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Sharon BM, Arute AP, Nguyen A, Tiwari S, Reddy Bonthu SS, Hulyalkar NV, Neugent ML, Palacios Araya D, Dillon NA, Zimmern PE, Palmer KL, De Nisco NJ. Genetic and functional enrichments associated with Enterococcus faecalis isolated from the urinary tract. mBio 2023; 14:e0251523. [PMID: 37962362 PMCID: PMC10746210 DOI: 10.1128/mbio.02515-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 10/05/2023] [Indexed: 11/15/2023] Open
Abstract
IMPORTANCE Urinary tract infection (UTI) is a global health issue that imposes a substantial burden on healthcare systems. Women are disproportionately affected by UTI, with >60% of women experiencing at least one UTI in their lifetime. UTIs can recur, particularly in postmenopausal women, leading to diminished quality of life and potentially life-threatening complications. Understanding how pathogens colonize and survive in the urinary tract is necessary to identify new therapeutic targets that are urgently needed due to rising rates of antimicrobial resistance. How Enterococcus faecalis, a bacterium commonly associated with UTI, adapts to the urinary tract remains understudied. Here, we generated a collection of high-quality closed genome assemblies of clinical urinary E. faecalis isolated from the urine of postmenopausal women that we used alongside detailed clinical metadata to perform a robust comparative genomic investigation of genetic factors that may be involved in E. faecalis survival in the urinary tract.
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Affiliation(s)
- Belle M. Sharon
- Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas, USA
| | - Amanda P. Arute
- Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas, USA
| | - Amber Nguyen
- Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas, USA
| | - Suman Tiwari
- Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas, USA
| | | | - Neha V. Hulyalkar
- Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas, USA
| | - Michael L. Neugent
- Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas, USA
| | - Dennise Palacios Araya
- Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas, USA
| | - Nicholas A. Dillon
- Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas, USA
| | - Philippe E. Zimmern
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Kelli L. Palmer
- Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas, USA
| | - Nicole J. De Nisco
- Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas, USA
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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Shirvani F, Hassanzadeh R, Attaran B, Ghandchi G, Abdollahi N, Gholinejad Z, Sheikhi Z, Behzad A, Fallah F, Azimi L, Safarkhani A, Karimi A, Mahdavi A, Armin S, Ghanaiee RM, Tabatabaei SR, Fahimzad SA, Alebouyeh M. The intestinal carrier status of Enterococcus spp. in children: clonal diversity and alterations in resistance phenotypes before and after admission to a pediatric intensive care unit. BMC Pediatr 2023; 23:434. [PMID: 37648974 PMCID: PMC10466818 DOI: 10.1186/s12887-023-04238-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 08/08/2023] [Indexed: 09/01/2023] Open
Abstract
BACKGROUND This study aimed to investigate the intestinal carrier status of Enterococcus spp. among children in a pediatric intensive care unit (PICU) and reveal the role of hospitalization in the alteration of resistance phenotypes and clonal diversity of the isolates during admission and discharge periods. METHODS Two separate stool samples were collected from hospitalized patients in the pediatric intensive care unit at admission and discharge times. The culture was done, and Enterococcus species were tested for antimicrobial susceptibility and carriage of vanA-D gene subtypes. Random Amplified Polymorphic DNA (RAPD)-PCR was used for a phylogenetic study to check the homology of pairs of isolates. RESULTS The results showed carriage of Enterococci at admission, discharge, and at both time points in 31%, 28.7%, and 40.1% of the cases, respectively. High frequencies of the fecal Enterococcus isolates with vancomycin-resistance (VR, 32.6% and 41.9%), high-level of gentamicin-resistance (HLGR, 25.6% and 27.9%), and multi-drug resistance phenotypes (MDR, 48.8% and 65.1%) were detected at admission and discharge times, respectively. Resistance to vancomycin, ampicillin, and rifampicin was higher among E. faecium, but resistance to ciprofloxacin was higher in E. faecalis isolates. The increased length of hospital stay was correlated with the carriage of resistant strains to vancomycin, ampicillin, and ciprofloxacin. While the homology of the isolates was low among different patients during hospitalization, identical (9%) and similar (21%) RAPD-PCR patterns were detected between pairs of isolates from each patient. CONCLUSIONS The high rate of intestinal carriage of VR, HLGR-, and MDR-Enterococci at admission and during hospitalization in the PICU, and the impact of increased length of hospital stay on the fecal carriage of the resistant strains show the importance of antibiotic stewardship programs to control their transmission and spread in children.
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Affiliation(s)
- Fariba Shirvani
- Pediatric Infections Research Center, Research Institute for Children's Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Romina Hassanzadeh
- Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran
| | - Bahareh Attaran
- Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran
| | - Ghazale Ghandchi
- Pediatric Infections Research Center, Research Institute for Children's Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Nafiseh Abdollahi
- Pediatric Infections Research Center, Research Institute for Children's Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zari Gholinejad
- Pediatric Infections Research Center, Research Institute for Children's Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zahra Sheikhi
- Pediatric Intensive Care Unit, Mofid Children's Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Azita Behzad
- Pediatric Intensive Care Department, Mofid Children's Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Fatemeh Fallah
- Pediatric Infections Research Center, Research Institute for Children's Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Leila Azimi
- Pediatric Infections Research Center, Research Institute for Children's Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Azam Safarkhani
- Pediatric Intensive Care Unit, Mofid Children's Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Abdollah Karimi
- Pediatric Infections Research Center, Research Institute for Children's Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Alireza Mahdavi
- Anesthesiology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Shahnaz Armin
- Pediatric Infections Research Center, Research Institute for Children's Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Roxana Mansour Ghanaiee
- Pediatric Infections Research Center, Research Institute for Children's Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sedigheh Rafiei Tabatabaei
- Pediatric Infections Research Center, Research Institute for Children's Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Seyed Alireza Fahimzad
- Pediatric Infections Research Center, Research Institute for Children's Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Masoud Alebouyeh
- Pediatric Infections Research Center, Research Institute for Children's Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Almasian Tehrani N, Azimi L, Armin S, Soleimani N, Fallah F, Karimi A, Shamsian BS, Nazari S, Alebouyeh M. Endogenous Bacteremia Caused by Intestinal Colonization of Carbapenem-Resistant Enterobacteriaceae (CR E) in Immunocompromised Children. Trop Med Infect Dis 2023; 8:402. [PMID: 37624340 PMCID: PMC10458169 DOI: 10.3390/tropicalmed8080402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/24/2023] [Accepted: 08/04/2023] [Indexed: 08/26/2023] Open
Abstract
OBJECTIVE Carbapenem-resistant Enterobacteriaceae (CRE) infection is life-threatening, especially for immunocompromised children. The source tracking of CRE could prevent bacteremia during hospitalization. In this study, the intestinal colonization of CRE and their translocation to blood were investigated. METHODS Stool samples from immunocompromised pediatric patients were collected after admission, and secondary stool and blood samples were collected in case of fever. After CRE phonotypic detection, the OXA-48, NDM-1, VIM, IMP, and KPC genes were detected by PCR. Enterobacterial Repetitive Intergenic Consensus Polymerase Chain Reaction (ERIC-PCR) was used to determine the phylogenic relatedness of the blood and fecal isolates. RESULTS Bacteremia was recorded in 71.4% of the patients. Enterobacteriaceae spp. were recorded in 100% of the stool samples and 31% of the blood samples. The correlation between the length of stay (LOS), days of fever, chemotherapy regimens, and death rate was significant (p-value ≤ 0.05). OXA-48 was present in all CRE isolates in both the primary and the secondary stool samples and the blood samples. According to the phylogenetic data, 58.33% of the patients with bacteremia had identical blood and stool isolates. The death rate was 24.4% in children with CRE bacteremia. CONCLUSIONS The primary intestinal colonization with CRE in immunocompromised pediatrics and their translocation to blood was established in this study. The implementation of infection control programs and the application of infection prevention strategies for immunocompromised children is necessary.
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Affiliation(s)
- Nasim Almasian Tehrani
- Pediatric Infections Research Center, Research Institute for Children's Health, Shahid Beheshti University of Medical Sciences, Tehran 1546815514, Iran
- Department of Microbiology and Microbial Biotechnology, Shahid Beheshti University, Tehran 1983969411, Iran
| | - Leila Azimi
- Pediatric Infections Research Center, Research Institute for Children's Health, Shahid Beheshti University of Medical Sciences, Tehran 1546815514, Iran
| | - Shahnaz Armin
- Pediatric Infections Research Center, Research Institute for Children's Health, Shahid Beheshti University of Medical Sciences, Tehran 1546815514, Iran
| | - Neda Soleimani
- Department of Microbiology and Microbial Biotechnology, Shahid Beheshti University, Tehran 1983969411, Iran
| | - Fatemeh Fallah
- Pediatric Infections Research Center, Research Institute for Children's Health, Shahid Beheshti University of Medical Sciences, Tehran 1546815514, Iran
| | - Abdollah Karimi
- Pediatric Infections Research Center, Research Institute for Children's Health, Shahid Beheshti University of Medical Sciences, Tehran 1546815514, Iran
| | - Bibi Shahin Shamsian
- Pediatric Congenital Hematologic Disorders Research Center, Research Institute for Children's Health, Shahid Beheshti University of Medical Sciences, Tehran 1546815514, Iran
| | - Shiva Nazari
- Pediatric Infections Research Center, Research Institute for Children's Health, Shahid Beheshti University of Medical Sciences, Tehran 1546815514, Iran
| | - Masoud Alebouyeh
- Pediatric Infections Research Center, Research Institute for Children's Health, Shahid Beheshti University of Medical Sciences, Tehran 1546815514, Iran
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Deng R, Meng X, Li R, Wang A, Song Y. Asymptomatic Candida glabrata urinary tract infection in an immunocompetent young female: A case report. Medicine (Baltimore) 2023; 102:e33798. [PMID: 37335701 DOI: 10.1097/md.0000000000033798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 06/21/2023] Open
Abstract
INTRODUCTION Fungal urinary tract infections (UTIs) are becoming increasingly common in hospitalized patients and Candida species are the most prevalent organisms. However, recurrent candiduria in young healthy outpatients is rare thus require further examination to find the etiologic factors. CASE PRESENTATION We described a case of recurrent asymptomatic c caused by azole-resistant C. glabrata in a healthy young female who only had previous use of antibiotics without other risk factors. However, after removal of the predisposing factor and the use of sensitive antifungal agents, the patient's urine cultures remained positive. This phenomenon indicated to us that the patient might have an immune-related genetic deficiency. We found a novel caspase-associated recruitment domain-containing protein 9 (CARD9) gene mutation (c.808-11G > T) which might be the cause of recurrent asymptomatic candiduria in this immune-competent young female without any underlying diseases. CONCLUSIONS We report a case of recurrent asymptomatic candiduria caused by azole-resistant Candida glabrata in a young healthy female with a novel CARD9 mutation. A functional study of this mutation should be performed in the future to determine its effect on asymptomatic fungal UTIs.
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Affiliation(s)
- Ruixin Deng
- Department of Dermatology and Venerology, Peking University First Hospital, Beijing, China
- National Clinical Research Center for Skin and Immune Diseases, Beijing, China
- Research Center for Medical Mycology, Peking University, Beijing, China
- Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China
| | - Xingye Meng
- Department of Dermatology and Venerology, Peking University First Hospital, Beijing, China
- National Clinical Research Center for Skin and Immune Diseases, Beijing, China
- Research Center for Medical Mycology, Peking University, Beijing, China
- Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China
| | - Ruoyu Li
- Department of Dermatology and Venerology, Peking University First Hospital, Beijing, China
- National Clinical Research Center for Skin and Immune Diseases, Beijing, China
- Research Center for Medical Mycology, Peking University, Beijing, China
- Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China
| | - Aiping Wang
- Department of Dermatology and Venerology, Peking University First Hospital, Beijing, China
- National Clinical Research Center for Skin and Immune Diseases, Beijing, China
- Research Center for Medical Mycology, Peking University, Beijing, China
- Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China
| | - Yinggai Song
- Department of Dermatology and Venerology, Peking University First Hospital, Beijing, China
- National Clinical Research Center for Skin and Immune Diseases, Beijing, China
- Research Center for Medical Mycology, Peking University, Beijing, China
- Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China
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Sharon BM, Arute AP, Nguyen A, Tiwari S, Bonthu SSR, Hulyalkar NV, Neugent ML, Araya DP, Dillon NA, Zimmern PE, Palmer KL, De Nisco NJ. Functional and genetic adaptations contributing to Enterococcus faecalis persistence in the female urinary tract. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.18.541374. [PMID: 37293065 PMCID: PMC10245761 DOI: 10.1101/2023.05.18.541374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Enterococcus faecalis is the leading Gram-positive bacterial species implicated in urinary tract infection (UTI). An opportunistic pathogen, E. faecalis is a commensal of the human gastrointestinal tract (GIT) and its presence in the GIT is a predisposing factor for UTI. The mechanisms by which E. faecalis colonizes and survives in the urinary tract (UT) are poorly understood, especially in uncomplicated or recurrent UTI. The UT is distinct from the GIT and is characterized by a sparse nutrient landscape and unique environmental stressors. In this study, we isolated and sequenced a collection of 37 clinical E. faecalis strains from the urine of primarily postmenopausal women. We generated 33 closed genome assemblies and four highly contiguous draft assemblies and conducted a comparative genomics to identify genetic features enriched in urinary E. faecalis with respect to E. faecalis isolated from the human GIT and blood. Phylogenetic analysis revealed high diversity among urinary strains and a closer relatedness between urine and gut isolates than blood isolates. Plasmid replicon (rep) typing further underscored possible UT-GIT interconnection identifying nine shared rep types between urine and gut E. faecalis . Both genotypic and phenotypic analysis of antimicrobial resistance among urinary E. faecalis revealed infrequent resistance to front-line UTI antibiotics nitrofurantoin and fluoroquinolones and no vancomycin resistance. Finally, we identified 19 candidate genes enriched among urinary strains that may play a role in adaptation to the UT. These genes are involved in the core processes of sugar transport, cobalamin import, glucose metabolism, and post-transcriptional regulation of gene expression. IMPORTANCE Urinary tract infection (UTI) is a global health issue that imposes substantial burden on healthcare systems. Women are disproportionately affected by UTI with >60% of women experiencing at least one UTI in their lifetime. UTIs can recur, particularly in postmenopausal women, leading to diminished quality of life and potentially life-threatening complications. Understanding how pathogens colonize and survive in the urinary tract is necessary to identify new therapeutic targets that are urgently needed due to rising rates of antimicrobial resistance. How Enterococcus faecalis , a bacterium commonly associated with UTI, adapts to the urinary tract remains understudied. Here, we generated a collection of high-quality closed genome assemblies of clinical urinary E. faecalis isolated from the urine of postmenopausal women that we used alongside detailed clinical metadata to perform a robust comparative genomic investigation of genetic factors that may mediate urinary E. faecalis adaptation to the female urinary tract.
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Maślak E, Miśta W, Złoch M, Błońska D, Pomastowski P, Monedeiro F, Buszewski B, Mrochem-Kwarciak J, Bojarska K, Gabryś D. A New Approach to Imaging and Rapid Microbiome Identification for Prostate Cancer Patients Undergoing Radiotherapy. Biomedicines 2022; 10:biomedicines10081806. [PMID: 36009352 PMCID: PMC9405325 DOI: 10.3390/biomedicines10081806] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/18/2022] [Accepted: 07/25/2022] [Indexed: 11/16/2022] Open
Abstract
(1) Background: Little is known about the impact of urinary microflora, in particular, its effects on side effects after radiotherapy. The use of mass spectrometry identification method (MALDI) may bring a new look at the issue of the composition and significance of the urinary microbiome. This study aimed to use the mass spectrometry identification method (MALDI) to identify the microbiome of urine samples collected from 50 irradiated prostate cancer patients. (2) Methods: Blood and urine samples were collected before gold marker implantation, at the start and last day of radiotherapy, 1, 4 months after. Patients do not always collect the urine from the midstream; therefore, samples were collected from the first void and midstream in 12 patients for MALDI analysis; in the remaining 38 patients—from the midstream void for MALDI and biochemical analysis. (3) Results: Microorganisms were present in 140/181 urine samples. We found 33 different species 3G(−) and 30G(+). The most frequently isolated strains were: Staphylococcus haemolyticus, Staphylococcus epidermidis, Staphylococcus hominis, Enterococcus faecalis, and Micrococcus luteus. When comparing the type of urine samples, bacteria were more common in samples from the first-void urine than from the midstream one. The absence of bacteria was found in 12.2% of samples from the first-void urine and in 24.7% from the midstream. There was no difference in the total incidence of species between streams (p = 0.85). Before fiducial implantation, the total number of detected bacterial species was significantly higher in comparison to the end of radiotherapy (p = 0.038), indicating that the administered therapy resulted in depleting the local microbiome. One month after radiotherapy, an increase in the number of isolated bacteria was observed. The number of bacterial species in urine did not correlate with blood parameters. The presence of leukocytes (p = 0.013) and proteins (p = 0.004) in urine was related to a greater variety of bacteria found in urine specimens. (4) Conclusions: We obtained a similar spectrum of bacteria from the initial and middle urine streams. We also showed that there is a change in bacteria species affected by the treatment of prostate cancer patients, with both antibiotics before gold fiducial implantation and radiotherapy.
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Affiliation(s)
- Ewelina Maślak
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wileńska 4 Str., 87-100 Toruń, Poland; (E.M.); (M.Z.); (D.B.); (P.P.); (F.M.); (B.B.)
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, Gagarina 7 Str., 87-100 Toruń, Poland
| | - Wioletta Miśta
- Radiotherapy Department, Maria Sklodowska-Curie National Research Institute of Oncology, Gliwice Branch, Wybrzeże Armii Krajowej 15 Str., 44-102 Gliwice, Poland;
| | - Michał Złoch
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wileńska 4 Str., 87-100 Toruń, Poland; (E.M.); (M.Z.); (D.B.); (P.P.); (F.M.); (B.B.)
| | - Dominika Błońska
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wileńska 4 Str., 87-100 Toruń, Poland; (E.M.); (M.Z.); (D.B.); (P.P.); (F.M.); (B.B.)
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, Gagarina 7 Str., 87-100 Toruń, Poland
| | - Paweł Pomastowski
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wileńska 4 Str., 87-100 Toruń, Poland; (E.M.); (M.Z.); (D.B.); (P.P.); (F.M.); (B.B.)
| | - Fernanda Monedeiro
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wileńska 4 Str., 87-100 Toruń, Poland; (E.M.); (M.Z.); (D.B.); (P.P.); (F.M.); (B.B.)
| | - Bogusław Buszewski
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wileńska 4 Str., 87-100 Toruń, Poland; (E.M.); (M.Z.); (D.B.); (P.P.); (F.M.); (B.B.)
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, Gagarina 7 Str., 87-100 Toruń, Poland
| | - Jolanta Mrochem-Kwarciak
- Analytics and Clinical Biochemistry Department, Maria Sklodowska-Curie National Research Institute of Oncology, Gliwice Branch, Wybrzeże Armii Krajowej 15 Str., 44-102 Gliwice, Poland; (J.M.-K.); (K.B.)
| | - Katarzyna Bojarska
- Analytics and Clinical Biochemistry Department, Maria Sklodowska-Curie National Research Institute of Oncology, Gliwice Branch, Wybrzeże Armii Krajowej 15 Str., 44-102 Gliwice, Poland; (J.M.-K.); (K.B.)
| | - Dorota Gabryś
- Radiotherapy Department, Maria Sklodowska-Curie National Research Institute of Oncology, Gliwice Branch, Wybrzeże Armii Krajowej 15 Str., 44-102 Gliwice, Poland;
- Correspondence: ; Tel.: +48-32-278-80-51
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Genetic Diversity, Antimicrobial Resistance, and Virulence Factors of Enterococcus Faecalis Isolates Obtained from Stool Samples of Hospitalized Patients. Jundishapur J Microbiol 2022. [DOI: 10.5812/jjm-121379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Background: Enterococcus faecalis rapidly develops resistance to different antibiotics, thereby resulting in serious nosocomial infections associated with high mortality rates and different problems in the healthcare systems. Objectives: This study aimed to analyze the genetic diversity, antimicrobial resistance, and virulence factors of E. faecalis isolates obtained from the stool samples of patients in a hospital in the center of Iran. Methods: In this cross-sectional descriptive-analytical study, 108 stool samples were collected from September 2019 to February 2020 from 108 patients hospitalized in a hospital in the center of Iran. Enterococcus faecalis isolates were detected using the ddlE gene detection technique, and antimicrobial resistance testing was performed using the disc agar diffusion method. Moreover, polymerase chain reaction (PCR) was used to detect antimicrobial resistance genes and virulence factors. Genetic diversity was also analyzed by enterobacterial repetitive intergenic consensus using PCR (ERIC-PCR). The BioNumerics software was used to construct a dendrogram. Results: Of 108 isolates, 50 samples were E. faecalis (46.2%). The prevalence of multidrug resistance among E. faecalis isolates was 62%, and most isolates were resistant to antibiotics tetracycline (70%), erythromycin (68%), and rifampin (60%). Among the E. faecalis isolates, the most prevalent antimicrobial resistance genes were ermB (96%), aph (2′′) Ia (66%), aac(6′)-Ie (40%), and ermC (30%), and the most prevalent virulence genes were gelE (78%), asa1 (74%), and esp (74%). The genetic diversity analysis showed 25 ERIC types in two major clusters (ie, clusters H and J) and eight minor clusters (ie, clusters A-G and I). There was no significant difference between clusters H and J in terms of antimicrobial resistance and resistance genes (P > 0.05). In contrast, the prevalence of the asa1 gene was significantly higher in cluster J than in cluster H (P < 0.05). Conclusions: This study showed the high prevalence of multidrug resistance, and high heterogeneity among the E. faecalis isolates obtained from the stool samples of hospitalized patients.
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Nana T, Bhoora S, Chibabhai V. Trends in the epidemiology of urinary tract infections in pregnancy at a tertiary hospital in Johannesburg: Are contemporary treatment recommendations appropriate? S Afr J Infect Dis 2021; 36:328. [PMID: 34957292 PMCID: PMC8678934 DOI: 10.4102/sajid.v36i1.328] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 10/19/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Urinary tract infections (UTIs) are common during pregnancy and are associated with maternal and foetal complications. Empiric antibiotic choices in pregnancy require consideration of efficacy and safety, resulting in limited oral options. With rapidly evolving antibiotic resistance, surveillance to guide empiric treatment recommendations is essential. METHODS A retrospective analysis of urine culture isolates from the Charlotte Maxeke Johannesburg Academic Hospital (CMJAH) Obstetrics Department for 1 January 2015 to 31 December 2020 was performed. RESULTS The top 3 pathogens were Escherichia coli, Enterococcus faecalis and Klebsiella pneumoniae. For E. coli susceptibility to cefuroxime declined (95% to 81%, p < 0.0001). Similarly, the E. coli extended spectrum beta-lactamase rate increased from 5% to 10% (p = 0.04). E. coli susceptibility to nitrofurantoin (93%) and fosfomycin (96%) remained high. In 2019, carbapenem-resistant K. pneumoniae emerged. Ampicillin susceptibility was high amongst the E. faecalis isolates. Amoxicillin-clavulanate demonstrated high levels of activity against the top 3 uropathogens. CONCLUSION The Essential Drug List recommended antibiotics for lower UTIs, nitrofurantoin and fosfomycin, are appropriate empiric options for E. coli, the most common uropathogen in the CMJAH obstetric population. The high rate of E. faecalis susceptibility to nitrofurantoin reported from other Gauteng tertiary obstetric patients, suggests that nitrofurantoin will provide adequate empiric cover for a large proportion of UTIs. However, the determination of the E. faecalis nitrofurantoin and fosfomycin susceptibility rates in the CMJAH obstetric population will provide useful data. Periodic surveillance at the various levels of antenatal care in different regions of South Africa and the determination of risk factors for infections with resistant uropathogens is needed.
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Affiliation(s)
- Trusha Nana
- Department of Clinical Microbiology and Infectious Diseases, University of the Witwatersrand, Johannesburg, South Africa
- Microbiology Laboratory, Charlotte Maxeke Johannesburg Academic Hospital, National Health Laboratory Services, Johannesburg, South Africa
| | - Shastra Bhoora
- Department of Obstetrics and Gynaecology, University of the Witwatersrand, Johannesburg, South Africa
- Department of Obstetrics and Gynaecology, Charlotte Maxeke Johannesburg Academic Hospital, South Africa
- Gauteng Department of Health, Johannesburg, South Africa
- Department of Obstetrics and Gynaecology, Faculty of Medicine, Baylor College, Houston, United States of America
| | - Vindana Chibabhai
- Department of Clinical Microbiology and Infectious Diseases, University of the Witwatersrand, Johannesburg, South Africa
- Microbiology Laboratory, Charlotte Maxeke Johannesburg Academic Hospital, National Health Laboratory Services, Johannesburg, South Africa
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Xiao X, Sun H, Liu X, Guo Z, Zheng S, Xu J, Sun J, Lan Y, Shao C, Sun W. Qualitative and quantitative proteomic and metaproteomic analyses of healthy human urine sediment. Proteomics Clin Appl 2021; 16:e2100007. [PMID: 34687263 DOI: 10.1002/prca.202100007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 09/30/2021] [Accepted: 10/17/2021] [Indexed: 11/07/2022]
Abstract
PURPOSE The healthy human urine sediment proteome and metaproteome are investigated, to shed light on the variations of urine sediment proteins and metaproteins associated with sex and age. EXPERIMENTAL DESIGN Urine sediment samples are collected from 19 healthy subjects. Protein identification and quantification are performed by liquid chromatography coupled high-resolution mass spectrometry. RESULTS A total of 2736 human proteins were identified, which were primarily associated with inflammatory response and energy metabolism. For the metaproteome, 65 genera were identified that were primarily involved in translation and carbohydrate metabolic processes. The median biological coefficient variation of the proteome/metaproteome of human urine sediment was 0.5/0.72, similar to the proteome of human urine supernatant. In addition, sex and age were observed to affect the proteome and metaproteome of healthy human urine sediment. CONCLUSION AND CLINICAL RELEVANCE The healthy human urine sediment were characterized, indicating that urine sediment might represent an alternative resource for disease research in addition to urine supernatant, but the influence of sex and age must be considered in the study design process.
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Affiliation(s)
- XiaoLian Xiao
- Core Facility of Instrument, School of Basic Medicine, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Haidan Sun
- Core Facility of Instrument, School of Basic Medicine, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Xiaoyan Liu
- Core Facility of Instrument, School of Basic Medicine, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Zhengguang Guo
- Core Facility of Instrument, School of Basic Medicine, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Shuxin Zheng
- Core Facility of Instrument, School of Basic Medicine, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Jiyu Xu
- Core Facility of Instrument, School of Basic Medicine, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Jiameng Sun
- Core Facility of Instrument, School of Basic Medicine, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Ying Lan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Chen Shao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Wei Sun
- Core Facility of Instrument, School of Basic Medicine, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
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Quan J, Dai H, Liao W, Zhao D, Shi Q, Zhang L, Shi K, Akova M, Yu Y. Etiology and prevalence of ESBLs in adult community-onset urinary tract infections in East China: A prospective multicenter study. J Infect 2021; 83:175-181. [PMID: 34116075 DOI: 10.1016/j.jinf.2021.06.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 06/05/2021] [Indexed: 01/08/2023]
Abstract
OBJECTIVES Community onset urinary tract infections (COUTIs) drew attention recently owing to their increased prevalence and associations with resistant pathogens. The study is aimed at investigating the etiology of COUTIs as well as prevalence and the related risk factors of extended-spectrum β-lactamase (ESBL) in COUTIs in China. METHODS The prospective study was performed in nineteen hospitals during November 1, 2017 and August 31, 2019. Non-duplicated isolates from COUTIs were included. The ESBL phenotypic confirmation test was performed and whole genomes were sequenced for all the ESBL-positive bacteria for further analysis. The risk factors for ESBL-producing bacterial infections were analyzed using binary logistic regression. RESULTS A total of 1760 COUTI cases were included in this study. Escherichia coli (1332, 75.7%), Klebsiella pneumoniae (110, 6.3%) and Enterococcus faecalis (52, 3.0%) were the top three common pathogens of COUTIs in China. The overall positive rate of ESBLs in Enterobacterales was 37.2% (562/1512). The age (OR=1.007, P = 0.041), solid malignant tumor (OR=1.668, P = 0.016), prostate diseases (OR=2.035, P = 0.010), history of lithotripsy for urinary calculi (OR=2.009, P = 0.030), history of urological surgery (OR=1.869, P = 0.009) and cephalosporin use within 3 months (OR=1.503, P = 0.025) were independent risk factors for ESBL-producing organisms causing COUTIs. The predominant ESBL types were CTX-Ms, among which CTX-M-14, CTX-M-55 and CTX-M-27 were the most common subtypes. ST131 and ST1193 were the predominant sequence types of ESBL-producing E. coli (ESBL-EC). Most of the tested antimicrobial agents showed significantly higher non-susceptible rates in the ESBL positive group as compared with ESBL-negative group (P < 0.05). CONCLUSIONS Enterobacterales, especially E. coli, is the most common pathogen in COUTIs in China and ESBL-producers are highly prevalent. Thus, early prediction depending on risk factors seems to be crucial to determine the appropriate empirical therapy for infections caused by ESBL-producing pathogens.
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Affiliation(s)
- Jingjing Quan
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, Zhejiang, China; Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Honglei Dai
- Department of General Practice, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Weichao Liao
- Department of Intensive Care Unit, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Dongdong Zhao
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, Zhejiang, China; Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qiucheng Shi
- Department of Clinical Laboratory, The Children's Hospital, National Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Linghong Zhang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, Zhejiang, China; Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Keren Shi
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, Zhejiang, China; Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Murat Akova
- Department of Infectious Disease, Hacettepe University School of Medicine, Ankara 06100, Turkey
| | - Yunsong Yu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, Zhejiang, China; Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.
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