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Singh SR, Tang CY, Mao B, Soeng S, Ling CL, Teo JQM, Vonthanak S, Turner P, Hsu LY, Ong RTH. Whole genome sequencing of multidrug resistant Enterobacterales identified in children and their household members within Siem Reap, Cambodia. JAC Antimicrob Resist 2023; 5:dlad067. [PMID: 37325250 PMCID: PMC10265595 DOI: 10.1093/jacamr/dlad067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 05/02/2023] [Indexed: 06/17/2023] Open
Abstract
Objectives To explore the association of recent hospitalization and asymptomatic carriage of multidrug-resistant Enterobacterales (MDRE) and determine the prevailing strains and antibiotic resistance genes in Siem Reap, Cambodia using WGS. Methods In this cross-sectional study, faecal samples were collected from two arms: a hospital-associated arm consisted of recently hospitalized children (2-14 years), with their family members; and a community-associated arm comprising children in the matching age group and their family members with no recent hospitalization. Forty-two families in each study arm were recruited, with 376 enrolled participants (169 adults and 207 children) and 290 stool specimens collected from participants. The DNA of ESBL- and carbapenemase-producing Enterobacterales cultured from the faecal samples was subject to WGS on the Illumina NovaSeq platform. Results Of the 290 stool specimens, 277 Escherichia coli isolates and 130 Klebsiella spp. were identified on CHROMagar ESBL and KPC plates. The DNA of 276 E. coli (one isolate failed quality control test), 89 Klebsiella pneumoniae, 40 Klebsiella quasipneumoniae and 1 Klebsiella variicola was sequenced. CTX-M-15 was the most common ESBL gene found in E. coli (n = 104, 38%), K. pneumoniae (n = 50, 56%) and K. quasipneumoniae (n = 16, 40%). The prevalence of bacterial lineages and ESBL genes was not associated with any specific arm. Conclusions Our results demonstrate that MDRE is likely to be endemic within the Siem Reap community. ESBL genes, specifically blaCTX-M, can be found in almost all E. coli commensals, indicating that these genes are continuously propagated in the community through various unknown channels at present.
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Affiliation(s)
- Shweta R Singh
- Saw Swee Hock School of Public Health, Tahir Foundation Building, National University of Singapore, Singapore
| | - Cheng Yee Tang
- Saw Swee Hock School of Public Health, Tahir Foundation Building, National University of Singapore, Singapore
| | - Bunsoth Mao
- University of Health Sciences, Phnom Penh, Cambodia
| | - Sona Soeng
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Clare L Ling
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | | | | | - Paul Turner
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Li Yang Hsu
- Saw Swee Hock School of Public Health, Tahir Foundation Building, National University of Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, NUHS Tower Block, National University of Singapore, Singapore
- Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore
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Gysin M, Hon PY, Tan P, Sengduangphachanh A, Simmalavong M, Hinfonthong P, Kaewphanderm N, Pham TD, Nguyen TH, Haldimann K, Becker K, van Doorn HR, Hopkins J, Simpson AJH, Ashley EA, Kesteman T, Tran HH, Vasoo S, Ling CL, Roberts T, Turner P, Hobbie SN. Apramycin susceptibility of multidrug-resistant Gram-negative blood culture isolates in five countries in Southeast Asia. Int J Antimicrob Agents 2022; 60:106659. [PMID: 35988665 DOI: 10.1016/j.ijantimicag.2022.106659] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 07/21/2022] [Accepted: 08/11/2022] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Bloodstream infections (BSIs) are a leading cause of sepsis, which is a life-threatening condition that significantly contributes to the mortality of bacterial infections. Aminoglycoside antibiotics such as gentamicin or amikacin are essential medicines in the treatment of BSIs, but their clinical efficacy is increasingly being compromised by antimicrobial resistance. The aminoglycoside apramycin has demonstrated preclinical efficacy against aminoglycoside-resistant and multidrug-resistant (MDR) Gram-negative bacilli (GNB) and is currently in clinical development for the treatment of critical systemic infections. METHODS This study collected a panel of 470 MDR GNB isolates from healthcare facilities in Cambodia, Laos, Singapore, Thailand and Vietnam for a multicentre assessment of their antimicrobial susceptibility to apramycin in comparison with other aminoglycosides and colistin by broth microdilution assays. RESULTS Apramycin and amikacin MICs ≤ 16 µg/mL were found for 462 (98.3%) and 408 (86.8%) GNB isolates, respectively. Susceptibility to gentamicin and tobramycin (MIC ≤ 4 µg/mL) was significantly lower at 122 (26.0%) and 101 (21.5%) susceptible isolates, respectively. Of note, all carbapenem and third-generation cephalosporin-resistant Enterobacterales, all Acinetobacter baumannii and all Pseudomonas aeruginosa isolates tested in this study appeared to be susceptible to apramycin. Of the 65 colistin-resistant isolates tested, four (6.2%) had an apramycin MIC > 16 µg/mL. CONCLUSION Apramycin demonstrated best-in-class activity against a panel of GNB isolates with resistances to other aminoglycosides, carbapenems, third-generation cephalosporins and colistin, warranting continued consideration of apramycin as a drug candidate for the treatment of MDR BSIs.
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Affiliation(s)
- Marina Gysin
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Pei Yun Hon
- National Centre for Infectious Diseases and Tan Tock Seng Hospital, Singapore
| | - Pisey Tan
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Amphonesavanh Sengduangphachanh
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
| | - Manivone Simmalavong
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
| | - Pattaraporn Hinfonthong
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Napaporn Kaewphanderm
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Thai Duy Pham
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Thanh Ha Nguyen
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Klara Haldimann
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Katja Becker
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - H Rogier van Doorn
- Oxford University Clinical Research Unit, Hanoi, Vietnam; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Jill Hopkins
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Andrew J H Simpson
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Elizabeth A Ashley
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Thomas Kesteman
- Oxford University Clinical Research Unit, Hanoi, Vietnam; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Hoang Huy Tran
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Shawn Vasoo
- National Centre for Infectious Diseases and Tan Tock Seng Hospital, Singapore
| | - Clare L Ling
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Tamalee Roberts
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Paul Turner
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.
| | - Sven N Hobbie
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.
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Roberts T, Chandna A, Watthanaworawit W, Thaiprakong A, Soeng S, Simmalavong M, Phoumin P, Saengchun W, Khatta N, Hinfonthong P, Kaewpundoem N, Lee SJ, Perrone C, Amos B, Turner P, Ashley EA, Ling CL. Impact of delayed processing of positive blood cultures on organism detection: a prospective multi-centre study. BMC Infect Dis 2022; 22:517. [PMID: 35659576 PMCID: PMC9167519 DOI: 10.1186/s12879-022-07504-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 05/26/2022] [Indexed: 11/10/2022] Open
Abstract
Background Blood cultures remain the gold standard investigation for the diagnosis of bloodstream infections. In many locations, quality-assured processing of positive blood cultures is not possible. One solution is to incubate blood cultures locally, and then transport bottles that flag positive to a central reference laboratory for organism identification and antimicrobial susceptibility testing. However, the impact of delay between the bottle flagging positive and subsequent sub-culture on the viability of the isolate has received little attention. Methods This study evaluated the impact of delays to sub-culture (22 h to seven days) in three different temperature conditions (2–8 °C, 22–27 °C and 35 ± 2 °C) for bottles that had flagged positive in automated detection systems using a mixture of spiked and routine clinical specimens. Ninety spiked samples for five common bacterial causes of sepsis (Escherichia coli, Haemophilus influenzae, Staphylococcus aureus, Streptococcus agalactiae and Streptococcus pneumoniae) and 125 consecutive positive clinical blood cultures were evaluated at four laboratories located in Cambodia, Lao PDR and Thailand. In addition, the utility of transport swabs for preserving organism viability was investigated. Results All organisms were recoverable from all sub-cultures in all temperature conditions with the exception of S. pneumoniae, which was less likely to be recoverable after longer delays (> 46–50 h), when stored in hotter temperatures (35 °C), and from BacT/ALERT when compared with BACTEC blood culture bottles. Storage of positive blood culture bottles in cooler temperatures (22–27 °C or below) and the use of Amies bacterial transport swabs helped preserve viability of S. pneumoniae. Conclusions These results have practical implications for the optimal workflow for blood culture bottles that have flagged positive in automated detection systems located remotely from a central processing laboratory, particularly in tropical resource-constrained contexts. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-022-07504-1.
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Dennis TPW, Mable BK, Brunelle B, Devault A, Carter RW, Ling CL, Mmbaga BT, Halliday JEB, Oravcova K, Forde TL. Target-enrichment sequencing yields valuable genomic data for challenging-to-culture bacteria of public health importance. Microb Genom 2022; 8. [PMID: 35622897 PMCID: PMC9465068 DOI: 10.1099/mgen.0.000836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Genomic data contribute invaluable information to the epidemiological investigation of pathogens of public health importance. However, whole-genome sequencing (WGS) of bacteria typically relies on culture, which represents a major hurdle for generating such data for a wide range of species for which culture is challenging. In this study, we assessed the use of culture-free target-enrichment sequencing as a method for generating genomic data for two bacterial species: (1) Bacillus anthracis, which causes anthrax in both people and animals and whose culture requires high-level containment facilities; and (2) Mycoplasma amphoriforme, a fastidious emerging human respiratory pathogen. We obtained high-quality genomic data for both species directly from clinical samples, with sufficient coverage (>15×) for confident variant calling over at least 80% of the baited genomes for over two thirds of the samples tested. Higher qPCR cycle threshold (Ct) values (indicative of lower pathogen concentrations in the samples), pooling libraries prior to capture, and lower captured library concentration were all statistically associated with lower capture efficiency. The Ct value had the highest predictive value, explaining 52 % of the variation in capture efficiency. Samples with Ct values ≤30 were over six times more likely to achieve the threshold coverage than those with a Ct > 30. We conclude that target-enrichment sequencing provides a valuable alternative to standard WGS following bacterial culture and creates opportunities for an improved understanding of the epidemiology and evolution of many clinically important pathogens for which culture is challenging.
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Affiliation(s)
- Tristan P. W. Dennis
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Barbara K. Mable
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | | | | | - Ryan W. Carter
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Clare L. Ling
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Blandina T. Mmbaga
- Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | - Jo E. B. Halliday
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Katarina Oravcova
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Taya L. Forde
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
- *Correspondence: Taya L. Forde,
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Vihta KD, Gordon NC, Stoesser N, Quan TP, Tyrrell CSB, Vongsouvath M, Ashley EA, Chansamouth V, Turner P, Ling CL, Eyre DW, White NJ, Crook D, Peto TEA, Walker AS. Antimicrobial resistance in commensal opportunistic pathogens isolated from non-sterile sites can be an effective proxy for surveillance in bloodstream infections. Sci Rep 2021; 11:23359. [PMID: 34862445 PMCID: PMC8642463 DOI: 10.1038/s41598-021-02755-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 11/23/2021] [Indexed: 11/10/2022] Open
Abstract
Antimicrobial resistance (AMR) surveillance in bloodstream infections (BSIs) is challenging in low/middle-income countries (LMICs) given limited laboratory capacity. Other specimens are easier to collect and process and are more likely to be culture-positive. In 8102 E. coli BSIs, 322,087 E. coli urinary tract infections, 6952 S. aureus BSIs and 112,074 S. aureus non-sterile site cultures from Oxfordshire (1998-2018), and other (55,296 isolates) rarer commensal opportunistic pathogens, antibiotic resistance trends over time in blood were strongly associated with those in other specimens (maximum cross-correlation per drug 0.51-0.99). Resistance prevalence was congruent across drug-years for each species (276/312 (88%) species-drug-years with prevalence within ± 10% between blood/other isolates). Results were similar across multiple countries in high/middle/low income-settings in the independent ATLAS dataset (103,559 isolates, 2004-2017) and three further LMIC hospitals/programmes (6154 isolates, 2008-2019). AMR in commensal opportunistic pathogens cultured from BSIs is strongly associated with AMR in commensal opportunistic pathogens cultured from non-sterile sites over calendar time, suggesting the latter could be used as an effective proxy for AMR surveillance in BSIs.
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Affiliation(s)
- Karina-Doris Vihta
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK.
- National Institute for Health Research Health Protection Research Unit, Oxford, UK.
- Microbiology Research Level 7, John Radcliffe Hospital, Headley Way, Oxford, OX3 9DU, UK.
| | | | - Nicole Stoesser
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- National Institute for Health Research Health Protection Research Unit, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - T Phuong Quan
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- National Institute for Health Research Health Protection Research Unit, Oxford, UK
| | | | | | - Elizabeth A Ashley
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Vientiane, Laos
- Centre for Tropical Medicine & Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Vilada Chansamouth
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Vientiane, Laos
- Centre for Tropical Medicine & Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Paul Turner
- Centre for Tropical Medicine & Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Clare L Ling
- Centre for Tropical Medicine & Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - David W Eyre
- National Institute for Health Research Health Protection Research Unit, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Big Data Institute, University of Oxford, Oxford, UK
| | - Nicholas J White
- Centre for Tropical Medicine & Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Derrick Crook
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- National Institute for Health Research Health Protection Research Unit, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Tim E A Peto
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- National Institute for Health Research Health Protection Research Unit, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Ann Sarah Walker
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- National Institute for Health Research Health Protection Research Unit, Oxford, UK
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Roberts T, Luangasanatip N, Ling CL, Hopkins J, Jaksuwan R, Lubell Y, Vongsouvath M, van Doorn HR, Ashley EA, Turner P. Antimicrobial resistance detection in Southeast Asian hospitals is critically important from both patient and societal perspectives, but what is its cost? PLOS Glob Public Health 2021; 1:e0000018. [PMID: 34746931 PMCID: PMC7611947 DOI: 10.1371/journal.pgph.0000018] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 09/13/2021] [Indexed: 11/19/2022]
Abstract
Antimicrobial resistance (AMR) is a major threat to global health. Improving laboratory capacity for AMR detection is critically important for patient health outcomes and population level surveillance. We aimed to estimate the financial cost of setting up and running a microbiology laboratory for organism identification and antimicrobial susceptibility testing as part of an AMR surveillance programme. Financial costs for setting up and running a microbiology laboratory were estimated using a top-down approach based on resource and cost data obtained from three clinical laboratories in the Mahidol Oxford Tropical Medicine Research Unit network. Costs were calculated for twelve scenarios, considering three levels of automation, with equipment sourced from either of the two leading manufacturers, and at low and high specimen throughput. To inform the costs of detection of AMR in existing labs, the unit cost per specimen and per isolate were also calculated using a micro-costing approach. Establishing a laboratory with the capacity to process 10,000 specimens per year ranged from $254,000 to $660,000 while the cost for a laboratory processing 100,000 specimens ranged from $394,000 to $887,000. Excluding capital costs to set up the laboratory, the cost per specimen ranged from $22-31 (10,000 specimens) and $11-12 (100,000 specimens). The cost per isolate ranged from $215-304 (10,000 specimens) and $105-122 (100,000 specimens). This study provides a conservative estimate of the costs for setting up and running a microbiology laboratory for AMR surveillance from a healthcare provider perspective. In the absence of donor support, these costs may be prohibitive in many low- and middle- income country (LMIC) settings. With the increased focus on AMR detection and surveillance, the high laboratory costs highlight the need for more focus on developing cheaper and cost-effective equipment and reagents so that laboratories in LMICs have the potential to improve laboratory capacity and participate in AMR surveillance.
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Affiliation(s)
- Tamalee Roberts
- Lao- Oxford-Mahosot Hospital- Wellcome Trust Research Unit, Mahosot Hospital, Vientiane, Lao People’s Democratic Republic
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - Nantasit Luangasanatip
- Faculty of Tropical Medicine, Mahidol- Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Clare L. Ling
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
- Shoklo Malaria Research Unit, Mahidol- Oxford Tropical Medicine Research Unit, Mae Sot, Thailand
| | - Jill Hopkins
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Risara Jaksuwan
- Lao- Oxford-Mahosot Hospital- Wellcome Trust Research Unit, Mahosot Hospital, Vientiane, Lao People’s Democratic Republic
| | - Yoel Lubell
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
- Faculty of Tropical Medicine, Mahidol- Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Manivanh Vongsouvath
- Lao- Oxford-Mahosot Hospital- Wellcome Trust Research Unit, Mahosot Hospital, Vientiane, Lao People’s Democratic Republic
| | - H. Rogier van Doorn
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
- Oxford University Clinical Research Unit, National Hospital for Tropical Diseases, Hanoi, Vietnam
| | - Elizabeth A. Ashley
- Lao- Oxford-Mahosot Hospital- Wellcome Trust Research Unit, Mahosot Hospital, Vientiane, Lao People’s Democratic Republic
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - Paul Turner
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
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7
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Watthanaworawit W, Roberts T, Hopkins J, Gassiep I, Norton R, Robinson MT, Silisouk J, Sar P, Sao S, Amornchai P, Limmathurotsakul D, Wuthiekanun V, Nosten F, Simpson AJH, Turner P, Ling CL. A multi-country study using MALDI-TOF mass spectrometry for rapid identification of Burkholderia pseudomallei. BMC Microbiol 2021; 21:213. [PMID: 34266382 PMCID: PMC8283998 DOI: 10.1186/s12866-021-02276-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 06/21/2021] [Indexed: 11/10/2022] Open
Abstract
Background Burkholderia pseudomallei is the bacterial causative agent of melioidosis, a difficult disease to diagnose clinically with high mortality if not appropriately treated. Definitive diagnosis requires isolation and identification of the organism. With the increased adoption of MALDI-TOF MS for the identification of bacteria, we established a method for rapid identification of B. pseudomallei using the Vitek MS, a system that does not currently have B. pseudomallei in its in-vitro diagnostic database. Results A routine direct spotting method was employed to create spectra and SuperSpectra. An initial B. pseudomallei SuperSpectrum was created at Shoklo Malaria Research Unit (SMRU) from 17 reference isolates (46 spectra). When tested, this initial SMRU SuperSpectrum was able to identify 98.2 % (54/55) of Asian isolates, but just 46.7 % (35/75) of Australian isolates. Using spectra (430) from different reference and clinical isolates, two additional SMRU SuperSpectra were created. Using the combination of all SMRU SuperSpectra with seven existing SuperSpectra from Townsville, Australia 119 (100 %) Asian isolates and 31 (100 %) Australian isolates were correctly identified. In addition, no misidentifications were obtained when using these 11 SuperSpectra when tested with 34 isolates of other bacteria including the closely related species Burkholderia thailandensis and Burkholderia cepacia. Conclusions This study has established a method for identification of B. pseudomallei using Vitek MS, and highlights the impact of geographical differences between strains for identification using this technique. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02276-1.
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Affiliation(s)
- Wanitda Watthanaworawit
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand.
| | - Tamalee Roberts
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
| | - Jill Hopkins
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Ian Gassiep
- University of Queensland Centre for Clinical Research, Herston, Queensland, Australia
| | - Robert Norton
- Pathology, Townsville Hospital, Townsville, Queensland, Australia.,Faculty of Medicine, University of Queensland, Brisbane, Australia
| | - Matthew T Robinson
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Joy Silisouk
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
| | - Poda Sar
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Sena Sao
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Premjit Amornchai
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Direk Limmathurotsakul
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Vanaporn Wuthiekanun
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Francois Nosten
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Andrew J H Simpson
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Paul Turner
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Clare L Ling
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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8
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Win MM, Win KKN, Wah TT, Aye SN, Htwe TT, Zin KN, Aung MT, Aung WW, Ashley EA, Smithuis F, Rigas V, Currie BJ, Mayo M, Webb JR, Ling CL, Htun ZT, Dance DA. Enhanced melioidosis surveillance in patients attending four tertiary hospitals in Yangon, Myanmar. Epidemiol Infect 2021; 149:1-23. [PMID: 34158136 PMCID: PMC8276317 DOI: 10.1017/s095026882100128x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/21/2021] [Accepted: 06/01/2021] [Indexed: 11/05/2022] Open
Abstract
To investigate the current epidemiology of melioidosis in Yangon, Myanmar, between June 2017 and May 2019 we conducted enhanced surveillance for melioidosis in four tertiary hospitals in Yangon, where the disease was first discovered in 1911. Oxidase-positive Gram-negative rods were obtained from the microbiology laboratories and further analysed at the Department of Medical Research. Analysis included culture on Ashdown agar, the three disc sensitivity test (gentamicin, colistin and co-amoxiclav), latex agglutination, API 20 NE, antibiotic susceptibility testing, and a subset underwent molecular confirmation with a Burkholderia pseudomallei specific assay. Twenty one of 364 isolates (5.7%) were confirmed as B. pseudomallei and were mostly susceptible to the antibiotics used in standard therapy for melioidosis. Ten patients were from Yangon Region, nine were from Ayeyarwaddy region, and one each was from Kayin and Rakhine States. A history of soil contact was given by seven patients, five had diabetes mellitus and one had renal insufficiency. The patients presented with septicaemia (12 cases), pneumonia (three cases), urinary tract infection (two cases) and wound infection (four cases). Eighteen patients survived to hospital discharge. This study highlights the likelihood that melioidosis may be far more common, but underdiagnosed, in more rural parts of Myanmar as in other countries in SE Asia.
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Affiliation(s)
- Mo Mo Win
- Department of Medical Research, Yangon, Myanmar
| | | | | | | | | | | | | | | | - Elizabeth A. Ashley
- Myanmar-Oxford Clinical Research Unit, Yangon, Myanmar
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Frank Smithuis
- Myanmar-Oxford Clinical Research Unit, Yangon, Myanmar
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Vanessa Rigas
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Bart J. Currie
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Mark Mayo
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Jessica R. Webb
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Clare L. Ling
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Shoklo Malaria Research Unit, Mahidol Oxford Tropical Medicine Research Unit, Maesot, Thailand
| | | | - David A.B. Dance
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Vientiane, Lao PDR
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
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9
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Ling CL, Roberts T, Soeng S, Cusack TP, Dance DAB, Lee SJ, Reed TAN, Hinfonthong P, Sihalath S, Sengduangphachanh A, Watthanaworawit W, Wangrangsimakul T, Newton PN, Nosten FH, Turner P, Ashley EA. Impact of delays to incubation and storage temperature on blood culture results: a multi-centre study. BMC Infect Dis 2021; 21:173. [PMID: 33579205 PMCID: PMC7881545 DOI: 10.1186/s12879-021-05872-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 02/04/2021] [Indexed: 02/07/2023] Open
Abstract
Background Blood cultures are one of the most important tests performed by microbiology laboratories. Many hospitals, particularly in low and middle-income countries, lack either microbiology services or staff to provide 24 h services resulting in delays to blood culture incubation. There is insufficient guidance on how to transport/store blood cultures if delays before incubation are unavoidable, particularly if ambient temperatures are high. This study set out to address this knowledge gap. Methods In three South East Asian countries, four different blood culture systems (two manual and two automated) were used to test blood cultures spiked with five common bacterial pathogens. Prior to incubation the spiked blood culture bottles were stored at different temperatures (25 °C, in a cool-box at ambient temperature, or at 40 °C) for different lengths of time (0 h, 6 h, 12 h or 24 h). The impacts of these different storage conditions on positive blood culture yield and on time to positivity were examined. Results There was no significant loss in yield when blood cultures were stored < 24 h at 25 °C, however, storage for 24 h at 40 °C decreased yields and longer storage times increased times to detection. Conclusion Blood cultures should be incubated with minimal delay to maximize pathogen recovery and timely result reporting, however, this study provides some reassurance that unavoidable delays can be managed to minimize negative impacts. If delays to incubation ≥ 12 h are unavoidable, transportation at a temperature not exceeding 25 °C, and blind sub-cultures prior to incubation should be considered. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-021-05872-8.
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Affiliation(s)
- Clare L Ling
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand. .,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.
| | - Tamalee Roberts
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
| | - Sona Soeng
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Tomas-Paul Cusack
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic.,Present address: Department of Infection, University Hospital Southampton, Southampton, UK
| | - David A B Dance
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.,Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic.,Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Sue J Lee
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.,Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Thomas A N Reed
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia.,Present address: London North West University Healthcare NHS Trust, Northwick Park Hospital, London, UK
| | - Pattaraporn Hinfonthong
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Somsavanh Sihalath
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
| | - Amphone Sengduangphachanh
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
| | - Wanitda Watthanaworawit
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Tri Wangrangsimakul
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.,Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Paul N Newton
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.,Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic.,Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK.,Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Francois H Nosten
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Paul Turner
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.,Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Elizabeth A Ashley
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.,Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic.,Myanmar Oxford Clinical Research Unit, Yangon, Myanmar
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10
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Reed TAN, Watson G, Kheng C, Tan P, Roberts T, Ling CL, Miliya T, Turner P. Elizabethkingia anophelis Infection in Infants, Cambodia, 2012-2018. Emerg Infect Dis 2021; 26:320-322. [PMID: 31961289 PMCID: PMC6986841 DOI: 10.3201/eid2602.190345] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
We describe 6 clinical isolates of Elizabethkingia anophelis from a pediatric referral hospital in Cambodia, along with 1 isolate reported from Thailand. Improving diagnostic microbiological methods in resource-limited settings will increase the frequency of reporting for this pathogen. Consensus on therapeutic options is needed, especially for resource-limited settings.
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11
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Turner P, Ashley EA, Celhay OJ, Douangnouvong A, Hamers RL, Ling CL, Lubell Y, Miliya T, Roberts T, Soputhy C, Ngoc Thach P, Vongsouvath M, Waithira N, Wannapinij P, van Doorn HR. ACORN (A Clinically-Oriented Antimicrobial Resistance Surveillance Network): a pilot protocol for case based antimicrobial resistance surveillance. Wellcome Open Res 2020; 5:13. [PMID: 32509968 PMCID: PMC7250055 DOI: 10.12688/wellcomeopenres.15681.2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/27/2020] [Indexed: 11/20/2022] Open
Abstract
Background: Antimicrobial resistance (AMR) / drug resistant infections (DRIs) are a major global health priority. Surveillance data is critical to inform infection treatment guidelines, monitor trends, and to assess interventions. However, most existing AMR / DRI surveillance systems are passive and pathogen-based with many potential biases. Addition of clinical and patient outcome data would provide considerable added value to pathogen-based surveillance. Methods: The aim of the ACORN project is to develop an efficient clinically-oriented AMR surveillance system, implemented alongside routine clinical care in hospitals in low- and middle-income country settings. In an initial pilot phase, clinical and microbiology data will be collected from patients presenting with clinically suspected meningitis, pneumonia, or sepsis. Community-acquired infections will be identified by daily review of new admissions, and hospital-acquired infections will be enrolled during weekly point prevalence surveys, on surveillance wards. Clinical variables will be collected at enrolment, hospital discharge, and at day 28 post-enrolment using an electronic questionnaire on a mobile device. These data will be merged with laboratory data onsite using a flexible automated computer script. Specific target pathogens will be
Streptococcus pneumoniae, Staphylococcus aureus, Salmonella spp
., Klebsiella pneumoniae, Escherichia coli, and
Acinetobacter baumannii. A bespoke browser-based app will provide sites with fully interactive data visualisation, analysis, and reporting tools. Discussion: ACORN will generate data on the burden of DRI which can be used to inform local treatment guidelines / national policy and serve as indicators to measure the impact of interventions. Following development, testing and iteration of the surveillance tools during an initial six-month pilot phase, a wider rollout is planned.
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Affiliation(s)
- Paul Turner
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Elizabeth A Ashley
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
| | - Olivier J Celhay
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Anousone Douangnouvong
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
| | - Raph L Hamers
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Eijkman-Oxford Clinical Research Unit, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Clare L Ling
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Yoel Lubell
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Thyl Miliya
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Tamalee Roberts
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
| | - Chansovannara Soputhy
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | | | - Manivanh Vongsouvath
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
| | - Naomi Waithira
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Prapass Wannapinij
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - H Rogier van Doorn
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Oxford University Clinical Research Unit, National Hospital for Tropical Diseases, Hanoi, Vietnam
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12
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Turner P, Ashley EA, Celhay OJ, Douangnouvong A, Hamers RL, Ling CL, Lubell Y, Miliya T, Roberts T, Soputhy C, Ngoc Thach P, Vongsouvath M, Waithira N, Wannapinij P, van Doorn HR. ACORN (A Clinically-Oriented Antimicrobial Resistance Surveillance Network): a pilot protocol for case based antimicrobial resistance surveillance. Wellcome Open Res 2020; 5:13. [PMID: 32509968 DOI: 10.12688/wellcomeopenres.15681.1] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/22/2020] [Indexed: 12/13/2022] Open
Abstract
Background: Antimicrobial resistance (AMR) / drug resistant infections (DRIs) are a major global health priority. Surveillance data is critical to inform infection treatment guidelines, monitor trends, and to assess interventions. However, most existing AMR / DRI surveillance systems are passive and pathogen-based with many potential biases. Addition of clinical and patient outcome data would provide considerable added value to pathogen-based surveillance. Methods: The aim of the ACORN project is to develop an efficient clinically-oriented AMR surveillance system, implemented alongside routine clinical care in hospitals in low- and middle-income country settings. In an initial pilot phase, clinical and microbiology data will be collected from patients presenting with clinically suspected meningitis, pneumonia, or sepsis. Community-acquired infections will be identified by daily review of new admissions, and hospital-acquired infections will be enrolled during weekly point prevalence surveys, on surveillance wards. Clinical variables will be collected at enrolment, hospital discharge, and at day 28 post-enrolment using an electronic questionnaire on a mobile device. These data will be merged with laboratory data onsite using a flexible automated computer script. Specific target pathogens will be Streptococcus pneumoniae, Staphylococcus aureus, Salmonella spp ., Klebsiella pneumoniae, Escherichia coli, and Acinetobacter baumannii. A bespoke browser-based app will provide sites with fully interactive data visualisation, analysis, and reporting tools. Discussion: ACORN will generate data on the burden of DRI which can be used to inform local treatment guidelines / national policy and serve as indicators to measure the impact of interventions. Following development, testing and iteration of the surveillance tools during an initial six-month pilot phase, a wider rollout is planned.
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Affiliation(s)
- Paul Turner
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Elizabeth A Ashley
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
| | - Olivier J Celhay
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Anousone Douangnouvong
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
| | - Raph L Hamers
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Eijkman-Oxford Clinical Research Unit, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Clare L Ling
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Yoel Lubell
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Thyl Miliya
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Tamalee Roberts
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
| | - Chansovannara Soputhy
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | | | - Manivanh Vongsouvath
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
| | - Naomi Waithira
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Prapass Wannapinij
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - H Rogier van Doorn
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Oxford University Clinical Research Unit, National Hospital for Tropical Diseases, Hanoi, Vietnam
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13
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Wyres KL, Nguyen TNT, Lam MMC, Judd LM, van Vinh Chau N, Dance DAB, Ip M, Karkey A, Ling CL, Miliya T, Newton PN, Lan NPH, Sengduangphachanh A, Turner P, Veeraraghavan B, Vinh PV, Vongsouvath M, Thomson NR, Baker S, Holt KE. Genomic surveillance for hypervirulence and multi-drug resistance in invasive Klebsiella pneumoniae from South and Southeast Asia. Genome Med 2020; 12:11. [PMID: 31948471 DOI: 10.1101/557785v1.full] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 12/12/2019] [Indexed: 05/26/2023] Open
Abstract
BACKGROUND Klebsiella pneumoniae is a leading cause of bloodstream infection (BSI). Strains producing extended-spectrum beta-lactamases (ESBLs) or carbapenemases are considered global priority pathogens for which new treatment and prevention strategies are urgently required, due to severely limited therapeutic options. South and Southeast Asia are major hubs for antimicrobial-resistant (AMR) K. pneumoniae and also for the characteristically antimicrobial-sensitive, community-acquired "hypervirulent" strains. The emergence of hypervirulent AMR strains and lack of data on exopolysaccharide diversity pose a challenge for K. pneumoniae BSI control strategies worldwide. METHODS We conducted a retrospective genomic epidemiology study of 365 BSI K. pneumoniae from seven major healthcare facilities across South and Southeast Asia, extracting clinically relevant information (AMR, virulence, K and O antigen loci) using Kleborate, a K. pneumoniae-specific genomic typing tool. RESULTS K. pneumoniae BSI isolates were highly diverse, comprising 120 multi-locus sequence types (STs) and 63 K-loci. ESBL and carbapenemase gene frequencies were 47% and 17%, respectively. The aerobactin synthesis locus (iuc), associated with hypervirulence, was detected in 28% of isolates. Importantly, 7% of isolates harboured iuc plus ESBL and/or carbapenemase genes. The latter represent genotypic AMR-virulence convergence, which is generally considered a rare phenomenon but was particularly common among South Asian BSI (17%). Of greatest concern, we identified seven novel plasmids carrying both iuc and AMR genes, raising the prospect of co-transfer of these phenotypes among K. pneumoniae. CONCLUSIONS K. pneumoniae BSI in South and Southeast Asia are caused by different STs from those predominating in other regions, and with higher frequency of acquired virulence determinants. K. pneumoniae carrying both iuc and AMR genes were also detected at higher rates than have been reported elsewhere. The study demonstrates how genomics-based surveillance-reporting full molecular profiles including STs, AMR, virulence and serotype locus information-can help standardise comparisons between sites and identify regional differences in pathogen populations.
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Affiliation(s)
- Kelly L Wyres
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, 3004, Australia
| | - To N T Nguyen
- Hospital of Tropical Diseases, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Margaret M C Lam
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, 3004, Australia
| | - Louise M Judd
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, 3004, Australia
| | | | - David A B Dance
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- London School of Hygiene and Tropical Medicine, London, UK
| | - Margaret Ip
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Abhilasha Karkey
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- Patan Academy of Health Sciences, Oxford University Clinical Research Unit, Kathmandu, Nepal
| | - Clare L Ling
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, 63110, Thailand
| | - Thyl Miliya
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Paul N Newton
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- London School of Hygiene and Tropical Medicine, London, UK
| | | | - Amphone Sengduangphachanh
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
| | - Paul Turner
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Balaji Veeraraghavan
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Phat Voong Vinh
- Hospital of Tropical Diseases, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Manivanh Vongsouvath
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
| | - Nicholas R Thomson
- London School of Hygiene and Tropical Medicine, London, UK
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Stephen Baker
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID) Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0AW, UK.
| | - Kathryn E Holt
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, 3004, Australia
- London School of Hygiene and Tropical Medicine, London, UK
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14
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Wyres KL, Nguyen TNT, Lam MMC, Judd LM, van Vinh Chau N, Dance DAB, Ip M, Karkey A, Ling CL, Miliya T, Newton PN, Lan NPH, Sengduangphachanh A, Turner P, Veeraraghavan B, Vinh PV, Vongsouvath M, Thomson NR, Baker S, Holt KE. Genomic surveillance for hypervirulence and multi-drug resistance in invasive Klebsiella pneumoniae from South and Southeast Asia. Genome Med 2020; 12:11. [PMID: 31948471 PMCID: PMC6966826 DOI: 10.1186/s13073-019-0706-y] [Citation(s) in RCA: 144] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 12/12/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Klebsiella pneumoniae is a leading cause of bloodstream infection (BSI). Strains producing extended-spectrum beta-lactamases (ESBLs) or carbapenemases are considered global priority pathogens for which new treatment and prevention strategies are urgently required, due to severely limited therapeutic options. South and Southeast Asia are major hubs for antimicrobial-resistant (AMR) K. pneumoniae and also for the characteristically antimicrobial-sensitive, community-acquired "hypervirulent" strains. The emergence of hypervirulent AMR strains and lack of data on exopolysaccharide diversity pose a challenge for K. pneumoniae BSI control strategies worldwide. METHODS We conducted a retrospective genomic epidemiology study of 365 BSI K. pneumoniae from seven major healthcare facilities across South and Southeast Asia, extracting clinically relevant information (AMR, virulence, K and O antigen loci) using Kleborate, a K. pneumoniae-specific genomic typing tool. RESULTS K. pneumoniae BSI isolates were highly diverse, comprising 120 multi-locus sequence types (STs) and 63 K-loci. ESBL and carbapenemase gene frequencies were 47% and 17%, respectively. The aerobactin synthesis locus (iuc), associated with hypervirulence, was detected in 28% of isolates. Importantly, 7% of isolates harboured iuc plus ESBL and/or carbapenemase genes. The latter represent genotypic AMR-virulence convergence, which is generally considered a rare phenomenon but was particularly common among South Asian BSI (17%). Of greatest concern, we identified seven novel plasmids carrying both iuc and AMR genes, raising the prospect of co-transfer of these phenotypes among K. pneumoniae. CONCLUSIONS K. pneumoniae BSI in South and Southeast Asia are caused by different STs from those predominating in other regions, and with higher frequency of acquired virulence determinants. K. pneumoniae carrying both iuc and AMR genes were also detected at higher rates than have been reported elsewhere. The study demonstrates how genomics-based surveillance-reporting full molecular profiles including STs, AMR, virulence and serotype locus information-can help standardise comparisons between sites and identify regional differences in pathogen populations.
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Affiliation(s)
- Kelly L Wyres
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, 3004, Australia
| | - To N T Nguyen
- Hospital of Tropical Diseases, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Margaret M C Lam
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, 3004, Australia
| | - Louise M Judd
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, 3004, Australia
| | | | - David A B Dance
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- London School of Hygiene and Tropical Medicine, London, UK
| | - Margaret Ip
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Abhilasha Karkey
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- Patan Academy of Health Sciences, Oxford University Clinical Research Unit, Kathmandu, Nepal
| | - Clare L Ling
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, 63110, Thailand
| | - Thyl Miliya
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Paul N Newton
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- London School of Hygiene and Tropical Medicine, London, UK
| | | | - Amphone Sengduangphachanh
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
| | - Paul Turner
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Balaji Veeraraghavan
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Phat Voong Vinh
- Hospital of Tropical Diseases, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Manivanh Vongsouvath
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
| | - Nicholas R Thomson
- London School of Hygiene and Tropical Medicine, London, UK
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Stephen Baker
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID) Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0AW, UK.
| | - Kathryn E Holt
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, 3004, Australia
- London School of Hygiene and Tropical Medicine, London, UK
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15
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Turner P, Fox-Lewis A, Shrestha P, Dance DAB, Wangrangsimakul T, Cusack TP, Ling CL, Hopkins J, Roberts T, Limmathurotsakul D, Cooper BS, Dunachie S, Moore CE, Dolecek C, van Doorn HR, Guerin PJ, Day NPJ, Ashley EA. Microbiology Investigation Criteria for Reporting Objectively (MICRO): a framework for the reporting and interpretation of clinical microbiology data. BMC Med 2019; 17:70. [PMID: 30922309 PMCID: PMC6440102 DOI: 10.1186/s12916-019-1301-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 03/06/2019] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND There is a pressing need to understand better the extent and distribution of antimicrobial resistance on a global scale, to inform development of effective interventions. Collation of datasets for meta-analysis, mathematical modelling and temporo-spatial analysis is hampered by the considerable variability in clinical sampling, variable quality in laboratory practice and inconsistencies in antimicrobial susceptibility testing and reporting. METHODS The Microbiology Investigation Criteria for Reporting Objectively (MICRO) checklist was developed by an international working group of clinical and laboratory microbiologists, infectious disease physicians, epidemiologists and mathematical modellers. RESULTS In keeping with the STROBE checklist, but applicable to all study designs, MICRO defines items to be included in reports of studies involving human clinical microbiology data. It provides a concise and comprehensive reference for clinicians, researchers, reviewers and journals working on, critically appraising, and publishing clinical microbiology datasets. CONCLUSIONS Implementation of the MICRO checklist will enhance the quality and scientific reporting of clinical microbiology data, increasing data utility and comparability to improve surveillance, grade data quality, facilitate meta-analyses and inform policy and interventions from local to global levels.
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Affiliation(s)
- Paul Turner
- Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Andrew Fox-Lewis
- Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Poojan Shrestha
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Infectious Diseases Data Observatory, Oxford, UK
| | - David A. B. Dance
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People’s Democratic Republic
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Tri Wangrangsimakul
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Tomas-Paul Cusack
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People’s Democratic Republic
- National Infection Service, Public Health England, London, UK
| | - Clare L. Ling
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Jill Hopkins
- Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Tamalee Roberts
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People’s Democratic Republic
| | - Direk Limmathurotsakul
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Ben S. Cooper
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Susanna Dunachie
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Catrin E. Moore
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Christiane Dolecek
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - H. Rogier van Doorn
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford University Clinical Research Unit, Hanoi, Vietnam
| | - Philippe J. Guerin
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Infectious Diseases Data Observatory, Oxford, UK
| | - Nicholas P. J. Day
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Elizabeth A. Ashley
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Myanmar Oxford Clinical Research Unit, Yangon, Myanmar
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16
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Cusack TP, Ashley EA, Ling CL, Roberts T, Turner P, Wangrangsimakul T, Dance DAB. Time to switch from CLSI to EUCAST? A Southeast Asian perspective. Clin Microbiol Infect 2019; 25:782-785. [PMID: 30922928 PMCID: PMC6587905 DOI: 10.1016/j.cmi.2019.03.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 03/15/2019] [Accepted: 03/16/2019] [Indexed: 11/25/2022]
Affiliation(s)
- T P Cusack
- Lao-Oxford-Mahosot Hospital Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic; National Infection Service, Public Health England, London, UK.
| | - E A Ashley
- Myanmar Oxford Clinical Research Unit, Yangon, Myanmar; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - C L Ling
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - T Roberts
- Lao-Oxford-Mahosot Hospital Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
| | - P Turner
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - T Wangrangsimakul
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - D A B Dance
- Lao-Oxford-Mahosot Hospital Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
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17
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Cusack TP, Ashley EA, Ling CL, Rattanavong S, Roberts T, Turner P, Wangrangsimakul T, Dance DAB. Impact of CLSI and EUCAST breakpoint discrepancies on reporting of antimicrobial susceptibility and AMR surveillance. Clin Microbiol Infect 2019; 25:910-911. [PMID: 30910717 PMCID: PMC6587648 DOI: 10.1016/j.cmi.2019.03.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 03/10/2019] [Indexed: 11/29/2022]
Affiliation(s)
- T P Cusack
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic; National Infection Service, Public Health England, London, UK.
| | - E A Ashley
- Myanmar Oxford Clinical Research Unit, Yangon, Myanmar; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - C L Ling
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - S Rattanavong
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
| | - T Roberts
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
| | - P Turner
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - T Wangrangsimakul
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - D A B Dance
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
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18
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Salter SJ, Scott P, Page AJ, Tracey A, de Goffau MC, Cormie C, Ochoa-Montaño B, Ling CL, Tangmanakit J, Turner P, Parkhill J. 'Candidatus Ornithobacterium hominis': insights gained from draft genomes obtained from nasopharyngeal swabs. Microb Genom 2019; 5. [PMID: 30720420 PMCID: PMC6421346 DOI: 10.1099/mgen.0.000247] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
'Candidatus Ornithobacterium hominis' represents a new member of the Flavobacteriaceae detected in 16S rRNA gene surveys of people from South-East Asia, Africa and Australia. It frequently colonizes the infant nasopharynx at high proportional abundance, and we demonstrate its presence in 42 % of nasopharyngeal swabs from 12-month-old children in the Maela refugee camp in Thailand. The species, a Gram-negative bacillus, has not yet been cultured, but the cells can be identified in mixed samples by fluorescent hybridization. Here, we report seven genomes assembled from metagenomic data, two to improved draft standard. The genomes are approximately 1.9 Mb, sharing 62 % average amino acid identity with the only other member of the genus, the bird pathogen Ornithobacterium rhinotracheale. The draft genomes encode multiple antibiotic-resistance genes, competition factors, Flavobacterium johnsoniae-like gliding motility genes and a homologue of the Pasteurella multocida mitogenic toxin. Intra- and inter-host genome comparison suggests that colonization with this bacterium is both persistent and strain exclusive.
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Affiliation(s)
| | - Paul Scott
- 1Pathogen Genomics, Wellcome Sanger Institute, Hinxton, UK
| | - Andrew J Page
- 1Pathogen Genomics, Wellcome Sanger Institute, Hinxton, UK.,†Present address: Quadram Institute Bioscience, Norwich, UK
| | - Alan Tracey
- 1Pathogen Genomics, Wellcome Sanger Institute, Hinxton, UK
| | | | - Claire Cormie
- 1Pathogen Genomics, Wellcome Sanger Institute, Hinxton, UK
| | - Bernardo Ochoa-Montaño
- 2Department of Biochemistry, University of Cambridge, Cambridge, UK.,‡Present address: Illumina Cambridge Ltd, Little Chesterford, UK
| | - Clare L Ling
- 3Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand.,4Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jiraporn Tangmanakit
- 3Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Paul Turner
- 4Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,5Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
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19
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Thi SS, Parker DM, Swe LL, Pukrittayakamee S, Ling CL, Amornpaisarnloet K, Vincenti-Delmas M, Nosten FH. Migration histories of multidrug-resistant tuberculosis patients from the Thailand-Myanmar border, 2012-2014. Int J Tuberc Lung Dis 2018. [PMID: 28633699 DOI: 10.5588/ijtld.16.0658] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
SETTING Multidrug-resistant tuberculosis (MDR-TB) is a growing public health threat in South-East Asia. TB is typically a disease of poverty and can be spread by infectious humans who migrate from one region to another. DESIGN We interviewed 20 MDR-TB patients on the Thailand-Myanmar border with regard to their migration histories. Migration origins and destinations were mapped. RESULTS All but one participant had a history of migration, and maps of migration ranges revealed wide geographic dispersal. Most described living and work conditions that could contribute to the spread of drug-resistant TB, including numerous contacts and crowded living quarters. CONCLUSION Our results show that at least some migrant workers in the region carry MDR-TB, and indicate that this subgroup of the population is important with regard to the transmission of MDR-TB throughout the region. Migrants in this region come into contact with high numbers of people and may be able to spread the disease across wide geographic ranges. Access to diagnosis and treatment and socio-economic development are at least as important as any TB control measures, meaning that innovative and bold approaches that extend across international borders are needed to address these problems.
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Affiliation(s)
- S S Thi
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Tak
| | - D M Parker
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Tak, Mahidol-Oxford Tropical Medicine Research Unit
| | - L L Swe
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Tak
| | | | - C L Ling
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Tak, Mahidol-Oxford Tropical Medicine Research Unit, Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - M Vincenti-Delmas
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Tak, Mahidol-Oxford Tropical Medicine Research Unit
| | - F H Nosten
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Tak, Mahidol-Oxford Tropical Medicine Research Unit, Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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20
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Win MM, Ashley EA, Zin KN, Aung MT, Swe MMM, Ling CL, Nosten F, Thein WM, Zaw NN, Aung MY, Tun KM, Dance DAB, Smithuis FM. Melioidosis in Myanmar. Trop Med Infect Dis 2018; 3:tropicalmed3010028. [PMID: 30274425 PMCID: PMC6136617 DOI: 10.3390/tropicalmed3010028] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 02/20/2018] [Accepted: 02/23/2018] [Indexed: 11/17/2022] Open
Abstract
Sporadic cases of melioidosis have been diagnosed in Myanmar since the disease was first described in Yangon in 1911. Published and unpublished cases are summarized here, along with results from environmental and serosurveys. A total of 298 cases have been reported from seven states or regions between 1911 and 2018, with the majority of these occurring before 1949. Findings from soil surveys confirm the presence of Burkholderia pseudomallei in the environment in all three regions examined. The true epidemiology of the disease in Myanmar is unknown. Important factors contributing to the current gaps in knowledge are lack of awareness among clinicians and insufficient laboratory diagnostic capacity in many parts of the country. This is likely to have led to substantial under-reporting.
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Affiliation(s)
- Mo Mo Win
- Department of Medical Research, Yangon, Myanmar.
| | - Elizabeth A Ashley
- Myanmar Oxford Clinical Research Unit, Yangon, Myanmar.
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Old Road Campus, University of Oxford, Oxford OX3 7FZ, UK.
| | - Khwar Nyo Zin
- Department of Microbiology, Yangon General Hospital, University of Medicine 1, Yangon, Myanmar.
| | - Myint Thazin Aung
- Pathology Department, Microbiology Section, North Okkapala General Hospital, University of Medicine 2, Yangon, Myanmar.
| | | | - Clare L Ling
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Old Road Campus, University of Oxford, Oxford OX3 7FZ, UK.
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot 63110, Thailand.
| | - François Nosten
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Old Road Campus, University of Oxford, Oxford OX3 7FZ, UK.
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot 63110, Thailand.
| | - Win May Thein
- Mandalay General Hospital, University of Medicine, Mandalay, Myanmar.
| | - Ni Ni Zaw
- Mandalay General Hospital, University of Medicine, Mandalay, Myanmar.
| | - May Yee Aung
- Pathology Department, Microbiology section, Thingungyun Hospital, University of Medicine 1, Yangon, Myanmar.
| | - Kyaw Myo Tun
- Department of Preventive & Social Medicine, Defence Services Medical Academy, Yangon, Myanmar.
| | - David A B Dance
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Old Road Campus, University of Oxford, Oxford OX3 7FZ, UK.
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos.
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK.
| | - Frank M Smithuis
- Myanmar Oxford Clinical Research Unit, Yangon, Myanmar.
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Old Road Campus, University of Oxford, Oxford OX3 7FZ, UK.
- Medical Action Myanmar, Yangon, Myanmar.
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21
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Das S, Jang IK, Barney B, Peck R, Rek JC, Arinaitwe E, Adrama H, Murphy M, Imwong M, Ling CL, Proux S, Haohankhunnatham W, Rist M, Seilie AM, Hanron A, Daza G, Chang M, Nakamura T, Kalnoky M, Labarre P, Murphy SC, McCarthy JS, Nosten F, Greenhouse B, Allauzen S, Domingo GJ. Performance of a High-Sensitivity Rapid Diagnostic Test for Plasmodium falciparum Malaria in Asymptomatic Individuals from Uganda and Myanmar and Naive Human Challenge Infections. Am J Trop Med Hyg 2017; 97:1540-1550. [PMID: 28820709 PMCID: PMC5817764 DOI: 10.4269/ajtmh.17-0245] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Sensitive field-deployable diagnostic tests can assist malaria programs in achieving elimination. The performance of a new Alere™ Malaria Ag P.f Ultra Sensitive rapid diagnostic test (uRDT) was compared with the currently available SD Bioline Malaria Ag P.f RDT in blood specimens from asymptomatic individuals in Nagongera, Uganda, and in a Karen Village, Myanmar, representative of high- and low-transmission areas, respectively, as well as in pretreatment specimens from study participants from four Plasmodium falciparum-induced blood-stage malaria (IBSM) studies. A quantitative reverse transcription PCR (qRT-PCR) and a highly sensitive enzyme-linked immunosorbent assay (ELISA) test for histidine-rich protein II (HRP2) were used as reference assays. The uRDT showed a greater than 10-fold lower limit of detection for HRP2 compared with the RDT. The sensitivity of the uRDT was 84% and 44% against qRT-PCR in Uganda and Myanmar, respectively, and that of the RDT was 62% and 0% for the same two sites. The specificities of the uRDT were 92% and 99.8% against qRT-PCR for Uganda and Myanmar, respectively, and 99% and 99.8% against the HRP2 reference ELISA. The RDT had specificities of 95% and 100% against qRT-PCR for Uganda and Myanmar, respectively, and 96% and 100% against the HRP2 reference ELISA. The uRDT detected new infections in IBSM study participants 1.5 days sooner than the RDT. The uRDT has the same workflow as currently available RDTs, but improved performance characteristics to identify asymptomatic malaria infections. The uRDT may be a useful tool for malaria elimination strategies.
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Affiliation(s)
- Smita Das
- Diagnostics Program, PATH, Seattle, Washington
| | | | | | - Roger Peck
- Diagnostics Program, PATH, Seattle, Washington
| | - John C Rek
- Infectious Disease Research Collaboration, Kampala, Uganda
| | | | - Harriet Adrama
- Infectious Disease Research Collaboration, Kampala, Uganda
| | - Maxwell Murphy
- University of California San Francisco, San Francisco, California
| | - Mallika Imwong
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Clare L Ling
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Stephane Proux
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Warat Haohankhunnatham
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Melissa Rist
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Annette M Seilie
- Department of Laboratory Medicine, University of Washington, Seattle, Washington
| | - Amelia Hanron
- Department of Laboratory Medicine, University of Washington, Seattle, Washington
| | - Glenda Daza
- Department of Laboratory Medicine, University of Washington, Seattle, Washington
| | - Ming Chang
- Department of Laboratory Medicine, University of Washington, Seattle, Washington
| | | | | | | | - Sean C Murphy
- Center for Emerging and Re-emerging Infectious Diseases, University of Washington, Seattle, Washington.,Department of Microbiology, University of Washington, Seattle, Washington.,Department of Laboratory Medicine, University of Washington, Seattle, Washington
| | | | - Francois Nosten
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.,Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Bryan Greenhouse
- University of California San Francisco, San Francisco, California
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22
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van Enter BJD, Lau YL, Ling CL, Watthanaworawit W, Sukthana Y, Lee WC, Nosten F, McGready R. Seroprevalence of Toxoplasma gondii Infection in Refugee and Migrant Pregnant Women along the Thailand-Myanmar Border. Am J Trop Med Hyg 2017; 97:232-235. [PMID: 28719309 PMCID: PMC5508912 DOI: 10.4269/ajtmh.16-0999] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Toxoplasma gondii primary infection in pregnancy is associated with poor obstetric outcomes. This study aimed to determine the seroprevalence of Toxoplasma infection in pregnant migrant and refugee women from Myanmar attending antenatal care in Thailand. A random selection of 199 residual blood samples from first antenatal screen in 2014–2015 was tested for Toxoplasma IgG and IgM antibodies. Seroprevalence of Toxoplasma infection was 31.7% (95% confidence interval = 25.6–38.4). Avidity testing in the three positive IgM cases indicated all were past infections. Multiparity (≥ 3 children) was significantly associated with higher Toxoplasma seropositivity rates. Seroprevalence of T. gondii infection in this pregnant population is similar to the only other report from Myanmar, where multiparity was also identified as a significant association. Toxoplasma infection is important in pregnant women. Nevertheless, in this marginalized population, this infection may be given less priority, due to resource constraints in providing the most basic components of safe motherhood programs.
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Affiliation(s)
- Bert J D van Enter
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Yee-Ling Lau
- Department of Parasitology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Clare L Ling
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom.,Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Wanitda Watthanaworawit
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.,Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Yaowalark Sukthana
- Department of Protozoology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Wenn-Chyau Lee
- Singapore Immunology Network (SIgN), A*STAR, Singapore, Singapore
| | - François Nosten
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom.,Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Rose McGready
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom.,Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
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23
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Bancone G, Chowwiwat N, Somsakchaicharoen R, Poodpanya L, Moo PK, Gornsawun G, Kajeechiwa L, Thwin MM, Rakthinthong S, Nosten S, Thinraow S, Nyo SN, Ling CL, Wiladphaingern J, Kiricharoen NL, Moore KA, White NJ, Nosten F. Single Low Dose Primaquine (0.25 mg/kg) Does Not Cause Clinically Significant Haemolysis in G6PD Deficient Subjects. PLoS One 2016; 11:e0151898. [PMID: 27010542 PMCID: PMC4807095 DOI: 10.1371/journal.pone.0151898] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 03/04/2016] [Indexed: 11/19/2022] Open
Abstract
Background Primaquine is the only drug consistently effective against mature gametocytes of Plasmodium falciparum. The transmission blocking dose of primaquine previously recommended was 0.75mg/kg (adult dose 45mg) but its deployment was limited because of concerns over haemolytic effects in patients with glucose-6-phosphate dehydrogenase (G6PD) deficiency. G6PD deficiency is an inherited X-linked enzymatic defect that affects an estimated 400 million people around the world with high frequencies (15–20%) in populations living in malarious areas. To reduce transmission in low transmission settings and facilitate elimination of P. falciparum, the World Health Organization now recommends adding a single dose of 0.25mg/kg (adult dose 15mg) to Artemisinin-based Combination Therapies (ACTs) without G6PD testing. Direct evidence of the safety of this low dose is lacking. Adverse events and haemoglobin variations after this treatment were assessed in both G6PD normal and deficient subjects in the context of targeted malaria elimination in a malaria endemic area on the North-Western Myanmar-Thailand border where prevalence of G6PD deficiency (Mahidol variant) approximates 15%. Methods and Findings The tolerability and safety of primaquine (single dose 0.25 mg base/kg) combined with dihydroartemisinin-piperaquine (DHA-PPQ) given three times at monthly intervals was assessed in 819 subjects. Haemoglobin concentrations were estimated over the six months preceding the ACT + primaquine rounds of mass drug administration. G6PD deficiency was assessed with a phenotypic test and genotyping was performed in male subjects with deficient phenotypes and in all females. Fractional haemoglobin changes in relation to G6PD phenotype and genotype and primaquine round were assessed using linear mixed-effects models. No adverse events related to primaquine were reported during the trial. Mean fractional haemoglobin changes after each primaquine treatment in G6PD deficient subjects (-5.0%, -4.2% and -4.7%) were greater than in G6PD normal subjects (0.3%, -0.8 and -1.7%) but were clinically insignificant. Fractional drops in haemoglobin concentration larger than 25% following single dose primaquine were observed in 1.8% of the population but were asymptomatic. Conclusions The single low dose (0.25mg/kg) of primaquine is clinically well tolerated and can be used safely without prior G6PD testing in populations with high prevalence of G6PD deficiency. The present evidence supports a broader use of low dose primaquine without G6PD testing for the treatment and elimination of falciparum malaria. Trial Registration ClinicalTrials.gov NCT01872702
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Affiliation(s)
- Germana Bancone
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
- * E-mail:
| | - Nongnud Chowwiwat
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Raweewan Somsakchaicharoen
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Lalita Poodpanya
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Paw Khu Moo
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Gornpan Gornsawun
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Ladda Kajeechiwa
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - May Myo Thwin
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Santisuk Rakthinthong
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Suphak Nosten
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Suradet Thinraow
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Slight Naw Nyo
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Clare L. Ling
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Jacher Wiladphaingern
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Naw Lily Kiricharoen
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Kerryn A. Moore
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Macfarlane Burnet Institute for Medical Research and Public Health, Melbourne, Victoria, Australia
| | - Nicholas J. White
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Francois Nosten
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
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24
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McGready R, Prakash JAJ, Benjamin SJ, Watthanaworawit W, Anantatat T, Tanganuchitcharnchai A, Ling CL, Tan SO, Ashley EA, Pimanpanarak M, Blacksell SD, Day NP, Singhasivanon P, White NJ, Nosten F, Paris DH. Pregnancy outcome in relation to treatment of murine typhus and scrub typhus infection: a fever cohort and a case series analysis. PLoS Negl Trop Dis 2014; 8:e3327. [PMID: 25412503 PMCID: PMC4238995 DOI: 10.1371/journal.pntd.0003327] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 10/08/2014] [Indexed: 11/18/2022] Open
Abstract
Background There is a paucity of published reports on pregnancy outcome following scrub and murine typhus despite these infections being leading causes of undifferentiated fever in Asia. This study aimed to relate pregnancy outcome with treatment of typhus. Methodology/Principal Findings Data were analyzed from: i) pregnant women with a diagnosis of scrub and/or murine typhus from a fever cohort studies; ii) case series of published studies in PubMed using the search terms “scrub typhus” (ST), “murine typhus” (MT), “Orientia tsutsugamushi”, “Rickettsia tsutsugamushi”, “Rickettsia typhi”, “rickettsiae”, “typhus”, or “rickettsiosis”; and “pregnancy”, until February 2014 and iii) an unpublished case series. Fever clearance time (FCT) and pregnancy outcome (miscarriage and delivery) were compared to treatment. Poor neonatal outcome was a composite measure for pregnancies sustained to 28 weeks or more of gestation ending in stillbirth, preterm birth, or delivery of a growth restricted or low birth weight newborn. Results There were 26 women in the fever cohort. MT and ST were clinically indistinguishable apart from two ST patients with eschars. FCTs (median [range] hours) were 25 [16–42] for azithromycin (n = 5), 34 [20–53] for antimalarials (n = 5) and 92 [6–260] for other antibiotics/supportive therapy (n = 16). There were 36.4% (8/22) with a poor neonatal outcome. In 18 years, 97 pregnancies were collated, 82 with known outcomes, including two maternal deaths. Proportions of miscarriage 17.3% (14/81) and poor neonatal outcomes 41.8% (28/67) were high, increasing with longer FCTs (p = 0.050, linear trend). Use of azithromycin was not significantly associated with improved neonatal outcomes (p = 0.610) Conclusion The published ST and MT world literature amounts to less than 100 pregnancies due to under recognition and under diagnosis. Evidence supporting the most commonly used treatment, azithromycin, is weak. Collaborative, prospective clinical trials in pregnant women are urgently required to reduce the burden of adverse maternal and newborn outcomes and to determine the safety and efficacy of antimicrobial treatment. Typhus is an under-recognised and under-studied public health problem in Asia. In rural areas of Southeast Asia murine and scrub typhus are probably the most common treatable cause of fever. The estimated number of scrub typhus cases in Southeast Asia, more than 1 million yearly, results in approximately 50–80,000 deaths per year. Treatment delays due to lack of appropriate diagnostics and lack of awareness lead to a substantial health and economic impact in the one of the world's most densely populated regions. Only 97 cases in pregnancy are available from the published world literature over the past 18 years. Only 82 of these had known outcomes, including two maternal deaths. The proportion of poor neonatal outcome including stillbirth, prematurity and low birth weight was high occurring in more than 40% of pregnancies, and higher when the fever clearance time was longer. While poor neonatal outcomes were observed with all antibiotics prescribed, azithromycin appeared to be associated with shorter fever clearance times but this was not statistically significant. Evidence to support the use of azithromycin is weak. The correct antimicrobial or combination for undifferentiated fever in pregnant women in Southeast Asia is unknown.
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Affiliation(s)
- Rose McGready
- Shoklo Malaria Research Unit (SMRU), Mahidol-Oxford Tropical Medicine Research Unit, Mae Sot, Tak, Thailand
- Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- * E-mail:
| | - John Antony Jude Prakash
- Immunology Laboratories, Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Santosh Joseph Benjamin
- Immunology Laboratories, Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Wanitda Watthanaworawit
- Shoklo Malaria Research Unit (SMRU), Mahidol-Oxford Tropical Medicine Research Unit, Mae Sot, Tak, Thailand
| | - Tippawan Anantatat
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Ampai Tanganuchitcharnchai
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Clare L. Ling
- Shoklo Malaria Research Unit (SMRU), Mahidol-Oxford Tropical Medicine Research Unit, Mae Sot, Tak, Thailand
- Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Saw Oo Tan
- Shoklo Malaria Research Unit (SMRU), Mahidol-Oxford Tropical Medicine Research Unit, Mae Sot, Tak, Thailand
| | - Elizabeth A. Ashley
- Shoklo Malaria Research Unit (SMRU), Mahidol-Oxford Tropical Medicine Research Unit, Mae Sot, Tak, Thailand
- Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Mupawjay Pimanpanarak
- Shoklo Malaria Research Unit (SMRU), Mahidol-Oxford Tropical Medicine Research Unit, Mae Sot, Tak, Thailand
| | - Stuart D. Blacksell
- Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Nicholas P. Day
- Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Pratap Singhasivanon
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Nicholas J. White
- Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - François Nosten
- Shoklo Malaria Research Unit (SMRU), Mahidol-Oxford Tropical Medicine Research Unit, Mae Sot, Tak, Thailand
- Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Daniel H. Paris
- Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
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25
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Gillespie SH, Ling CL, Oravcova K, Pinheiro M, Wells L, Bryant JM, McHugh TD, Bébéar C, Webster D, Harris SR, Seth-Smith HMB, Thomson NR. Genomic Investigations unmask Mycoplasma amphoriforme, a new respiratory pathogen. Clin Infect Dis 2014; 60:381-8. [PMID: 25344534 PMCID: PMC4293396 DOI: 10.1093/cid/ciu820] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The results of high-resolution whole-genome sequencing data provide compelling evidence that Mycoplasma amphoriforme produces chronic relapsing infection and, importantly, is transmitted in a hospital environment. Background. Mycoplasma amphoriforme has been associated with infection in patients with primary antibody deficiency (PAD). Little is known about the natural history of infection with this organism and its ability to be transmitted in the community. Methods. The bacterial load was estimated in sequential sputum samples from 9 patients by quantitative polymerase chain reaction. The genomes of all available isolates, originating from patients in the United Kingdom, France, and Tunisia, were sequenced along with the type strain. Genomic data were assembled and annotated, and a high-resolution phylogenetic tree was constructed. Results. By using high-resolution whole-genome sequencing (WGS) data, we show that patients can be chronically infected with M. amphoriforme manifesting as a relapsing-remitting bacterial load, interspersed by periods when the organism is undetectable. Importantly, we demonstrate transmission of strains within a clinical environment. Antibiotic resistance mutations accumulate in isolates taken from patients who received multiple courses of antibiotics. Conclusions. Mycoplasma amphoriforme isolates form a closely related species responsible for a chronic relapsing and remitting infection in PAD patients in the United Kingdom and from immunocompetent patients in other countries. We provide strong evidence of transmission between patients attending the same clinic, suggesting that screening and isolation may be necessary for susceptible patients. This work demonstrates the critical role that WGS can play in rapidly unraveling the biology of a novel pathogen.
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Affiliation(s)
| | - Clare L Ling
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand University College London Centre for Clinical Microbiology, Royal Free Campus, and
| | | | - Miguel Pinheiro
- School of Medicine, University of St Andrews, United Kingdom
| | - Louise Wells
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | | | - Timothy D McHugh
- University College London Centre for Clinical Microbiology, Royal Free Campus, and
| | | | - David Webster
- Department of Immunology, Royal Free Hospital NHS Trust, London, United Kingdom
| | - Simon R Harris
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
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26
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Tan JJL, Capozzoli M, Sato M, Watthanaworawit W, Ling CL, Mauduit M, Malleret B, Grüner AC, Tan R, Nosten FH, Snounou G, Rénia L, Ng LFP. An integrated lab-on-chip for rapid identification and simultaneous differentiation of tropical pathogens. PLoS Negl Trop Dis 2014; 8:e3043. [PMID: 25078474 PMCID: PMC4117454 DOI: 10.1371/journal.pntd.0003043] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Accepted: 06/10/2014] [Indexed: 01/03/2023] Open
Abstract
Tropical pathogens often cause febrile illnesses in humans and are responsible for considerable morbidity and mortality. The similarities in clinical symptoms provoked by these pathogens make diagnosis difficult. Thus, early, rapid and accurate diagnosis will be crucial in patient management and in the control of these diseases. In this study, a microfluidic lab-on-chip integrating multiplex molecular amplification and DNA microarray hybridization was developed for simultaneous detection and species differentiation of 26 globally important tropical pathogens. The analytical performance of the lab-on-chip for each pathogen ranged from 102 to 103 DNA or RNA copies. Assay performance was further verified with human whole blood spiked with Plasmodium falciparum and Chikungunya virus that yielded a range of detection from 200 to 4×105 parasites, and from 250 to 4×107 PFU respectively. This lab-on-chip was subsequently assessed and evaluated using 170 retrospective patient specimens in Singapore and Thailand. The lab-on-chip had a detection sensitivity of 83.1% and a specificity of 100% for P. falciparum; a sensitivity of 91.3% and a specificity of 99.3% for P. vivax; a positive 90.0% agreement and a specificity of 100% for Chikungunya virus; and a positive 85.0% agreement and a specificity of 100% for Dengue virus serotype 3 with reference methods conducted on the samples. Results suggested the practicality of an amplification microarray-based approach in a field setting for high-throughput detection and identification of tropical pathogens. Tropical diseases consist of a group of debilitating and fatal infections that occur primarily in rural and urban settings of tropical and subtropical countries. While the primary indices of an infection are mostly the presentation of clinical signs and symptoms, outcomes due to an infection with tropical pathogens are often unspecific. Accurate diagnosis is crucial for timely intervention, appropriate and adequate treatments, and patient management to prevent development of sequelae and transmission. Although, multiplex assays are available for the simultaneous detection of tropical pathogens, they are generally of low throughput. Performing parallel assays to cover the detection for a comprehensive scope of tropical infections that include protozoan, bacterial and viral infections is undoubtedly labor-intensive and time consuming. We present an integrated lab-on-chip using microfluidics technology coupled with reverse transcription (RT), PCR amplification, and microarray hybridization for the simultaneous identification and differentiation of 26 tropical pathogens that cause 14 globally important tropical diseases. Such diagnostics capacity would facilitate evidence-based management of patients, improve the specificity of treatment and, in some cases, even allow contact tracing and other disease-control measures.
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Affiliation(s)
- Jeslin J. L. Tan
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Biopolis, Singapore
| | - Monica Capozzoli
- CI Group, Molecular Diagnostic Business Unit, Microfluidics Division, ST Microelectronics, Catania, Italy
| | - Mitsuharu Sato
- Veredus Laboratories Pte Ltd, Singapore Science Park, Singapore
| | - Wanitda Watthanaworawit
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Clare L. Ling
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Marjorie Mauduit
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Biopolis, Singapore
| | - Benoît Malleret
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Biopolis, Singapore
| | - Anne-Charlotte Grüner
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Biopolis, Singapore
| | - Rosemary Tan
- Veredus Laboratories Pte Ltd, Singapore Science Park, Singapore
| | - François H. Nosten
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
- Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Georges Snounou
- Université Pierre et Marie Curie (Paris VI), Centre Hospitalo-Universitaire Pitié-Salpêtrière, Paris, France
- INSERM UMR S 945, Paris, France
| | - Laurent Rénia
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Biopolis, Singapore
- * E-mail: (LR); (LFPN)
| | - Lisa F. P. Ng
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Biopolis, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- * E-mail: (LR); (LFPN)
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27
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Abstract
The accurate diagnosis of lower respiratory tract infection remains a challenge, with conventional diagnostic methods often failing to identify a causative agent. Here we describe a multiplex real-time PCR assay that has been validated for the detection of the rarely identified atypical bacterial pathogens: Legionella pneumophila, Mycoplasma pneumoniae, and Chlamydophila pneumoniae. Due to the complexity and poor performance of the existing cultural and serological methods for the detection of these pathogens, investigation for them is rarely initiated. This is likely to result in underdetection and empirical treatment regardless of a microbiological diagnosis. The assay described here is designed to address this need.
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Affiliation(s)
- Clare L Ling
- London Regional Microbiology Network, Health Protection Agency, London, UK.
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28
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Jenkins C, Ling CL, Ciesielczuk HL, Lockwood J, Hopkins S, McHugh TD, Gillespie SH, Kibbler CC. Detection and identification of bacteria in clinical samples by 16S rRNA gene sequencing: comparison of two different approaches in clinical practice. J Med Microbiol 2012; 61:483-488. [DOI: 10.1099/jmm.0.030387-0] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Claire Jenkins
- Colindale Microbiological Services, Health Protection Agency, Colindale, London NW9 5AT, UK
- Department of Medical Microbiology, Royal Free Hospital NHS Trust, Pond Street, London NW3 2PF, UK
| | - Clare L. Ling
- Colindale Microbiological Services, Health Protection Agency, Colindale, London NW9 5AT, UK
- Department of Medical Microbiology, Royal Free Hospital NHS Trust, Pond Street, London NW3 2PF, UK
| | - Holly L. Ciesielczuk
- Centre for Clinical Microbiology, Department of Infection, Royal Free Campus, UCL, London NW3 2QG, UK
- Department of Medical Microbiology, Royal Free Hospital NHS Trust, Pond Street, London NW3 2PF, UK
| | - Julianne Lockwood
- Department of Medical Microbiology, Royal Free Hospital NHS Trust, Pond Street, London NW3 2PF, UK
| | - Susan Hopkins
- Centre for Clinical Microbiology, Department of Infection, Royal Free Campus, UCL, London NW3 2QG, UK
- Department of Medical Microbiology, Royal Free Hospital NHS Trust, Pond Street, London NW3 2PF, UK
| | - Timothy D. McHugh
- Centre for Clinical Microbiology, Department of Infection, Royal Free Campus, UCL, London NW3 2QG, UK
| | - Stephen H. Gillespie
- School of Medicine, University of St Andrews, North Haugh, St Andrews, Fife KY16 9TF, UK
- Centre for Clinical Microbiology, Department of Infection, Royal Free Campus, UCL, London NW3 2QG, UK
| | - Christopher C. Kibbler
- Department of Medical Microbiology, Royal Free Hospital NHS Trust, Pond Street, London NW3 2PF, UK
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29
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Williams KJ, Ling CL, Jenkins C, Gillespie SH, McHugh TD. A paradigm for the molecular identification of Mycobacterium species in a routine diagnostic laboratory. J Med Microbiol 2007; 56:598-602. [PMID: 17446280 DOI: 10.1099/jmm.0.46855-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The aim of this study was to improve the identification ofMycobacteriumspecies in the context of a UK teaching hospital. Real-time PCR assays were established to enable the rapid differentiation betweenMycobacterium tuberculosis(MTB) complex andMycobacteriumspecies other thantuberculosis(MOTT), followed by 16S rRNA gene sequencing for the speciation of MOTT. Real-time PCR assays gave comparable results to those from the reference laboratory. The implementation of these PCR assays using an improved bead extraction method has enhanced the mycobacterial diagnostic service at the Royal Free Hospital by providing a rapid means of differentiating between MTB complex and MOTT, and would be simple to implement in similar laboratories. Sequence analysis successfully identified a range ofMycobacteriumspp. representative of those encountered in the clinical setting of the authors, includingMycobacterium aviumcomplex,Mycobacterium fortuitumgroup,Mycobacterium chelonae–Mycobacterium abscessusgroup,Mycobacterium xenopiandMycobacterium gordonae. It provides a useful tool for the identification of MOTT when clinically indicated.
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Affiliation(s)
- K J Williams
- Department of Microbiology, Royal Free Hospital, London NW3 2QG, UK
| | - C L Ling
- Department of Microbiology, Royal Free Hospital, London NW3 2QG, UK
| | - C Jenkins
- Department of Microbiology, Royal Free Hospital, London NW3 2QG, UK
| | - S H Gillespie
- Centre for Medical Microbiology, Hampstead Campus, University College London, London NW3 2PF, UK
| | - T D McHugh
- Centre for Medical Microbiology, Hampstead Campus, University College London, London NW3 2PF, UK
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30
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McHugh TD, Pope CF, Ling CL, Patel S, Billington OJ, Gosling RD, Lipman MC, Gillespie SH. Prospective evaluation of BDProbeTec strand displacement amplification (SDA) system for diagnosis of tuberculosis in non-respiratory and respiratory samples. J Med Microbiol 2004; 53:1215-1219. [PMID: 15585500 DOI: 10.1099/jmm.0.45780-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Nucleic acid amplification techniques (NAATs) have been demonstrated to make significant improvements in the diagnosis of tuberculosis (TB), particularly in the time to diagnosis and the diagnosis of smear-negative TB. The BD ProbeTec strand displacement amplification (SDA) system for the diagnosis of pulmonary and non-pulmonary tuberculosis was evaluated. A total of 689 samples were analysed from patients with clinically suspected TB. Compared with culture, the sensitivity and specificity for pulmonary samples were 98 and 89 %, and against final clinical diagnosis 93 and 92 %, respectively. This assay has undergone limited evaluation for non-respiratory samples and so 331 non-respiratory samples were tested, identifying those specimens that were likely to yield a useful result. These were CSF (n = 104), fine needle aspirates (n = 64) and pus (n = 41). Pleural fluid (n = 47) was identified as a poor specimen. A concern in using the SDA assay was that low-positive samples were difficult to interpret; 7.8 % of specimens fell into this category. Indeed, 64 % of the discrepant results, when compared to final clinical diagnosis, could be assigned as low-positive samples. Specimen type did not predict likelihood of a sample being in the low-positive zone. Although the manufacturers do not describe the concept of a low-positive zone, we have found that it aids clinical diagnosis.
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Affiliation(s)
- T D McHugh
- Centre for Medical Microbiology, Department of Infection, Royal Free & University College Medical School, Pond Street, London NW3 2PF, UK 2Department of Thoracic Medicine, Royal Free Hospital NHS Trust, Pond Street, London NW3 2PF, UK
| | - C F Pope
- Centre for Medical Microbiology, Department of Infection, Royal Free & University College Medical School, Pond Street, London NW3 2PF, UK 2Department of Thoracic Medicine, Royal Free Hospital NHS Trust, Pond Street, London NW3 2PF, UK
| | - C L Ling
- Centre for Medical Microbiology, Department of Infection, Royal Free & University College Medical School, Pond Street, London NW3 2PF, UK 2Department of Thoracic Medicine, Royal Free Hospital NHS Trust, Pond Street, London NW3 2PF, UK
| | - S Patel
- Centre for Medical Microbiology, Department of Infection, Royal Free & University College Medical School, Pond Street, London NW3 2PF, UK 2Department of Thoracic Medicine, Royal Free Hospital NHS Trust, Pond Street, London NW3 2PF, UK
| | - O J Billington
- Centre for Medical Microbiology, Department of Infection, Royal Free & University College Medical School, Pond Street, London NW3 2PF, UK 2Department of Thoracic Medicine, Royal Free Hospital NHS Trust, Pond Street, London NW3 2PF, UK
| | - R D Gosling
- Centre for Medical Microbiology, Department of Infection, Royal Free & University College Medical School, Pond Street, London NW3 2PF, UK 2Department of Thoracic Medicine, Royal Free Hospital NHS Trust, Pond Street, London NW3 2PF, UK
| | - M C Lipman
- Centre for Medical Microbiology, Department of Infection, Royal Free & University College Medical School, Pond Street, London NW3 2PF, UK 2Department of Thoracic Medicine, Royal Free Hospital NHS Trust, Pond Street, London NW3 2PF, UK
| | - S H Gillespie
- Centre for Medical Microbiology, Department of Infection, Royal Free & University College Medical School, Pond Street, London NW3 2PF, UK 2Department of Thoracic Medicine, Royal Free Hospital NHS Trust, Pond Street, London NW3 2PF, UK
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Abstract
AIM To characterise 12 Borrelia burgdorferi sensu lato isolates cultured from ticks collected in the Highlands of Scotland. METHODS Three molecular methods were used: an outer surface membrane protein A (OSP A) gene polymerase chain reaction (PCR) designed to give different molecular weight products with different genomic groups, randomly amplified polymorphic DNA (RAPD) analysis, and ribosomal RNA (rRNA) gene PCRs using genomic group specific primers. RESULTS All of the molecular methods used were quick and easy to perform and capable of differentiating between the different genomic groups of B burgdorferi sensu lato. All 12 tick isolates were characterised successfully with each method: five were characterised as B afzelii and seven were characterised as B burgdorferi sensu stricto. RAPD also identified differences within these genomic groups. CONCLUSIONS From this study, it is now known that at least two different B burgdorferi sensu lato genomic groups are present in the Highlands of Scotland: B afzelii and B burgdorferi sensu stricto. This information can now be used to develop appropriate serological tests, which should improve the diagnosis and management of patients with Lyme disease in Scotland. The molecular methods chosen were found to be useful typing tools and will allow rapid identification of any future isolates.
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Affiliation(s)
- C L Ling
- Microbiology Department, Raigmore Hospital, Inverness, UK
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Abstract
The aim of this study was to make an evidence-based comparison of four commercial enzyme immunoassays (EIAs) (Serion Classics, Sigma Diagnostics, Cambridge Biotech and ICN Diagnostics) and an in-house enzyme immunoassay (EIA) in order to select the most appropriate screening assay for diagnosis of Lyme disease. Borrelia burgdorferi sensu stricto cultured in BSK-H medium was used to develop the in-house assay. Escherichia coli antigen (0.9 mg/ml) was included in the serum diluent to reduce non-specific background. Comparison of the number of tests needed to diagnose (i.e. to indicate a positive result) and the cost per positive diagnosis for the five assays was made using a panel of 176 Western blot-characterised sera. The Cambridge Biotech and Sigma assays had the highest sensitivity but poorer specificity, whereas the Serion and ICN assays had highest specificity but poorer sensitivity. The in-house assay had average sensitivity and specificity, the number of tests needed to diagnose being 2.32 compared to 1.92 for Serion, 2.17 for ICN, 2.5 for Sigma and 2.7 for Cambridge Biotech. In a diagnostic protocol that uses an EIA as screening test, with confirmation by Western blot, a good balance of sensitivity and specificity is essential. The in-house assay was the most cost-effective (lowest cost per positive diagnosis), and is probably the best option for specialist laboratories in Europe.
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Affiliation(s)
- M M Davidson
- Microbiology Department, Raigmore Hospital NHS Trust, Inverness, UK
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Davidson MM, Evans R, Ling CL, Wiseman AD, Joss AWL, Ho-Yen DO. Isolation of Borrelia burgdorferi from ticks in the Highlands of Scotland. J Med Microbiol 1999; 48:59-65. [PMID: 9920126 DOI: 10.1099/00222615-48-1-59] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Borrelia burgdorferi, the causative agent of Lyme disease, was first isolated in 1982 and since then has been regularly isolated from ticks and clinical material in both Continental Europe and the USA. However, only three isolations have been reported in Britain. During the summer of 1997, 128 ticks were collected from two sites in the Highlands of Scotland and examined by the polymerase chain reaction (PCR) and culture. Eleven fresh isolates were obtained from culture and passed up to 22 times. Seven of the tick emulsions were also positive by flagellin gene PCR, and a further one was positive by PCR but negative on culture. All 11 isolate cultures were positive by the flagellin gene PCR. Further studies on four of these isolates confirmed their identity by immunofluorescence, but also detected possible differences between them and B. burgdorferi ACA-1 by enzyme profiles and by PCR with OspA gene primers. Culture of these new strains provides antigens that should improve diagnostic serological tests in Britain.
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