
- Molecular Biology and Bioinformatics Laboratory, Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, 1706, Bangladesh
| | - Zannatara Moyna
- Molecular Biology and Bioinformatics Laboratory, Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, 1706, Bangladesh
| | - Md Aminul Islam
- Advanced Molecular Lab, Department of Microbiology, President Abdul Hamid Medical College, Karimganj, 2310, Bangladesh
| | - Anup Kumar Talukder
- Molecular Biology and Bioinformatics Laboratory, Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, 1706, Bangladesh
| | | | - Ziban Chandra Das
- Molecular Biology and Bioinformatics Laboratory, Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, 1706, Bangladesh
| | - Tofazzal Isalm
- Institute of Biotechnology and Genetic Engineering (IBGE), BSMRAU, Gazipur, 1706, Bangladesh
| | - M. Anwar Hossain
- Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Abu Nasar Md Aminoor Rahman
- Molecular Biology and Bioinformatics Laboratory, Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, 1706, Bangladesh
| |
Collapse
|