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Kuruwa S, Zade A, Shah S, Moidu R, Lad S, Chande C, Joshi A, Hirani N, Nikam C, Bhattacharya S, Poojary A, Kapoor M, Kondabagil K, Chatterjee A. An integrated method for targeted Oxford Nanopore sequencing and automated bioinformatics for the simultaneous detection of bacteria, fungi, and ARG. J Appl Microbiol 2024; 135:lxae037. [PMID: 38346849 DOI: 10.1093/jambio/lxae037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 01/26/2024] [Accepted: 02/10/2024] [Indexed: 02/24/2024]
Abstract
AIMS The use of metagenomics for pathogen identification in clinical practice has been limited. Here we describe a workflow to encourage the clinical utility and potential of NGS for the screening of bacteria, fungi, and antimicrobial resistance genes (ARGs). METHODS AND RESULTS The method includes target enrichment, long-read sequencing, and automated bioinformatics. Evaluation of several tools and databases was undertaken across standard organisms (n = 12), clinical isolates (n = 114), and blood samples from patients with suspected bloodstream infections (n = 33). The strategy used could offset the presence of host background DNA, error rates of long-read sequencing, and provide accurate and reproducible detection of pathogens. Eleven targets could be successfully tested in a single assay. Organisms could be confidently identified considering ≥60% of best hits of a BLAST-based threshold of e-value 0.001 and a percent identity of >80%. For ARGs, reads with percent identity of >90% and >60% overlap of the complete gene could be confidently annotated. A kappa of 0.83 was observed compared to standard diagnostic methods. Thus, a workflow for the direct-from-sample, on-site sequencing combined with automated genomics was demonstrated to be reproducible. CONCLUSION NGS-based technologies overcome several limitations of current day diagnostics. Highly sensitive and comprehensive methods of pathogen screening are the need of the hour. We developed a framework for reliable, on-site, screening of pathogens.
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Affiliation(s)
- Sanjana Kuruwa
- HaystackAnalytics Pvt. Ltd, SINE, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Amrutraj Zade
- HaystackAnalytics Pvt. Ltd, SINE, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Sanchi Shah
- HaystackAnalytics Pvt. Ltd, SINE, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Rameez Moidu
- HaystackAnalytics Pvt. Ltd, SINE, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Shailesh Lad
- HaystackAnalytics Pvt. Ltd, SINE, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Chhaya Chande
- Department of Microbiology, Sir J. J. Group of Hospitals, Mumbai 400008, India
| | - Ameeta Joshi
- Department of Microbiology, Sir J. J. Group of Hospitals, Mumbai 400008, India
| | - Nilma Hirani
- Department of Microbiology, Sir J. J. Group of Hospitals, Mumbai 400008, India
| | - Chaitali Nikam
- HaystackAnalytics Pvt. Ltd, SINE, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
- Thyrocare Technologies Pvt. Ltd, Navi Mumbai 400703, India
| | - Sanjay Bhattacharya
- Department of Microbiology, Tata Medical Center, 14, MAR(E-W), DH Block (Newtown), Action Area I, Newtown, Kolkata, Chakpachuria 700160, India
| | - Aruna Poojary
- Department of Microbiology, Breach Candy Hospital and Research Center, Mumbai 400026, India
| | - Mahua Kapoor
- HaystackAnalytics Pvt. Ltd, SINE, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Kiran Kondabagil
- Department of Bioscience and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Anirvan Chatterjee
- HaystackAnalytics Pvt. Ltd, SINE, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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Graspeuntner S, Lupatsii M, Dashdorj L, Rody A, Rupp J, Bossung V, Härtel C. First-Day-of-Life Rectal Swabs Fail To Represent Meconial Microbiota Composition and Underestimate the Presence of Antibiotic Resistance Genes. Microbiol Spectr 2023; 11:e0525422. [PMID: 37097170 PMCID: PMC10269712 DOI: 10.1128/spectrum.05254-22] [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: 12/22/2022] [Accepted: 04/10/2023] [Indexed: 04/26/2023] Open
Abstract
The human gut microbiome plays a vital role in health and disease. In particular, the first days of life provide a unique window of opportunity for development and establishment of microbial community. Currently, stool samples are known to be the most widely used sampling approach for studying the gut microbiome. However, complicated sample acquisition at certain time points, challenges in transportation, and patient discomfort underline the need for development of alternative sampling approaches. One of the alternatives is rectal swabs, shown to be a reliable proxy for gut microbiome analysis when obtained from adults. Here, we compare the usability of rectal swabs and meconium paired samples collected from infants on the first days of life. Our results indicate that the two sampling approaches display significantly distinct patterns in microbial composition and alpha and beta diversity as well as detection of resistance genes. Moreover, the dissimilarity between the two collection methods was greater than the interindividual variation. Therefore, we conclude that rectal swabs are not a reliable proxy compared to stool samples for gut microbiome analysis when collected on the first days of a newborn's life. IMPORTANCE Currently, there are numerous suggestions on how to ease the notoriously complex and error-prone methodological setups to study the gut microbiota of newborns during the first days of life. Especially, meconium samples are regularly failing to yield meaningful data output and therefore have been suggested to be replaced by rectal swabs as done in adults as well. We find this development toward a simplified method to be producing dramatically erroneous results, skewing data interpretation away from the real aspects to be considered for neonatal health during the first days of life. We have put together our knowledge on this critical aspect with careful consideration and identified the failure of rectal swabs to be a replacement for sampling of meconium in term-born newborns.
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Affiliation(s)
- S. Graspeuntner
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Lübeck, Germany
| | - M. Lupatsii
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
| | - L. Dashdorj
- Department of Obstetrics and Gynecology, University Hospital of Schleswig-Holstein, Lübeck, Germany
| | - A. Rody
- Department of Obstetrics and Gynecology, University Hospital of Schleswig-Holstein, Lübeck, Germany
| | - J. Rupp
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Lübeck, Germany
| | - V. Bossung
- Department of Obstetrics and Gynecology, University Hospital of Schleswig-Holstein, Lübeck, Germany
- Department of Pediatrics, University Hospital of Würzburg, Würzburg, Germany
| | - C. Härtel
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Lübeck, Germany
- Department of Obstetrics, University Hospital of Zurich, Zurich, Switzerland
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Bossung V, Lupatsii M, Dashdorj L, Tassiello O, Jonassen S, Pagel J, Demmert M, Wolf EA, Rody A, Waschina S, Graspeuntner S, Rupp J, Härtel C. Timing of antimicrobial prophylaxis for cesarean section is critical for gut microbiome development in term born infants. Gut Microbes 2022; 14:2038855. [PMID: 35184691 PMCID: PMC8865290 DOI: 10.1080/19490976.2022.2038855] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Animal models imply that the perinatal exposure to antibiotics has a substantial impact on microbiome establishment of the offspring. We aimed to evaluate the effect of timing of antimicrobial prophylaxis for cesarean section before versus after cord clamping on gut microbiome composition of term born infants. We performed an exploratory, single center randomized controlled clinical trial. We included forty pregnant women with elective cesarean section at term. The intervention group received single dose intravenous cefuroxime after cord clamping (n = 19), the control group single dose intravenous cefuroxime 30 minutes before skin incision (n = 21). The primary endpoint was microbiome signature of infants and metabolic prediction in the first days of life as determined in meconium samples by 16S rRNA gene sequencing. Secondary endpoints were microbiome composition at one month and 1 year of life. In meconium samples of the intervention group, the genus Staphylococcus pre-dominated. In the control group, the placental cross-over of cefuroxime was confirmed in cord blood. A higher amino acid and nitrogen metabolism as well as increased abundance of the genera Cutibacterium, Corynebacterium and Streptophyta were noted (indicator families: Cytophagaceae, Lactobacilaceae, Oxalobacteraceae). Predictive models of metabolic function revealed higher 2'fucosyllactose utilization in control group samples. In the follow-up visits, a higher abundance of the genus Clostridium was evident in the intervention group. Our exploratory randomized controlled trial suggests that timing of antimicrobial prophylaxis is critical for early microbiome engraftment but not antimicrobial resistance emergence in term born infants.
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Affiliation(s)
- Verena Bossung
- Department of Obstetrics and Gynecology, University Hospital of Schleswig-Holstein, Campus, Lübeck, Germany,CONTACT Verena Bossung Department of Obstetrics and Gynecology University Hospital of Schleswig-Holstein, Campus Lübeck Ratzeburger Allee 160, D −23538Luebeck, Germany
| | - Mariia Lupatsii
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany,German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Lübeck, Germany
| | | | - Oronzo Tassiello
- Institute for Human Nutrition and Food Science, Nutriinformatics, University of Kiel, Kiel, Germany
| | - Sinje Jonassen
- Department of Obstetrics and Gynecology, University Hospital of Schleswig-Holstein, Campus, Lübeck, Germany
| | - Julia Pagel
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Lübeck, Germany,Department of Pediatrics, University Hospital of Schleswig-Holstein, Campus, Lübeck, Germany
| | - Martin Demmert
- Department of Pediatrics, University Hospital of Schleswig-Holstein, Campus, Lübeck, Germany
| | - Ellinor Anna Wolf
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
| | - Achim Rody
- Department of Obstetrics and Gynecology, University Hospital of Schleswig-Holstein, Campus, Lübeck, Germany
| | - Silvio Waschina
- Institute for Human Nutrition and Food Science, Nutriinformatics, University of Kiel, Kiel, Germany
| | - Simon Graspeuntner
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany,German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Lübeck, Germany
| | - Jan Rupp
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany,German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Lübeck, Germany
| | - Christoph Härtel
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Lübeck, Germany,Department of Pediatrics, University Hospital of Schleswig-Holstein, Campus, Lübeck, Germany,Department of Pediatrics, University Hospital of Würzburg, Wurzburg, Germany
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Prevalence of vancomycin-resistant enterococcus in Africa in one health approach: a systematic review and meta-analysis. Sci Rep 2020; 10:20542. [PMID: 33239734 PMCID: PMC7688635 DOI: 10.1038/s41598-020-77696-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 11/02/2020] [Indexed: 11/08/2022] Open
Abstract
Vancomycin-resistant enterococci are a global challenge currently as reported by the World Health Organization. It is also important to recognize that combating antimicrobial resistance needs to recognize the interconnections between people, animals, plants and their shared environment in creating public health, the so-called One Health approach. Although the presence of VRE has been described in many regions of the world, there is a lack of comprehensive data indicating their prevalence of in Africa. Therefore, this study aimed to aggregate the result of studies describing VRE reported across multiple regions in Africa. A literature search was conducted on PubMed, Google scholar, and Hinari with the term “Vancomycin resistance enterococcus in Africa” on August 1–3, 2019. All available articles were downloaded to “Endnote version 7.1” then to Microsoft Word 2013. Articles determined to meet our criteria for the review was extracted to Microsoft Excel 2013. Those articles that reported the prevalence of vancomycin resistance Enterococcus obtained from all sample types and published from 2010 to 2019 in the English language were included for the review. A meta-analysis was conducted with OpenMetaAnalyst version R.3.1.0 software. The effect size was determined using a binary random effect model and statically significant considered when p < 0.05. Heterogeneity determined with the inconsistency index. A leave one out analysis used to perform the sensitivity analysis. There were 151 articles identified from the database searches; of this, 36 articles included after extensive review with two independent authors. Out of 4073 samples collected, 1488 isolates identified with an overall pooled prevalence of VRE 26.8% (95% CI; 10.7–43.0%) in Africa with a one-health perspective. The analysis showed that considerable heterogeneity among the studies (I2 = 99.97%; p < 0.001). Subgroup analysis in-country, African region, laboratory method, year of publication, and sample source showed that a high prevalence was identified from South Africa (74.8%), South African regions (74.8%), PCR (959.2%), 2010–2015 years (30.3%) and environmental (52.2%), respectively. This meta-analysis indicates that there was a high-pooled prevalence of vancomycin-resistant enterococci in African. A lot should be done to prevent and control the transmission of vancomycin resistance enterococci to a human being from the environment in the continent.
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Antimicrobial Resistance of Enterococcus Faecium Isolated from the Urinary System Of Dogs. MACEDONIAN VETERINARY REVIEW 2019. [DOI: 10.2478/macvetrev-2018-0026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Abstract
The purpose of the present study was to determine the antimicrobial susceptibility of vancomycin-resistant and Enterococcus faecium strains isolated from urine samples of dogs. A total of 22 Enterococcus sp. samples were isolated and identified from 100 urine samples collected by cystocentesis from dogs of both sexes. The identification with species specific primers for multiplex PCR revealed that all 22 isolates (100%) belonged to E. faecium. Vancomycin resistance was found in 10 (45%) samples of E. faecium strains with PCR study by vanA and vanB primers.
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Moosavian M, Ghadri H, Samli Z. Molecular detection of vanA and vanB genes among vancomycin-resistant enterococci in ICU-hospitalized patients in Ahvaz in southwest of Iran. Infect Drug Resist 2018; 11:2269-2275. [PMID: 30532561 PMCID: PMC6245376 DOI: 10.2147/idr.s177886] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Objective Nosocomial infections due to vancomycin-resistant enterococci (VRE) are known as a source of spreading these bacteria. The aim of this prospective study was molecular detection of vanA and vanB genes among VRE isolated from patients admitted to intensive care units (ICUs) in Ahvaz in southwest of Iran. Materials and methods Overall, 243 non-duplicate rectal swab specimens were collected from ICU-hospitalized patients in teaching hospitals affiliated to Ahvaz Jundishapur University of Medical Sciences, Iran. The specimens were inoculated on suitable culture media, and isolates were identified by standard biochemical tests. The susceptibility and resistance of enterococci to 10 antibiotics were determined based on the Clinical and Laboratory Standards Institute guidelines. Resistance to vancomycin was phenotypically detected by vancomycin screening test, and the vanA and vanB genes in vancomycin-resistant isolates were amplified by multiplex PCR method. Results Of 175 specimens containing enterococci, 129 (73.7%) isolates were detected as Enterococcus faecium and Enterococcus faecalis and 46 (26.3%) isolates as Enterococcus spp. The results of susceptibility test showed high rates of resistance to tetracycline, erythromycin, ciprofloxacin, and ampicillin. Moreover, based on this test, out of 129 Enterococcus isolates, 56 (43.4%) were resistant to vancomycin and teicoplanin. Also, among 59 vancomycin-resistant or semi-susceptible isolates, vanA gene was detected in 54 (91.5%) isolates, while none of the isolates had vanB gene. Conclusion According to the results of this study, to prevent the spread of vancomycin-resistant Enterococcus strains, especially in nosocomial infections, the susceptibility of isolates should be determined before vancomycin prescription.
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Affiliation(s)
- Mojtaba Moosavian
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran, .,Department of Microbiology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran,
| | - Hosein Ghadri
- Department of Microbiology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran,
| | - Zahra Samli
- School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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Huang TS, Lee SSJ, Lee CC, Chen CY, Chen FC, Chen BC, Sy CL, Wu KS. Evaluation of a matrix-assisted laser desorption ionization-time of flight mass spectrometry assisted, selective broth method to screen for vancomycin-resistant enterococci in patients at high risk. PLoS One 2017; 12:e0179455. [PMID: 28609453 PMCID: PMC5469485 DOI: 10.1371/journal.pone.0179455] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Accepted: 05/29/2017] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Bile esculin azide with vancomycin (BEAV) medium is a sensitive, but slightly less specific method for vancomycin-resistant enterococci (VRE) screening. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a rapid method for identification of clinical pathogens. This study aimed to assess the performance of a novel combination screening test for VRE, using BEAV broth combined with MALDI-TOF MS. MATERIALS AND METHODS Clinical specimens were collected from patients at risk of VRE carriage, and tested by the novel combination method, using selective BEAV broth culture method followed by MALDI-TOF MS identification (SBEAVM). The reference method used for comparison was the ChromID VRE agar method. RESULTS A total of 135 specimens were collected from 78 patients, and 63 specimens tested positive for VRE positive using the ChromID VRE method (positive rate 46.7%). The sensitivity, specificity, positive predictive value, and negative predictive value of SBEAVM method after an incubation period of 28 hours were 93.7%, 90.3%, 89.4%, and 94.2%, respectively. The SBEAVM method when compared to the ChromID VRE method had a shorter turnaround time (29 vs. 48-72 hours) and lower laboratory cost ($2.11 vs. $3.23 per test). CONCLUSIONS This study demonstrates that SBEAVM is a rapid, inexpensive, and accurate method for use in VRE screening.
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Affiliation(s)
- Tsi-Shu Huang
- Division of Microbiology, Department of pathology and laboratory medicine, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Susan Shin-Jung Lee
- Division of Microbiology, Department of pathology and laboratory medicine, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
- Division of Infectious Diseases, Department of Internal Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
- School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Chia-Chien Lee
- Division of Microbiology, Department of pathology and laboratory medicine, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Chiu-Yen Chen
- Department of Nursing, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Fang-Chen Chen
- Department of Nursing, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
- Infection Control Unit, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Bao-Chen Chen
- Division of Microbiology, Department of pathology and laboratory medicine, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Cheng Len Sy
- Division of Infectious Diseases, Department of Internal Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Kuan-Sheng Wu
- Division of Infectious Diseases, Department of Internal Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
- School of Medicine, National Yang-Ming University, Taipei, Taiwan
- * E-mail:
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Kim HJ, Kim YJ, Yong DE, Lee K, Park JH, Lee JM, Yoon SS. Loop-mediated isothermal amplification of vanA gene enables a rapid and naked-eye detection of vancomycin-resistant enterococci infection. J Microbiol Methods 2014; 104:61-6. [PMID: 24925601 DOI: 10.1016/j.mimet.2014.05.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 05/29/2014] [Accepted: 05/29/2014] [Indexed: 11/26/2022]
Abstract
Vancomycin-resistant enterococci (VRE) are one of the leading causes of nosocomial infection at intensive care unit (ICU). A rapid and sensitive detection of VRE infection is in high demand for timely and suitable antibiotic treatment. Here, we optimized a distinct DNA-based diagnostic technique, loop-mediated isothermal amplification (LAMP) for a rapid detection of the presence of vanA gene, a critical component of the gene cluster required for vancomycin resistance. Amplification efficiency was optimal at 62°C and with 2mM MgSO4. The detection limit of the DNA template was 80pg and LAMP amplicons were detected within 40min; thereby suggesting a potential applicability of LAMP as a sensitive and urgent diagnostic method. Furthermore, positive LAMP reaction was directly detected with the naked-eye by monitoring the formation of a white precipitate or the color change induced by hydroxy naphthol blue (HNB) dye. Finally, 56 clinical isolates were successfully tested for the presence of vanA gene by LAMP, which was determined to be more sensitive than PCR. Together, our results clearly demonstrate the usefulness of LAMP for the diagnosis of VRE infection.
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Affiliation(s)
- Hye Jin Kim
- Department of Microbiology and Immunology, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Yu Jin Kim
- Department of Microbiology and Immunology, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Dong Eun Yong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Kyungwon Lee
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jeon Han Park
- Department of Microbiology and Immunology, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea; Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jae Myun Lee
- Department of Microbiology and Immunology, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea; Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, Republic of Korea.
| | - Sang Sun Yoon
- Department of Microbiology and Immunology, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea; Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, Republic of Korea.
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Prevalence of Vancomycin-resistant Enterococci Colonization, and Susceptibility to linezolid in Pediatric Intensive Care Units of a Referral Pediatric Center in Tehran, Iran. ARCHIVES OF PEDIATRIC INFECTIOUS DISEASES 2014. [DOI: 10.5812/pedinfect.16970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Penas PP, Mayer MP, Gomes BP, Endo M, Pignatari AC, Bauab KC, Pinheiro ET. Analysis of Genetic Lineages and Their Correlation with Virulence Genes in Enterococcus faecalis Clinical Isolates from Root Canal and Systemic Infections. J Endod 2013; 39:858-64. [DOI: 10.1016/j.joen.2013.01.009] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Revised: 01/21/2013] [Accepted: 01/30/2013] [Indexed: 10/27/2022]
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Nosocomial bloodstream infections in Brazilian hospitals: analysis of 2,563 cases from a prospective nationwide surveillance study. J Clin Microbiol 2011; 49:1866-71. [PMID: 21411591 DOI: 10.1128/jcm.00376-11] [Citation(s) in RCA: 142] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Nosocomial bloodstream infections (nBSIs) are an important cause of morbidity and mortality. Data from a nationwide, concurrent surveillance study, Brazilian SCOPE (Surveillance and Control of Pathogens of Epidemiological Importance), were used to examine the epidemiology and microbiology of nBSIs at 16 Brazilian hospitals. In our study 2,563 patients with nBSIs were included from 12 June 2007 to 31 March 2010. Ninety-five percent of BSIs were monomicrobial. Gram-negative organisms caused 58.5% of these BSIs, Gram-positive organisms caused 35.4%, and fungi caused 6.1%. The most common pathogens (monomicrobial) were Staphylococcus aureus (14.0%), coagulase-negative staphylococci (CoNS) (12.6%), Klebsiella spp. (12.0%), and Acinetobacter spp. (11.4%). The crude mortality was 40.0%. Forty-nine percent of nBSIs occurred in the intensive-care unit (ICU). The most frequent underlying conditions were malignancy, in 622 patients (24.3%). Among the potential factors predisposing patients to BSI, central venous catheters were the most frequent (70.3%). Methicillin resistance was detected in 157 S. aureus isolates (43.7%). Of the Klebsiella sp. isolates, 54.9% were resistant to third-generation cephalosporins. Of the Acinetobacter spp. and Pseudomonas aeruginosa isolates, 55.9% and 36.8%, respectively, were resistant to imipenem. In our multicenter study, we found high crude mortality and a high proportion of nBSIs due to antibiotic-resistant organisms.
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