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Bell SFE, Ware RS, Lewis DA, Lahra MM, Whiley DM. Antimicrobial susceptibility assays for Neisseria gonorrhoeae: a proof-of-principle population-based retrospective analysis. THE LANCET. MICROBE 2023; 4:e544-e551. [PMID: 37336225 DOI: 10.1016/s2666-5247(23)00071-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 12/09/2022] [Accepted: 02/17/2023] [Indexed: 06/21/2023]
Abstract
BACKGROUND Neisseria gonorrhoeae treatment guided by molecular antimicrobial susceptibility assays could improve treatment options and antimicrobial stewardship; however, few commercial assays are available. We aimed to investigate antimicrobial susceptibility of N gonorrhoeae isolates in New South Wales, Australia, and estimate the potential usefulness of hypothetical combinations of rapid molecular antimicrobial susceptibility assays. METHODS In this proof-of-principle, population-based, retrospective analysis, we assessed N gonorrhoeae susceptibility data for ceftriaxone, azithromycin, ciprofloxacin, and penicillin. Isolates were previously collected as part of the Australian Gonococcal Surveillance Programme between Jan 1, 2008, and Dec 31, 2019. All cultured N gonorrhoeae isolates with susceptibility data to all four antimicrobials were included. However, only one isolate was included if several isolates originated from the same individual within 13 days of the previous isolate originating from that individual, and there were less than two standard double-dilution minimum inhibitory concentrations between the isolates. We assessed the use of different combinations of hypothetical antimicrobial susceptibility assays and treatment combinations in terms of their ability to minimise overall ceftriaxone use, and use specifically in isolates with decreased susceptibility to ceftriaxone, compared with standard non-assay-guided empirical ceftriaxone treatment. FINDINGS We included 23 089 N gonorrhoeae isolates. The prevalence of antimicrobial sensitivity fluctuated significantly during the study. Isolates with decreased susceptibility to ceftriaxone were more likely to be resistant to one or more antimicrobials than isolates without decreased susceptibility (782 [98·6%] of 793 vs 10 661 [47·8%] of 22 296), particularly ciprofloxacin (p<0·0001) and penicillin (p<0·0001). Compared with empirical ceftriaxone treatment, we estimated that strategies based on the use of hypothetical antimicrobial susceptibility would reduce ceftriaxone use (p<0·0001). However, because of co-resistance, most assay-directed treatment strategies, including those involving use of assays for two antibiotics, would result in only moderate reductions in ceftriaxone use among isolates with decreased susceptibility to ceftriaxone. INTERPRETATION Individualised treatment guided by molecular antimicrobial susceptibility diagnostics could help to reduce overall ceftriaxone use in gonorrhoea. However, the use of these assays needs to be informed by the non-random nature of co-resistance among circulating N gonorrhoeae strains. FUNDING Australian Government and Queensland Government.
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Affiliation(s)
- Sara F E Bell
- Centre for Clinical Research, The University of Queensland, Royal Brisbane and Women's Hospital, Herston, QLD, Australia.
| | - Robert S Ware
- Menzies Health Institute Queensland and School of Medicine and Dentistry, Griffith University, Nathan, QLD, Australia
| | - David A Lewis
- Western Sydney Sexual Health Centre, Parramatta, NSW, Australia; Westmead Clinical School, Faculty of Medicine and Health and Sydney Institute for Infectious Diseases, University of Sydney, Westmead, NSW, Australia
| | - Monica M Lahra
- WHO Collaborating Centre for STI and AMR, NSW Health Pathology Microbiology, Prince of Wales Hospital, Randwick, NSW, Australia
| | - David M Whiley
- Centre for Clinical Research, The University of Queensland, Royal Brisbane and Women's Hospital, Herston, QLD, Australia.
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Rapid Detection of MCR-Mediated Colistin Resistance in Escherichia coli. Microbiol Spectr 2022; 10:e0092022. [PMID: 35616398 PMCID: PMC9241874 DOI: 10.1128/spectrum.00920-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Colistin is one of the last-resort antibiotics for infections caused by multidrug-resistant Gram-negative bacteria. However, the wide spread of novel plasmid-carrying colistin resistance genes mcr-1 and its variants substantially compromise colistin's therapeutic effectiveness and pose a severe danger to public health. To detect colistin-resistant microorganisms induced by mcr genes, rapid and reliable antibiotic susceptibility testing (AST) is imminently needed. In this study, we identified an RNA-based AST (RBAST) to discriminate between colistin-susceptible and mcr-1-mediated colistin-resistant bacteria. After short-time colistin treatment, RBAST can detect differentially expressed RNA biomarkers in bacteria. Those candidate mRNA biomarkers were successfully verified within colistin exposure temporal shifts, concentration shifts, and other mcr-1 variants. Furthermore, a group of clinical strains were effectively distinguished by using the RBAST approach during the 3-h test duration with over 93% accuracy. Taken together, our findings imply that certain mRNA transcripts produced in response to colistin treatment might be useful indicators for the development of fast AST for mcr-positive bacteria. IMPORTANCE The emergence and prevalence of mcr-1 and its variants in humans, animals, and the environment pose a global public health threat. There is a pressing urgency to develop rapid and accurate methods to identify MCR-positive colistin-resistant bacteria in the clinical samples, providing a basis for subsequent effective antibiotic treatment. Using the specific mRNA signatures, we develop an RNA-based antibiotic susceptibility testing (RBAST) for effectively distinguishing colistin-susceptible and mcr-1-mediated colistin-resistant strains. Meanwhile, the detection efficiency of these RNA biomarkers was evidenced in other mcr variants-carrying strains. By comparing with the traditional AST method, the RBAST method was verified to successfully characterize a set of clinical isolates during 3 h assay time with over 93% accuracy. Our study provides a feasible method for the rapid detection of colistin-resistant strains in clinical practice.
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Waskito LA, Rezkitha YAA, Vilaichone RK, Wibawa IDN, Mustika S, Sugihartono T, Miftahussurur M. Antimicrobial Resistance Profile by Metagenomic and Metatranscriptomic Approach in Clinical Practice: Opportunity and Challenge. Antibiotics (Basel) 2022; 11:antibiotics11050654. [PMID: 35625299 PMCID: PMC9137939 DOI: 10.3390/antibiotics11050654] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/29/2022] [Accepted: 05/09/2022] [Indexed: 01/15/2023] Open
Abstract
The burden of bacterial resistance to antibiotics affects several key sectors in the world, including healthcare, the government, and the economic sector. Resistant bacterial infection is associated with prolonged hospital stays, direct costs, and costs due to loss of productivity, which will cause policy makers to adjust their policies. Current widely performed procedures for the identification of antibiotic-resistant bacteria rely on culture-based methodology. However, some resistance determinants, such as free-floating DNA of resistance genes, are outside the bacterial genome, which could be potentially transferred under antibiotic exposure. Metagenomic and metatranscriptomic approaches to profiling antibiotic resistance offer several advantages to overcome the limitations of the culture-based approach. These methodologies enhance the probability of detecting resistance determinant genes inside and outside the bacterial genome and novel resistance genes yet pose inherent challenges in availability, validity, expert usability, and cost. Despite these challenges, such molecular-based and bioinformatics technologies offer an exquisite advantage in improving clinicians’ diagnoses and the management of resistant infectious diseases in humans. This review provides a comprehensive overview of next-generation sequencing technologies, metagenomics, and metatranscriptomics in assessing antimicrobial resistance profiles.
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Affiliation(s)
- Langgeng Agung Waskito
- Department of Internal Medicine, Faculty of Medicine, Universitas Airlangga, Surabaya 60132, Indonesia;
- Helicobacter pylori and Microbiota Study Group, Institute of Tropical Diseases, Universitas Airlangga, Surabaya 60115, Indonesia;
- Department of Physiology and Medical Biochemistry, Faculty of Medicine, Universitas Airlangga, Surabaya 60132, Indonesia
| | - Yudith Annisa Ayu Rezkitha
- Helicobacter pylori and Microbiota Study Group, Institute of Tropical Diseases, Universitas Airlangga, Surabaya 60115, Indonesia;
- Department of Internal Medicine, Faculty of Medicine, Universitas Muhammadiyah Surabaya, Surabaya 60115, Indonesia
| | - Ratha-korn Vilaichone
- Gastroenterology Unit, Department of Medicine, Faculty of Medicine, Thammasat University Hospital, Khlong Nueng 12120, Pathumthani, Thailand;
- Digestive Diseases Research Center (DRC), Thammasat University, Khlong Nueng 12121, Pathumthani, Thailand
- Department of Medicine, Chulabhorn International College of Medicine (CICM), Thammasat University, Khlong Nueng 12121, Pathumthani, Thailand
- Division of Gastroentero-Hepatology, Department of Internal Medicine, Faculty of Medicine, Dr. Soetomo Teaching Hospital, Universitas Airlangga, Surabaya 60286, Indonesia;
| | - I Dewa Nyoman Wibawa
- Division of Gastroentero-Hepatology, Department of Internal Medicine, Sanglah General Hospital, Faculty of Medicine, Universitas Udayana, Denpasar 80232, Indonesia;
| | - Syifa Mustika
- Division of Gastroentero-Hepatology, Department of Internal Medicine, Dr. Saiful Anwar Hospital, Malang 65112, Indonesia;
| | - Titong Sugihartono
- Division of Gastroentero-Hepatology, Department of Internal Medicine, Faculty of Medicine, Dr. Soetomo Teaching Hospital, Universitas Airlangga, Surabaya 60286, Indonesia;
| | - Muhammad Miftahussurur
- Helicobacter pylori and Microbiota Study Group, Institute of Tropical Diseases, Universitas Airlangga, Surabaya 60115, Indonesia;
- Division of Gastroentero-Hepatology, Department of Internal Medicine, Faculty of Medicine, Dr. Soetomo Teaching Hospital, Universitas Airlangga, Surabaya 60286, Indonesia;
- Correspondence: ; Tel.: +62-31-502-3865; Fax: +62-31-502-3865
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Hsieh K, Melendez JH, Gaydos CA, Wang TH. Bridging the gap between development of point-of-care nucleic acid testing and patient care for sexually transmitted infections. LAB ON A CHIP 2022; 22:476-511. [PMID: 35048928 PMCID: PMC9035340 DOI: 10.1039/d1lc00665g] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
The incidence rates of sexually transmitted infections (STIs), including the four major curable STIs - chlamydia, gonorrhea, trichomoniasis and, syphilis - continue to increase globally, causing medical cost burden and morbidity especially in low and middle-income countries (LMIC). There have seen significant advances in diagnostic testing, but commercial antigen-based point-of-care tests (POCTs) are often insufficiently sensitive and specific, while near-point-of-care (POC) instruments that can perform sensitive and specific nucleic acid amplification tests (NAATs) are technically complex and expensive, especially for LMIC. Thus, there remains a critical need for NAAT-based STI POCTs that can improve diagnosis and curb the ongoing epidemic. Unfortunately, the development of such POCTs has been challenging due to the gap between researchers developing new technologies and healthcare providers using these technologies. This review aims to bridge this gap. We first present a short introduction of the four major STIs, followed by a discussion on the current landscape of commercial near-POC instruments for the detection of these STIs. We present relevant research toward addressing the gaps in developing NAAT-based STI POCT technologies and supplement this discussion with technologies for HIV and other infectious diseases, which may be adapted for STIs. Additionally, as case studies, we highlight the developmental trajectory of two different POCT technologies, including one approved by the United States Food and Drug Administration (FDA). Finally, we offer our perspectives on future development of NAAT-based STI POCT technologies.
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Affiliation(s)
- Kuangwen Hsieh
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
| | - Johan H Melendez
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Charlotte A Gaydos
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Tza-Huei Wang
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, USA
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5
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Melendez JH, Chen FE, Wang TH. Antimicrobial susceptibility testing of Neisseria gonorrhoeae using a phenotypic-molecular assay and lyophilized antimicrobials. Diagn Microbiol Infect Dis 2022; 102:115590. [PMID: 34871932 PMCID: PMC9241851 DOI: 10.1016/j.diagmicrobio.2021.115590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 10/19/2021] [Accepted: 10/24/2021] [Indexed: 02/03/2023]
Abstract
Gonorrhea is an urgent global public health threat as Neisseria gonorrhoeae (Ng) has progressively developed resistance to all antibiotics commonly used for treatment. Surveillance of antimicrobial susceptibility trends is critical to monitor the emergence and spread of antimicrobial resistance. The gold standard methods for antimicrobial susceptibility testing (AST) of Ng are laborious and time-consuming. We evaluated a phenotypic molecular approach, involving a short cultivation step and quantitative PCR, with lyophilized antimicrobials to characterize antimicrobial susceptibility in Ng. There was excellent concordance between AST performed with liquid and lyophilized ciprofloxacin, penicillin, and tetracycline using the pheno-molecular assay, following a 4-hour incubation step. The categorical agreement between the pheno-molecular assay and the gold standard AST results was 92.4% for characterization of antimicrobial susceptibility. Essential agreement between the 2 methods was 91.9%. Characterization of ceftriaxone susceptibility in Ng using the pheno-molecular assay required a 6-hour incubation step.
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Affiliation(s)
- Johan H. Melendez
- Division of Infectious Diseases, School of Medicine, Johns Hopkins University, Baltimore, MD 21205
| | - Fan-En Chen
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218
| | - Tza-Huei Wang
- Division of Infectious Diseases, School of Medicine, Johns Hopkins University, Baltimore, MD 21205.,Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218,Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218
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Golparian D, Unemo M. Antimicrobial resistance prediction in Neisseria gonorrhoeae: Current status and future prospects. Expert Rev Mol Diagn 2021; 22:29-48. [PMID: 34872437 DOI: 10.1080/14737159.2022.2015329] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Several nucleic acid amplification tests (NAATs), mostly real-time PCRs, to detect antimicrobial resistance (AMR) determinants and predict AMR in Neisseria gonorrhoeae are promising, and some may be ready to apply at the point-of-care (POC), but important limitations remain with most NAATs. Next-generation sequencing (NGS) can overcome many of these limitations.Areas covered: Recent advances, with main focus on publications since 2017, in the development and use of NAATs and NGS to predict gonococcal AMR for surveillance and clinical use, and pros and cons of these tests as well as future perspectives for appropriate use of molecular AMR prediction for N. gonorrhoeae.Expert Commentary: NAATs and/or NGS for AMR prediction should supplement culture-based AMR surveillance, which will remain because it detects also AMR due to unknown AMR determinants, and translation into POC tests is imperative for the end-goal of individualized treatment, sparing ceftriaxone±azithromycin. Several challenges for direct testing of clinical, especially pharyngeal, specimens and for accurate prediction of cephalosporins and azithromycin resistance, especially using NAATs, remain. The choice of AMR prediction assay needs to carefully consider the intended use of the assay; limitations intrinsic to the AMR prediction technology, algorithms and specific to chosen methodology; specimen types analyzed; and cost-effectiveness.
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Affiliation(s)
- Daniel Golparian
- WHO Collaborating Centre for Gonorrhoea and other STIs, National Reference Laboratory for STIs, Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Magnus Unemo
- WHO Collaborating Centre for Gonorrhoea and other STIs, National Reference Laboratory for STIs, Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
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Unemo M, Lahra MM, Escher M, Eremin S, Cole MJ, Galarza P, Ndowa F, Martin I, Dillon JAR, Galas M, Ramon-Pardo P, Weinstock H, Wi T. WHO global antimicrobial resistance surveillance for Neisseria gonorrhoeae 2017-18: a retrospective observational study. THE LANCET. MICROBE 2021; 2:e627-e636. [PMID: 35544082 DOI: 10.1016/s2666-5247(21)00171-3] [Citation(s) in RCA: 113] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 05/27/2021] [Accepted: 06/16/2021] [Indexed: 01/13/2023]
Abstract
BACKGROUND Gonorrhoea and antimicrobial resistance (AMR) in Neisseria gonorrhoeae are major health concerns globally. Increased global surveillance of gonococcal AMR is essential. We aimed to describe the 2017-18 data from WHO's global gonococcal AMR surveillance, and to discuss priorities essential for the effective management and control of gonorrhoea. METHODS We did a retrospective observational study of the AMR data of gonococcal isolates reported to WHO by 73 countries in 2017-18. WHO recommends that each country collects at least 100 gonococcal isolates per year, and that quantitative methods to determine the minimum inhibitory concentration of antimicrobials, interpreted by internationally standardised resistance breakpoints, are used. FINDINGS In 2017-18, 73 countries provided AMR data for one or more drug. Decreased susceptibility or resistance to ceftriaxone was reported by 21 (31%) of 68 reporting countries and to cefixime by 24 (47%) of 51 reporting countries. Resistance to azithromycin was reported by 51 (84%) of 61 reporting countries and to ciprofloxacin by all 70 (100%) reporting countries. The annual proportion of decreased susceptibility or resistance across countries was 0-21% to ceftriaxone and 0-22% to cefixime, and that of resistance was 0-60% to azithromycin and 0-100% to ciprofloxacin. The number of countries reporting gonococcal AMR and resistant isolates, and the number of examined isolates, have increased since 2015-16. Surveillance remains scarce in central America and the Caribbean and eastern Europe, and in the WHO African, Eastern Mediterranean, and South-East Asian regions. INTERPRETATION In many countries, ciprofloxacin resistance was exceedingly high, azithromycin resistance was increasing, and decreased susceptibility or resistance to ceftriaxone and cefixime continued to emerge. WHO's global surveillance of gonococcal AMR needs to expand internationally to provide imperative data for national and international management guidelines and public health policies. Improved prevention, early diagnosis, treatment of index patients and partners, enhanced surveillance (eg, infection, AMR, treatment failures, and antimicrobial use or misuse), and increased knowledge on antimicrobial selection, stewardship, and pharmacokinetics or pharmacodynamics are essential. The development of rapid, accurate, and affordable point-of-care gonococcal diagnostic tests, new antimicrobials, and gonococcal vaccines is imperative. FUNDING None.
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Affiliation(s)
- Magnus Unemo
- WHO Collaborating Centre for Gonorrhoea and Other STIs, Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden.
| | - Monica M Lahra
- WHO Collaborating Centre for Sexually Transmitted Infections and Antimicrobial Resistance, New South Wales Health Pathology, Microbiology, Randwick, NSW, Australia
| | - Martina Escher
- Department of the Global HIV, Hepatitis and STI programmes, WHO, Geneva, Switzerland
| | - Sergey Eremin
- Surveillance, Evidence and Laboratory Strengthening, Antimicrobial Resistance Division, WHO, Geneva, Switzerland
| | - Michelle J Cole
- National Infection Service, Public Health England, London, UK
| | - Patricia Galarza
- WHO Collaborating Centre for Antimicrobial Resistance, National Reference Laboratory for STDs, National Institute of Infectious Diseases-ANLIS Dr Carlos G Malbrán, Buenos Aires, Argentina
| | - Francis Ndowa
- Skin and Genitourinary Medicine Clinic, Harare, Zimbabwe
| | - Irene Martin
- Public Health Agency of Canada, National Microbiology Laboratory, Winnipeg, MB, Canada
| | - Jo-Anne R Dillon
- Vaccine and Infecious Disease Organization-International Vaccine Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Marcelo Galas
- Communicable Diseases and Environmental Determinants of Health, Pan American Health Organization, Washington, DC, USA
| | - Pilar Ramon-Pardo
- Communicable Diseases and Environmental Determinants of Health, Pan American Health Organization, Washington, DC, USA
| | - Hillard Weinstock
- Division of STD Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Teodora Wi
- Department of the Global HIV, Hepatitis and STI programmes, WHO, Geneva, Switzerland
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Arumugam A, Markham C, Aykar SS, Van Der Pol B, Dixon P, Wu M, Wong S. PrintrLab incubator: A portable and low-cost CO2 incubator based on an open-source 3D printer architecture. PLoS One 2021; 16:e0251812. [PMID: 34077426 PMCID: PMC8172042 DOI: 10.1371/journal.pone.0251812] [Citation(s) in RCA: 1] [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: 10/27/2020] [Accepted: 05/03/2021] [Indexed: 11/18/2022] Open
Abstract
Growth in open-source hardware designs combined with the decreasing cost of high-quality 3D printers have supported a resurgence of in-house custom lab equipment development. Herein, we describe a low-cost (< $400), open-source CO2 incubator. The system is comprised of a Raspberry Pi computer connected to a 3D printer controller board that has controls for a CO2 sensor, solenoid valve, heater, and thermistors. CO2 is supplied through the sublimation of dry ice stored inside a thermos to create a sustained 5% CO2 supply. The unit is controlled via G-Code commands sent by the Raspberry Pi to the controller board. In addition, we built a custom software application for remote control and used the open-source Grafana dashboard for remote monitoring. Our data show that we can maintain consistent CO2 and temperature levels for over three days without manual interruption. The results from our culture plates and real-time PCR indicate that our incubator performed equally well when compared to a much more expensive commercial CO2 incubator. We have also demonstrated that the antibiotic susceptibility assay can be performed in this low-cost CO2 incubator. Our work also indicates that the system can be connected to incubator chambers of various chamber volumes.
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Affiliation(s)
| | - Cole Markham
- AI Biosciences, Inc., College Station, Texas, United States of America
| | | | - Barbara Van Der Pol
- University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Paula Dixon
- University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Michelle Wu
- AI Biosciences, Inc., College Station, Texas, United States of America
| | - Season Wong
- AI Biosciences, Inc., College Station, Texas, United States of America
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9
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Kost GJ. Geospatial Spread of Antimicrobial Resistance, Bacterial and Fungal Threats to Coronavirus Infectious Disease 2019 (COVID-19) Survival, and Point-of-Care Solutions. Arch Pathol Lab Med 2021; 145:145-167. [PMID: 32886738 DOI: 10.5858/arpa.2020-0284-ra] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/23/2020] [Indexed: 12/15/2022]
Abstract
CONTEXT.— Point-of-care testing (POCT) is inherently spatial, that is, performed where needed, and intrinsically temporal, because it accelerates decision-making. POCT efficiency and effectiveness have the potential to facilitate antimicrobial resistance (AMR) detection, decrease risks of coinfections for critically ill patients with coronavirus infectious disease 2019 (COVID-19), and improve the cost-effectiveness of health care. OBJECTIVES.— To assess AMR identification by using POCT, describe the United States AMR Diagnostic Challenge, and improve global standards of care for infectious diseases. DATA SOURCES.— PubMed, World Wide Web, and other sources were searched for papers focusing on AMR and POCT. EndNote X9.1 (Clarivate Analytics) consolidated abstracts, URLs, and PDFs representing approximately 500 articles were assessed for relevance. Panelist insights at Tri•Con 2020 in San Francisco and finalist POC technologies competing for a US $20,000,000 AMR prize are summarized. CONCLUSIONS.— Coinfections represent high risks for COVID-19 patients. POCT potentially will help target specific pathogens, refine choices for antimicrobial drugs, and prevent excess morbidity and mortality. POC assays that identify patterns of pathogen resistance can help tell us how infected individuals spread AMR, where geospatial hotspots are located, when delays cause death, and how to deploy preventative resources. Shared AMR data "clouds" could help reduce critical care burden during pandemics and optimize therapeutic options, similar to use of antibiograms in individual hospitals. Multidisciplinary health care personnel should learn the principles and practice of POCT, so they can meet needs with rapid diagnostic testing. The stakes are high. Antimicrobial resistance is projected to cause millions of deaths annually and cumulative financial loses in the trillions by 2050.
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Affiliation(s)
- Gerald J Kost
- From Knowledge Optimization, Davis, California; and Point-of-Care Testing Center for Teaching and Research (POCT•CTR), University of California, Davis
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Al Suwayyid BA, Rankine-Wilson L, Speers DJ, Wise MJ, Coombs GW, Kahler CM. Meningococcal Disease-Associated Prophage-Like Elements Are Present in Neisseria gonorrhoeae and Some Commensal Neisseria Species. Genome Biol Evol 2020; 12:3938-3950. [PMID: 32031617 PMCID: PMC7058167 DOI: 10.1093/gbe/evaa023] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/04/2020] [Indexed: 12/14/2022] Open
Abstract
Neisseria spp. possess four genogroups of filamentous prophages, termed Nf1 to 4. A filamentous bacteriophage from the Nf1 genogroup termed meningococcal disease-associated phage (MDA φ) is associated with clonal complexes of Neisseria meningitidis that cause invasive meningococcal disease. Recently, we recovered an isolate of Neisseria gonorrhoeae (ExNg63) from a rare case of gonococcal meningitis, and found that it possessed a region with 90% similarity to Nf1 prophages, specifically, the meningococcal MDA φ. This led to the hypothesis that the Nf1 prophage may be more widely distributed amongst the genus Neisseria. An analysis of 92 reference genomes revealed the presence of intact Nf1 prophages in the commensal species, Neisseria lactamica and Neisseria cinerea in addition to the pathogen N. gonorrhoeae. In N. gonorrhoeae, Nf1 prophages had a restricted distribution but were present in all representatives of MLST ST1918. Of the 160 phage integration sites identified, only one common insertion site was found between one isolate of N. gonorrhoeae and N. meningitidis. There was an absence of any obvious conservation of the receptor for prophage entry, PilE, suggesting that the phage may have been obtained by natural transformation. An examination of the restriction modification systems and mutated mismatch repair systems with prophage presence suggested that there was no obvious preference for these hosts. A timed phylogeny inferred that N. meningitidis was the donor of the Nf1 prophages in N. lactamica and N. gonorrhoeae. Further work is required to determine whether Nf1 prophages are active and can act as accessory colonization factors in these species.
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Affiliation(s)
- Barakat A Al Suwayyid
- The Marshall Centre for Infectious Diseases Research and Training, The University of Western Australia, Crawley, Australia.,School of Biomedical Sciences, The University of Western Australia, Crawley, Australia.,Ministry of Education, Riyadh, Saudi Arabia
| | - Leah Rankine-Wilson
- The Marshall Centre for Infectious Diseases Research and Training, The University of Western Australia, Crawley, Australia.,School of Biomedical Sciences, The University of Western Australia, Crawley, Australia
| | - David J Speers
- Department of Microbiology, PathWest Laboratory Medicine WA, Queen Elizabeth II Medical Centre, Nedlands, Australia.,School of Medicine and Pharmacology, University of Western Australia, Crawley, Australia
| | - Michael J Wise
- The Marshall Centre for Infectious Diseases Research and Training, The University of Western Australia, Crawley, Australia.,Computer Science and Software Engineering, The University of Western Australia, Crawley, Australia
| | - Geoffrey W Coombs
- Department of Microbiology, PathWest Laboratory Medicine WA, Fiona Stanley Hospital, Murdoch, Australia.,Antimicrobial Resistance and Infectious Diseases Research Laboratory, School of Veterinary Life Sciences, Murdoch University, Australia
| | - Charlene M Kahler
- The Marshall Centre for Infectious Diseases Research and Training, The University of Western Australia, Crawley, Australia.,School of Biomedical Sciences, The University of Western Australia, Crawley, Australia
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A Novel Platform Using RNA Signatures To Accelerate Antimicrobial Susceptibility Testing in Neisseria gonorrhoeae. J Clin Microbiol 2020; 58:JCM.01152-20. [PMID: 32967905 DOI: 10.1128/jcm.01152-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 09/09/2020] [Indexed: 12/27/2022] Open
Abstract
The rise of antimicrobial-resistant pathogens can be attributed to the lack of a rapid pathogen identification (ID) or antimicrobial susceptibility testing (AST), resulting in delayed therapeutic decisions at the point of care. Gonorrhea is usually empirically treated, with no AST results available before treatment, thus contributing to the rapid rise in drug resistance. Here, we present a rapid AST platform using RNA signatures for Neisseria gonorrhoeae Transcriptome sequencing (RNA-seq) followed by bioinformatic tools was applied to explore potential markers in the transcriptome profile of N. gonorrhoeae upon minutes of azithromycin exposure. Validation of candidate markers using quantitative real-time PCR (qRT-PCR) showed that two markers (arsR [NGO1562] and rpsO) can deliver accurate AST results across 14 tested isolates. Further validation of our susceptibility threshold in comparison to MIC across 64 more isolates confirmed the reliability of our platform. Our RNA markers combined with emerging molecular point-of-care systems has the potential to greatly accelerate both ID and AST to inform treatment.
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Zhu Z, Surujon D, Ortiz-Marquez JC, Huo W, Isberg RR, Bento J, van Opijnen T. Entropy of a bacterial stress response is a generalizable predictor for fitness and antibiotic sensitivity. Nat Commun 2020; 11:4365. [PMID: 32868761 PMCID: PMC7458919 DOI: 10.1038/s41467-020-18134-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 08/06/2020] [Indexed: 02/07/2023] Open
Abstract
Current approaches explore bacterial genes that change transcriptionally upon stress exposure as diagnostics to predict antibiotic sensitivity. However, transcriptional changes are often specific to a species or antibiotic, limiting implementation to known settings only. While a generalizable approach, predicting bacterial fitness independent of strain, species or type of stress, would eliminate such limitations, it is unclear whether a stress-response can be universally captured. By generating a multi-stress and species RNA-Seq and experimental evolution dataset, we highlight the strengths and limitations of existing gene-panel based methods. Subsequently, we build a generalizable method around the observation that global transcriptional disorder seems to be a common, low-fitness, stress response. We quantify this disorder using entropy, which is a specific measure of randomness, and find that in low fitness cases increasing entropy and transcriptional disorder results from a loss of regulatory gene-dependencies. Using entropy as a single feature, we show that fitness and quantitative antibiotic sensitivity predictions can be made that generalize well beyond training data. Furthermore, we validate entropy-based predictions in 7 species under antibiotic and non-antibiotic conditions. By demonstrating the feasibility of universal predictions of bacterial fitness, this work establishes the fundamentals for potentially new approaches in infectious disease diagnostics.
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Affiliation(s)
- Zeyu Zhu
- Biology Department, Boston College, Chestnut Hill, MA, 02467, USA
| | - Defne Surujon
- Biology Department, Boston College, Chestnut Hill, MA, 02467, USA
| | | | - Wenwen Huo
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, 02111, USA
| | - Ralph R Isberg
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, 02111, USA
| | - José Bento
- Computer Science Department, Boston College, Chestnut Hill, MA, 02467, USA
| | - Tim van Opijnen
- Biology Department, Boston College, Chestnut Hill, MA, 02467, USA.
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Abstract
INTRODUCTION Point-of-care (POC) tests for Neisseria gonorrhoeae (Ng) are urgently needed to control the gonorrhea epidemic, so patients can receive immediate diagnoses and treatment. While the advent of nucleic acid amplification tests (NAATs) has improved the accuracy of Ng identification, very few POC assays are able to provide results of such tests at the clinical visit. Additionally, antimicrobial resistance (AMR) presents a unique treatment challenge for Ng. AREAS COVERED This review notes that older POC tests have lower sensitivity for Ng, compared to the currently-available NAATs, and are not adequate for the current demand for high sensitivity. Promising newer assays, which can be used at the POC are covered. This review also includes data about clinicians' and patients' acceptability and expectations of POC tests for Ng, testing of extragenital specimens, pooling studies, as well as their impact clinically, and use in low-resource settings. EXPERT OPINION The ability to use POC tests to identify and immediately treat Ng infections at the patient encounter offers many benefits and opportunities. POC tests for Ng are currently available, but not widely used especially in low-resource settings. Further development of POC tests with AMR testing capacity is needed to help guide antimicrobial stewardship.
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Affiliation(s)
- Charlotte A Gaydos
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University , Baltimore, Maryland, USA
| | - Johan H Melendez
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University , Baltimore, Maryland, USA
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Rubin DHF, Ross JDC, Grad YH. The frontiers of addressing antibiotic resistance in Neisseria gonorrhoeae. Transl Res 2020; 220:122-137. [PMID: 32119845 PMCID: PMC7293957 DOI: 10.1016/j.trsl.2020.02.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 02/08/2020] [Accepted: 02/10/2020] [Indexed: 12/21/2022]
Abstract
The sexually transmitted infection gonorrhea, caused by the Gram-negative bacterium Neisseria gonorrhoeae, can cause urethritis, cervicitis, and systemic disease, among other manifestations. N. gonorrhoeae has rapidly rising incidence along with increasing levels of antibiotic resistance to a broad range of drugs including first-line treatments. The rise in resistance has led to fears of untreatable gonorrhea causing substantial disease globally. In this review, we will describe multiple approaches being undertaken to slow and control this spread of resistance. First, a number of old drugs have been repurposed and new drugs are being developed with activity against Neisseria gonorrhoeae. Second, vaccine development, long an important goal, is advancing. Third, new diagnostics promise rapid detection of antibiotic resistance and a shift from empiric to tailored treatment. The deployment of these new tools for addressing the challenge of antibiotic resistance will require careful consideration to provide optimal care for all patients while extending the lifespan of treatment regimens.
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Affiliation(s)
- Daniel H F Rubin
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts
| | - Jonathan D C Ross
- Department of Sexual Health and HIV, Birmingham University Hospitals NHS Foundation Trust, Birmingham, UK
| | - Yonatan H Grad
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts; Center for Communicable Disease Dynamics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts; Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts.
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15
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Genomic Characterization of Neisseria gonorrhoeae Strains from 2016 U.S. Sentinel Surveillance Displaying Reduced Susceptibility to Azithromycin. Antimicrob Agents Chemother 2020; 64:AAC.02420-19. [PMID: 32071056 DOI: 10.1128/aac.02420-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 02/12/2020] [Indexed: 11/20/2022] Open
Abstract
In 2016, the proportion of Neisseria gonorrhoeae isolates with reduced susceptibility to azithromycin rose to 3.6%. A phylogenetic analysis of 334 N. gonorrhoeae isolates collected in 2016 revealed a single, geographically diverse lineage of isolates with MICs of 2 to 16 μg/ml that carried a mosaic-like mtr locus, whereas the majority of isolates with MICs of ≥16 μg/ml appeared sporadically and carried 23S rRNA mutations. Continued molecular surveillance of N. gonorrhoeae isolates will identify new resistance mechanisms.
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Savela ES, Schoepp NG, Cooper MM, Rolando JC, Klausner JD, Soge OO, Ismagilov RF. Surfactant-enhanced DNA accessibility to nuclease accelerates phenotypic β-lactam antibiotic susceptibility testing of Neisseria gonorrhoeae. PLoS Biol 2020; 18:e3000651. [PMID: 32191696 PMCID: PMC7081974 DOI: 10.1371/journal.pbio.3000651] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Accepted: 02/14/2020] [Indexed: 11/19/2022] Open
Abstract
Rapid antibiotic susceptibility testing (AST) for Neisseria gonorrhoeae (Ng) is critically needed to counter widespread antibiotic resistance. Detection of nucleic acids in genotypic AST can be rapid, but it has not been successful for β-lactams (the largest antibiotic class used to treat Ng). Rapid phenotypic AST for Ng is challenged by the pathogen's slow doubling time and the lack of methods to quickly quantify the pathogen's response to β-lactams. Here, we asked two questions: (1) Is it possible to use nucleic acid quantification to measure the β-lactam susceptibility phenotype of Ng very rapidly, using antibiotic-exposure times much shorter than the 1- to 2-h doubling time of Ng? (2) Would such short-term antibiotic exposures predict the antibiotic resistance profile of Ng measured by plate growth assays over multiple days? To answer these questions, we devised an innovative approach for performing a rapid phenotypic AST that measures DNA accessibility to exogenous nucleases after exposure to β-lactams (termed nuclease-accessibility AST [nuc-aAST]). We showed that DNA in antibiotic-susceptible cells has increased accessibility upon exposure to β-lactams and that a judiciously chosen surfactant permeabilized the outer membrane and enhanced this effect. We tested penicillin, cefixime, and ceftriaxone and found good agreement between the results of the nuc-aAST after 15-30 min of antibiotic exposure and the results of the gold-standard culture-based AST measured over days. These results provide a new pathway toward developing a critically needed phenotypic AST for Ng and additional global-health threats.
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Affiliation(s)
- Emily S. Savela
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Nathan G. Schoepp
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Matthew M. Cooper
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Justin C. Rolando
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Jeffrey D. Klausner
- David Geffen School of Medicine, Division of Infectious Disease, University of California Los Angeles, Los Angeles, California, United States of America
| | - Olusegun O. Soge
- Neisseria Reference Laboratory, Department of Global Health, University of Washington, Seattle, Washington, United States of America
| | - Rustem F. Ismagilov
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, United States of America
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Palace SG, Wang Y, Rubin DHF, Welsh MA, Mortimer TD, Cole K, Eyre DW, Walker S, Grad YH. RNA polymerase mutations cause cephalosporin resistance in clinical Neisseria gonorrhoeae isolates. eLife 2020; 9:e51407. [PMID: 32011233 PMCID: PMC7012608 DOI: 10.7554/elife.51407] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 02/01/2020] [Indexed: 02/06/2023] Open
Abstract
Increasing Neisseria gonorrhoeae resistance to ceftriaxone, the last antibiotic recommended for empiric gonorrhea treatment, poses an urgent public health threat. However, the genetic basis of reduced susceptibility to ceftriaxone is not completely understood: while most ceftriaxone resistance in clinical isolates is caused by target site mutations in penA, some isolates lack these mutations. We show that penA-independent ceftriaxone resistance has evolved multiple times through distinct mutations in rpoB and rpoD. We identify five mutations in these genes that each increase resistance to ceftriaxone, including one mutation that arose independently in two lineages, and show that clinical isolates from multiple lineages are a single nucleotide change from ceftriaxone resistance. These RNA polymerase mutations cause large-scale transcriptional changes without altering susceptibility to other antibiotics, reducing growth rate, or deranging cell morphology. These results underscore the unexpected diversity of pathways to resistance and the importance of continued surveillance for novel resistance mutations.
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Affiliation(s)
- Samantha G Palace
- Department of Immunology and Infectious DiseasesHarvard T. H. Chan School of Public HealthBostonUnited States
- Center for Communicable Disease DynamicsHarvard T. H. Chan School of Public HealthBostonUnited States
| | - Yi Wang
- Department of Immunology and Infectious DiseasesHarvard T. H. Chan School of Public HealthBostonUnited States
| | - Daniel HF Rubin
- Department of Immunology and Infectious DiseasesHarvard T. H. Chan School of Public HealthBostonUnited States
| | - Michael A Welsh
- Department of MicrobiologyHarvard Medical SchoolBostonUnited States
| | - Tatum D Mortimer
- Department of Immunology and Infectious DiseasesHarvard T. H. Chan School of Public HealthBostonUnited States
| | - Kevin Cole
- Public Health England, Royal Sussex County HospitalBrightonUnited Kingdom
| | - David W Eyre
- Big Data Institute, University of OxfordOxfordUnited Kingdom
| | - Suzanne Walker
- Department of MicrobiologyHarvard Medical SchoolBostonUnited States
| | - Yonatan H Grad
- Department of Immunology and Infectious DiseasesHarvard T. H. Chan School of Public HealthBostonUnited States
- Center for Communicable Disease DynamicsHarvard T. H. Chan School of Public HealthBostonUnited States
- Division of Infectious DiseasesBrigham and Women’s Hospital, Harvard Medical SchoolBostonUnited States
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Meyer T, Buder S. The Laboratory Diagnosis of Neisseria gonorrhoeae: Current Testing and Future Demands. Pathogens 2020; 9:E91. [PMID: 32024032 PMCID: PMC7169389 DOI: 10.3390/pathogens9020091] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 01/28/2020] [Accepted: 01/29/2020] [Indexed: 02/05/2023] Open
Abstract
The ideal laboratory test to detect Neisseria gonorrhoeae (Ng) should be sensitive, specific, easy to use, rapid, and affordable and should provide information about susceptibility to antimicrobial drugs. Currently, such a test is not available and presumably will not be in the near future. Thus, diagnosis of gonococcal infections presently includes application of different techniques to address these requirements. Microscopy may produce rapid results but lacks sensitivity in many cases (except symptomatic urogenital infections in males). Highest sensitivity to detect Ng was shown for nucleic acid amplification technologies (NAATs), which, however, are less specific than culture. In addition, comprehensive analysis of antibiotic resistance is accomplished only by in vitro antimicrobial susceptibility testing of cultured isolates. As a light at the end of the tunnel, new developments of molecular techniques and microfluidic systems represent promising opportunities to design point-of-care tests for rapid detection of Ng with high sensitivity and specificity, and there is reason to hope that such tests may also provide antimicrobial resistance data in the future.
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Affiliation(s)
- Thomas Meyer
- Department of Dermatology, Venerology and Allergology, St. Josef Hospital, Ruhr-University, 44791 Bochum, Germany
| | - Susanne Buder
- German Consiliary Laboratory for Gonococci, Department of Dermatology and Venerology, Vivantes Hospital Berlin, 12351 Berlin, Germany;
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