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Nieto-Rosado M, Sands K, Portal EAR, Thomson KM, Carvalho MJ, Mathias J, Milton R, Dyer C, Akpulu C, Boostrom I, Hogan P, Saif H, Sanches Ferreira AD, Hender T, Portal B, Andrews R, Watkins WJ, Zahra R, Shirazi H, Muhammad A, Ullah SN, Jan MH, Akif S, Iregbu KC, Modibbo F, Uwaezuoke S, Audu L, Edwin CP, Yusuf AH, Adeleye A, Mukkadas AS, Mazarati JB, Rucogoza A, Gaju L, Mehtar S, Bulabula ANH, Whitelaw A, Roberts L, Chan G, Bekele D, Solomon S, Abayneh M, Metaferia G, Walsh TR. Colonisation of hospital surfaces from low- and middle-income countries by extended spectrum β-lactamase- and carbapenemase-producing bacteria. Nat Commun 2024; 15:2758. [PMID: 38553439 PMCID: PMC10980694 DOI: 10.1038/s41467-024-46684-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 03/06/2024] [Indexed: 04/02/2024] Open
Abstract
Hospital surfaces can harbour bacterial pathogens, which may disseminate and cause nosocomial infections, contributing towards mortality in low- and middle-income countries (LMICs). During the BARNARDS study, hospital surfaces from neonatal wards were sampled to assess the degree of environmental surface and patient care equipment colonisation by Gram-negative bacteria (GNB) carrying antibiotic resistance genes (ARGs). Here, we perform PCR screening for extended-spectrum β-lactamases (blaCTX-M-15) and carbapenemases (blaNDM, blaOXA-48-like and blaKPC), MALDI-TOF MS identification of GNB carrying ARGs, and further analysis by whole genome sequencing of bacterial isolates. We determine presence of consistently dominant clones and their relatedness to strains causing neonatal sepsis. Higher prevalence of carbapenemases is observed in Pakistan, Bangladesh, and Ethiopia, compared to other countries, and are mostly found in surfaces near the sink drain. Klebsiella pneumoniae, Enterobacter hormaechei, Acinetobacter baumannii, Serratia marcescens and Leclercia adecarboxylata are dominant; ST15 K. pneumoniae is identified from the same ward on multiple occasions suggesting clonal persistence within the same environment, and is found to be identical to isolates causing neonatal sepsis in Pakistan over similar time periods. Our data suggests persistence of dominant clones across multiple time points, highlighting the need for assessment of Infection Prevention and Control guidelines.
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Affiliation(s)
- Maria Nieto-Rosado
- Department of Biology, Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK.
- Division of Infection and Immunity, Cardiff University, Cardiff, UK.
| | - Kirsty Sands
- Department of Biology, Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
- Division of Infection and Immunity, Cardiff University, Cardiff, UK
| | - Edward A R Portal
- Department of Biology, Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
- Division of Infection and Immunity, Cardiff University, Cardiff, UK
| | - Kathryn M Thomson
- Department of Biology, Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
- Division of Infection and Immunity, Cardiff University, Cardiff, UK
| | - Maria J Carvalho
- Division of Infection and Immunity, Cardiff University, Cardiff, UK
- Department of Medical Sciences, Institute of Biomedicine, University of Aveiro, Aveiro, Portugal
| | - Jordan Mathias
- Division of Infection and Immunity, Cardiff University, Cardiff, UK
| | - Rebecca Milton
- Division of Infection and Immunity, Cardiff University, Cardiff, UK
- Centre for Trials Research, Cardiff University, Cardiff, UK
| | - Calie Dyer
- Division of Infection and Immunity, Cardiff University, Cardiff, UK
- Centre for Trials Research, Cardiff University, Cardiff, UK
| | - Chinenye Akpulu
- Department of Biology, Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
- Division of Infection and Immunity, Cardiff University, Cardiff, UK
| | - Ian Boostrom
- Division of Infection and Immunity, Cardiff University, Cardiff, UK
| | - Patrick Hogan
- Division of Infection and Immunity, Cardiff University, Cardiff, UK
| | - Habiba Saif
- Division of Infection and Immunity, Cardiff University, Cardiff, UK
| | - Ana D Sanches Ferreira
- Division of Infection and Immunity, Cardiff University, Cardiff, UK
- Parasites and Microbes Programme, Wellcome Sanger Institute Hinxton, Hinxton, UK
| | - Thomas Hender
- Division of Infection and Immunity, Cardiff University, Cardiff, UK
| | - Barbra Portal
- Division of Infection and Immunity, Cardiff University, Cardiff, UK
| | - Robert Andrews
- Division of Infection and Immunity, Cardiff University, Cardiff, UK
| | - W John Watkins
- Division of Infection and Immunity, Cardiff University, Cardiff, UK
| | - Rabaab Zahra
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Haider Shirazi
- Pakistan Institute of Medical Sciences, Islamabad, Pakistan
| | - Adil Muhammad
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Syed Najeeb Ullah
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Muhammad Hilal Jan
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Shermeen Akif
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
| | | | | | | | | | - Chinago P Edwin
- Department of Microbiology, Medway Maritime Hospital NHS Foundation Trust, Gillingham, Kent, UK
- Aminu Kano Teaching Hospital, Kano, Nigeria
| | | | - Adeola Adeleye
- Murtala Muhammad Specialist Hospital, Kano City, Nigeria
| | | | | | - Aniceth Rucogoza
- The National Reference Laboratory, Rwanda Biomedical Centre, Kigali, Rwanda
| | - Lucie Gaju
- The National Reference Laboratory, Rwanda Biomedical Centre, Kigali, Rwanda
| | - Shaheen Mehtar
- Unit of IPC, Stellenbosch University, Cape Town, South Africa
- Infection Control Africa Network, Cape Town, South Africa
| | - Andrew N H Bulabula
- Infection Control Africa Network, Cape Town, South Africa
- Department of Global Health, Stellenbosch University, Cape Town, South Africa
| | - Andrew Whitelaw
- Division of Medical Microbiology, Stellenbosch University, Cape Town, South Africa
- National Health Laboratory Service, Tygerberg Hospital, Cape Town, South Africa
| | - Lauren Roberts
- Division of Medical Microbiology, Stellenbosch University, Cape Town, South Africa
| | - Grace Chan
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatrics and Child Health, St Paul's Hospital Millennium Medical College, Addis Ababa, Ethiopia
| | - Delayehu Bekele
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, USA
- Department of Obstetrics and Gynecology, St Paul's Hospital Millennium Medical College, Addis Ababa, Ethiopia
| | - Semaria Solomon
- Department of Microbiology, Immunology and Parasitology, St Paul's Hospital Millennium Medical College, Addis Ababa, Ethiopia
| | - Mahlet Abayneh
- Department of Pediatrics and Child Health, St Paul's Hospital Millennium Medical College, Addis Ababa, Ethiopia
| | - Gesit Metaferia
- Department of Microbiology, Immunology and Parasitology, St Paul's Hospital Millennium Medical College, Addis Ababa, Ethiopia
| | - Timothy R Walsh
- Department of Biology, Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
- Division of Infection and Immunity, Cardiff University, Cardiff, UK
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Portal EAR, Sands K, Farley C, Boostrom I, Jones E, Barrell M, Carvalho MJ, Milton R, Iregbu K, Modibbo F, Uwaezuoke S, Akpulu C, Audu L, Edwin C, Yusuf AH, Adeleye A, Mukkadas AS, Maduekwe D, Gambo S, Sani J, Walsh TR, Spiller OB. Characterisation of colistin resistance in Gram-negative microbiota of pregnant women and neonates in Nigeria. Nat Commun 2024; 15:2302. [PMID: 38485761 PMCID: PMC10940312 DOI: 10.1038/s41467-024-45673-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 01/30/2024] [Indexed: 03/18/2024] Open
Abstract
A mobile colistin resistance gene mcr was first reported in 2016 in China and has since been found with increasing prevalence across South-East Asia. Here we survey the presence of mcr genes in 4907 rectal swabs from mothers and neonates from three hospital sites across Nigeria; a country with limited availability or history of colistin use clinically. Forty mother and seven neonatal swabs carried mcr genes in a range of bacterial species: 46 Enterobacter spp. and single isolates of; Shigella, E. coli and Klebsiella quasipneumoniae. Ninety percent of the genes were mcr-10 (n = 45) we also found mcr-1 (n = 3) and mcr-9 (n = 1). While the prevalence during this collection (2015-2016) was low, the widespread diversity of mcr-gene type and range of bacterial species in this sentinel population sampling is concerning. It suggests that agricultural colistin use was likely encouraging sustainment of mcr-positive isolates in the community and implementation of medical colistin use will rapidly select and expand resistant isolates.
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Affiliation(s)
- E A R Portal
- Department of Medical Microbiology, Division of Infection and Immunity, Cardiff University, Cardiff, UK.
- Ineos Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, Oxford, UK.
| | - K Sands
- Department of Medical Microbiology, Division of Infection and Immunity, Cardiff University, Cardiff, UK.
- Ineos Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, Oxford, UK.
| | - C Farley
- Department of Medical Microbiology, Division of Infection and Immunity, Cardiff University, Cardiff, UK
| | - I Boostrom
- Department of Medical Microbiology, Division of Infection and Immunity, Cardiff University, Cardiff, UK
| | - E Jones
- Department of Medical Microbiology, Division of Infection and Immunity, Cardiff University, Cardiff, UK
| | - M Barrell
- Department of Medical Microbiology, Division of Infection and Immunity, Cardiff University, Cardiff, UK
| | - M J Carvalho
- Department of Medical Microbiology, Division of Infection and Immunity, Cardiff University, Cardiff, UK
- Institute of Biomedicine, Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - R Milton
- Department of Medical Microbiology, Division of Infection and Immunity, Cardiff University, Cardiff, UK
- Centre for Trials Research, Cardiff University, Cardiff, UK
| | - K Iregbu
- National Hospital Abuja, Abuja, Nigeria
| | - F Modibbo
- Murtala Muhammad Specialist Hospital, Kano, Nigeria
| | - S Uwaezuoke
- Federal Medical Centre -Jabi, Abuja, Nigeria
| | - C Akpulu
- Ineos Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, Oxford, UK
- National Hospital Abuja, Abuja, Nigeria
- Interdisciplinary Biosciences DTP, University of Oxford, Oxford, UK
| | - L Audu
- National Hospital Abuja, Abuja, Nigeria
| | - C Edwin
- Department of Medical Microbiology Aminu Kano Teaching Hospital, Kano, Nigeria
| | - A H Yusuf
- Department of Medical Microbiology Aminu Kano Teaching Hospital, Kano, Nigeria
| | - A Adeleye
- Department of Medical Microbiology Aminu Kano Teaching Hospital, Kano, Nigeria
| | - A S Mukkadas
- Department of Medical Microbiology Aminu Kano Teaching Hospital, Kano, Nigeria
| | - D Maduekwe
- Wuse General Hospital Abuja, Abuja, Nigeria
| | - S Gambo
- Department of Paediatrics, Murtala Muhammed Specialist Hospital, Kano, Nigeria
| | - J Sani
- Department of Paediatrics Abdullahi Wase Teaching Hospital, Kano, Nigeria
| | - T R Walsh
- Department of Medical Microbiology, Division of Infection and Immunity, Cardiff University, Cardiff, UK
- Ineos Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, Oxford, UK
| | - O B Spiller
- Department of Medical Microbiology, Division of Infection and Immunity, Cardiff University, Cardiff, UK
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Naha S, Basak P, Sands K, Milton R, Carvalho MJ, Mitra S, Bhattacharjee A, Sinha A, Mukherjee S, Saha B, Chattopadhyay P, Chakravorty PS, Nandy RK, Dutta S, Walsh TR, Basu S. Carriage and within-host diversity of mcr-1.1-harbouring Escherichia coli from pregnant mothers: inter- and intra-mother transmission dynamics of mcr-1.1. Emerg Microbes Infect 2023; 12:2278899. [PMID: 37929689 PMCID: PMC10773534 DOI: 10.1080/22221751.2023.2278899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 10/30/2023] [Indexed: 11/07/2023]
Abstract
Exchange of antimicrobial resistance genes via mobile genetic elements occur in the gut which can be transferred from mother to neonate during birth. This study is the first to analyse transmissible colistin resistance gene, mcr, in pregnant mothers and neonates. Samples were collected from pregnant mothers (rectal) and septicaemic neonates (rectal and blood) and analysed for the presence of mcr, its transmissibility, genome diversity, and exchange of mcr between isolates within an individual and across different individuals (not necessarily mother-baby pairs). mcr-1.1 was detected in rectal samples of pregnant mothers (n = 10, 0.9%), but not in neonates. All mcr-positive mothers gave birth to healthy neonates from whom rectal specimen were not collected. Hence, the transmission of mcr between these mother-neonate pairs could not be studied. mcr-1.1 was noted only in Escherichia coli (phylogroup A & B1), and carried few resistance and virulence genes. Isolates belonged to diverse sequence types (n = 11) with two novel STs (ST12452, ST12455). mcr-1.1 was borne on conjugative IncHI2 bracketed between ISApl1 on Tn6630, and the plasmids exhibited similarities in sequences across the study isolates. Phylogenetic comparison showed that study isolates were related to mcr-positive isolates of animal origin from Southeast Asian countries. Spread of mcr-1.1 within this study occurred either via similar mcr-positive clones or similar mcr-bearing plasmids in mothers. Though this study could not build evidence for mother-baby transmission but the presence of such genes in the maternal specimen may enhance the chances of transmission to neonates.
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Affiliation(s)
- Sharmi Naha
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Priyanka Basak
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Kirsty Sands
- Institute of Infection and Immunity, Cardiff University, Cardiff, UK
- Department of Zoology, Ineos Oxford Institute of Antimicrobial Research, University of Oxford, Oxford, UK
| | - Rebecca Milton
- Institute of Infection and Immunity, Cardiff University, Cardiff, UK
- Centre for Trials Research, Cardiff University, Cardiff, UK
| | - Maria J. Carvalho
- Institute of Infection and Immunity, Cardiff University, Cardiff, UK
- Department of Medical Sciences, Institute of Biomedicine, University of Aveiro, Aveiro, Portugal
| | - Shravani Mitra
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Amrita Bhattacharjee
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Anuradha Sinha
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Suchandra Mukherjee
- Department of Neonatology, Institute of Post-Graduate and Medical Education & Research, Kolkata, India
| | - Bijan Saha
- Department of Neonatology, Institute of Post-Graduate and Medical Education & Research, Kolkata, India
| | - Pinaki Chattopadhyay
- Department of Neonatology, Institute of Post-Graduate and Medical Education & Research, Kolkata, India
| | - Partha Sarathi Chakravorty
- Department of Obstetrics & Gynecology, Institute of Post-Graduate and Medical Education & Research, Kolkata, India
| | - Ranjan Kumar Nandy
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Shanta Dutta
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Timothy R. Walsh
- Institute of Infection and Immunity, Cardiff University, Cardiff, UK
- Department of Zoology, Ineos Oxford Institute of Antimicrobial Research, University of Oxford, Oxford, UK
| | - Sulagna Basu
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
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Baumann BC, Laugeman E, Kohlmyer S, Levine L, Russell K, Smith Z, Reimers M, Michalski JM, Picus J, Pachynski R, Sivaraman A, Thomas L, Smelser W, Sands K, Kim E, Frankel J, Moravan MJ, Gay HA, Price AT. ARTIA-Bladder: Daily Online Adaptive Short-Course Radiation Therapy (RT) and Concurrent Chemotherapy for Muscle-Invasive Bladder Cancer (MIBC): A Prospective Trial of an Individualized Approach for Reducing Bowel and Bladder Toxicity. Int J Radiat Oncol Biol Phys 2023; 117:e366. [PMID: 37785254 DOI: 10.1016/j.ijrobp.2023.06.2461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) Concurrent chemo-radiotherapy is commonly prescribed for muscle-invasive bladder cancer (MIBC). Post hoc analysis of two large, randomized trials found that hypofractionation improves loco-regional control (LRC) vs. standard fractionation in this population. A challenge in traditional image-guided radiotherapy of the bladder is that daily changes in bladder position and size requires large margins to ensure target coverage. This makes it difficult to spare uninvolved bladder from high-dose treatment, increases the risk of bowel toxicity, and results in historical rates of acute G3+ toxicity exceeding 20-30%. Daily online adaptive RT (ART) may enable reduced, personalized margins that maintain target coverage while reducing dose to OARs. This prospective clinical trial will test whether: 1) participants undergoing ART for MIBC have a lower rate of acute G3+ GI/GU toxicity compared with the 31% historical control rate (Stage III BC2001 trial), and 2) 2-year LRC with ART will be non-inferior to historical controls (75%). MATERIALS/METHODS This multi-national trial will enroll 165 adult subjects with stage cT2-T4aN0M0 urothelial MIBC. Subjects will have undergone an attempt at maximal transurethral resection of bladder tumor. Patients with clinically involved nodes or G2+ GI or G3+ GU symptoms/conditions at baseline are ineligible. Concurrent with chemotherapy, participants will receive (at the discretion of the investigator) either 55 Gy in 20 fx to whole-bladder or 46 Gy in 20 fx to whole-bladder plus simultaneous in-field boost of 55 Gy in 20 fx to tumor bed. A personalized ITV will be derived for each subject based on bladder expansion, as assessed on two CT simulations separated by 30 min. Daily ART will be attempted for all subjects. The primary endpoint is acute G3+ GI/GU toxicity. Secondary endpoints are LRC; quality of life (EORTC QLQ-BLM30, EPIC 26 bowel and urinary); global function (EQ-5D-5L ); 2-year disease-free, bladder intact event-free, and overall survival; 2-year bladder cancer-specific mortality; NTCP model of acute GI toxicity for hypofractionated bladder RT; workflow feasibility of ART; improved target coverage ± reduced dose to critical OARs vs. non-ART dosimetry; acute G3+ GI/GU toxicity rate in subjects with ≥75% of their treatments as ART; and acute G3+ GI/GU toxicity in the cohort treated with partial bladder boost. Exploratory translational and correlative endpoints will also be examined. RESULTS This trial opened to enrollment on Feb 2, 2023; the study duration is expected to be 4-5 years. CONCLUSION This prospective clinical trial will provide robust clinical data to inform healthcare providers' decisions on the use of daily online ART and hypofractionation as a bladder preservation strategy for this population.
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Affiliation(s)
- B C Baumann
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO
| | - E Laugeman
- Washington University School of Medicine in St. Louis, Department of Radiation Oncology, St. Louis, MO
| | | | - L Levine
- Varian Medical Systems, A Siemens Healthineers Company, Palo Alto, CA
| | - K Russell
- Varian Medical Systems, Palo Alto, CA
| | - Z Smith
- Department of Surgery, Division of Urology, Washington University School of Medicine, St. Louis, MO
| | - M Reimers
- Washington University School of Medicine, Department of Medicine, Division of Medical Oncology, St. Louis, MO
| | - J M Michalski
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO
| | - J Picus
- Department of Medicine, Division of Hematology and Oncology, Washington University School of Medicine, St. Louis, MO
| | - R Pachynski
- Department of Medicine, Division of Hematology and Oncology, Washington University School of Medicine, St. Louis, MO
| | - A Sivaraman
- Washington University in St. Louis, St. Louis, MO
| | - L Thomas
- Washington University in St. Louis, St. Louis, MO
| | - W Smelser
- Washington University in St. Louis, St Louis, MO
| | - K Sands
- Washington University in St. Louis, St. Louis, MO
| | - E Kim
- Department of Surgery, Division of Urology, Washington University School of Medicine, St. Louis, MO
| | - J Frankel
- Washington University in St. Louis, St. Louis, MO
| | - M J Moravan
- Department of Radiation Oncology, Washington University in St. Louis, St. Louis, MO
| | - H A Gay
- Washington University School of Medicine in St. Louis, Department of Radiation Oncology, St. Louis, MO
| | - A T Price
- University Hospitals, Department of Radiation Oncology, Case Western Reserve University, Cleveland, OH
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Bhattacharjee A, Sands K, Mitra S, Basu R, Saha B, Clermont O, Dutta S, Basu S. A Decade-Long Evaluation of Neonatal Septicaemic Escherichia coli: Clonal Lineages, Genomes, and New Delhi Metallo-Beta-Lactamase Variants. Microbiol Spectr 2023; 11:e0521522. [PMID: 37367488 PMCID: PMC10434172 DOI: 10.1128/spectrum.05215-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 05/27/2023] [Indexed: 06/28/2023] Open
Abstract
Longitudinal studies of extraintestinal pathogenic Escherichia coli (ExPEC) and epidemic clones of E. coli in association with New Delhi metallo-β-lactamase (blaNDM) in septicaemic neonates are rare. This study captured the diversity of 80 E. coli isolates collected from septicaemic neonates in terms of antibiotic susceptibility, resistome, phylogroups, sequence types (ST), virulome, plasmids, and integron types over a decade (2009 to 2019). Most of the isolates were multidrug-resistant and, 44% of them were carbapenem-resistant, primarily due to blaNDM. NDM-1 was the sole NDM-variant present in conjugative IncFIA/FIB/FII replicons until 2013, and it was subsequently replaced by other variants, such as NDM-5/-7 found in IncX3/FII. A core genome analysis for blaNDM+ve isolates showed the heterogeneity of the isolates. Fifty percent of the infections were caused by isolates of phylogroups B2 (34%), D (11.25%), and F (4%), whereas the other half were caused by phylogroups A (25%), B1 (11.25%), and C (14%). The isolates were further distributed in approximately 20 clonal complexes (STC), including five epidemic clones (ST131, ST167, ST410, ST648, and ST405). ST167 and ST131 (subclade H30Rx) were dominant, with most of the ST167 being blaNDM+ve and blaCTX-M-15+ve. In contrast, the majority of ST131 isolates were blaNDM-ve but blaCTX-M-15+ve, and they possessed more virulence determinants than did ST167. A single nucleotide polymorphism (SNP)-based comparative genome analysis of epidemic clones ST167 and ST131 in a global context revealed that the study isolates were present in close proximity but were distant from global isolates. The presence of antibiotic-resistant epidemic clones causing sepsis calls for a modification of the recommended antibiotics with which to treat neonatal sepsis. IMPORTANCE Multidrug-resistant and virulent ExPEC causing sepsis in neonates is a challenge to neonatal health. The presence of enzymes, such as carbapenemases (blaNDM) that hydrolyze most β-lactam antibiotic compounds, result in difficulties when treating neonates. The characterization of ExPECs collected over 10 years showed that 44% of ExPECs were carbapenem-resistant, possessing transmissible blaNDM genes. The isolates belonged to different phylogroups that are considered to be either commensals or virulent. The isolates were distributed in around 20 clonal complexes (STC), including two predominant epidemic clones (ST131 and ST167). ST167 possessed few virulence determinants but was blaNDM+ve. In contrast, ST131 harbored several virulence determinants but was blaNDM-ve. A comparison of the genomes of these epidemic clones in a global context revealed that the study isolates were present in close proximity but were distant from global isolates. The presence of epidemic clones in a vulnerable population with contrasting characteristics and the presence of resistance genes call for strict vigilance.
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Affiliation(s)
- Amrita Bhattacharjee
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, West Bengal, India
| | - Kirsty Sands
- Division of Medical Microbiology, Institute of Infection and Immunity, Cardiff University, United Kingdom
- Ineos Oxford Institute of Antimicrobial Research, Department of Biology, University of Oxford, United Kingdom
| | - Shravani Mitra
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, West Bengal, India
| | - Ritojeet Basu
- Department of Economics, University of Warwick, Coventry, United Kingdom
| | - Bijan Saha
- Department of Neonatology, Institute of Post-Graduate Medical Education & Research and SSKM Hospital, Kolkata, West Bengal, India
| | - Olivier Clermont
- Université de Paris, IAME, UMR1137, INSERM, Paris, France
- Université Sorbonne Paris Nord, IAME, Paris, France
| | - Shanta Dutta
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, West Bengal, India
| | - Sulagna Basu
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, West Bengal, India
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6
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Kumar CK, Sands K, Walsh TR, O'Brien S, Sharland M, Lewnard JA, Hu H, Srikantiah P, Laxminarayan R. Global, regional, and national estimates of the impact of a maternal Klebsiella pneumoniae vaccine: A Bayesian modeling analysis. PLoS Med 2023; 20:e1004239. [PMID: 37216371 DOI: 10.1371/journal.pmed.1004239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 04/26/2023] [Indexed: 05/24/2023] Open
Abstract
BACKGROUND Despite significant global progress in reducing neonatal mortality, bacterial sepsis remains a major cause of neonatal deaths. Klebsiella pneumoniae (K. pneumoniae) is the leading pathogen globally underlying cases of neonatal sepsis and is frequently resistant to antibiotic treatment regimens recommended by the World Health Organization (WHO), including first-line therapy with ampicillin and gentamicin, second-line therapy with amikacin and ceftazidime, and meropenem. Maternal vaccination to prevent neonatal infection could reduce the burden of K. pneumoniae neonatal sepsis in low- and middle-income countries (LMICs) but the potential impact of vaccination remains poorly quantified. We estimated the potential impact of such vaccination on cases and deaths of K. pneumoniae neonatal sepsis and project the global effects of routine immunization of pregnant women with the K. pneumoniae vaccine as antimicrobial resistance (AMR) increases. METHODS AND FINDINGS We developed a Bayesian mixture-modeling framework to estimate the effects of a hypothetical K. pneumoniae maternal vaccine with 70% efficacy administered with coverage equivalent to that of the maternal tetanus vaccine on neonatal sepsis infections and mortality. To parameterize our model, we used data from 3 global studies of neonatal sepsis and/or mortality-with 2,330 neonates who died with sepsis surveilled from 2016 to 2020 undertaken in 18 mainly LMICs across all WHO regions (Ethiopia, Kenya, Mali, Mozambique, Nigeria, Rwanda, Sierra Leone, South Africa, Uganda, Brazil, Italy, Greece, Pakistan, Bangladesh, India, Thailand, China, and Vietnam). Within these studies, 26.95% of fatal neonatal sepsis cases were culture-positive for K. pneumoniae. We analyzed 9,070 K. pneumoniae genomes from human isolates gathered globally from 2001 to 2020 to quantify the temporal rate of acquisition of AMR genes in K. pneumoniae isolates to predict the future number of drug-resistant cases and deaths that could be averted by vaccination. Resistance rates to carbapenems are increasing most rapidly and 22.43% [95th percentile Bayesian credible interval (CrI): 5.24 to 41.42] of neonatal sepsis deaths are caused by meropenem-resistant K. pneumoniae. Globally, we estimate that maternal vaccination could avert 80,258 [CrI: 18,084 to 189,040] neonatal deaths and 399,015 [CrI: 334,523 to 485,442] neonatal sepsis cases yearly worldwide, accounting for more than 1.49% [CrI: 0.33 to 3.51] of all neonatal deaths. The largest relative benefits are in Africa (Sierra Leone, Mali, Niger) and South-East Asia (Bangladesh) where vaccination could avert over 5% of all neonatal deaths. Nevertheless, our modeling only considers country-level trends in K. pneumoniae neonatal sepsis deaths and is unable to consider within-country variability in bacterial prevalence that may impact the projected burden of sepsis. CONCLUSIONS A K. pneumoniae maternal vaccine could have widespread, sustained global benefits as AMR in K. pneumoniae continues to increase.
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Affiliation(s)
- Chirag K Kumar
- Princeton University, Princeton, New Jersey, United States of America
| | - Kirsty Sands
- Ineos Oxford Institute for Antimicrobial Resistance, Department of Zoology, Oxford, United Kingdom
| | - Timothy R Walsh
- Ineos Oxford Institute for Antimicrobial Resistance, Department of Zoology, Oxford, United Kingdom
| | - Seamus O'Brien
- Global Antibiotic Research and Development Partnership, Geneva, Switzerland
| | - Mike Sharland
- Center for Neonatal and Paediatric Infection (CNPI), Institute of Infection and Immunity, St George's University of London, London, United Kingdom
| | - Joseph A Lewnard
- Division of Epidemiology, School of Public Health, University of California at Berkeley, Berkeley, California, United States of America
| | - Hao Hu
- Bill & Melinda Gates Foundation, Seattle, Washington, United States of America
| | - Padmini Srikantiah
- Bill & Melinda Gates Foundation, Seattle, Washington, United States of America
| | - Ramanan Laxminarayan
- Princeton University, Princeton, New Jersey, United States of America
- One Health Trust, Bengaluru, India
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7
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David S, Mentasti M, Sands K, Portal E, Graham L, Watkins J, Williams C, Healy B, Spiller OB, Aanensen DM, Wootton M, Jones L. Genomic surveillance of multidrug-resistant Klebsiella in Wales reveals persistent spread of Klebsiella pneumoniae ST307 and adaptive evolution of pOXA-48-like plasmids. Microb Genom 2023; 9. [PMID: 37227259 DOI: 10.1099/mgen.0.001016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023] Open
Affiliation(s)
- Sophia David
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford OX3 7LF, UK
| | - Massimo Mentasti
- Specialist Antimicrobial Chemotherapy Unit, Public Health Wales Microbiology, Cardiff CF14 4XW, UK
| | - Kirsty Sands
- Department of Zoology, University of Oxford, Oxford OX1 3SZ, UK
- Division of Infection and Immunity, Cardiff University, Cardiff CF14 4XN, UK
| | - Edward Portal
- Division of Infection and Immunity, Cardiff University, Cardiff CF14 4XN, UK
| | - Lee Graham
- Pathogen Genomics Unit, Public Health Wales Microbiology, Cardiff CF14 4XW, UK
| | - Joanne Watkins
- Pathogen Genomics Unit, Public Health Wales Microbiology, Cardiff CF14 4XW, UK
| | - Catie Williams
- Pathogen Genomics Unit, Public Health Wales Microbiology, Cardiff CF14 4XW, UK
| | - Brendan Healy
- Public Health Wales Microbiology, Swansea SA2 8QA, UK
| | - Owen B Spiller
- Division of Infection and Immunity, Cardiff University, Cardiff CF14 4XN, UK
| | - David M Aanensen
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford OX3 7LF, UK
| | - Mandy Wootton
- Specialist Antimicrobial Chemotherapy Unit, Public Health Wales Microbiology, Cardiff CF14 4XW, UK
| | - Lim Jones
- Specialist Antimicrobial Chemotherapy Unit, Public Health Wales Microbiology, Cardiff CF14 4XW, UK
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8
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Umair M, Hassan B, Farzana R, Ali Q, Sands K, Mathias J, Afegbua S, Haque MN, Walsh TR, Mohsin M. International manufacturing and trade in colistin, its implications in colistin resistance and One Health global policies: a microbiological, economic, and anthropological study. Lancet Microbe 2023; 4:e264-e276. [PMID: 36931291 DOI: 10.1016/s2666-5247(22)00387-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 11/27/2022] [Accepted: 11/29/2022] [Indexed: 03/16/2023]
Abstract
BACKGROUND The emergence of colistin-resistant Enterobacterales is a global public health concern, yet colistin is still widely used in animals that are used for food as treatment, metaphylaxis, prophylaxis, and growth promotion. Herein, we investigate the effect of colistin-resistant Enterobacterales in Pakistan, global trade of colistin, colistin use at the farm level, and relevant socioeconomic factors. METHODS We conducted a microbiological, economic, and anthropological study of colistin-resistant Escherichia coli in humans, animals, and the environment and international trade and knowledge of colistin in Pakistan, Bangladesh, Nigeria, China, India, and Viet Nam. We collected backyard poultry cloacal swabs, commercial broiler cloacal swabs, cattle and buffalo rectal swabs, human rectal swabs, wild bird droppings, cattle and buffalo meat, sewage water, poultry flies, chicken meat, and canal water from 131 sites across Faisalabad, Pakistan, to be tested for mcr-1-positive and mcr-3-positive Escherichia coli. We recruited new patients admitted to Allied Hospital, Faisalabad, Pakistan, with abdominal pain and diarrhoea for rectal swabs. Patients with dysentery and those who were already on antibiotic treatment were excluded. Data for colistin trade between 2017 and 2020, including importation, manufacturing, and usage, were accessed from online databases and government sources in Pakistan, Bangladesh, and Nigeria. We recruited participants from poultry farms and veterinary drug stores in Pakistan and Nigeria to be interviewed using a structured questionnaire. International manufacturing, import, and export data; value analysis; and trade routes of colistin pharmaceutical raw material (PRM), feed additive, and finished pharmaceutical products (FPPs) were accessed from 2017-21 export data sets. FINDINGS We collected 1131 samples between May 12, 2018, and July 1, 2019: backyard poultry cloacal swabs (n=100), commercial broiler cloacal swabs (n=102), cattle and buffalo rectal swabs (n=188), human rectal swabs (n=200), wild bird droppings (n=100), cattle and buffalo meat (n=100), sewage water (n=90), poultry flies (n=100), chicken meat (n=100), and canal water (n=51). We recruited 200 inpatients at Allied Hospital, Faisalabad, Pakistan, between Nov 15, 2018, and Dec 14, 2018, for rectal swabs. We recruited 21 participants between Jan 1, 2020, and Dec 31, 2020, from poultry farms and drug stores in Pakistan and Nigeria to be interviewed. 75 (7%) of 1131 samples contained mcr-1-positive E coli, including wild bird droppings (25 [25%] of 100), commercial broiler cloacal swabs (17 [17%] of 100), backyard poultry cloacal swabs (one [1%] of 100), chicken meat (13 [13%] of 100), cattle and buffalo meat (two [2%] of 100), poultry flies (eight [8%] of 100), sewage water (six [7%] of 90), and human rectal swabs (three [2%] of 200). During 2017-20, Pakistan imported 275·5 tonnes (68·9 tonnes per year, 95% CI 41·2-96·6) of colistin as PRM, all sourced from China, 701·9 tonnes (175·5 tonnes per year, 140·9-210·1) of colistin as feed additives from China and Viet Nam, and 63·0 tonnes (15·8 tonnes per year, 10·4-21·1) of colistin as FPPs from various countries in Asia and Europe. For Bangladesh and Nigeria, colistin PRM and FPPs were imported from China and Europe. Colistin knowledge and usage practices in Pakistan and Nigeria were unsatisfactory in terms of understanding of the effects on human medicine and usage other than for treatment purposes. China is the major manufacturer of PRM and feed additive colistin and exported a total of 2664·8 tonnes (666·2 tonnes per year, 95% CI 262·1 to 1070·2) of PRM and 2570·2 tonnes (642·6 tonnes per year, -89·4 to 1374·5) of feed additive in 1330 shipments during 2018-21 to 21 countries. INTERPRETATION Regardless of 193 countries signing the UN agreement to tackle antimicrobial resistance, trading of colistin as PRM, FPPs, and feed additive or growth promoter in low-income and middle-income countries continues unabated. Robust national and international laws are urgently required to mitigate the international trade of this antimicrobial listed on WHO Critically Important Antimicrobials for Human Medicine. FUNDING Pakistan Agricultural Research Council and INEOS Oxford Institute for Antimicrobial Research TRANSLATION: For the Urdu translation of the abstract see Supplementary Materials section.
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Affiliation(s)
- Muhammad Umair
- Institute of Microbiology, University of Agriculture, Faisalabad, Pakistan; INEOS Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, Oxford, UK
| | - Brekhna Hassan
- School of Medicine, Department of Medical Microbiology, Institute of Infection and Immunity, Cardiff University, Cardiff, UK
| | - Refath Farzana
- INEOS Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, Oxford, UK
| | - Qasim Ali
- Institute of Microbiology, University of Agriculture, Faisalabad, Pakistan; Department of Virology, National Institutes of Health, Islamabad, Pakistan
| | - Kirsty Sands
- INEOS Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, Oxford, UK; School of Medicine, Department of Medical Microbiology, Institute of Infection and Immunity, Cardiff University, Cardiff, UK
| | - Jordan Mathias
- School of Medicine, Department of Medical Microbiology, Institute of Infection and Immunity, Cardiff University, Cardiff, UK
| | - Seniyat Afegbua
- Department of Microbiology, Faculty of Life Sciences, Ahmadu Bello University, Zaria, Nigeria
| | | | - Timothy R Walsh
- INEOS Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, Oxford, UK.
| | - Mashkoor Mohsin
- Institute of Microbiology, University of Agriculture, Faisalabad, Pakistan.
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Khan UB, Portal EAR, Sands K, Lo S, Chalker VJ, Jauneikaite E, Spiller OB. Genomic Analysis Reveals New Integrative Conjugal Elements and Transposons in GBS Conferring Antimicrobial Resistance. Antibiotics (Basel) 2023; 12:544. [PMID: 36978411 PMCID: PMC10044541 DOI: 10.3390/antibiotics12030544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/02/2023] [Accepted: 03/03/2023] [Indexed: 03/11/2023] Open
Abstract
Streptococcus agalactiae or group B streptococcus (GBS) is a leading cause of neonatal sepsis and increasingly found as an invasive pathogen in older patient populations. Beta-lactam antibiotics remain the most effective therapeutic with resistance rarely reported, while the majority of GBS isolates carry the tetracycline resistance gene tet(M) in fixed genomic positions amongst five predominant clonal clades. In the UK, GBS resistance to clindamycin and erythromycin has increased from 3% in 1991 to 11.9% (clindamycin) and 20.2% (erythromycin), as reported in this study. Here, a systematic investigation of antimicrobial resistance genomic content sought to fully characterise the associated mobile genetic elements within phenotypically resistant GBS isolates from 193 invasive and non-invasive infections of UK adult patients collected during 2014 and 2015. Resistance to erythromycin and clindamycin was mediated by erm(A) (16/193, 8.2%), erm(B) (16/193, 8.2%), mef(A)/msr(D) (10/193, 5.1%), lsa(C) (3/193, 1.5%), lnu(C) (1/193, 0.5%), and erm(T) (1/193, 0.5%) genes. The integrative conjugative elements (ICEs) carrying these genes were occasionally found in combination with high gentamicin resistance mediating genes aac(6')-aph(2″), aminoglycoside resistance genes (ant(6-Ia), aph(3'-III), and/or aad(E)), alternative tetracycline resistance genes (tet(O) and tet(S)), and/or chloramphenicol resistance gene cat(Q), mediating resistance to multiple classes of antibiotics. This study provides evidence of the retention of previously reported ICESag37 (n = 4), ICESag236 (n = 2), and ICESpy009 (n = 3), as well as the definition of sixteen novel ICEs and three novel transposons within the GBS lineage, with no evidence of horizontal transfer.
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Affiliation(s)
- Uzma Basit Khan
- Department of Medical Microbiology, Division of Infection and Immunity, Cardiff University, 6th Floor University Hospital of Wales, Cardiff CF14 4XN, UK
- Parasites and Microbes Programme, The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Edward A. R. Portal
- Department of Medical Microbiology, Division of Infection and Immunity, Cardiff University, 6th Floor University Hospital of Wales, Cardiff CF14 4XN, UK
- Bacterial Reference Department, UK Health Security Agency, London NW9 5DF, UK
- Department of Biology, Ineos Oxford Institute, University of Oxford, Oxford OX1 3RE, UK
| | - Kirsty Sands
- Department of Medical Microbiology, Division of Infection and Immunity, Cardiff University, 6th Floor University Hospital of Wales, Cardiff CF14 4XN, UK
- Department of Biology, Ineos Oxford Institute, University of Oxford, Oxford OX1 3RE, UK
| | - Stephanie Lo
- Parasites and Microbes Programme, The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Victoria J. Chalker
- Bacterial Reference Department, UK Health Security Agency, London NW9 5DF, UK
| | - Elita Jauneikaite
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London W12 0NN, UK
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London W2 1PG, UK
| | - Owen B. Spiller
- Department of Medical Microbiology, Division of Infection and Immunity, Cardiff University, 6th Floor University Hospital of Wales, Cardiff CF14 4XN, UK
- Bacterial Reference Department, UK Health Security Agency, London NW9 5DF, UK
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10
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Acolatse JEE, Portal EAR, Boostrom I, Akafity G, Dakroah MP, Chalker VJ, Sands K, Spiller OB. Environmental surveillance of ESBL and carbapenemase-producing gram-negative bacteria in a Ghanaian Tertiary Hospital. Antimicrob Resist Infect Control 2022; 11:49. [PMID: 35296353 PMCID: PMC8925048 DOI: 10.1186/s13756-022-01090-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 02/27/2022] [Indexed: 11/29/2022] Open
Abstract
Background The burden of antibiotic resistant infection is mainly felt in low-to-middle income countries, where the rate of antimicrobial resistance is largely under-surveyed and under huge pressure from unregulated, disparate and often self-guided access to antimicrobials. Nosocomial infections from hospital environments have been shown to be a particularly prevalent source of multi-drug resistant strains, yet surveillance of hospital environmental contamination is often not investigated. Methods The study was prospective, observational and cross-sectional, sampling 231 high and low touch surfaces from 15th March to 13th April 2021, from five wards in the Cape Coast Teaching Hospital, Ghana. Microbial growth in the presence of vancomycin and either meropenem or cefotaxime was examined and bacterial species were identified by MALDI-TOF. The presence of common extended-spectrum β-lactamases (ESBL) and carbapenemase antimicrobial resistance genes (ARG) were identified through PCR screening, which were confirmed by phenotypic antimicrobial susceptibility determination. Isolates positive for carbapenem resistance genes were sequenced using a multi-platform approach. Results We recovered microbial growth from 99% of swabs (n = 229/231) plated on agar in the absence of antimicrobials. Multiple sites were found to be colonised with resistant bacteria throughout the hospital setting. Bacteria with multi-drug resistance and ARG of concern were isolated from high and low touch points with evidence of strain dissemination throughout the environment. A total of 21 differing species of bacteria carrying ARG were isolated. The high prevalence of Acinetobacter baumannii carrying blaNDM-1 observed was further characterised by whole genome sequencing and phylogenetic analysis to determine the relationship between resistant strains found in different wards.
Conclusion Evidence of multiple clonal incursions of MDR bacteria of high sepsis risk were found in two separate wards for a regional hospital in Ghana. The prevalence of multiple blaNDM carrying species in combination with combinations of ESBLs was particularly concerning and unexpected in Africa. We also identify strains carrying tet(X3), blaVIM-5 or blaDIM-1 showing a high diversity of carbapenamases present as a reservoir in a hospital setting. Findings of multi-drug resistant bacteria from multiple environmental sites throughout the hospital will inform future IPC practices and aid research prioritisation for AMR in Ghana. Supplementary Information The online version contains supplementary material available at 10.1186/s13756-022-01090-2.
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11
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Martins WMBS, Li M, Sands K, Lenzi MH, Portal E, Mathias J, Dantas PP, Migliavacca R, Hunter JR, Medeiros EA, Gales AC, Toleman MA. Effective phage cocktail to combat the rising incidence of extensively drug-resistant Klebsiella pneumoniae sequence type 16. Emerg Microbes Infect 2022; 11:1015-1023. [PMID: 35259067 PMCID: PMC9004492 DOI: 10.1080/22221751.2022.2051752] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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] [Indexed: 11/18/2022]
Abstract
Bacteriophages are the most abundant organisms on Earth. As there are few effective treatment options against some pathogens, the interest in the bacteriophage control of multi-drug-resistant bacterial pathogens is escalating, especially for Klebsiella pneumoniae. This study aimed to develop a phage-based solution to the rising incidence of extensively drug-resistant clinical Klebsiella pneumoniae sequence type (ST16) infections starting from a set of phages recently characterized against this lineage. A phage-cocktail (Katrice-16) composed of eight lytic phages was characterized for potential use in humans. In vitro and in vivo broth inhibition and Galleria mellonella rescue assays were used to demonstrate the efficacy of this approach using a collection of 56 strains of K. pneumoniae ST16, with distinct genetic backgrounds that were collected from clinical infections from four disparate nations. Additionally, Katrice-16 anti-biofilm activity, synergism with meropenem, and activity in human body fluids were also assessed. Katrice-16 was highly active in vitro against our K. pneumoniae ST16 collection (AUC% median = 86.48%; Q1 = 83.8%; Q2 = 96.85%; Q3 = 98.85%). It additionally demonstrated excellent in vivo activity in G. mellonella rescue assays, even with larvae infected by isolates that exhibited moderate in vitro inhibition. We measured significant anti-biofilm activity over 12 h (p = .0113) and synergic activity with meropenem. In addition, we also demonstrate that Katrice-16 maintained high activity in human body fluids. Our results indicate that our cocktail will likely be an effective solution for human infections with this increasingly prevalent and often highly resistant bacterial clone.
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Affiliation(s)
- Willames M B S Martins
- Department of Medical Microbiology, Division of Infection and Immunity, Cardiff University, Cardiff, UK.,Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina/Universidade Federal de São Paulo - UNIFESP, São Paulo, Brazil
| | - Mei Li
- Department of Medical Microbiology, Division of Infection and Immunity, Cardiff University, Cardiff, UK
| | - Kirsty Sands
- Department of Medical Microbiology, Division of Infection and Immunity, Cardiff University, Cardiff, UK.,Department of Zoology, University of Oxford, Oxford, UK
| | - Michael H Lenzi
- Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina/Universidade Federal de São Paulo - UNIFESP, São Paulo, Brazil
| | - Edward Portal
- Department of Medical Microbiology, Division of Infection and Immunity, Cardiff University, Cardiff, UK
| | - Jordan Mathias
- Department of Medical Microbiology, Division of Infection and Immunity, Cardiff University, Cardiff, UK
| | - Priscila P Dantas
- Division of Infection Control and Hospital Epidemiology, Hospital São Paulo, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Roberta Migliavacca
- Department of Clinical-Surgical, Diagnostic and Pediatric Sciences, Unit of Microbiology and Clinical Microbiology, University of Pavia, Pavia, Italy
| | - James R Hunter
- Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina/Universidade Federal de São Paulo - UNIFESP, São Paulo, Brazil
| | - Eduardo A Medeiros
- Division of Infection Control and Hospital Epidemiology, Hospital São Paulo, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Ana C Gales
- Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina/Universidade Federal de São Paulo - UNIFESP, São Paulo, Brazil
| | - Mark A Toleman
- Department of Medical Microbiology, Division of Infection and Immunity, Cardiff University, Cardiff, UK
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Martins WMBS, Cino J, Lenzi MH, Sands K, Portal E, Hassan B, Dantas PP, Migliavacca R, Medeiros EA, Gales AC, Toleman MA. Diversity of lytic bacteriophages against XDR Klebsiella pneumoniae sequence type 16 recovered from sewage samples in different parts of the world. Sci Total Environ 2022; 839:156074. [PMID: 35623509 DOI: 10.1016/j.scitotenv.2022.156074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 04/27/2022] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
Bacteriophages (phages) are viruses considered to be natural bacterial predators and widely detected in aquatic environments. Sewage samples are an important source of phage isolation since high density and diversity of bacterial cells are present, due to human, animal and household fluids. This study aims to investigate and characterise phages against an extremely drug-resistant (XDR) lineage, Klebsiella pneumoniae ST16, using sewage samples from different parts of the World. Sewage samples from Brazil, Bangladesh, Saudi Arabia, Thailand and the United Kingdom were collected and used to investigate phages against ten K. pneumoniae ST16 (hosts) recovered from infection sites. The phages were microbiological and genetically characterised by double-agar overlay (DLA), transmission electron microscopy and Illumina WGS. The host range against K. pneumoniae belonging to different sequence types was evaluated at different temperatures by spot test. Further phage characterisation, such as efficiency of plating, optimal phage temperature, and pH/temperature susceptibility, were conducted. Fourteen lytic phages were isolated, belonging to Autographiviridae, Ackermannviridae, Demerecviridae, Drexlerviridae, and Myoviridae families, from Brazil, Bangladesh, Saudi Arabia and Thailand and demonstrated a great genetic diversity. The viruses had good activity against our collection of clinical K. pneumoniae ST16 at room temperature and 37 °C, but also against other important Klebsiella clones such as ST11, ST15, and ST258. Temperature assays showed lytic activity in different temperatures, except for PWKp18 which only had activity at room temperature. Phages were stable between pH 5 and 10 with minor changes in phage activity, and 70 °C was the temperature able to kill all phages in this study. Using sewage from different parts of the World allowed us to have a set of highly efficient phages against an K. pneumoniae ST16 that can be used in the future to develop new tools to combat infections in humans or animals caused by this pathogen.
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Affiliation(s)
- Willames M B S Martins
- Department of Medical Microbiology, Division of Infection and Immunity, Cardiff University, Cardiff, United Kingdom; Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina/Universidade Federal de São Paulo-UNIFESP, São Paulo, Brazil.
| | - Juliana Cino
- Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina/Universidade Federal de São Paulo-UNIFESP, São Paulo, Brazil
| | - Michael H Lenzi
- Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina/Universidade Federal de São Paulo-UNIFESP, São Paulo, Brazil
| | - Kirsty Sands
- Department of Medical Microbiology, Division of Infection and Immunity, Cardiff University, Cardiff, United Kingdom; Department of Zoology, University of Oxford, United Kingdom
| | - Edward Portal
- Department of Medical Microbiology, Division of Infection and Immunity, Cardiff University, Cardiff, United Kingdom
| | - Brekhna Hassan
- Department of Medical Microbiology, Division of Infection and Immunity, Cardiff University, Cardiff, United Kingdom
| | - Priscila P Dantas
- Universidade Federal de São Paulo, Hospital Epidemiology Committee, Hospital São Paulo, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina, São Paulo, Brazil
| | - Roberta Migliavacca
- Department of Clinical-Surgical, Diagnostic and Pediatric Sciences, Unit of Microbiology and Clinical Microbiology, University of Pavia, 27100 Pavia, Italy
| | - Eduardo A Medeiros
- Universidade Federal de São Paulo, Hospital Epidemiology Committee, Hospital São Paulo, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina, São Paulo, Brazil
| | - Ana C Gales
- Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina/Universidade Federal de São Paulo-UNIFESP, São Paulo, Brazil
| | - Mark A Toleman
- Department of Medical Microbiology, Division of Infection and Immunity, Cardiff University, Cardiff, United Kingdom.
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13
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Sands K, Carvalho MJ, Spiller OB, Portal EAR, Thomson K, Watkins WJ, Mathias J, Dyer C, Akpulu C, Andrews R, Ferreira A, Hender T, Milton R, Nieto M, Zahra R, Shirazi H, Muhammad A, Akif S, Jan MH, Iregbu K, Modibbo F, Uwaezuoke S, Chan GJ, Bekele D, Solomon S, Basu S, Nandy RK, Naha S, Mazarati JB, Rucogoza A, Gaju L, Mehtar S, Bulabula ANH, Whitelaw A, Walsh TR. Characterisation of Staphylococci species from neonatal blood cultures in low- and middle-income countries. BMC Infect Dis 2022; 22:593. [PMID: 35790903 PMCID: PMC9254428 DOI: 10.1186/s12879-022-07541-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 06/15/2022] [Indexed: 11/14/2022] Open
Abstract
Background In low- and middle-income countries (LMIC) Staphylococcus aureus is regarded as one of the leading bacterial causes of neonatal sepsis, however there is limited knowledge on the species diversity and antimicrobial resistance caused by Gram-positive bacteria (GPB). Methods We characterised GPB isolates from neonatal blood cultures from LMICs in Africa (Ethiopia, Nigeria, Rwanda, and South Africa) and South-Asia (Bangladesh and Pakistan) between 2015–2017. We determined minimum inhibitory concentrations and performed whole genome sequencing (WGS) on Staphylococci isolates recovered and clinical data collected related to the onset of sepsis and the outcome of the neonate up to 60 days of age. Results From the isolates recovered from blood cultures, Staphylococci species were most frequently identified. Out of 100 S. aureus isolates sequenced, 18 different sequence types (ST) were found which unveiled two small epidemiological clusters caused by methicillin resistant S. aureus (MRSA) in Pakistan (ST8) and South Africa (ST5), both with high mortality (n = 6/17). One-third of S. aureus was MRSA, with methicillin resistance also detected in Staphylococcus epidermidis, Staphylococcus haemolyticus and Mammaliicoccus sciuri. Through additional WGS analysis we report a cluster of M. sciuri in Pakistan identified between July-November 2017. Conclusions In total we identified 14 different GPB bacterial species, however Staphylococci was dominant. These findings highlight the need of a prospective genomic epidemiology study to comprehensively assess the true burden of GPB neonatal sepsis focusing specifically on mechanisms of resistance and virulence across species and in relation to neonatal outcome. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-022-07541-w.
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Milton R, Gillespie D, Dyer C, Taiyari K, Carvalho MJ, Thomson K, Sands K, Portal EAR, Hood K, Ferreira A, Hender T, Kirby N, Mathias J, Nieto M, Watkins WJ, Bekele D, Abayneh M, Solomon S, Basu S, Nandy RK, Saha B, Iregbu K, Modibbo FZ, Uwaezuoke S, Zahra R, Shirazi H, Najeeb SU, Mazarati JB, Rucogoza A, Gaju L, Mehtar S, Bulabula ANH, Whitelaw AC, Walsh TR, Chan GJ, Odumade O, Ambachew R, Yohannes ZG, Metaferia G, Workneh R, Biteye T, Mohammed YZ, Teklu AM, Nigatu B, Gezahegn W, Chakravorty PS, Naha S, Mukherjee A, Umar KM, Akunna AV, Nsude Q, Uke I, Okenu MJ, Akpulu C, Mmadueke C, Yakubu S, Audu L, Idris N, Gambo S, Ibrahim J, Chinago E, Yusuf A, Gwadabe S, Adeleye A, Aliyu M, Muhammad A, Kassim A, Mukaddas AS, Khalid RY, Alkali FI, Muhammad MY, Tukur FM, Muhammad SM, Shittu A, Bello M, Sa ad FH, Zulfiqar S, Muhammad A, Jan MH, Paterson L. Neonatal sepsis and mortality in low-income and middle-income countries from a facility-based birth cohort: an international multisite prospective observational study. The Lancet Global Health 2022; 10:e661-e672. [PMID: 35427523 PMCID: PMC9023753 DOI: 10.1016/s2214-109x(22)00043-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 01/14/2022] [Accepted: 01/26/2022] [Indexed: 02/08/2023] Open
Abstract
Background Neonatal sepsis is a primary cause of neonatal mortality and is an urgent global health concern, especially within low-income and middle-income countries (LMICs), where 99% of global neonatal mortality occurs. The aims of this study were to determine the incidence and associations with neonatal sepsis and all-cause mortality in facility-born neonates in LMICs. Methods The Burden of Antibiotic Resistance in Neonates from Developing Societies (BARNARDS) study recruited mothers and their neonates into a prospective observational cohort study across 12 clinical sites from Bangladesh, Ethiopia, India, Pakistan, Nigeria, Rwanda, and South Africa. Data for sepsis-associated factors in the four domains of health care, maternal, birth and neonatal, and living environment were collected for all mothers and neonates enrolled. Primary outcomes were clinically suspected sepsis, laboratory-confirmed sepsis, and all-cause mortality in neonates during the first 60 days of life. Incidence proportion of livebirths for clinically suspected sepsis and laboratory-confirmed sepsis and incidence rate per 1000 neonate-days for all-cause mortality were calculated. Modified Poisson regression was used to investigate factors associated with neonatal sepsis and parametric survival models for factors associated with all-cause mortality. Findings Between Nov 12, 2015 and Feb 1, 2018, 29 483 mothers and 30 557 neonates were enrolled. The incidence of clinically suspected sepsis was 166·0 (95% CI 97·69–234·24) per 1000 livebirths, laboratory-confirmed sepsis was 46·9 (19·04–74·79) per 1000 livebirths, and all-cause mortality was 0·83 (0·37–2·00) per 1000 neonate-days. Maternal hypertension, previous maternal hospitalisation within 12 months, average or higher monthly household income, ward size (>11 beds), ward type (neonatal), living in a rural environment, preterm birth, perinatal asphyxia, and multiple births were associated with an increased risk of clinically suspected sepsis, laboratory-confirmed sepsis, and all-cause mortality. The majority (881 [72·5%] of 1215) of laboratory-confirmed sepsis cases occurred within the first 3 days of life. Interpretation Findings from this study highlight the substantial proportion of neonates who develop neonatal sepsis, and the high mortality rates among neonates with sepsis in LMICs. More efficient and effective identification of neonatal sepsis is needed to target interventions to reduce its incidence and subsequent mortality in LMICs. Funding Bill & Melinda Gates Foundation.
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Farzana R, Jones LS, Rahman MA, Sands K, van Tonder AJ, Portal E, Criollo JM, Parkhill J, Guest MF, Watkins WJ, Pervin M, Boostrom I, Hassan B, Mathias J, Kalam MA, Walsh TR. Genomic Insights Into the Mechanism of Carbapenem Resistance Dissemination in Enterobacterales From a Tertiary Public Heath Setting in South Asia. Clin Infect Dis 2022; 76:119-133. [PMID: 35412593 PMCID: PMC9825829 DOI: 10.1093/cid/ciac287] [Citation(s) in RCA: 6] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 04/01/2022] [Accepted: 04/07/2022] [Indexed: 01/12/2023] Open
Abstract
SUMMARY 10.6% patients were CRE positive. Only 27% patients were prescribed at least 1 antibiotic to which infecting pathogen was susceptible. Burn and ICU admission and antibiotics exposures facilitate CRE acquisition. Escherichia coli ST167 was the dominant CRE clone. BACKGROUND Given the high prevalence of multidrug resistance (MDR) across South Asian (SA) hospitals, we documented the epidemiology of carbapenem-resistant Enterobacterales (CRE) infections at Dhaka Medical College Hospital between October 2016 and September 2017. METHODS We enrolled patients and collected epidemiology and outcome data. All Enterobacterales were characterized phenotypically and by whole-genome sequencing. Risk assessment for the patients with CRE was performed compared with patients with carbapenem-susceptible Enterobacterales (CSE). RESULTS 10.6% of all 1831 patients with a clinical specimen collected had CRE. In-hospital 30-day mortality was significantly higher with CRE [50/180 (27.8%)] than CSE [42/312 (13.5%)] (P = .001); however, for bloodstream infections, this was nonsignificant. Of 643 Enterobacterales isolated, 210 were CRE; blaNDM was present in 180 isolates, blaOXA-232 in 26, blaOXA-181 in 24, and blaKPC-2 in 5. Despite this, ceftriaxone was the most commonly prescribed empirical antibiotic and only 27% of patients were prescribed at least 1 antibiotic to which their infecting pathogen was susceptible. Significant risk factors for CRE isolation included burns unit and intensive care unit admission, and prior exposure to levofloxacin, amikacin, clindamycin, and meropenem. Escherichia coli ST167 was the dominant CRE clone. Clustering suggested clonal transmission of Klebsiella pneumoniae ST15 and the MDR hypervirulent clone, ST23. The major trajectories involved in horizontal gene transfer were IncFII and IncX3, IS26, and Tn3. CONCLUSIONS This is the largest study from an SA public hospital combining outcome, microbiology, and genomics. The findings indicate the urgent implementation of targeted diagnostics, appropriate antibiotic use, and infection-control interventions in SA public institutions.
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Affiliation(s)
- Refath Farzana
- Correspondence: R. Farzana, Department of Zoology, University of Oxford, Oxford, United Kingdom; Department of Medical Microbiology, Institute of Infection and Immunity, School of Medicine, Cardiff University, UK ()
| | - Lim S Jones
- Public Health Wales Microbiology, University Hospital of Wales, Cardiff, United Kingdom
| | | | - Kirsty Sands
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Andries J van Tonder
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Edward Portal
- Department of Medical Microbiology, Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Jose Munoz Criollo
- Advanced Research Computing @Cardiff (ARCCA), Cardiff University, Cardiff, United Kingdom
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Martyn F Guest
- Advanced Research Computing @Cardiff (ARCCA), Cardiff University, Cardiff, United Kingdom
| | - W John Watkins
- Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Monira Pervin
- Department of Virology, Dhaka Medical College, Dhaka, Bangladesh
| | - Ian Boostrom
- Department of Medical Microbiology, Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Brekhna Hassan
- Department of Medical Microbiology, Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Jordan Mathias
- Department of Medical Microbiology, Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Md Abul Kalam
- Sheikh Hasina National Institute of Burn and Plastic Surgery, Dhaka, Bangladesh
| | - Timothy R Walsh
- Department of Zoology, University of Oxford, Oxford, United Kingdom
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Sands K, Spiller OB, Thomson K, Portal EAR, Iregbu KC, Walsh TR. Early-Onset Neonatal Sepsis in Low- and Middle-Income Countries: Current Challenges and Future Opportunities. Infect Drug Resist 2022; 15:933-946. [PMID: 35299860 PMCID: PMC8921667 DOI: 10.2147/idr.s294156] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 02/17/2022] [Indexed: 12/18/2022] Open
Abstract
Neonatal sepsis is defined as a systemic infection within the first 28 days of life, with early-onset sepsis (EOS) occurring within the first 72h, although the definition of EOS varies in literature. Whilst the global incidence has dramatically reduced over the last decade, neonatal sepsis remains an important cause of neonatal mortality, highest in low- and middle-income countries (LMICs). Symptoms at the onset of neonatal sepsis can be subtle, and therefore EOS is often difficult to diagnose from clinical presentation and laboratory testing and blood cultures are not always conclusive or accessible, especially in resource limited countries. Although the World Health Organisation (WHO) currently advocates a ß-lactam, and gentamicin for first line treatment, availability and cost influence the empirical antibiotic therapy administered. Antibiotic treatment of neonatal sepsis in LMICs is highly variable, partially caused by factors such as cost of antibiotics (and who pays for them) and access to certain antibiotics. Antimicrobial resistance (AMR) has increased considerably over the past decade and this review discusses current microbiology data available in the context of the diagnosis, and treatment for EOS. Importantly, this review highlights a large variability in data availability, methodology, availability of diagnostics, and aetiology of sepsis pathogens.
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Affiliation(s)
- Kirsty Sands
- Ineos Institute of Antimicrobial Research, Department of Zoology, University of Oxford, Oxford, UK
- Division of Infection and Immunity, Cardiff University, Cardiff, UK
| | - Owen B Spiller
- Division of Infection and Immunity, Cardiff University, Cardiff, UK
| | - Kathryn Thomson
- Ineos Institute of Antimicrobial Research, Department of Zoology, University of Oxford, Oxford, UK
- Division of Infection and Immunity, Cardiff University, Cardiff, UK
| | | | | | - Timothy R Walsh
- Ineos Institute of Antimicrobial Research, Department of Zoology, University of Oxford, Oxford, UK
- Division of Infection and Immunity, Cardiff University, Cardiff, UK
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Boostrom I, Portal EAR, Spiller OB, Walsh TR, Sands K. Comparing Long-Read Assemblers to Explore the Potential of a Sustainable Low-Cost, Low-Infrastructure Approach to Sequence Antimicrobial Resistant Bacteria With Oxford Nanopore Sequencing. Front Microbiol 2022; 13:796465. [PMID: 35308384 PMCID: PMC8928191 DOI: 10.3389/fmicb.2022.796465] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [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: 10/16/2021] [Accepted: 01/26/2022] [Indexed: 12/24/2022] Open
Abstract
Long-read sequencing (LRS) can resolve repetitive regions, a limitation of short read (SR) data. Reduced cost and instrument size has led to a steady increase in LRS across diagnostics and research. Here, we re-basecalled FAST5 data sequenced between 2018 and 2021 and analyzed the data in relation to gDNA across a large dataset (n = 200) spanning a wide GC content (25-67%). We examined whether re-basecalled data would improve the hybrid assembly, and, for a smaller cohort, compared long read (LR) assemblies in the context of antimicrobial resistance (AMR) genes and mobile genetic elements. We included a cost analysis when comparing SR and LR instruments. We compared the R9 and R10 chemistries and reported not only a larger yield but increased read quality with R9 flow cells. There were often discrepancies with ARG presence/absence and/or variant detection in LR assemblies. Flye-based assemblies were generally efficient at detecting the presence of ARG on both the chromosome and plasmids. Raven performed more quickly but inconsistently recovered small plasmids, notably a ∼15-kb Col-like plasmid harboring bla KPC . Canu assemblies were the most fragmented, with genome sizes larger than expected. LR assemblies failed to consistently determine multiple copies of the same ARG as identified by the Unicycler reference. Even with improvements to ONT chemistry and basecalling, long-read assemblies can lead to misinterpretation of data. If LR data are currently being relied upon, it is necessary to perform multiple assemblies, although this is resource (computing) intensive and not yet readily available/useable.
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Affiliation(s)
- Ian Boostrom
- Division of Infection and Immunity, Department of Medical Microbiology, Cardiff University, Cardiff, United Kingdom
| | - Edward A. R. Portal
- Division of Infection and Immunity, Department of Medical Microbiology, Cardiff University, Cardiff, United Kingdom
| | - Owen B. Spiller
- Division of Infection and Immunity, Department of Medical Microbiology, Cardiff University, Cardiff, United Kingdom
| | - Timothy R. Walsh
- Division of Infection and Immunity, Department of Medical Microbiology, Cardiff University, Cardiff, United Kingdom
- Department of Zoology, Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, United Kingdom
| | - Kirsty Sands
- Division of Infection and Immunity, Department of Medical Microbiology, Cardiff University, Cardiff, United Kingdom
- Department of Zoology, Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, United Kingdom
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Martins WM, Lenzi MH, Narciso AC, Dantas P, Andrey DO, Yang QE, Sands K, Medeiros EA, Walsh TR, Gales AC. Silent Circulation of BKC-1-producing Klebsiella pneumoniae ST442: Molecular and Clinical Characterisation of an Early and Unreported Outbreak. Int J Antimicrob Agents 2022; 59:106568. [DOI: 10.1016/j.ijantimicag.2022.106568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 01/25/2022] [Accepted: 03/06/2022] [Indexed: 11/29/2022]
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Affiliation(s)
- Sharmi Naha
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, West Bengal, India
| | - Kirsty Sands
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Suchandra Mukherjee
- Department of Neonatology, Institute of Post-Graduate Medical Education & Research and SSKM Hospital, Kolkata, West Bengal, India
| | - Shanta Dutta
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, West Bengal, India
| | - Sulagna Basu
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, West Bengal, India
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20
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Thomson KM, Dyer C, Liu F, Sands K, Portal E, Carvalho MJ, Barrell M, Boostrom I, Dunachie S, Farzana R, Ferreira A, Frayne F, Hassan B, Jones E, Jones L, Mathias J, Milton R, Rees J, Chan GJ, Bekele D, Mahlet A, Basu S, Nandy RK, Saha B, Iregbu K, Modibbo F, Uwaezuoke S, Zahra R, Shirazi H, Syed NU, Mazarati JB, Rucogoza A, Gaju L, Mehtar S, Bulabula ANH, Whitelaw A, van Hasselt JGC, Walsh TR. Effects of antibiotic resistance, drug target attainment, bacterial pathogenicity and virulence, and antibiotic access and affordability on outcomes in neonatal sepsis: an international microbiology and drug evaluation prospective substudy (BARNARDS). Lancet Infect Dis 2021; 21:1677-1688. [PMID: 34384533 PMCID: PMC8612937 DOI: 10.1016/s1473-3099(21)00050-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 12/01/2020] [Accepted: 01/22/2021] [Indexed: 12/30/2022]
Abstract
BACKGROUND Sepsis is a major contributor to neonatal mortality, particularly in low-income and middle-income countries (LMICs). WHO advocates ampicillin-gentamicin as first-line therapy for the management of neonatal sepsis. In the BARNARDS observational cohort study of neonatal sepsis and antimicrobial resistance in LMICs, common sepsis pathogens were characterised via whole genome sequencing (WGS) and antimicrobial resistance profiles. In this substudy of BARNARDS, we aimed to assess the use and efficacy of empirical antibiotic therapies commonly used in LMICs for neonatal sepsis. METHODS In BARNARDS, consenting mother-neonates aged 0-60 days dyads were enrolled on delivery or neonatal presentation with suspected sepsis at 12 BARNARDS clinical sites in Bangladesh, Ethiopia, India, Pakistan, Nigeria, Rwanda, and South Africa. Stillborn babies were excluded from the study. Blood samples were collected from neonates presenting with clinical signs of sepsis, and WGS and minimum inhibitory concentrations for antibiotic treatment were determined for bacterial isolates from culture-confirmed sepsis. Neonatal outcome data were collected following enrolment until 60 days of life. Antibiotic usage and neonatal outcome data were assessed. Survival analyses were adjusted to take into account potential clinical confounding variables related to the birth and pathogen. Additionally, resistance profiles, pharmacokinetic-pharmacodynamic probability of target attainment, and frequency of resistance (ie, resistance defined by in-vitro growth of isolates when challenged by antibiotics) were assessed. Questionnaires on health structures and antibiotic costs evaluated accessibility and affordability. FINDINGS Between Nov 12, 2015, and Feb 1, 2018, 36 285 neonates were enrolled into the main BARNARDS study, of whom 9874 had clinically diagnosed sepsis and 5749 had available antibiotic data. The four most commonly prescribed antibiotic combinations given to 4451 neonates (77·42%) of 5749 were ampicillin-gentamicin, ceftazidime-amikacin, piperacillin-tazobactam-amikacin, and amoxicillin clavulanate-amikacin. This dataset assessed 476 prescriptions for 442 neonates treated with one of these antibiotic combinations with WGS data (all BARNARDS countries were represented in this subset except India). Multiple pathogens were isolated, totalling 457 isolates. Reported mortality was lower for neonates treated with ceftazidime-amikacin than for neonates treated with ampicillin-gentamicin (hazard ratio [adjusted for clinical variables considered potential confounders to outcomes] 0·32, 95% CI 0·14-0·72; p=0·0060). Of 390 Gram-negative isolates, 379 (97·2%) were resistant to ampicillin and 274 (70·3%) were resistant to gentamicin. Susceptibility of Gram-negative isolates to at least one antibiotic in a treatment combination was noted in 111 (28·5%) to ampicillin-gentamicin; 286 (73·3%) to amoxicillin clavulanate-amikacin; 301 (77·2%) to ceftazidime-amikacin; and 312 (80·0%) to piperacillin-tazobactam-amikacin. A probability of target attainment of 80% or more was noted in 26 neonates (33·7% [SD 0·59]) of 78 with ampicillin-gentamicin; 15 (68·0% [3·84]) of 27 with amoxicillin clavulanate-amikacin; 93 (92·7% [0·24]) of 109 with ceftazidime-amikacin; and 70 (85·3% [0·47]) of 76 with piperacillin-tazobactam-amikacin. However, antibiotic and country effects could not be distinguished. Frequency of resistance was recorded most frequently with fosfomycin (in 78 isolates [68·4%] of 114), followed by colistin (55 isolates [57·3%] of 96), and gentamicin (62 isolates [53·0%] of 117). Sites in six of the seven countries (excluding South Africa) stated that the cost of antibiotics would influence treatment of neonatal sepsis. INTERPRETATION Our data raise questions about the empirical use of combined ampicillin-gentamicin for neonatal sepsis in LMICs because of its high resistance and high rates of frequency of resistance and low probability of target attainment. Accessibility and affordability need to be considered when advocating antibiotic treatments with variance in economic health structures across LMICs. FUNDING The Bill & Melinda Gates Foundation.
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Affiliation(s)
- Kathryn M Thomson
- Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, UK,Oxford Institute of Antimicrobial Research, Department of Zoology, University of Oxford, Oxford, UK,Correspondence to: Kathryn M Thomson, Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK and Ineos Oxford Institute of Antimicrobial Research, Department of Zoology, University of Oxford, Oxford, OX1 3SZ, UK
| | - Calie Dyer
- Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, UK,Centre for Trials Research, Cardiff University, Cardiff, UK
| | - Feiyan Liu
- Leiden Academic Centre for Drug Research, Leiden University, Leiden, Netherlands
| | - Kirsty Sands
- Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, UK,Oxford Institute of Antimicrobial Research, Department of Zoology, University of Oxford, Oxford, UK
| | - Edward Portal
- Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, UK
| | - Maria J Carvalho
- Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, UK,Institute of Biomedicine, Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Matthew Barrell
- Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, UK
| | - Ian Boostrom
- Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, UK
| | - Susanna Dunachie
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK,Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Refath Farzana
- Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, UK,Oxford Institute of Antimicrobial Research, Department of Zoology, University of Oxford, Oxford, UK
| | - Ana Ferreira
- Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, UK
| | - Francis Frayne
- Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, UK
| | - Brekhna Hassan
- Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, UK
| | - Ellis Jones
- Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, UK
| | - Lim Jones
- Public Health Wales Microbiology, University Hospital of Wales, Cardiff, UK
| | - Jordan Mathias
- Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, UK
| | - Rebecca Milton
- Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, UK,Centre for Trials Research, Cardiff University, Cardiff, UK
| | - Jessica Rees
- Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, UK
| | - Grace J Chan
- Division of Medicine Critical Care, Boston Children's Hospital, Boston, MA, USA,Department of Epidemiology, Harvard T H Chan School of Public Health, Boston, MA, USA,Department of Paediatrics, St Paul's Hospital Millennium Medical College, Addis Ababa, Ethiopia
| | - Delayehu Bekele
- Department of Obstetrics and Gynecology, St Paul's Hospital Millennium Medical College, Addis Ababa, Ethiopia
| | - Abayneh Mahlet
- Department of Paediatrics, St Paul's Hospital Millennium Medical College, Addis Ababa, Ethiopia
| | - Sulagna Basu
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases Beliaghata, Kolkata, India
| | - Ranjan K Nandy
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases Beliaghata, Kolkata, India
| | - Bijan Saha
- Department of Neonatology, Institute of Postgraduate Medical Education & Research, Kolkata, India
| | | | | | | | | | - Haider Shirazi
- Pakistan Institute of Medical Sciences, Islamabad, Pakistan
| | | | | | - Aniceth Rucogoza
- University Teaching Hospital, Kigali, Rwanda,National Reference Laboratory, Rwanda Biomedical Center, Kigali, Rwanda
| | - Lucie Gaju
- University Teaching Hospital, Kigali, Rwanda
| | - Shaheen Mehtar
- Department of Global Health, Stellenbosch University, Cape Town, South Africa
| | - Andre N H Bulabula
- Department of Global Health, Stellenbosch University, Cape Town, South Africa
| | - Andrew Whitelaw
- Division of Medical Microbiology, Stellenbosch University, Cape Town, South Africa,National Health Laboratory Service, Tygerberg Hospital, Cape Town, South Africa
| | | | - Timothy R Walsh
- Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, UK,Ineos Oxford Institute of Antimicrobial Research, Department of Zoology, University of Oxford, Oxford, UK,Prof Timothy R Walsh, Ineos Oxford Institute of Antimicrobial Research, Department of Zoology, University of Oxford, Oxford, OX1 3SZ, UK
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Sharratt M, Sands K, Portal EAR, Boostrom I, Mondeja BA, Rodríguez NM, Jones LC, Spiller OB. Defining Fluoroquinolone Resistance-Mediating Mutations from Non-Resistance Polymorphisms in Mycoplasma hominis Topoisomerases. Antibiotics (Basel) 2021; 10:antibiotics10111379. [PMID: 34827317 PMCID: PMC8614649 DOI: 10.3390/antibiotics10111379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 10/26/2021] [Accepted: 10/30/2021] [Indexed: 12/02/2022] Open
Abstract
Often dismissed as a commensal, Mycoplasma hominis is an increasingly prominent target of research due to its role in septic arthritis and organ transplant failure in immunosuppressed patients, particularly lung transplantation. As a mollicute, its highly reductive genome and structure render it refractile to most forms of treatment and growing levels of resistance to the few sources of treatment left, such as fluoroquinolones. We examined antimicrobial susceptibility (AST) to fluoroquinolones on 72 isolates and observed resistance in three (4.1%), with corresponding mutations in the quinolone resistance-determining region (QRDR) of S83L or E87G in gyrA and S81I or E85V in parC. However, there were high levels of polymorphism identified between all isolates outside of the QRDR, indicating caution for a genomics-led approach for resistance screening, particularly as we observed a further two quinolone-susceptible isolates solely containing gyrA mutation S83L. However, both isolates spontaneously developed a second spontaneous E85K parC mutation and resistance following prolonged incubation in 4 mg/L levofloxacin for an extra 24–48 h. Continued AST surveillance and investigation is required to understand how gyrA QRDR mutations predispose M. hominis to rapid spontaneous mutation and fluoroquinolone resistance, absent from other susceptible isolates. The unusually high prevalence of polymorphisms in M. hominis also warrants increased genomics’ surveillance.
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Affiliation(s)
- Martin Sharratt
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK; (M.S.); (K.S.); (E.A.R.P.); (I.B.)
| | - Kirsty Sands
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK; (M.S.); (K.S.); (E.A.R.P.); (I.B.)
- Department of Zoology, Oxford University, Oxford OX1 3RE, UK
| | - Edward A. R. Portal
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK; (M.S.); (K.S.); (E.A.R.P.); (I.B.)
- Bacteriology Reference Department, UK Health Security Agency, London NW9 5EQ, UK
| | - Ian Boostrom
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK; (M.S.); (K.S.); (E.A.R.P.); (I.B.)
| | - Brian A. Mondeja
- Pedro Kourí Tropical Medicine Institute, Havana 11400, Cuba; (B.A.M.); (N.M.R.)
- Center for Advance Research of Cuba, Havana CP17100, Cuba
| | - Nadia M. Rodríguez
- Pedro Kourí Tropical Medicine Institute, Havana 11400, Cuba; (B.A.M.); (N.M.R.)
| | - Lucy C. Jones
- Department of Integrated Sexual Health, Cwm Taf Morgannwg University Health Board, Pontypridd CF37 1LB, UK;
| | - Owen B. Spiller
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK; (M.S.); (K.S.); (E.A.R.P.); (I.B.)
- Bacteriology Reference Department, UK Health Security Agency, London NW9 5EQ, UK
- Correspondence:
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Spiller-Boulter O, Paukner S, Boostrom I, Sands K, Portal EAR, Spiller OB. Determination of In Vitro Antimicrobial Susceptibility for Lefamulin (Pleuromutilin) for Ureaplasma Spp. and Mycoplasma hominis. Antibiotics (Basel) 2021; 10:antibiotics10111370. [PMID: 34827308 PMCID: PMC8614837 DOI: 10.3390/antibiotics10111370] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/29/2021] [Accepted: 11/03/2021] [Indexed: 11/30/2022] Open
Abstract
Lefamulin is the first of the pleuromutilin class of antimicrobials to be available for therapeutic use in humans. Minimum inhibitory concentrations of lefamulin were determined by microbroth dilution for 90 characterised clinical isolates (25 Ureaplasma parvum, 25 Ureaplasma urealyticum, and 40 Mycoplasma hominis). All Mycoplasma hominis isolates possessed lefamulin MICs of ≤0.25 mg/L after 48 h (MIC50/90 of 0.06/0.12 mg/L), despite an inherent resistance to macrolides; while Ureaplasma isolates had MICs of ≤2 mg/L after 24 h (MIC50/90 of 0.25/1 mg/L), despite inherent resistance to clindamycin. Two U. urealyticum isolates with additional A2058G mutations of 23S rRNA, and one U. parvum isolate with a R66Q67 deletion (all of which had a combined resistance to macrolides and clindamycin) only showed a 2-fold increase in lefamulin MIC (1–2 mg/L) relative to macrolide-susceptible strains. Lefamulin could be an effective alternative antimicrobial for treating Ureaplasma spp. and Mycoplasma hominis infections irrespective of intrinsic or acquired resistance to macrolides, lincosamides, and ketolides. Based on this potent in vitro activity and the known good, rapid, and homogenous tissue penetration of female and male urogenital tissues and glands, further exploration of clinical efficacy of lefamulin for the treatment of Mycoplasma and Ureaplasma urogenital infections is warranted.
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Affiliation(s)
| | | | - Ian Boostrom
- Division of Infection and Immunity, Department of Medical Microbiology, Cardiff University, 6th Floor University Hospital of Wales, Cardiff CF14 4XN, UK; (I.B.); (K.S.); (E.A.R.P.)
| | - Kirsty Sands
- Division of Infection and Immunity, Department of Medical Microbiology, Cardiff University, 6th Floor University Hospital of Wales, Cardiff CF14 4XN, UK; (I.B.); (K.S.); (E.A.R.P.)
- Department of Zoology, University of Oxford, Oxford OX1 3RE, UK
| | - Edward A. R. Portal
- Division of Infection and Immunity, Department of Medical Microbiology, Cardiff University, 6th Floor University Hospital of Wales, Cardiff CF14 4XN, UK; (I.B.); (K.S.); (E.A.R.P.)
- Bacterial Reference Department, UK Health Security Agency, London NW9 5DF, UK
| | - Owen B. Spiller
- Division of Infection and Immunity, Department of Medical Microbiology, Cardiff University, 6th Floor University Hospital of Wales, Cardiff CF14 4XN, UK; (I.B.); (K.S.); (E.A.R.P.)
- Bacterial Reference Department, UK Health Security Agency, London NW9 5DF, UK
- Correspondence:
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Hassan B, Ijaz M, Khan A, Sands K, Serfas GI, Clayfield L, El-Bouseary MM, Lai G, Portal E, Khan A, Watkins WJ, Parkhill J, Walsh TR. A role for arthropods as vectors of multidrug-resistant Enterobacterales in surgical site infections from South Asia. Nat Microbiol 2021; 6:1259-1270. [PMID: 34580444 DOI: 10.1038/s41564-021-00965-1] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 08/19/2021] [Indexed: 02/07/2023]
Abstract
Understanding how multidrug-resistant Enterobacterales (MDRE) are transmitted in low- and middle-income countries (LMICs) is critical for implementing robust policies to curb the increasing burden of antimicrobial resistance (AMR). Here, we analysed samples from surgical site infections (SSIs), hospital surfaces (HSs) and arthropods (summer and winter 2016) to investigate the incidence and transmission of MDRE in a public hospital in Pakistan. We investigated Enterobacterales containing resistance genes (blaCTX-M-15, blaNDM and blaOXA-48-like) for identification, antimicrobial susceptibility testing and whole-genome sequencing. Genotypes, phylogenetic relationships and transmission events for isolates from different sources were investigated using single-nucleotide polymorphism (SNP) analysis with a cut-off of ≤20 SNPs. Escherichia coli (14.3%), Klebsiella pneumoniae (10.9%) and Enterobacter cloacae (16.3%) were the main MDRE species isolated. The carbapenemase gene blaNDM was most commonly detected, with 15.5%, 15.1% and 13.3% of samples positive in SSIs, HSs and arthropods, respectively. SNP (≤20) and spatiotemporal analysis revealed linkages in bacteria between SSIs, HSs and arthropods supporting the One Health approach to underpin infection control policies across LMICs and control AMR.
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Affiliation(s)
- Brekhna Hassan
- Institute of Infection and Immunity, Cardiff University, Cardiff, UK.
| | | | | | - Kirsty Sands
- Institute of Infection and Immunity, Cardiff University, Cardiff, UK
- Ineos Institute of Antimicrobial Research, Department of Zoology, University of Oxford, Oxford, UK
| | | | - Liam Clayfield
- Institute of Infection and Immunity, Cardiff University, Cardiff, UK
| | | | - Giulia Lai
- Institute of Infection and Immunity, Cardiff University, Cardiff, UK
| | - Edward Portal
- Institute of Infection and Immunity, Cardiff University, Cardiff, UK
| | - Afifah Khan
- School of Biosciences, Cardiff University, Cardiff, UK
| | - William J Watkins
- Institute of Infection and Immunity, Cardiff University, Cardiff, UK
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, USA
| | - Timothy R Walsh
- Institute of Infection and Immunity, Cardiff University, Cardiff, UK
- Ineos Institute of Antimicrobial Research, Department of Zoology, University of Oxford, Oxford, UK
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Mohsin M, Hassan B, Martins WMBS, Li R, Abdullah S, Sands K, Walsh TR. Emergence of plasmid-mediated tigecycline resistance tet(X4) gene in Escherichia coli isolated from poultry, food and the environment in South Asia. Sci Total Environ 2021; 787:147613. [PMID: 33992939 DOI: 10.1016/j.scitotenv.2021.147613] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/23/2021] [Accepted: 05/03/2021] [Indexed: 06/12/2023]
Abstract
The recent emergence of mobile-tigecycline resistance tet(X) genes in human and animals in China seriously threats the clinical utility of tigecycline. Here we focused on the isolation and molecular characterization of plasmid-mediated tigecycline resistance tet(X4)-positive E. coli from different sources in Pakistan using MinION and Illumina sequencing. The tet(X4) gene was detected in four E. coli isolates from poultry, chicken meat, wild bird and the slaughterhouse wastewater in Pakistan. Co-existence of colistin resistance mcr-1 gene was also detected in three isolates. The four isolates belonged to different sequence types and the tet(X4) gene was located on plasmids ranging from 12,331 bp to 113,610 bp belonging to IncFII and IncQ replicon types with two genetic contexts ISCR2-tet(X4)-abh-ISCR2-lysR-floR-virD2 and ΔISCR2-abh-tet(X4)-ISCR2-virD2-floR, respectively. In all the four E. coli strains, tet(X4) was transferable by conjugation to E. coli J53 host strain. In addition, three of four strains transferred tet(X4) to a wild-type carbapenem resistant E. coli strain. To our knowledge, this is the first report of the emergence of plasmid-mediated tet(X4) gene from Pakistan. The convergence of tigecycline and colistin resistance in South Asia is a serious threat to human health.
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Affiliation(s)
- Mashkoor Mohsin
- Institute of Microbiology, University of Agriculture, Faisalabad, Pakistan.
| | - Brekhna Hassan
- School of Medicine, Department of Medical Microbiology, Institute of Infection and Immunity, Cardiff University, Cardiff, United Kingdom
| | - Willames M B S Martins
- School of Medicine, Department of Medical Microbiology, Institute of Infection and Immunity, Cardiff University, Cardiff, United Kingdom
| | - Ruichao Li
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, PR China
| | - Sabahat Abdullah
- Institute of Microbiology, University of Agriculture, Faisalabad, Pakistan
| | - Kirsty Sands
- Ineos Oxford Institute of Antimicrobial Research, Department of Zoology, University of Oxford, United Kingdom
| | - Timothy R Walsh
- Ineos Oxford Institute of Antimicrobial Research, Department of Zoology, University of Oxford, United Kingdom.
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25
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Boostrom I, Bala Y, Vasic JM, Gluvakov J, Chanard E, Barratt AH, Sands K, Portal E, Devigne L, Jones LC, Spiller OB. Evaluation of the MYCOPLASMA IST3 urogenital mycoplasma assay in an international multicentre trial. J Antimicrob Chemother 2021; 76:3175-3182. [PMID: 34477840 PMCID: PMC8678932 DOI: 10.1093/jac/dkab320] [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] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 08/04/2021] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES To evaluate the accuracy, susceptibility and specificity of MYCOPLASMA IST3, the next generation of the most popular culture-based in vitro diagnostic device designed to detect, identify and test the susceptibility of urogenital mycoplasma infections. METHODS MYCOPLASMA IST3 was evaluated against culture- and molecular-based gold standard methodologies to detect, identify, enumerate and determine antimicrobial resistance for Mycoplasma hominis and Ureaplasma species in 516 clinical samples collected across France, Serbia and the UK. Sample types included vulvovaginal/endocervical or urethral swabs (dry swab or eSwab®), semen and urine samples, which included blinded analysis following addition of a panel of 80 characterized control strains. RESULTS Overall species identification was excellent for both Ureaplasma spp. (98.4% sensitivity, 99.7% specificity) and M. hominis (95.7% sensitivity, 100% specificity) relative to combined colony morphology on agar and quantitative PCR standards. Non-dilution-based bacterial load estimation by the assay was accurate between 83.7% (M. hominis) and 86.3% (Ureaplasma spp.) of the time (increased to 94.2% and 100%, respectively, if ±10-fold variance was allowed) relative to colonies counted on agar. Resistance accuracy for Ureaplasma spp. varied from gold standards for only 11/605 of individual tests (major error rate = 1.8%) and for 14/917 individual tests for M. hominis (major error rate = 1.5%). CONCLUSIONS The redesigned MYCOPLASMA IST3 assay eliminated previous shortcomings by providing independent accurate resistance screening of M. hominis and Ureaplasma species, even in mixed infections, with CLSI-compliant thresholds. Specificity, sensitivity and enumeration estimates correlated closely with the confirmatory methods.
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Affiliation(s)
- Ian Boostrom
- Cardiff University, Division of Infection and Immunity, Department of Medical Microbiology, University Hospital of Wales, Cardiff, UK
| | - Yohan Bala
- bioMérieux Global Clinical Affairs, Marcy, L'Étoile, France
| | | | | | | | - Andrew H Barratt
- Cardiff University, Division of Infection and Immunity, Department of Medical Microbiology, University Hospital of Wales, Cardiff, UK
| | - Kirsty Sands
- Cardiff University, Division of Infection and Immunity, Department of Medical Microbiology, University Hospital of Wales, Cardiff, UK.,Department of Zoology, University of Oxford, Oxford, UK
| | - Edward Portal
- Cardiff University, Division of Infection and Immunity, Department of Medical Microbiology, University Hospital of Wales, Cardiff, UK
| | | | - Lucy C Jones
- Cardiff University, Division of Infection and Immunity, Department of Medical Microbiology, University Hospital of Wales, Cardiff, UK.,Department of Integrated Sexual Health, Dewi Sant Hospital Cwm Taf Morgannwg University Health Board, Pontypridd, UK.,HealthFirst Consulting, Research Division, Blackwood, UK
| | - Owen B Spiller
- Cardiff University, Division of Infection and Immunity, Department of Medical Microbiology, University Hospital of Wales, Cardiff, UK.,Public Heath England, Bacterial Reference Department, London, UK
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Solomon S, Akeju O, Odumade OA, Ambachew R, Gebreyohannes Z, Van Wickle K, Abayneh M, Metaferia G, Carvalho MJ, Thomson K, Sands K, Walsh TR, Milton R, Goddard FGB, Bekele D, Chan GJ. Prevalence and risk factors for antimicrobial resistance among newborns with gram-negative sepsis. PLoS One 2021; 16:e0255410. [PMID: 34343185 PMCID: PMC8330902 DOI: 10.1371/journal.pone.0255410] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [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: 03/09/2021] [Accepted: 07/16/2021] [Indexed: 11/18/2022] Open
Abstract
INTRODUCTION Newborn sepsis accounts for more than a third of neonatal deaths globally and one in five neonatal deaths in Ethiopia. The first-line treatment recommended by WHO is the combination of gentamicin with ampicillin or benzylpenicillin. Gram-negative bacteria (GNB) are increasingly resistant to previously effective antibiotics. OBJECTIVES Our goal was to estimate the prevalence of antibiotic-resistant gram-negative bacteremia and identify risk factors for antibiotic resistance, among newborns with GNB sepsis. METHODS At a tertiary hospital in Ethiopia, we enrolled a cohort pregnant women and their newborns, between March and December 2017. Newborns who were followed up until 60 days of life for clinical signs of sepsis. Among the newborns with clinical signs of sepsis, blood samples were cultured; bacterial species were identified and tested for antibiotic susceptibility. We described the prevalence of antibiotic resistance, identified newborn, maternal, and environmental factors associated with multidrug resistance (MDR), and combined resistance to ampicillin and gentamicin (AmpGen), using multivariable regression. RESULTS Of the 119 newborns with gram-negative bacteremia, 80 (67%) were born preterm and 82 (70%) had early-onset sepsis. The most prevalent gram-negative species were Klebsiella pneumoniae 94 (79%) followed by Escherichia coli 10 (8%). Ampicillin resistance was found in 113 cases (95%), cefotaxime 104 (87%), gentamicin 101 (85%), AmpGen 101 (85%), piperacillin-tazobactam 47 (39%), amikacin 10 (8.4%), and Imipenem 1 (0.8%). Prevalence of MDR was 88% (n = 105). Low birthweight and late-onset sepsis (LOS) were associated with higher risks of AmpGen-resistant infections. All-cause mortality was higher among newborns treated with ineffective antibiotics. CONCLUSION There was significant resistance to current first-line antibiotics and cephalosporins. Additional data are needed from primary care and community settings. Amikacin and piperacillin-tazobactam had lower rates of resistance; however, context-specific assessments of their potential adverse effects, their local availability, and cost-effectiveness would be necessary before selecting a new first-line regimen to help guide clinical decision-making.
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Affiliation(s)
- Semaria Solomon
- St. Paul’s Hospital Millennium Medical College, Addis Ababa, Ethiopia
| | - Oluwasefunmi Akeju
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Oludare A. Odumade
- Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Rozina Ambachew
- St. Paul’s Hospital Millennium Medical College, Addis Ababa, Ethiopia
| | | | - Kimi Van Wickle
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Mahlet Abayneh
- St. Paul’s Hospital Millennium Medical College, Addis Ababa, Ethiopia
| | - Gesit Metaferia
- St. Paul’s Hospital Millennium Medical College, Addis Ababa, Ethiopia
| | - Maria J. Carvalho
- Division of Infection and Immunity, Cardiff University, Cardiff, United Kingdom
- Department of Medical Sciences, Institute of Biomedicine, University of Aveiro, Aveiro, Portugal
| | - Kathryn Thomson
- Division of Infection and Immunity, Cardiff University, Cardiff, United Kingdom
| | - Kirsty Sands
- Division of Infection and Immunity, Cardiff University, Cardiff, United Kingdom
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Timothy R. Walsh
- Division of Infection and Immunity, Cardiff University, Cardiff, United Kingdom
- Department of Zoology, Ineos Oxford Institute of Antimicrobial Research, University of Oxford, Oxford, United Kingdom
| | - Rebecca Milton
- Division of Infection and Immunity, Cardiff University, Cardiff, United Kingdom
- Centre for Trials Research, Cardiff University, Cardiff, United Kingdom
| | | | - Delayehu Bekele
- St. Paul’s Hospital Millennium Medical College, Addis Ababa, Ethiopia
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Grace J. Chan
- St. Paul’s Hospital Millennium Medical College, Addis Ababa, Ethiopia
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
- Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
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Yu Y, Andrey DO, Yang RS, Sands K, Tansawai U, Li M, Portal E, Gales AC, Niumsup PR, Sun J, Liao X, Liu YH, Walsh TR. A Klebsiella pneumoniae strain co-harbouring mcr-1 and mcr-3 from a human in Thailand. J Antimicrob Chemother 2021; 75:2372-2374. [PMID: 32294160 DOI: 10.1093/jac/dkaa133] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Yang Yu
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou 510642, China.,Department of Medical Microbiology and Infectious Disease, Division of Infection and Immunity, Cardiff University, Cardiff CF14 4XN, UK
| | - Diego O Andrey
- Department of Medical Microbiology and Infectious Disease, Division of Infection and Immunity, Cardiff University, Cardiff CF14 4XN, UK.,Service of Infectious Diseases, Geneva University Hospitals and Faculty of Medicine, 1211 Geneva, Switzerland
| | - Run-Shi Yang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou 510642, China
| | - Kirsty Sands
- Department of Medical Microbiology and Infectious Disease, Division of Infection and Immunity, Cardiff University, Cardiff CF14 4XN, UK
| | - Uttapoln Tansawai
- Department of Medical Microbiology and Infectious Disease, Division of Infection and Immunity, Cardiff University, Cardiff CF14 4XN, UK.,Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok 65000, Thailand
| | - Mei Li
- Department of Medical Microbiology and Infectious Disease, Division of Infection and Immunity, Cardiff University, Cardiff CF14 4XN, UK
| | - Edward Portal
- Department of Medical Microbiology and Infectious Disease, Division of Infection and Immunity, Cardiff University, Cardiff CF14 4XN, UK
| | - Ana C Gales
- Federal University of Sao Paulo - UNIFESP, Infectious Diseases Department, Escola Paulista de Medicina, São Paulo, Brazil
| | - Pannika R Niumsup
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok 65000, Thailand
| | - Jian Sun
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou 510642, China.,Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Xiaoping Liao
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou 510642, China.,Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Ya-Hong Liu
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou 510642, China.,Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Timothy R Walsh
- Department of Medical Microbiology and Infectious Disease, Division of Infection and Immunity, Cardiff University, Cardiff CF14 4XN, UK
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Andrey DO, Pereira Dantas P, Martins WBS, Marques De Carvalho F, Almeida LGP, Sands K, Portal E, Sauser J, Cayô R, Nicolas MF, Vasconcelos ATR, Medeiros EA, Walsh TR, Gales AC. An Emerging Clone, Klebsiellapneumoniae Carbapenemase 2-Producing K. pneumoniae Sequence Type 16, Associated With High Mortality Rates in a CC258-Endemic Setting. Clin Infect Dis 2021; 71:e141-e150. [PMID: 31712802 PMCID: PMC7583420 DOI: 10.1093/cid/ciz1095] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [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: 04/18/2019] [Accepted: 11/09/2019] [Indexed: 12/15/2022] Open
Abstract
Background Carbapenemase-producing Klebsiella pneumoniae has become a global priority, not least in low- and middle-income countries. Here, we report the emergence and clinical impact of a novel Klebsiella pneumoniae carbapenemase–producing K. pneumoniae (KPC-KP) sequence type (ST) 16 clone in a clonal complex (CC) 258–endemic setting. Methods In a teaching Brazilian hospital, a retrospective cohort of adult KPC-KP bloodstream infection (BSI) cases (January 2014 to December 2016) was established to study the molecular epidemiology and its impact on outcome (30-day all-cause mortality). KPC-KP isolates underwent multilocus sequence typing. Survival analysis between ST/CC groups and risk factors for fatal outcome (logistic regression) were evaluated. Representative isolates underwent whole-genome sequencing and had their virulence tested in a Galleria larvae model. Results One hundred sixty-five unique KPC-KP BSI cases were identified. CC258 was predominant (66%), followed by ST16 (12%). The overall 30-day mortality rate was 60%; in contrast, 95% of ST16 cases were fatal. Patients’ severity scores were high and baseline clinical variables were not statistically different across STs. In multivariate analysis, ST16 (odds ratio [OR], 21.4; 95% confidence interval [CI], 2.3–202.8; P = .008) and septic shock (OR, 11.9; 95% CI, 4.2–34.1; P < .001) were independent risk factors for fatal outcome. The ST16 clone carried up to 14 resistance genes, including blaKPC-2 in an IncFIBpQIL plasmid, KL51 capsule, and yersiniabactin virulence determinants. The ST16 clone was highly pathogenic in the larvae model. Conclusions Mortality rates were high in this KPC-KP BSI cohort, where CC258 is endemic. An emerging ST16 clone was associated with high mortality. Our results suggest that even in endemic settings, highly virulent clones can rapidly emerge demanding constant monitoring.
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Affiliation(s)
- Diego O Andrey
- Department of Medical Microbiology, Division of Infection and Immunity, Cardiff University, Cardiff, United Kingdom.,Service of Infectious Diseases, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Priscila Pereira Dantas
- Universidade Federal de São Paulo, Hospital Epidemiology Committee, Hospital São Paulo, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina, São Paulo, Brazil
| | - Willames B S Martins
- Department of Medical Microbiology, Division of Infection and Immunity, Cardiff University, Cardiff, United Kingdom.,Universidade Federal de São Paulo, Laboratório Alerta, Disciplina de Infectologia, Departamento de Medicina, Escola Paulista de Medicina, São Paulo, Brazil
| | | | | | - Kirsty Sands
- Department of Medical Microbiology, Division of Infection and Immunity, Cardiff University, Cardiff, United Kingdom
| | - Edward Portal
- Department of Medical Microbiology, Division of Infection and Immunity, Cardiff University, Cardiff, United Kingdom
| | - Julien Sauser
- Infection Control Program, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Rodrigo Cayô
- Universidade Federal de São Paulo, Laboratório Alerta, Disciplina de Infectologia, Departamento de Medicina, Escola Paulista de Medicina, São Paulo, Brazil
| | - Marisa F Nicolas
- National Laboratory for Scientific Computing, Petrópolis, Rio de Janeiro, Brazil
| | | | - Eduardo A Medeiros
- Universidade Federal de São Paulo, Hospital Epidemiology Committee, Hospital São Paulo, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina, São Paulo, Brazil
| | - Timothy R Walsh
- Department of Medical Microbiology, Division of Infection and Immunity, Cardiff University, Cardiff, United Kingdom
| | - Ana C Gales
- Universidade Federal de São Paulo, Laboratório Alerta, Disciplina de Infectologia, Departamento de Medicina, Escola Paulista de Medicina, São Paulo, Brazil
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Portal E, Sands K, Portnojs A, Chalker VJ, Spiller OB. Legionella antimicrobial sensitivity testing: comparison of microbroth dilution with BCYE and LASARUS solid media. J Antimicrob Chemother 2021; 76:1197-1204. [PMID: 33367732 PMCID: PMC8050766 DOI: 10.1093/jac/dkaa535] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 08/19/2020] [Accepted: 11/20/2020] [Indexed: 01/11/2023] Open
Abstract
OBJECTIVES There is a lack of international unification for AST methodology for Legionella pneumophila. Current literature contains multiple possible methods and this study compares each of them to determine methodological concordance. METHODS Antibiotic susceptibility of 50 L. pneumophila strains was determined using broth microdilution (BMD), serial antimicrobial dilution in traditional buffered charcoal yeast extract (BCYE) agar (as well as comparison with gradient strip overlay on BCYE) and in a novel charcoal-free agar (LASARUS) for rifampicin, azithromycin, levofloxacin and doxycycline. RESULTS The deviation of tested media relative to BMD highlighted the overall similarity of BMD and LASARUS across all antimicrobials tested (within one serial dilution). BCYE agar dilution showed an increased MIC of up to five serial dilutions relative to BMD, while MICs by gradient strip overlay on BCYE were elevated by two to three serial dilutions, with the exception of doxycycline, which was decreased by three serial dilutions relative to MIC values determined by BMD. The MIC range for azithromycin was wider than for other antimicrobials tested and found to be caused by the presence or absence of the lpeAB gene. CONCLUSIONS BMD-based antimicrobial susceptibility testing (AST) methodology should be the internationally agreed gold standard for Legionella spp. AST, as is common for other bacterial species. Traditional BCYE gave significantly elevated MIC results and its use should be discontinued for Legionella spp., while MIC determination using LASARUS solid medium gave results concordant (within one serial dilution) with BMD for all antimicrobials tested. To the best of our knowledge, this study is the first to identify the lpeAB gene in UK isolates.
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Affiliation(s)
- Edward Portal
- Cardiff University, Division of Infection and Immunity, Department of Medical Microbiology, University Hospital of Wales, Cardiff, UK
- Public Heath England, Bacterial Reference Department, London, UK
| | - Kirsty Sands
- Cardiff University, Division of Infection and Immunity, Department of Medical Microbiology, University Hospital of Wales, Cardiff, UK
- Department of Zoology, University of Oxford, Oxford, UK
| | - Artjoms Portnojs
- Cardiff University, Division of Infection and Immunity, Department of Medical Microbiology, University Hospital of Wales, Cardiff, UK
| | | | - Owen B Spiller
- Cardiff University, Division of Infection and Immunity, Department of Medical Microbiology, University Hospital of Wales, Cardiff, UK
- Public Heath England, Bacterial Reference Department, London, UK
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Sands K, Carvalho MJ, Portal E, Thomson K, Dyer C, Akpulu C, Andrews R, Ferreira A, Gillespie D, Hender T, Hood K, Mathias J, Milton R, Nieto M, Taiyari K, Chan GJ, Bekele D, Solomon S, Basu S, Chattopadhyay P, Mukherjee S, Iregbu K, Modibbo F, Uwaezuoke S, Zahra R, Shirazi H, Muhammad A, Mazarati JB, Rucogoza A, Gaju L, Mehtar S, Bulabula ANH, Whitelaw A, Walsh TR. Characterization of antimicrobial-resistant Gram-negative bacteria that cause neonatal sepsis in seven low- and middle-income countries. Nat Microbiol 2021; 6:512-523. [PMID: 33782558 PMCID: PMC8007471 DOI: 10.1038/s41564-021-00870-7] [Citation(s) in RCA: 115] [Impact Index Per Article: 38.3] [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: 01/21/2020] [Accepted: 01/22/2021] [Indexed: 01/31/2023]
Abstract
Antimicrobial resistance in neonatal sepsis is rising, yet mechanisms of resistance that often spread between species via mobile genetic elements, ultimately limiting treatments in low- and middle-income countries (LMICs), are poorly characterized. The Burden of Antibiotic Resistance in Neonates from Developing Societies (BARNARDS) network was initiated to characterize the cause and burden of antimicrobial resistance in neonatal sepsis for seven LMICs in Africa and South Asia. A total of 36,285 neonates were enrolled in the BARNARDS study between November 2015 and December 2017, of whom 2,483 were diagnosed with culture-confirmed sepsis. Klebsiella pneumoniae (n = 258) was the main cause of neonatal sepsis, with Serratia marcescens (n = 151), Klebsiella michiganensis (n = 117), Escherichia coli (n = 75) and Enterobacter cloacae complex (n = 57) also detected. We present whole-genome sequencing, antimicrobial susceptibility and clinical data for 916 out of 1,038 neonatal sepsis isolates (97 isolates were not recovered from initial isolation at local sites). Enterobacterales (K. pneumoniae, E. coli and E. cloacae) harboured multiple cephalosporin and carbapenem resistance genes. All isolated pathogens were resistant to multiple antibiotic classes, including those used to treat neonatal sepsis. Intraspecies diversity of K. pneumoniae and E. coli indicated that multiple antibiotic-resistant lineages cause neonatal sepsis. Our results will underpin research towards better treatments for neonatal sepsis in LMICs.
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Affiliation(s)
- Kirsty Sands
- Division of Infection and Immunity, Cardiff University, Cardiff, UK.
- Department of Zoology, University of Oxford, Oxford, UK.
| | - Maria J Carvalho
- Division of Infection and Immunity, Cardiff University, Cardiff, UK.
- Institute of Biomedicine, Department of Medical Sciences, University of Aveiro, Aveiro, Portugal.
| | - Edward Portal
- Division of Infection and Immunity, Cardiff University, Cardiff, UK
| | - Kathryn Thomson
- Division of Infection and Immunity, Cardiff University, Cardiff, UK
| | - Calie Dyer
- Division of Infection and Immunity, Cardiff University, Cardiff, UK
- Centre for Trials Research, Cardiff University, Cardiff, UK
| | - Chinenye Akpulu
- Division of Infection and Immunity, Cardiff University, Cardiff, UK
- National Hospital Abuja, Abuja, Nigeria
- 54gene, Lagos, Nigeria
| | - Robert Andrews
- Division of Infection and Immunity, Cardiff University, Cardiff, UK
| | - Ana Ferreira
- Division of Infection and Immunity, Cardiff University, Cardiff, UK
| | | | - Thomas Hender
- Division of Infection and Immunity, Cardiff University, Cardiff, UK
| | - Kerenza Hood
- Centre for Trials Research, Cardiff University, Cardiff, UK
| | - Jordan Mathias
- Division of Infection and Immunity, Cardiff University, Cardiff, UK
| | - Rebecca Milton
- Division of Infection and Immunity, Cardiff University, Cardiff, UK
- Centre for Trials Research, Cardiff University, Cardiff, UK
| | - Maria Nieto
- Division of Infection and Immunity, Cardiff University, Cardiff, UK
| | | | - Grace J Chan
- Division of Medical Critical Care, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Delayehu Bekele
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Obstetrics and Gynecology, St Paul's Hospital Millennium Medical College, Addis Ababa, Ethiopia
| | - Semaria Solomon
- Department of Microbiology, Immunology and Parasitology, St Paul's Hospital Millennium Medical College, Addis Ababa, Ethiopia
| | - Sulagna Basu
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Pinaki Chattopadhyay
- Department of Neonatology, Institute of Postgraduate Medical Education & Research, Kolkata, India
| | - Suchandra Mukherjee
- Department of Neonatology, Institute of Postgraduate Medical Education & Research, Kolkata, India
| | | | - Fatima Modibbo
- National Hospital Abuja, Abuja, Nigeria
- 54gene, Lagos, Nigeria
| | | | - Rabaab Zahra
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Haider Shirazi
- Pakistan Institute of Medical Sciences, Islamabad, Pakistan
| | - Adil Muhammad
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
| | | | - Aniceth Rucogoza
- The National Reference Laboratory, Rwanda Biomedical Centre, Kigali, Rwanda
| | - Lucie Gaju
- The National Reference Laboratory, Rwanda Biomedical Centre, Kigali, Rwanda
| | - Shaheen Mehtar
- Unit of IPC, Stellenbosch University, Cape Town, South Africa
- Infection Control Africa Network, Cape Town, South Africa
| | - Andre N H Bulabula
- Infection Control Africa Network, Cape Town, South Africa
- Department of Global Health, Stellenbosch University, Cape Town, South Africa
| | - Andrew Whitelaw
- Division of Medical Microbiology, Stellenbosch University, Cape Town, South Africa
- National Health Laboratory Service, Tygerberg Hospital, Cape Town, South Africa
| | - Timothy R Walsh
- Division of Infection and Immunity, Cardiff University, Cardiff, UK
- Ineos Oxford Institute for Antimicrobial Research, Department of Zoology, Oxford, UK
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Tansawai U, Yu Y, Kiddee A, Assawatheptawee K, Sands K, Hassan B, Walsh TR, Niumsup PR. Emergence of mcr-3-mediated IncP and IncFII plasmids in Thailand. J Glob Antimicrob Resist 2021; 24:446-447. [PMID: 33618040 DOI: 10.1016/j.jgar.2021.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 01/19/2021] [Accepted: 02/05/2021] [Indexed: 11/18/2022] Open
Affiliation(s)
- Uttapoln Tansawai
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok 65000, Thailand
| | - Yang Yu
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Anong Kiddee
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok 65000, Thailand
| | - Kanit Assawatheptawee
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok 65000, Thailand
| | - Kirsty Sands
- Department of Medical Microbiology and Infectious Disease, Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Brekhna Hassan
- Department of Medical Microbiology and Infectious Disease, Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Timothy R Walsh
- Department of Medical Microbiology and Infectious Disease, Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Pannika R Niumsup
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok 65000, Thailand.
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Mentasti M, David S, Sands K, Khan S, Davies L, Turner L, Wootton M. Rapid detection and differentiation of mobile colistin resistance (mcr-1 to mcr-10) genes by real-time PCR and melt-curve analysis. J Hosp Infect 2021; 110:148-155. [PMID: 33485969 DOI: 10.1016/j.jhin.2021.01.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/13/2021] [Accepted: 01/13/2021] [Indexed: 10/22/2022]
Abstract
BACKGROUND The emergence of multi-drug-resistant (MDR) micro-organisms prompted new interest in older antibiotics, such as colistin, that had been abandoned previously due to limited efficacy or high toxicity. Over the years, several chromosomal-encoded colistin resistance mechanisms have been described; more recently, 10 plasmid-mediated mobile colistin resistance (mcr) genes have been identified. Spread of these genes among MDR Gram-negative bacteria is a matter of serious concern; therefore, reliable and timely mcr detection is paramount. AIM To design and validate a multiplex real-time polymerase chain reaction (PCR) assay for detection and differentiation of mcr genes. METHODS All available mcr alleles were downloaded from the National Center for Biotechnology Information Reference Gene Catalogue, aligned with Clustal Omega and primers designed using Primer-BLAST. Real-time PCR monoplexes were optimized and validated using a panel of 120 characterized Gram-negative strains carrying a wide range of resistance genes, often in combination. Melt-curve analysis was used to confirm positive results. FINDINGS In-silico analysis enabled the design of a 'screening' assay for detection of mcr-1/2/6, mcr-3, mcr-4, mcr-5, mcr-7, mcr-8 and mcr-9/10, paired with an internal control assay to discount inhibition. A 'supplementary' assay was subsequently designed to differentiate mcr-1, mcr-2, mcr-6, mcr-9 and mcr-10. Expected results were obtained for all strains (100% sensitivity and specificity). Melt-curve analysis showed consistent melting temperature results. Inhibition was not observed. CONCLUSIONS The assay is rapid and easy to perform, enabling unequivocal mcr detection and differentiation even when more than one variant is present. Adoption by clinical and veterinary microbiology laboratories would aid the surveillance of mcr genes amongst Gram-negative bacteria.
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Affiliation(s)
- M Mentasti
- Specialist Antimicrobial and Chemotherapy Unit, Public Health Wales, University Hospital of Wales, Cardiff, UK.
| | - S David
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Cambridge, UK
| | - K Sands
- School of Medicine, Cardiff University, Cardiff, UK; Department of Zoology, University of Oxford, Oxford, UK
| | - S Khan
- Specialist Antimicrobial and Chemotherapy Unit, Public Health Wales, University Hospital of Wales, Cardiff, UK
| | - L Davies
- Specialist Antimicrobial and Chemotherapy Unit, Public Health Wales, University Hospital of Wales, Cardiff, UK
| | - L Turner
- Specialist Antimicrobial and Chemotherapy Unit, Public Health Wales, University Hospital of Wales, Cardiff, UK
| | - M Wootton
- Specialist Antimicrobial and Chemotherapy Unit, Public Health Wales, University Hospital of Wales, Cardiff, UK
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Roch M, Sierra R, Sands K, Martins WMBS, Schrenzel J, Walsh TR, Gales AC, Andrey DO. Vertical and horizontal dissemination of an IncC plasmid harbouring rmtB 16S rRNA methylase gene, conferring resistance to plazomicin, among invasive ST258 and ST16 KPC-producing Klebsiella pneumoniae. J Glob Antimicrob Resist 2020; 24:183-189. [PMID: 33373732 DOI: 10.1016/j.jgar.2020.12.006] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 11/13/2020] [Accepted: 12/06/2020] [Indexed: 02/07/2023] Open
Abstract
OBJECTIVES Carbapenem resistance in Klebsiella pneumoniae is a major clinical challenge. Aminoglycosides remain an important asset in the current therapeutic arsenal to treat these infections. We examined aminoglycoside resistance phenotypes and genomics in a collection of 100 invasive KPC-producing K. pneumoniae isolates sequentially collected in a Brazilian tertiary hospital between 2014 and 2016. METHODS Aminoglycoside susceptibility testing was performed. We used a combined long-read (MinION) and short-read (Illumina) whole-genome sequencing strategy to provide a genomic picture of aminoglycoside resistance genes, with particular emphasis on 16S rRNA methyltransferases and related plasmids. RESULTS 68% of the strains were resistant to gentamicin and 42% to amikacin, with 35% resistant to both of these commonly used aminoglycosides. We identified the 16S rRNA methyltransferase gene rmtB in 30% of these isolates: 97% (29/30) belonged to sequence type 258 (ST258) and a single isolate to the emergent ST16 clone. In ST258 and ST16 the rmtB gene was located on large IncC plasmids of 177 kb and 174 kb, respectively, highly similar to a plasmid previously identified in Proteus mirabilis in the same hospital. Moreover, 99% of the isolates remained susceptible to the veterinary-approved drug apramycin, currently under clinical development for human medicine. CONCLUSION Such findings in geographically and temporally related isolates suggest a combination of vertical clonal spread as well as horizontal interspecies and intraspecies plasmid transfer. This broad rmtB dissemination in an endemic setting for KPC-producing clones is worrisome since it provides resistance to most clinically available aminoglycosides, including the novel aminoglycoside-modifying enzyme-resistant plazomicin.
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Affiliation(s)
- Mélanie Roch
- Service of Infectious Diseases, Department of Medicine, Geneva University Hospitals and Medical School, Geneva, Switzerland; Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Roberto Sierra
- Service of Infectious Diseases, Department of Medicine, Geneva University Hospitals and Medical School, Geneva, Switzerland; Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Kirsty Sands
- Department of Medical Microbiology, Division of Infection and Immunity, Cardiff University, Cardiff, UK
| | - Willames M B S Martins
- Department of Medical Microbiology, Division of Infection and Immunity, Cardiff University, Cardiff, UK; Universidade Federal de São Paulo (UNIFESP), Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo, Brazil
| | - Jacques Schrenzel
- Service of Infectious Diseases, Department of Medicine, Geneva University Hospitals and Medical School, Geneva, Switzerland; Genomic Research Laboratory, Service of Infectious Diseases, Geneva University Hospitals and University of Geneva, Geneva, Switzerland
| | - Timothy R Walsh
- Department of Medical Microbiology, Division of Infection and Immunity, Cardiff University, Cardiff, UK
| | - Ana C Gales
- Universidade Federal de São Paulo (UNIFESP), Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo, Brazil
| | - Diego O Andrey
- Service of Infectious Diseases, Department of Medicine, Geneva University Hospitals and Medical School, Geneva, Switzerland; Genomic Research Laboratory, Service of Infectious Diseases, Geneva University Hospitals and University of Geneva, Geneva, Switzerland.
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Martins WMBS, Seco BMS, Sampaio JLM, Sands K, Toleman MA, Gales AC. Detection of BKC-1 in Citrobacter freundii: A clue to mobilisation in an IncQ1 plasmid carrying bla BKC-1. Int J Antimicrob Agents 2020; 56:106042. [PMID: 32479892 DOI: 10.1016/j.ijantimicag.2020.106042] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 05/15/2020] [Accepted: 05/21/2020] [Indexed: 10/24/2022]
Affiliation(s)
- Willames M B S Martins
- Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina/Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil; Department of Medical Microbiology, Division of Infection and Immunity, Cardiff University, Cardiff, UK.
| | - Bruna M S Seco
- School of Pharmacy, Antimicrobial Resistance and Clinical Microbiology Laboratory, University of São Paulo, Av. Professor Lineu Prestes 580, São Paulo, Brazil
| | - Jorge L M Sampaio
- School of Pharmacy, Antimicrobial Resistance and Clinical Microbiology Laboratory, University of São Paulo, Av. Professor Lineu Prestes 580, São Paulo, Brazil; Microbiology Section, Fleury Medicine and Health, Av. General Valdomiro de Lima 508, São Paulo, Brazil
| | - Kirsty Sands
- Department of Medical Microbiology, Division of Infection and Immunity, Cardiff University, Cardiff, UK
| | - Mark A Toleman
- Department of Medical Microbiology, Division of Infection and Immunity, Cardiff University, Cardiff, UK
| | - Ana C Gales
- Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina/Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
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Farzana R, Jones LS, Rahman MA, Sands K, Portal E, Boostrom I, Kalam MA, Hasan B, Khan A, Walsh TR. Molecular and epidemiological analysis of a Burkholderia cepacia sepsis outbreak from a tertiary care hospital in Bangladesh. PLoS Negl Trop Dis 2020; 14:e0008200. [PMID: 32271750 PMCID: PMC7173934 DOI: 10.1371/journal.pntd.0008200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 08/22/2019] [Revised: 04/21/2020] [Accepted: 03/05/2020] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Burkholderia cepacia complex (Bcc) is a group of serious pathogens in cystic fibrosis patients and causes life threatening infections in immunocompromised patients. Species within the Bcc are widely distributed within the environment, can survive in the presence of disinfectants and antiseptics, and are inherently multidrug resistant (MDR). METHODS Dhaka Medical College Hospital (DMCH) patients with a B. cepacia positive blood culture between 20 October 2016 to 23rd September 2017 were considered as outbreak cases. Blood stream infections (BSIs) were detected using BacT/ALERT 3D at DMCH. B. cepacia was isolated on chromogenic UTI media followed by MALDI-TOF. Minimum inhibitory concentration (MIC) of clinically relevant antibiotics was determined by agar dilution. Whole genome sequencing was performed on an Illumina MiSeq platform. Patients' demographic and clinical data were collected. Patients' clinical history and genomic data of the outbreak strains were merged to investigate possible outbreaks. Ninety-one B. cepacia genomes were downloaded from 'Burkholderia Genome Database' and the genomic background of the global strains were compared with our outbreak strains. RESULTS Among 236 BSIs, 6.35% (15/236) were B. cepacia. Outbreak cases were confined to the burn critical care unit and, to a lesser extent, the paediatrics department. There was a continuum of overlapping cases at DMCH between 23 October 2016 to 30 August 2017. Core genome SNPs showed that the outbreak strains were confined to a single clade, corresponded to a common clone (ST1578). The strains were shown to be MDR and associated with a mortality of 31% excluding discharge against medical advice. MIC profiles of the strains suggested that antibiotics deployed as empirical therapy were invariably inappropriate. The genetic background of the outbreak strains was very similar; however, a few variations were found regarding the presence of virulence genes. Compared to global strains from the Burkholderia Genome Database, the Bangladeshi strains were genetically distinct. CONCLUSIONS Environmental surveillance is required to investigate the aetiology and mode of transmission of the B. cepacia outbreak. Systematic management of nosocomial outbreaks, particularly in resource limited regions, will mitigate transmission and will improve patients' outcomes.
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Affiliation(s)
- Refath Farzana
- Department of Medical Microbiology, Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
- * E-mail:
| | - Lim S. Jones
- Public Health Wales Microbiology, University Hospital of Wales, Cardiff, United Kingdom
| | | | - Kirsty Sands
- Department of Medical Microbiology, Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Edward Portal
- Department of Medical Microbiology, Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Ian Boostrom
- Department of Medical Microbiology, Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Md. Abul Kalam
- Department of Burn and Plastic Surgery, Sheikh Hasina National Institute of Burn and Plastic Surgery, Dhaka, Bangladesh
| | - Brekhna Hasan
- Department of Medical Microbiology, Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Afifah Khan
- Department of Medical Microbiology, Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Timothy R. Walsh
- Department of Medical Microbiology, Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
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Naha S, Sands K, Mukherjee S, Roy C, Rameez MJ, Saha B, Dutta S, Walsh TR, Basu S. KPC-2-producing Klebsiella pneumoniae ST147 in a neonatal unit: Clonal isolates with differences in colistin susceptibility attributed to AcrAB-TolC pump. Int J Antimicrob Agents 2020; 55:105903. [PMID: 31954832 DOI: 10.1016/j.ijantimicag.2020.105903] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [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: 06/17/2019] [Revised: 01/08/2020] [Accepted: 01/11/2020] [Indexed: 01/21/2023]
Abstract
This study characterizes four KPC-2-producing Klebsiella pneumoniae isolates from neonates belonging to a single sequence type 147 (ST147) in relation to carbapenem resistance and explores probable mechanisms of differential colistin resistance among the clonal cluster. Whole genome sequencing (WGS) revealed that the isolates were nearly 100% identical and harbored resistance genes (blaKPC-2,OXA-9,CTX-M-15,SHV-11,OXA-1,TEM-1B, oqxA, oqxB, qnrB1, fosA, arr-2, sul1, aacA4, aac(6')Ib-cr, aac(6')Ib), and several virulence genes. blaKPC-2 was the only carbapenem-resistant gene found, bracketed between ISKpn7 and ISKpn6 of Tn4401b on a non-conjugative IncFII plasmid. Remarkably, one of the clonal isolates was resistant to colistin, the mechanistic basis of which was not apparent from comparative genomics. The transmissible colistin resistance gene, mcr, was absent. Efflux pump inhibitor, carbonyl cyanide 3-chlorophenylhydrazone (CCCP) rendered a 32-fold decrease in the minimum inhibitory concentration (MIC) of colistin in the resistant isolate only. acrB, tolC, ramA, and soxS genes of the AcrAB-TolC pump system overexpressed exclusively in the colistin-resistant isolate, although the corresponding homologs of the AcrAB-TolC pump, regulators and promoters were mutually identical. No change was observed in the expression of other efflux genes (kpnE/F and kpnG/H) or two-component system (TCS) genes (phoP/phoQ, pmrA/pmrB). Colistin resistance in one of the clonal KPC-2-producing isolates is postulated to be due to overexpression of the AcrAB-TolC pump. This study is probably the first to report clinical clonal K. pneumoniae isolates with differences in colistin susceptibility. The presence of carbapenem-resistant isolates with differential behavior in the expression of a genomically identical pump system indicates the nuances of the resistance mechanisms and the difficulty of treatment thereof.
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Affiliation(s)
- Sharmi Naha
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, P33, CIT Road, Scheme XM, Beliaghata, Kolkata-700010, West Bengal, India
| | - Kirsty Sands
- Department of Medical Microbiology and Infectious Disease, Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK
| | - Subhankar Mukherjee
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, P33, CIT Road, Scheme XM, Beliaghata, Kolkata-700010, West Bengal, India
| | - Chayan Roy
- Department of Microbiology, Bose Institute, P-1/12 CIT Road, Scheme VIIM, Kolkata-700054, West Bengal, India
| | - Moidu Jameela Rameez
- Department of Microbiology, Bose Institute, P-1/12 CIT Road, Scheme VIIM, Kolkata-700054, West Bengal, India
| | - Bijan Saha
- Department of Neonatology, Institute of Post-Graduate Medical Education & Research and SSKM Hospital, Kolkata-700020, West Bengal, India
| | - Shanta Dutta
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, P33, CIT Road, Scheme XM, Beliaghata, Kolkata-700010, West Bengal, India
| | - Timothy R Walsh
- Department of Medical Microbiology and Infectious Disease, Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK
| | - Sulagna Basu
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, P33, CIT Road, Scheme XM, Beliaghata, Kolkata-700010, West Bengal, India.
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Lim SY, Dafydd M, Ong J, Ord-McDermott LA, Board-Davies E, Sands K, Williams D, Sloan AJ, Heard CM. Mucoadhesive thin films for the simultaneous delivery of microbicide and anti-inflammatory drugs in the treatment of periodontal diseases. Int J Pharm 2020; 573:118860. [DOI: 10.1016/j.ijpharm.2019.118860] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 11/04/2019] [Accepted: 11/06/2019] [Indexed: 12/19/2022]
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Farzana R, Jones LS, Rahman MA, Toleman MA, Sands K, Portal E, Boostrom I, Kalam MA, Hassan B, Uddin AKMN, Walsh TR. Emergence of mcr-1 mediated colistin resistant Escherichia coli from a hospitalized patient in Bangladesh. J Infect Dev Ctries 2019; 13:773-776. [DOI: 10.3855/jidc.11541] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Accepted: 07/24/2019] [Indexed: 10/31/2022] Open
Abstract
Introduction: The emergence of plasmid mediated mcr in bacteria has become global public health threat. Herein, we report a mcr-1 positive E. coli in normal human flora from a patient admitted in Dhaka Medical College Hospital (DMCH).
Methodology: In total, 700 non-duplicate rectal swabs were collected from DMCH during 13th May to 12th June 2018. E. coli from rectal swabs were isolated on chromogenic UTI media containing vancomycin 10mg/l (Liofilchem, Italy) and confirmed by MALDI-TOF. Minimum inhibitory concentrations (MIC) were determined by agar dilution and interpreted according to EUCAST breakpoints. Genomic analysis of mcr positive E. coli (MCRPEC) was performed by Illumina MiSeq sequencing and pulsed field gel electrophoresis (PFGE) using S1 nuclease DNA digests and blamcr-1 probing. Transferability of blamcr-1 were determined by conjugation assays.
Results: We found one MCRPEC from 700 rectal swab screening which was isolated from the rectal swab culture of a 17-year boy who was admitted to the burns ICU, DMCH with 53% flame burn involving much of the trunk and face. Genome sequencing revealed that mcr-1 was present on an IncH12 plasmid of 257,243 bp and flanked by ISApaI1. The colistin resistance can be transferred to the recipient Klebsiella varricola with a frequency of 8.3 × 10-5. Transconjugants were more resistant to colistin than donor (MIC 32 µg/mL).
Conclusions: This is the first human associated mcr in Bangladesh. These data indicate the need for a systematic “one health” surveillance in the country.
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Mentasti M, Prime K, Sands K, Khan S, Wootton M. Rapid detection of IMP, NDM, VIM, KPC and OXA-48-like carbapenemases from Enterobacteriales and Gram-negative non-fermenter bacteria by real-time PCR and melt-curve analysis. Eur J Clin Microbiol Infect Dis 2019; 38:2029-2036. [DOI: 10.1007/s10096-019-03637-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 07/10/2019] [Indexed: 10/26/2022]
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Yang QE, Tansawai U, Andrey DO, Wang S, Wang Y, Sands K, Kiddee A, Assawatheptawee K, Bunchu N, Hassan B, Walsh TR, Niumsup PR. Environmental dissemination of mcr-1 positive Enterobacteriaceae by Chrysomya spp. (common blowfly): An increasing public health risk. Environ Int 2019; 122:281-290. [PMID: 30455105 DOI: 10.1016/j.envint.2018.11.021] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 11/08/2018] [Accepted: 11/09/2018] [Indexed: 06/09/2023]
Abstract
Until recently, the role of insects, and particularly flies, in disseminating antimicrobial resistance (AMR) has been poorly studied. In this study, we screened blowflies (Chrysomya spp.) from different areas near the city of Phitsanulok, Northern Thailand, for the presence of AMR genes and in particular, mcr-1, using whole genome sequencing (WGS). In total, 48 mcr-1-positive isolates were recovered, consisting of 17 mcr-1-positive Klebsiella pneumoniae (MCRPKP) and 31 mcr-1-positive Escherichia coli (MCRPEC) strains. The 17 MCRPKP were shown to be clonal (ST43) with few single poly nucleomorphs (SNPs) by WGS analysis. In in-vitro models, the MCRPKP were shown to be highly virulent. In contrast, 31 recovered MCRPEC isolates are varied, belonging to 12 different sequence types shared with those causing human infections. The majority of mcr-1 gene are located on IncX4 plasmids (29/48, 60.42%), sharing an identical plasmid backbone. These findings highlight the contribution of flies to the AMR contagion picture in low- and middle-income countries and the challenges of tackling global AMR.
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Affiliation(s)
- Qiu E Yang
- Department of Medical Microbiology and Infectious Disease, Division of Infection and Immunity, Cardiff University, Cardiff CF14 4XN, UK.
| | - Uttapoln Tansawai
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok 65000, Thailand
| | - Diego O Andrey
- Department of Medical Microbiology and Infectious Disease, Division of Infection and Immunity, Cardiff University, Cardiff CF14 4XN, UK; Service of Infectious Diseases, Geneva University Hospitals and Faculty of Medicine, 1211 Geneva, Switzerland
| | - Shaolin Wang
- Beijing Advanced Innovation Centre for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Yang Wang
- Beijing Advanced Innovation Centre for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Kirsty Sands
- Department of Medical Microbiology and Infectious Disease, Division of Infection and Immunity, Cardiff University, Cardiff CF14 4XN, UK
| | - Anong Kiddee
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok 65000, Thailand
| | - Kanit Assawatheptawee
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok 65000, Thailand
| | - Nophawan Bunchu
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok 65000, Thailand
| | - Brekhna Hassan
- Department of Medical Microbiology and Infectious Disease, Division of Infection and Immunity, Cardiff University, Cardiff CF14 4XN, UK
| | - Timothy Rutland Walsh
- Department of Medical Microbiology and Infectious Disease, Division of Infection and Immunity, Cardiff University, Cardiff CF14 4XN, UK.
| | - Pannika R Niumsup
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok 65000, Thailand
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Farzana R, Jones LS, Rahman MA, Andrey DO, Sands K, Portal E, Watkins WJ, Pervin M, Banerjee M, Walsh TR. Outbreak of Hypervirulent Multidrug-resistant Klebsiella variicola Causing High Mortality in Neonates in Bangladesh. Clin Infect Dis 2018; 68:1225-1227. [DOI: 10.1093/cid/ciy778] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 09/06/2018] [Indexed: 12/18/2022] Open
Affiliation(s)
- Refath Farzana
- Department of Medical Microbiology, Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Lim S Jones
- Public Health Wales Microbiology, University Hospital of Wales, Cardiff, United Kingdom
| | | | - Diego O Andrey
- Department of Medical Microbiology, Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Kirsty Sands
- Department of Medical Microbiology, Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Edward Portal
- Department of Medical Microbiology, Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - W John Watkins
- Institute of Infection and Immunity, School of Medicine, Cardiff University, United Kingdom
| | - Monira Pervin
- Department of Virology, Dhaka Medical College, Bangladesh
| | | | - Timothy R Walsh
- Department of Medical Microbiology, Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
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Yang Q, Li M, Spiller OB, Andrey DO, Hinchliffe P, Li H, MacLean C, Niumsup P, Powell L, Pritchard M, Papkou A, Shen Y, Portal E, Sands K, Spencer J, Tansawai U, Thomas D, Wang S, Wang Y, Shen J, Walsh T. Balancing mcr-1 expression and bacterial survival is a delicate equilibrium between essential cellular defence mechanisms. Nat Commun 2017; 8:2054. [PMID: 29233990 PMCID: PMC5727292 DOI: 10.1038/s41467-017-02149-0] [Citation(s) in RCA: 121] [Impact Index Per Article: 17.3] [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: 05/09/2017] [Accepted: 11/09/2017] [Indexed: 12/20/2022] Open
Abstract
MCR-1 is a lipid A modifying enzyme that confers resistance to the antibiotic colistin. Here, we analyse the impact of MCR-1 expression on E. coli morphology, fitness, competitiveness, immune stimulation and virulence. Increased expression of mcr-1 results in decreased growth rate, cell viability, competitive ability and significant degradation in cell membrane and cytoplasmic structures, compared to expression of catalytically inactive MCR-1 (E246A) or MCR-1 soluble component. Lipopolysaccharide (LPS) extracted from mcr-1 strains induces lower production of IL-6 and TNF, when compared to control LPS. Compared to their parent strains, high-level colistin resistance mutants (HLCRMs) show reduced fitness (relative fitness is 0.41-0.78) and highly attenuated virulence in a Galleria mellonella infection model. Furthermore, HLCRMs are more susceptible to most antibiotics than their respective parent strains. Our results show that the bacterium is challenged to find a delicate equilibrium between expression of MCR-1-mediated colistin resistance and minimalizing toxicity and thus ensuring cell survival.
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Affiliation(s)
- Qiue Yang
- Department of Medical Microbiology and Infectious Disease, Division of Infection and Immunity, Cardiff University, Cardiff, CF14 4XN, UK.
| | - Mei Li
- Department of Medical Microbiology and Infectious Disease, Division of Infection and Immunity, Cardiff University, Cardiff, CF14 4XN, UK
| | - Owen B Spiller
- Department of Medical Microbiology and Infectious Disease, Division of Infection and Immunity, Cardiff University, Cardiff, CF14 4XN, UK
| | - Diego O Andrey
- Department of Medical Microbiology and Infectious Disease, Division of Infection and Immunity, Cardiff University, Cardiff, CF14 4XN, UK
- Service of Infectious Diseases, Geneva University Hospitals and Faculty of Medicine, 1211, Geneva, Switzerland
| | - Philip Hinchliffe
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK
| | - Hui Li
- Beijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, Beijing Center for Disease Prevention and Control, Beijing, 100013, China
| | - Craig MacLean
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
| | - Pannika Niumsup
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok, 65000, Thailand
| | - Lydia Powell
- Advanced Therapies Group, Oral and Biomedical Sciences, School of Dentistry, College of Biomedical and Life Sciences, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Manon Pritchard
- Advanced Therapies Group, Oral and Biomedical Sciences, School of Dentistry, College of Biomedical and Life Sciences, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Andrei Papkou
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
| | - Yingbo Shen
- Beijing Advanced Innovation Centre for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Edward Portal
- Department of Medical Microbiology and Infectious Disease, Division of Infection and Immunity, Cardiff University, Cardiff, CF14 4XN, UK
| | - Kirsty Sands
- Department of Medical Microbiology and Infectious Disease, Division of Infection and Immunity, Cardiff University, Cardiff, CF14 4XN, UK
| | - James Spencer
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK
| | - Uttapoln Tansawai
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok, 65000, Thailand
| | - David Thomas
- Advanced Therapies Group, Oral and Biomedical Sciences, School of Dentistry, College of Biomedical and Life Sciences, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Shaolin Wang
- Beijing Advanced Innovation Centre for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Yang Wang
- Beijing Advanced Innovation Centre for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Jianzhong Shen
- Beijing Advanced Innovation Centre for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Timothy Walsh
- Department of Medical Microbiology and Infectious Disease, Division of Infection and Immunity, Cardiff University, Cardiff, CF14 4XN, UK.
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Ellis AR, Fahie-Wilson M, Axcell M, Sands K, Hill RP. Macroprolactin(s): composition and reactivity in immunoassays and laboratory interpretation of results of an unusual patient serum. Ann Clin Biochem 2016; 43:57-62. [PMID: 16390610 DOI: 10.1258/000456306775141830] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [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]
Abstract
Background: Macroprolactin is a high molecular mass complex of prolactin that may be the cause of elevated serum prolactin as determined by immunoassay. The composition of macroprolactin and its reactivity in immunoassays are variable but the complex has minimal bioactivity in vivo. Hyperprolactinaemia due to unrecognized macroprolactinaemia can lead to misdiagnosis and mistreatment. Methods: Serum from a patient with an unusual pattern of immunoreactivity was distributed to three users of each of the most popular immunoassays represented in the UK National External Quality Assessment Scheme (NEQAS) for prolactin. Clinical details were provided and participating centres were invited to investigate the prolactin content of the specimen according to their local protocol, and to comment on their results. The nature of the macroprolactin in the specimen was investigated in detail by gel filtration chromatography of the native serum and of the serum after adsorption of IgG with protein A, and by affinity chromatography with concanavalin A. Results: Gel filtration studies revealed two peaks of macroprolactin in this serum. These macroprolactins were shown to be different in their IgG content and degree of glycosylation. All eight immunoassays reacted strongly with the macroprolactin present. The majority (78%) of centres that interpreted their results either demonstrated the presence of macroprolactin in the specimen, or suggested it as a likely cause of the hyperprolactinaemia. However, two centres inappropriately excluded macroprolactinaemia as the cause of the elevated prolactin, and a further two did not consider it at all. Data from previous UK NEQAS distributions (between 1996 and 2003) of macroprolactin containing sera are presented which suggest that the frequency of recognition of macroprolactin as a possible cause of hyperprolactinaemia has increased over time. Conclusions: Very high molecular mass forms of prolactin and the presence of multiple molecular mass forms, as detected in the case presented here, are uncommon. Also, the pattern of immunoreactivity reported in this specimen was unusual as most macroprolactins studied previously react less strongly in, for example, the Bayer ADVIA Centaur assay compared to the Roche E170 assay. Both peaks of macroprolactin in this serum reacted in all assays tested. This case highlights the variable nature and immunoreactive behaviour of macroprolactin species.
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Affiliation(s)
- A R Ellis
- UK NEQAS for Peptide Hormones, Department of Clinical Biochemistry, Royal Infirmary, Edinburgh EH16 4SA, UK.
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Sands K, Jansen R, Zaslau S, Greenwald D. Review article: the safety of therapeutic drugs in male inflammatory bowel disease patients wishing to conceive. Aliment Pharmacol Ther 2015; 41:821-34. [PMID: 25752753 DOI: 10.1111/apt.13142] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 04/27/2013] [Accepted: 02/05/2015] [Indexed: 12/20/2022]
Abstract
BACKGROUND Many therapeutic drugs are used by patients with inflammatory bowel disease, often around the time of conception. The pregnancy outcomes of males and females exposed to these therapeutics needs to be examined and this information is necessary to counsel patients appropriately. AIM To review the literature describing male infertility and inflammatory bowel disease to educate practitioners of the impact of inflammatory bowel disease on male reproduction and the impact of therapeutics on pregnancy outcomes. METHODS We performed a PubMed search using the search terms 'male infertility,' 'Crohn's disease,' 'inflammatory bowel disease,' 'ulcerative colitis,' 'ciprofloxacin AND infertility,' 'metronidazole AND infertility,' 'sulfasalazine AND infertility,' 'azathioprine AND infertility,' 'methotrexate AND infertility,' 'ciclosporin AND infertility,' 'corticosteroids AND infertility,' 'infliximab AND male fertility,' 'infliximab AND infertility,' 'infliximab AND foetus,' 'infliximab AND paternal exposure' and 'infliximab AND sperm.' References from selected papers were reviewed and used if relevant. RESULTS Over half of male patients with IBD have some degree of infertility, compared to 8-17% of the general population. Semen parameters including total count, motility and morphology may be adversely affected by therapeutics. IBD medications in males do not increase foetal risk with the possible exception of azathioprine and mercaptopurine; however, increased foetal risk is seen in other drugs if taken by female patients. CONCLUSIONS It is recognised that male infertility is often impacted with therapeutic drugs used to treat inflammatory bowel disease; however, the effects of the paternal drug exposure at the time of conception and exposure in utero should be considered to counsel patients appropriately.
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Affiliation(s)
- K Sands
- EW Sparrow Hospital Urology Residency, Michigan State University College of Osteopathic Medicine, Lansing, MI, USA
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Sands K, Williams DW, Wilson M, Lewis M, Wise MP. The Dynamics of Polymicrobial Biofilms. Am J Respir Crit Care Med 2013; 188:1266. [DOI: 10.1164/rccm.201305-0916le] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Grossman S, Lieberman R, Bar J, Fischer C, Lipsitz L, Mottley L, Sands K, Zimetbaum P, Shapiro N. Reducing Admissions Utilizing the Boston Syncope Criteria. Acad Emerg Med 2007. [DOI: 10.1197/j.aem.2007.03.824] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Grossman SA, Fischer C, Bar JL, Lipsitz LA, Mottley L, Sands K, Thompson S, Zimetbaum P, Shapiro NI. The yield of head CT in syncope: a pilot study. Intern Emerg Med 2007; 2:46-9. [PMID: 17551685 PMCID: PMC2780634 DOI: 10.1007/s11739-007-0010-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2006] [Accepted: 01/04/2007] [Indexed: 11/29/2022]
Abstract
UNLABELLED Although head CT is often routinely performed in emergency department (ED) patients with syncope, few studies have assessed its value. OBJECTIVES To determine the yield of routine head CT in ED patients with syncope and analyse the factors associated with a positive CT. METHODS Prospective, observational, cohort study of consecutive patients presenting with syncope to an urban tertiary-care ED (48,000 annual visits). INCLUSION CRITERIA age >or=18 and loss of consciousness (LOC). Exclusion criteria included persistent altered mental status, drug-related or post-trauma LOC, seizure or hypoglycaemia. Primary outcome was abnormal head CT including subarachnoid, subdural or parenchymal haemorrhage, infarction, signs of acute stroke and newly diagnosed brain mass. RESULTS Of 293 eligible patients, 113 (39%) underwent head CT and comprise the study cohort. Ninety-five patients (84%) were admitted to the hospital. Five patients, 5% (95% CI=0.8%-8%), had an abnormal head CT: 2 subarachnoid haemorrhage, 2 cerebral haemorrhage and 1 stroke. Post hoc examination of patients with an abnormal head CT revealed focal neurologic findings in 2 and a new headache in 1. The remaining 2 patients had no new neurologic findings but physical findings of trauma (head lacerations with periorbital ecchymoses suggestive of orbital fractures). All patients with positive findings on CT were >65 years of age. Of the 108 remaining patients who had head CT, 45 (32%-51%) had signs or symptoms of neurologic disease including headache, trauma above the clavicles or took coumadin. Limiting head CT to this population would potentially reduce scans by 56% (47%-65%). If age >60 were an additional criteria, scans would be reduced by 24% (16%-32%). Of the patients who did not have head CT, none were found to have new neurologic disease during hospitalisation or 30-day follow-up. CONCLUSIONS Our data suggest that the derivation of a prospectively derived decision rule has the potential to decrease the routine use of head CT in patients presenting to the ED with syncope.
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Affiliation(s)
- S A Grossman
- Department of Emergency Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, WCC2, One Deaconess Road, Boston, MA 02115, USA.
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Avery R, Kalaycio M, Pohlman B, Sobecks R, Kuczkowski E, Andresen S, Mossad S, Shamp J, Curtis J, Kosar J, Sands K, Serafin M, Bolwell B. Early vancomycin-resistant enterococcus (VRE) bacteremia after allogeneic bone marrow transplantation is associated with a rapidly deteriorating clinical course. Bone Marrow Transplant 2005; 35:497-9. [PMID: 15640812 DOI: 10.1038/sj.bmt.1704821] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.8] [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: 11/08/2022]
Abstract
Vancomycin-resistant enterococcal (VRE) infection is a growing threat. We studied the incidence, risk factors, and clinical course of early-onset VRE bacteremia in allogeneic hematopoietic stem cell transplant recipients. We carried out a chart review of 281 allogeneic hematopoietic stem cell transplant recipients from 1997-2003, including preparative regimen, diagnosis, status of disease, graft-versus-host disease prophylaxis, antimicrobial therapy, and survival. VRE bacteremia developed in 12/281 (4.3%) recipients; 10 (3.6%) were within 21 days of transplant. Diagnoses were acute leukemia (7), NHL (2), and MDS (1). In all, 70% had refractory/relapsed disease; 30% were in remission. In total, 50% had circulating blasts. Nine of 10 had matched unrelated donors (7/9 with CD8+ T-cell depletion). The average time to positive VRE cultures was 15 days; average WBC was 0.05, and 80% had concomitant infections. Despite treatment, all patients died within 73 days of VRE bacteremia. Intra-abdominal complications were common. Causes of death included bacterial or fungal infection, multiorgan failure, VOD, ARDS, and relapse. A total of 60% of patients engrafted neutrophils, but none engrafted platelets. Early VRE bacteremia after allogeneic bone marrow transplant is associated with a rapidly deteriorating clinical course, although not always directly due to VRE. Early VRE may be a marker for the critical condition of these high-risk patients at the time of transplant.
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Affiliation(s)
- R Avery
- Bone Marrow Transplantation Program and the Departments of Hematology-Oncology, Pharmacy, and Infectious Disease, Cleveland Clinic Foundation, OH 44195, USA
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Segal R, Poznansky MC, Connors L, Sands K, Barlam T. Changing patterns of presentations of patients with HIV-related disease at a tertiary referral centre and its implications for physician training. Int J STD AIDS 2001; 12:453-9. [PMID: 11394981 DOI: 10.1258/0956462011923480] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [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]
Abstract
Highly active antiretroviral therapy (HAART) has been shown to be highly effective in controlling HIV-related disease progression. Our objective was to determine whether HAART had altered the spectrum of HIV-related disease presentations at a tertiary medical referral centre and if a change in the clinical presentations of HIV-infected individuals to the hospital had impacted on physicians' training. A retrospective study which examined all admissions of HIV-infected patients identified between 1 October 1996 to 30 September 1998 using a hospital-designed computer database was undertaken at the Beth Israel Deaconess Medical Center (BIDMC) tertiary medical referral centre. All medical residents were surveyed in order to assess their knowledge of HIV-associated admissions and their confidence treating HIV-infected patients. There were significant changes in the admitting diagnosis for HIV-related illness between 1996 and 1998. Admissions for opportunistic infections (OIs) declined whereas admissions with bacterial infections increased significantly. Use of HAART remained stable between the 2 years of the study. Physicians' overestimated the use of HAART and only 8% of residents felt very comfortable taking care of an HIV-infected patient. In conclusion, the spectrum of presentations with HIV-related disease to a tertiary referral centre continues to change in the HAART era and impacts on physicians' experience of the management of HIV disease.
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Affiliation(s)
- R Segal
- Department of Infectious Diseases, Beth Israel and Deaconess Medical Center, Brookline Avenue, Boston, MA, USA
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Sands K. John Foxe: exorcist. Hist Today 2001; 51:37-43. [PMID: 18988361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
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