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Khawaja T, Mäklin T, Kallonen T, Gladstone RA, Pöntinen AK, Mero S, Thorpe HA, Samuelsen Ø, Parkhill J, Izhar M, Akhtar MW, Corander J, Kantele A. Deep sequencing of Escherichia coli exposes colonisation diversity and impact of antibiotics in Punjab, Pakistan. Nat Commun 2024; 15:5196. [PMID: 38890378 PMCID: PMC11189469 DOI: 10.1038/s41467-024-49591-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 06/10/2024] [Indexed: 06/20/2024] Open
Abstract
Multi-drug resistant (MDR) E. coli constitute a major public health burden globally, reaching the highest prevalence in the global south yet frequently flowing with travellers to other regions. However, our comprehension of the entire genetic diversity of E. coli colonising local populations remains limited. We quantified this diversity, its associated antimicrobial resistance (AMR), and assessed the impact of antibiotic use by recruiting 494 outpatients and 423 community dwellers in the Punjab province, Pakistan. Rectal swab and stool samples were cultured on CLED agar and DNA extracted from plate sweeps was sequenced en masse to capture both the genetic and AMR diversity of E. coli. We assembled 5,247 E. coli genomes from 1,411 samples, displaying marked genetic diversity in gut colonisation. Compared with high income countries, the Punjabi population generally showed a markedly different distribution of genetic lineages and AMR determinants, while use of antibiotics elevated the prevalence of well-known globally circulating MDR clinical strains. These findings implicate that longitudinal multi-regional genomics-based surveillance of both colonisation and infections is a prerequisite for developing mechanistic understanding of the interplay between ecology and evolution in the maintenance and dissemination of (MDR) E. coli.
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Affiliation(s)
- Tamim Khawaja
- Meilahti Infectious Diseases and Vaccine Research Center (MeiVac), Helsinki University Hospital and University of Helsinki, Helsinki, Finland
- Human Microbiome Research Program, University of Helsinki, Helsinki, Finland
- Multidiciplinary Center of Excellence in Antimicrobial Resistance Research, FIMAR, Medical Faculty, University of Helsinki, Helsinki, Finland
| | - Tommi Mäklin
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - Teemu Kallonen
- Department of Clinical Microbiology, Turku University Hospital, Turku, Finland
| | | | - Anna K Pöntinen
- Department of Biostatistics, University of Oslo, Oslo, Norway
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Sointu Mero
- Human Microbiome Research Program, University of Helsinki, Helsinki, Finland
- Multidiciplinary Center of Excellence in Antimicrobial Resistance Research, FIMAR, Medical Faculty, University of Helsinki, Helsinki, Finland
| | - Harry A Thorpe
- Department of Biostatistics, University of Oslo, Oslo, Norway
| | - Ørjan Samuelsen
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Mateen Izhar
- Department of Microbiology, Shaikh Zayed Post-Graduate Medical Institute, Lahore, Pakistan
| | - M Waheed Akhtar
- School of Biological Science, University of the Punjab, Lahore, Pakistan
| | - Jukka Corander
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland.
- Department of Biostatistics, University of Oslo, Oslo, Norway.
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, UK.
| | - Anu Kantele
- Meilahti Infectious Diseases and Vaccine Research Center (MeiVac), Helsinki University Hospital and University of Helsinki, Helsinki, Finland.
- Human Microbiome Research Program, University of Helsinki, Helsinki, Finland.
- Multidiciplinary Center of Excellence in Antimicrobial Resistance Research, FIMAR, Medical Faculty, University of Helsinki, Helsinki, Finland.
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El Chaar M, Khoury Y, Douglas GM, El Kazzi S, Jisr T, Soussi S, Merhi G, Moghnieh RA, Shapiro BJ. Longitudinal genomic surveillance of multidrug-resistant Escherichia coli carriage in critical care patients. Microbiol Spectr 2024; 12:e0312823. [PMID: 38171007 PMCID: PMC10846182 DOI: 10.1128/spectrum.03128-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 11/27/2023] [Indexed: 01/05/2024] Open
Abstract
Colonization with multidrug-resistant Escherichia coli strains causes a substantial health burden in hospitalized patients. We performed a longitudinal genomics study to investigate the colonization of resistant E. coli strains in critically ill patients and to identify evolutionary changes and strain replacement events within patients. Patients were admitted to the intensive care unit and hematology wards at a major hospital in Lebanon. Perianal swabs were collected from participants on admission and during hospitalization, which were screened for extended-spectrum beta-lactamases and carbapenem-resistant Enterobacterales. We performed whole-genome sequencing and analysis on E. coli strains isolated from patients at multiple time points. The E. coli isolates were genetically diverse, with 11 sequence types (STs) identified among 22 isolates sequenced. Five patients were colonized by E. coli sequence type 131 (ST131)-encoding CTX-M-27, an emerging clone not previously observed in clinical samples from Lebanon. Among the eight patients whose resident E. coli strains were tracked over time, five harbored the same E. coli strain with relatively few mutations over the 5 to 10 days of hospitalization. The other three patients were colonized by different E. coli strains over time. Our study provides evidence of strain diversity within patients during their hospitalization. While strains varied in their antimicrobial resistance profiles, the number of resistance genes did not increase over time. We also show that ST131-encoding CTX-M-27, which appears to be emerging as a globally important multidrug-resistant E. coli strain, is also prevalent among critical care patients and deserves further monitoring.IMPORTANCEUnderstanding the evolution of bacteria over time in hospitalized patients is of utmost significance in the field of infectious diseases. While numerous studies have surveyed genetic diversity and resistance mechanisms in nosocomial infections, time series of within-patient dynamics are rare, and high-income countries are over-represented, leaving low- and middle-income countries understudied. Our study aims to bridge these research gaps by conducting a longitudinal survey of critically ill patients in Lebanon. This allowed us to track Escherichia coli evolution and strain replacements within individual patients over extended periods. Through whole-genome sequencing, we found extensive strain diversity, including the first evidence of the emerging E. coli sequence type 131 clone encoding the CTX-M-27 beta-lactamase in a clinical sample from Lebanon, as well as likely strain replacement events during hospitalization.
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Affiliation(s)
- Mira El Chaar
- Faculty of Health Sciences, University of Balamand, Beirut, Lebanon
| | - Yaralynn Khoury
- Faculty of Health Sciences, University of Balamand, Beirut, Lebanon
| | - Gavin M. Douglas
- Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
| | - Samir El Kazzi
- Faculty of Health Sciences, University of Balamand, Beirut, Lebanon
| | - Tamima Jisr
- Clinical Laboratory Department, Makassed General Hospital, Beirut, Lebanon
| | - Shatha Soussi
- Clinical Laboratory Department, Makassed General Hospital, Beirut, Lebanon
| | - Georgi Merhi
- Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
| | - Rima A. Moghnieh
- Division of Infectious Diseases, Department of Internal Medicine, Lebanese American University Medical Center, Beirut, Lebanon
| | - B. Jesse Shapiro
- Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
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3
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Pöntinen AK, Gladstone RA, Pesonen H, Pesonen M, Cléon F, Parcell BJ, Kallonen T, Simonsen GS, Croucher NJ, McNally A, Parkhill J, Johnsen PJ, Samuelsen Ø, Corander J. Modulation of multidrug-resistant clone success in Escherichia coli populations: a longitudinal, multi-country, genomic and antibiotic usage cohort study. THE LANCET. MICROBE 2024; 5:e142-e150. [PMID: 38219757 DOI: 10.1016/s2666-5247(23)00292-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 08/24/2023] [Accepted: 09/01/2023] [Indexed: 01/16/2024]
Abstract
BACKGROUND The effect of antibiotic usage on the success of multidrug-resistant (MDR) clones in a population remains unclear. With this genomics-based molecular epidemiology study, we aimed to investigate the contribution of antibiotic use to Escherichia coli clone success, relative to intra-strain competition for colonisation and infection. METHODS We sequenced all the available E coli bloodstream infection isolates provided by the British Society for Antimicrobial Chemotherapy (BSAC) from 2012 to 2017 (n=718) and combined these with published data from the UK (2001-11; n=1090) and Norway (2002-17; n=3254). Defined daily dose (DDD) data from the European Centre for Disease Prevention and Control (retrieved on Sept 21, 2021) for major antibiotic classes (β-lactam, tetracycline, macrolide, sulfonamide, quinolone, and non-penicillin β-lactam) were used together with sequence typing, resistance profiling, regression analysis, and non-neutral Wright-Fisher simulation-based modelling to enable systematic comparison of resistance levels, clone success, and antibiotic usage between the UK and Norway. FINDINGS Sequence type (ST)73, ST131, ST95, and ST69 accounted for 892 (49·3%) of 1808 isolates in the BSAC collection. In the UK, the proportion of ST69 increased between 2001-10 and 2011-17 (p=0·0004), whereas the proportions of ST73 and ST95 did not vary between periods. ST131 expanded quickly after its emergence in 2003 and its prevalence remained consistent throughout the study period (apart from a brief decrease in 2009-10). The extended-spectrum β-lactamase (ESBL)-carrying, globally disseminated MDR clone ST131-C2 showed overall greater success in the UK (154 [56·8%] of 271 isolates in 2003-17) compared with Norway (51 [18·3%] of 278 isolates in 2002-17; p<0·0001). DDD data indicated higher total use of antimicrobials in the UK, driven mainly by the class of non-penicillin β-lactams, which were used between 2·7-times and 5·1-times more in the UK per annum (ratio mean 3·7 [SD 0·8]). This difference was associated with the higher success of the MDR clone ST131-C2 (pseudo-R2 69·1%). A non-neutral Wright-Fisher model replicated the observed expansion of non-MDR and MDR sequence types under higher DDD regimes. INTERPRETATION Our study indicates that resistance profiles of contemporaneously successful clones can vary substantially, warranting caution in the interpretation of correlations between aggregate measures of resistance and antibiotic usage. Our study further suggests that in countries with low-to-moderate use of antibiotics, such as the UK and Norway, the extent of non-penicillin β-lactam use modulates rather than determines the success of widely disseminated MDR ESBL-carrying E coli clones. Detailed understanding of underlying causal drivers of success is important for improved control of resistant pathogens. FUNDING Trond Mohn Foundation, Marie Skłodowska-Curie Actions, European Research Council, Royal Society, and Wellcome Trust.
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Affiliation(s)
- Anna K Pöntinen
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway; Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway.
| | - Rebecca A Gladstone
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Henri Pesonen
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Maiju Pesonen
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway; Oslo Centre for Biostatistics and Epidemiology, Oslo University Hospital Research Support Services, Oslo, Norway
| | - François Cléon
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | | | - Teemu Kallonen
- Department of Clinical Microbiology, Turku University Hospital, Turku, Finland
| | - Gunnar Skov Simonsen
- Research Group for Host-Microbe Interaction, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway; Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Nicholas J Croucher
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Alan McNally
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Pål J Johnsen
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Ørjan Samuelsen
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway; Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Jukka Corander
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway; Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK; Helsinki Institute of Information Technology, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland.
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Nadimpalli ML, Rojas Salvatierra L, Chakraborty S, Swarthout JM, Cabrera LZ, Pickering AJ, Calderon M, Saito M, Gilman RH, Pajuelo MJ. Effects of breastfeeding on children's gut colonization with multidrug-resistant Enterobacterales in peri-urban Lima, Peru. Gut Microbes 2024; 16:2309681. [PMID: 38300753 PMCID: PMC10841006 DOI: 10.1080/19490976.2024.2309681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 01/19/2024] [Indexed: 02/03/2024] Open
Abstract
Children living in low-resource settings are frequently gut-colonized with multidrug-resistant bacteria. We explored whether breastfeeding may protect against children's incident gut colonization with extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-Ec) and Klebsiella, Enterobacter, or Citrobacter spp. (ESBL-KEC). We screened 937 monthly stool samples collected from 112 children aged 1-16 months during a 2016-19 prospective cohort study of enteric infections in peri-urban Lima. We used 52,816 daily surveys to examine how exposures to breastfeeding in the 30 days prior to a stool sample were associated with children's risks of incident gut-colonization, controlling for antibiotic use and other covariates. We sequenced 78 ESBL-Ec from 47 children to explore their diversity. Gut-colonization with ESBL-Ec was increasingly prevalent as children aged, approaching 75% by 16 months, while ESBL-KEC prevalence fluctuated between 18% and 36%. Through 6 months of age, exclusively providing human milk in the 30 days prior to a stool sample did not reduce children's risk of incident gut-colonization with ESBL-Ec or ESBL-KEC. From 6 to 16 months of age, every 3 additional days of breastfeeding in the prior 30 days was associated with 6% lower risk of incident ESBL-Ec gut-colonization (95% CI: 0.90, 0.98, p = .003). No effects were observed on incident ESBL-KEC colonization. We detected highly diverse ESBL-Ec among children and few differences between children who were predominantly breastfed (mean age: 4.1 months) versus older children (10.8 months). Continued breastfeeding after 6 months conferred protection against children's incident gut colonization with ESBL-Ec in this setting. Policies supporting continued breastfeeding should be considered in efforts to combat antibiotic resistance.
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Affiliation(s)
- Maya L. Nadimpalli
- Gangarosa Department of Environmental Health, Emory Rollins School of Public Health, Atlanta, GA, USA
- Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance (Levy CIMAR), Tufts University, Boston, MA, USA
| | - Luismarcelo Rojas Salvatierra
- Laboratorio de Microbiología Molecular, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Subhra Chakraborty
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Jenna M. Swarthout
- Department of Civil and Environmental Engineering, Tufts University, Medford, MA, USA
| | - Lilia Z. Cabrera
- Asociación Benéfica Proyectos en Informática, Salud, Medicina, y Agricultura (PRISMA), Lima, Peru
| | - Amy J. Pickering
- Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance (Levy CIMAR), Tufts University, Boston, MA, USA
- Department of Civil and Environmental Engineering, University of California, Berkeley, CA, USA
- Blum Center for Developing Economies, University of California, Berkeley, CA, USA
| | - Maritza Calderon
- Laboratorio de Microbiología Molecular, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Mayuko Saito
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Robert H. Gilman
- Laboratorio de Microbiología Molecular, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia, Lima, Peru
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Monica J. Pajuelo
- Laboratorio de Microbiología Molecular, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia, Lima, Peru
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
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5
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Troth TD, McInnes RS, Dunn SJ, Mirza J, Whittaker AH, Goodchild SA, Loman NJ, Harding SV, van Schaik W. Differences in the gut microbiota between Gurkhas and soldiers of British origin. PLoS One 2023; 18:e0292645. [PMID: 38113233 PMCID: PMC10729956 DOI: 10.1371/journal.pone.0292645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 09/26/2023] [Indexed: 12/21/2023] Open
Abstract
Previous work indicated that the incidence of travellers' diarrhoea (TD) is higher in soldiers of British origin, when compared to soldiers of Nepalese descent (Gurkhas). We hypothesise that the composition of the gut microbiota may be a contributing factor in the risk of developing TD in soldiers of British origin. This study aimed to characterise the gut microbial composition of Gurkha and non-Gurkha soldiers of the British Army. Recruitment of 38 soldiers (n = 22 Gurkhas, n = 16 non-Gurkhas) and subsequent stool collection, enabled shotgun metagenomic sequencing-based analysis of the gut microbiota. The microbiota of Gurkhas had significantly (P < 0.05) lower diversity, for both Shannon and Simpson diversity indices, using species level markers than the gut microbiota of non-Gurkha soldiers. Non-metric Multidimensional Scaling (NMDS) of the Bray-Curtis distance matrix revealed a significant difference in the composition of the gut microbiota between Gurkhas and non-Gurkha soldiers, at both the species level (P = 0.0178) and the genus level (P = 0.0483). We found three genera and eight species that were significantly enriched in the non-Gurkha group and one genus (Haemophilus) and one species (Haemophilus parainfluenzae) which were enriched in the Gurkha group. The difference in the microbiota composition between Gurkha soldiers and soldiers of British origin may contribute to higher colonization resistance against diarrhoeal pathogens in the former group. Our findings may enable further studies into interventions that modulate the gut microbiota of soldiers to prevent TD during deployment.
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Affiliation(s)
- Thomas D. Troth
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Ross S. McInnes
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Steven J. Dunn
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Jeremy Mirza
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Annalise H. Whittaker
- CBR Division, Defence and Science Technology Laboratory, Salisbury, Wiltshire, United Kingdom
| | - Sarah A. Goodchild
- CBR Division, Defence and Science Technology Laboratory, Salisbury, Wiltshire, United Kingdom
| | - Nicholas J. Loman
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Sarah V. Harding
- CBR Division, Defence and Science Technology Laboratory, Salisbury, Wiltshire, United Kingdom
- School of Respiratory Sciences, University of Leicester, Leicester, United Kingdom
| | - Willem van Schaik
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
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Literacka E, Konior M, Izdebski R, Żabicka D, Herda M, Gniadkowski M, Korzeniewski K. High risk of intestinal colonization with ESBL-producing Escherichia coli among soldiers of military contingents in specific geographic regions. Eur J Clin Microbiol Infect Dis 2023; 42:1523-1530. [PMID: 37857920 PMCID: PMC10651695 DOI: 10.1007/s10096-023-04684-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 10/12/2023] [Indexed: 10/21/2023]
Abstract
One-hundred Polish soldiers of a contingent in Afghanistan in 2019 were screened for Enterobacterales resistant to newer-generation β-lactams at their departure and return. Seventeen percent were colonized in the gut at the departure, whereas 70% acquired carriage in Afghanistan. The commonest organisms were extended-spectrum β-lactamase (ESBL)-producing Escherichia coli (ESBL-Ec; 96.6%). All isolates were sequenced and were clonally diverse overall, even within the same sequence type, indicating that independent acquisitions mainly. ESBL-Ec were often multi-drug-resistant. Soldiers stationing in certain regions are at high risk of acquiring resistant bacteria that may cause endogenous infection, be transmitted to vulnerable individuals, and spread resistance genes.
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Affiliation(s)
- E Literacka
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Warsaw, Poland.
| | - M Konior
- Department of Epidemiology and Tropical Medicine, Military Institute of Medicine - National Research Institute, Warsaw, Poland
| | - R Izdebski
- Department of Molecular Microbiology, National Medicines Institute, Warsaw, Poland
| | - D Żabicka
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Warsaw, Poland
| | - M Herda
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Warsaw, Poland
| | - M Gniadkowski
- Department of Molecular Microbiology, National Medicines Institute, Warsaw, Poland
| | - K Korzeniewski
- Department of Epidemiology and Tropical Medicine, Military Institute of Medicine - National Research Institute, Warsaw, Poland
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7
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Khalil I, Anderson JD, Bagamian KH, Baqar S, Giersing B, Hausdorff WP, Marshall C, Porter CK, Walker RI, Bourgeois AL. Vaccine value profile for enterotoxigenic Escherichia coli (ETEC). Vaccine 2023; 41 Suppl 2:S95-S113. [PMID: 37951695 DOI: 10.1016/j.vaccine.2023.02.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 11/28/2022] [Accepted: 02/05/2023] [Indexed: 11/14/2023]
Abstract
Enterotoxigenic Escherichia coli (ETEC) is one of the leading bacterial causes of diarrhoea, especially among children in low-resource settings, and travellers and military personnel from high-income countries. WHO's primary strategic goal for ETEC vaccine development is to develop a safe, effective, and affordable ETEC vaccine that reduces mortality and morbidity due to moderate-to-severe diarrhoeal disease in infants and children under 5 years of age in LMICs, as well as the long-term negative health impact on infant physical and cognitive development resulting from infection with this enteric pathogen. An effective ETEC vaccine will also likely reduce the need for antibiotic treatment and help limit the further emergence of antimicrobial resistance bacterial pathogens. The lead ETEC vaccine candidate, ETVAX, has shown field efficacy in travellers and has moved into field efficacy testing in LMIC infants and children. A Phase 3 efficacy study in LMIC infants is projected to start in 2024 and plans for a Phase 3 trial in travellers are under discussion with the U.S. FDA. Licensing for both travel and LMIC indications is projected to be feasible in the next 5-8 years. Given increasing recognition of its negative impact on child health and development in LMICs and predominance as the leading etiology of travellers' diarrhoea (TD), a standalone vaccine for ETEC is more cost-effective than vaccines targeting other TD pathogens, and a viable commercial market also exists. In contrast, combination of an ETEC vaccine with other vaccines for childhood pathogens in LMICs would maximize protection in a more cost-effective manner than a series of stand-alone vaccines. This 'Vaccine Value Profile' (VVP) for ETEC is intended to provide a high-level, holistic assessment of available data to inform the potential public health, economic and societal value of pipeline vaccines and vaccine-like products. This VVP was developed by a working group of subject matter experts from academia, non-profit organizations, public private partnerships, and multi-lateral organizations. All contributors have extensive expertise on various elements of the ETEC VVP and collectively aimed to identify current research and knowledge gaps. The VVP was developed using only existing and publicly available information.
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Affiliation(s)
- Ibrahim Khalil
- Department of Global Health, University of Washington, Seattle, WA 98195, USA.
| | - John D Anderson
- Bagamian Scientific Consulting, LLC, Gainesville, FL 32601, USA; Office of Health Affairs, West Virginia University, Morgantown, WV 26505, USA
| | - Karoun H Bagamian
- Bagamian Scientific Consulting, LLC, Gainesville, FL 32601, USA; Department of Environmental and Global Health, University of Florida, Gainesville, FL 32603, USA
| | - Shahida Baqar
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Birgitte Giersing
- Department of Immunization, Vaccines and Biologicals (IVB), World Health Organization (WHO), Geneva, Switzerland
| | - William P Hausdorff
- PATH, Center for Vaccine Innovation and Access, 455 Massachusetts Ave NW, Washington, DC 20001 USA; Faculty of Medicine, Université Libre de Bruxelles, Brussels 1070, Belgium
| | - Caroline Marshall
- Department of Immunization, Vaccines and Biologicals (IVB), World Health Organization (WHO), Geneva, Switzerland
| | - Chad K Porter
- Directorate for DoD Infectious Diseases Research, Naval Medical Research Command, Silver Spring, MD 20190, USA
| | - Richard I Walker
- PATH, Center for Vaccine Innovation and Access, 455 Massachusetts Ave NW, Washington, DC 20001 USA
| | - A Louis Bourgeois
- PATH, Center for Vaccine Innovation and Access, 455 Massachusetts Ave NW, Washington, DC 20001 USA
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8
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Cummins EA, Moran RA, Snaith AE, Hall RJ, Connor CH, Dunn SJ, McNally A. Parallel loss of type VI secretion systems in two multi-drug-resistant Escherichia coli lineages. Microb Genom 2023; 9. [PMID: 37970873 DOI: 10.1099/mgen.0.001133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023] Open
Abstract
The repeated emergence of multi-drug-resistant (MDR) Escherichia coli clones is a threat to public health globally. In recent work, drug-resistant E. coli were shown to be capable of displacing commensal E. coli in the human gut. Given the rapid colonization observed in travel studies, it is possible that the presence of a type VI secretion system (T6SS) may be responsible for the rapid competitive advantage of drug-resistant E. coli clones. We employed large-scale genomic approaches to investigate this hypothesis. First, we searched for T6SS genes across a curated dataset of over 20 000 genomes representing the full phylogenetic diversity of E. coli. This revealed large, non-phylogenetic variation in the presence of T6SS genes. No association was found between T6SS gene carriage and MDR lineages. However, multiple clades containing MDR clones have lost essential structural T6SS genes. We characterized the T6SS loci of ST410 and ST131 and identified specific recombination and insertion events responsible for the parallel loss of essential T6SS genes in two MDR clones.
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Affiliation(s)
- Elizabeth A Cummins
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Robert A Moran
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Ann E Snaith
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Rebecca J Hall
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Christopher H Connor
- Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne 3000, Australia
| | - Steven J Dunn
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Alan McNally
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
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9
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Brown DG, Worby CJ, Pender MA, Brintz BJ, Ryan ET, Sridhar S, Oliver E, Harris JB, Turbett SE, Rao SR, Earl AM, LaRocque RC, Leung DT. Development of a prediction model for the acquisition of extended spectrum beta-lactam-resistant organisms in U.S. international travellers. J Travel Med 2023; 30:taad028. [PMID: 36864572 PMCID: PMC10628771 DOI: 10.1093/jtm/taad028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 02/20/2023] [Accepted: 02/21/2023] [Indexed: 03/04/2023]
Abstract
BACKGROUND Extended spectrum beta-lactamase producing Enterobacterales (ESBL-PE) present a risk to public health by limiting the efficacy of multiple classes of beta-lactam antibiotics against infection. International travellers may acquire these organisms and identifying individuals at high risk of acquisition could help inform clinical treatment or prevention strategies. METHODS We used data collected from a cohort of 528 international travellers enrolled in a multicentre US-based study to derive a clinical prediction rule (CPR) to identify travellers who developed ESBL-PE colonization, defined as those with new ESBL positivity in stool upon return to the United States. To select candidate features, we used data collected from pre-travel and post-travel questionnaires, alongside destination-specific data from external sources. We utilized LASSO regression for feature selection, followed by random forest or logistic regression modelling, to derive a CPR for ESBL acquisition. RESULTS A CPR using machine learning and logistic regression on 10 features has an internally cross-validated area under the receiver operating characteristic curve (cvAUC) of 0.70 (95% confidence interval 0.69-0.71). We also demonstrate that a four-feature model performs similarly to the 10-feature model, with a cvAUC of 0.68 (95% confidence interval 0.67-0.69). This model uses traveller's diarrhoea, and antibiotics as treatment, destination country waste management rankings and destination regional probabilities as predictors. CONCLUSIONS We demonstrate that by integrating traveller characteristics with destination-specific data, we could derive a CPR to identify those at highest risk of acquiring ESBL-PE during international travel.
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Affiliation(s)
- David Garrett Brown
- Division of Infectious Diseases, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Colin J Worby
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Melissa A Pender
- Division of Infectious Diseases, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Ben J Brintz
- Division of Epidemiology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Edward T Ryan
- Harvard Medical School, Boston, MA, USA
- Travelers’ Advice and Immunization Center, Massachusetts General Hospital, Boston, MA, USA
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Sushmita Sridhar
- Harvard Medical School, Boston, MA, USA
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Elizabeth Oliver
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Jason B Harris
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Sarah E Turbett
- Harvard Medical School, Boston, MA, USA
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Sowmya R Rao
- Department of Global Health, Boston University School of Public Health, Boston, MA, USA
| | - Ashlee M Earl
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Regina C LaRocque
- Harvard Medical School, Boston, MA, USA
- Travelers’ Advice and Immunization Center, Massachusetts General Hospital, Boston, MA, USA
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Daniel T Leung
- Division of Infectious Diseases, University of Utah School of Medicine, Salt Lake City, UT, USA
- Division of Microbiology & Immunology, University of Utah School of Medicine, Salt Lake City, UT, USA
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10
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Worby CJ, Sridhar S, Turbett SE, Becker MV, Kogut L, Sanchez V, Bronson RA, Rao SR, Oliver E, Walker AT, Walters MS, Kelly P, Leung DT, Knouse MC, Hagmann SHF, Harris JB, Ryan ET, Earl AM, LaRocque RC. Gut microbiome perturbation, antibiotic resistance, and Escherichia coli strain dynamics associated with international travel: a metagenomic analysis. THE LANCET. MICROBE 2023; 4:e790-e799. [PMID: 37716364 PMCID: PMC10680401 DOI: 10.1016/s2666-5247(23)00147-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 04/21/2023] [Accepted: 05/09/2023] [Indexed: 09/18/2023]
Abstract
BACKGROUND Culture-based studies have shown that acquisition of extended-spectrum β-lactamase-producing Enterobacterales is common during international travel; however, little is known about the role of the gut microbiome before and during travel, nor about acquisition of other antimicrobial-resistant organisms. We aimed to identify (1) whether the gut microbiome provided colonisation resistance against antimicrobial-resistant organism acquisition, (2) the effect of travel and travel behaviours on the gut microbiome, and (3) the scale and global heterogeneity of antimicrobial-resistant organism acquisition. METHODS In this metagenomic analysis, participants were recruited at three US travel clinics (Boston, MA; New York, NY; and Salt Lake City, UT) before international travel. Participants had to travel internationally between Dec 8, 2017, and April 30, 2019, and have DNA extractions for stool samples both before and after travel for inclusion. Participants were excluded if they had at least one low coverage sample (<1 million read pairs). Stool samples were collected at home before and after travel, sent to a clinical microbiology laboratory to be screened for three target antimicrobial-resistant organisms (extended-spectrum β-lactamase-producing Enterobacterales, carbapenem-resistant Enterobacterales, and mcr-mediated colistin-resistant Enterobacterales), and underwent DNA extraction and shotgun metagenomic sequencing. We profiled metagenomes for taxonomic composition, antibiotic-resistant gene content, and characterised the Escherichia coli population at the strain level. We analysed pre-travel samples to identify the gut microbiome risk factors associated with acquisition of the three targeted antimicrobial resistant organisms. Pre-travel and post-travel samples were compared to identify microbiome and resistome perturbation and E coli strain acquisition associated with travel. FINDINGS A total of 368 individuals travelled between the required dates, and 296 had DNA extractions available for both before and after travel. 29 travellers were excluded as they had at least one low coverage sample, leaving a final group of 267 participants. We observed a perturbation of the gut microbiota, characterised by a significant depletion of microbial diversity and enrichment of the Enterobacteriaceae family. Metagenomic strain tracking confirmed that 67% of travellers acquired new strains of E coli during travel that were phylogenetically distinct from their pre-travel strains. We observed widespread enrichment of antibiotic-resistant genes in the gut, with a median 15% (95% CI 10-20, p<1 × 10-10) increase in burden (reads per kilobase per million reads). This increase included antibiotic-resistant genes previously classified as threats to public health, which were 56% (95% CI 36-91, p=2 × 10-11) higher in abundance after travel than before. Fluoroquinolone antibiotic-resistant genes were aquired by 97 (54%) of 181 travellers with no detected pre-travel carriage. Although we found that visiting friends or relatives, travel to south Asia, and eating uncooked vegetables were risk factors for acquisition of the three targeted antimicrobial resistant organisms, we did not observe an association between the pre-travel microbiome structure and travel-related antimicrobial-resistant organism acquisition. INTERPRETATION This work highlights a scale of E coli and antimicrobial-resistant organism acquisition by US travellers not apparent from previous culture-based studies, and suggests that strategies to control antimicrobial-resistant organisms addressing international traveller behaviour, rather than modulating the gut microbiome, could be worthwhile. FUNDING US Centers for Disease Control and Prevention and National Institute of Allergy and Infectious Diseases.
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Affiliation(s)
- Colin J Worby
- Infectious Disease and Microbiome Program, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sushmita Sridhar
- Department of Medicine, Harvard Medical School, Boston, MA, USA; Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Sarah E Turbett
- Department of Medicine, Harvard Medical School, Boston, MA, USA; Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA; Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Margaret V Becker
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Lucyna Kogut
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Vanessa Sanchez
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Ryan A Bronson
- Infectious Disease and Microbiome Program, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sowmya R Rao
- Department of Global Health, Boston University School of Public Health, Boston, MA, USA
| | - Elizabeth Oliver
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Allison Taylor Walker
- Division of Global Migration and Quarantine, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Maroya Spalding Walters
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Disease, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Paul Kelly
- Division of Infectious Diseases, Bronx Care Center, Bronx, NY, USA
| | - Daniel T Leung
- Division of Infectious Diseases and Division of Microbiology and Immunology, University of Utah, Salt Lake City, UT, USA
| | - Mark C Knouse
- Department of Medicine, Lehigh Valley Health Network, Allentown, PA, USA
| | - Stefan H F Hagmann
- Division of Pediatric Infectious Diseases, Steven and Alexandra Cohen Children's Medical Center of New York/Northwell Health, New Hyde Park, NY, USA
| | - Jason B Harris
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA; Division of Pediatric Global Health, Massachusetts General Hospital for Children, Boston, MA, USA
| | - Edward T Ryan
- Department of Medicine, Harvard Medical School, Boston, MA, USA; Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA; Travellers' Advice and Immunization Center, Massachusetts General Hospital, Boston, MA, USA
| | - Ashlee M Earl
- Infectious Disease and Microbiome Program, The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Regina C LaRocque
- Department of Medicine, Harvard Medical School, Boston, MA, USA; Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA; Travellers' Advice and Immunization Center, Massachusetts General Hospital, Boston, MA, USA
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11
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Connor CH, Zucoloto AZ, Munnoch JT, Yu IL, Corander J, Hoskisson PA, McDonald B, McNally A. Multidrug-resistant E. coli encoding high genetic diversity in carbohydrate metabolism genes displace commensal E. coli from the intestinal tract. PLoS Biol 2023; 21:e3002329. [PMID: 37847672 PMCID: PMC10581457 DOI: 10.1371/journal.pbio.3002329] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 09/11/2023] [Indexed: 10/19/2023] Open
Abstract
Extra-intestinal pathogenic Escherichia coli (ExPEC) can cause a variety of infections outside of the intestine and are a major causative agent of urinary tract infections. Treatment of these infections is increasingly frustrated by antimicrobial resistance (AMR) diminishing the number of effective therapies available to clinicians. Incidence of multidrug resistance (MDR) is not uniform across the phylogenetic spectrum of E. coli. Instead, AMR is concentrated in select lineages, such as ST131, which are MDR pandemic clones that have spread AMR globally. Using a gnotobiotic mouse model, we demonstrate that an MDR E. coli ST131 is capable of out-competing and displacing non-MDR E. coli from the gut in vivo. This is achieved in the absence of antibiotic treatment mediating a selective advantage. In mice colonised with non-MDR E. coli strains, challenge with MDR E. coli either by oral gavage or co-housing with MDR E. coli colonised mice results in displacement and dominant intestinal colonisation by MDR E. coli ST131. To investigate the genetic basis of this superior gut colonisation ability by MDR E. coli, we assayed the metabolic capabilities of our strains using a Biolog phenotypic microarray revealing altered carbon metabolism. Functional pangenomic analysis of 19,571 E. coli genomes revealed that carriage of AMR genes is associated with increased diversity in carbohydrate metabolism genes. The data presented here demonstrate that independent of antibiotic selective pressures, MDR E. coli display a competitive advantage to colonise the mammalian gut and points to a vital role of metabolism in the evolution and success of MDR lineages of E. coli via carriage and spread.
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Affiliation(s)
- Christopher H. Connor
- Institute of Microbiology and Infection, College of Medical and Dental Science, University of Birmingham, Birmingham, United Kingdom
- International Microbiome Centre, University of Calgary, Calgary, Canada
| | - Amanda Z. Zucoloto
- International Microbiome Centre, University of Calgary, Calgary, Canada
- Department of Critical Care Medicine, Cumming School of Medicine, University of Calgary, Calgary, Canada
- Calvin, Phoebe, and Joan Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - John T. Munnoch
- Strathclyde Institute of Pharmaceutical and Biomedical Science, University of Strathclyde, Glasgow, United Kingdom
| | - Ian-Ling Yu
- Department of Critical Care Medicine, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Jukka Corander
- Department of Biostatistics, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, United Kingdom
- Helsinki Institute of Information Technology, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - Paul A. Hoskisson
- Strathclyde Institute of Pharmaceutical and Biomedical Science, University of Strathclyde, Glasgow, United Kingdom
| | - Braedon McDonald
- International Microbiome Centre, University of Calgary, Calgary, Canada
- Department of Critical Care Medicine, Cumming School of Medicine, University of Calgary, Calgary, Canada
- Calvin, Phoebe, and Joan Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Alan McNally
- Institute of Microbiology and Infection, College of Medical and Dental Science, University of Birmingham, Birmingham, United Kingdom
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12
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Yip AYG, King OG, Omelchenko O, Kurkimat S, Horrocks V, Mostyn P, Danckert N, Ghani R, Satta G, Jauneikaite E, Davies FJ, Clarke TB, Mullish BH, Marchesi JR, McDonald JAK. Antibiotics promote intestinal growth of carbapenem-resistant Enterobacteriaceae by enriching nutrients and depleting microbial metabolites. Nat Commun 2023; 14:5094. [PMID: 37607936 PMCID: PMC10444851 DOI: 10.1038/s41467-023-40872-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 08/11/2023] [Indexed: 08/24/2023] Open
Abstract
The intestine is the primary colonisation site for carbapenem-resistant Enterobacteriaceae (CRE) and serves as a reservoir of CRE that cause invasive infections (e.g. bloodstream infections). Broad-spectrum antibiotics disrupt colonisation resistance mediated by the gut microbiota, promoting the expansion of CRE within the intestine. Here, we show that antibiotic-induced reduction of gut microbial populations leads to an enrichment of nutrients and depletion of inhibitory metabolites, which enhances CRE growth. Antibiotics decrease the abundance of gut commensals (including Bifidobacteriaceae and Bacteroidales) in ex vivo cultures of human faecal microbiota; this is accompanied by depletion of microbial metabolites and enrichment of nutrients. We measure the nutrient utilisation abilities, nutrient preferences, and metabolite inhibition susceptibilities of several CRE strains. We find that CRE can use the nutrients (enriched after antibiotic treatment) as carbon and nitrogen sources for growth. These nutrients also increase in faeces from antibiotic-treated mice and decrease following intestinal colonisation with carbapenem-resistant Escherichia coli. Furthermore, certain microbial metabolites (depleted upon antibiotic treatment) inhibit CRE growth. Our results show that killing gut commensals with antibiotics facilitates CRE colonisation by enriching nutrients and depleting inhibitory microbial metabolites.
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Affiliation(s)
- Alexander Y G Yip
- Centre for Bacterial Resistance Biology, Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Olivia G King
- Centre for Bacterial Resistance Biology, Department of Infectious Disease, Imperial College London, London, SW7 2AZ, UK
| | - Oleksii Omelchenko
- Centre for Bacterial Resistance Biology, Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Sanjana Kurkimat
- Centre for Bacterial Resistance Biology, Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Victoria Horrocks
- Centre for Bacterial Resistance Biology, Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Phoebe Mostyn
- Centre for Bacterial Resistance Biology, Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Nathan Danckert
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, St Mary's Hospital Campus, Imperial College London, London, UK
| | - Rohma Ghani
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, St Mary's Hospital Campus, Imperial College London, London, UK
- Department of Infectious Disease, Imperial College Healthcare NHS Trust, London, UK
| | - Giovanni Satta
- UCL Centre for Clinical Microbiology, University College London, London, UK
| | - Elita Jauneikaite
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, UK
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK
| | - Frances J Davies
- Department of Infectious Disease, Imperial College Healthcare NHS Trust, London, UK
| | - Thomas B Clarke
- Centre for Bacterial Resistance Biology, Department of Infectious Disease, Imperial College London, London, SW7 2AZ, UK
| | - Benjamin H Mullish
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, St Mary's Hospital Campus, Imperial College London, London, UK
- Departments of Gastroenterology and Hepatology, St Mary's Hospital, Imperial College Healthcare NHS Trust, Paddington, London, UK
| | - Julian R Marchesi
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, St Mary's Hospital Campus, Imperial College London, London, UK
| | - Julie A K McDonald
- Centre for Bacterial Resistance Biology, Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK.
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13
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Jones DC, LaMartina EL, Lewis JR, Dahl AJ, Nadig N, Szabo A, Newton RJ, Skwor TA. One Health and Global Health View of Antimicrobial Susceptibility through the "Eye" of Aeromonas: Systematic Review and Meta-Analysis. Int J Antimicrob Agents 2023; 62:106848. [PMID: 37201798 PMCID: PMC10524465 DOI: 10.1016/j.ijantimicag.2023.106848] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 04/26/2023] [Accepted: 05/09/2023] [Indexed: 05/20/2023]
Abstract
Antimicrobial resistance (AMR) is one of the most pressing public health concerns; therefore, it is imperative to advance our understanding of the factors influencing AMR from Global and One Health perspectives. To address this, Aeromonas populations were identified using 16S rRNA gene libraries among human, agriculture, aquaculture, drinking water, surface water, and wastewater samples, supporting its use as indicator bacteria to study AMR. A systematic review and meta-analysis was then performed from Global and One Health perspectives, including data from 221 articles describing 15 891 isolates from 57 countries. The interconnectedness of different environments was evident as minimal differences were identified between sectors among 21 different antimicrobials. However, resistance to critically important antibiotics (aztreonam and cefepime) was significantly higher among wastewater populations compared with clinical isolates. Additionally, isolates from untreated wastewater typically exhibited increased AMR compared with those from treated wastewater. Furthermore, aquaculture was associated with increased AMR to ciprofloxacin and tetracycline compared with wild-caught seafood. Using the World Health Organization AWaRe classifications, countries with lower consumption of "Access" compared to "Watch" drugs from 2000 to 2015 demonstrated higher AMR levels. The current analysis revealed negative correlations between AMR and anthropogenic factors, such as environmental performance indices and socioeconomic standing. Environmental health and sanitation were two of the environmental factors most strongly correlated with AMR. The current analysis highlights the negative impacts of "Watch" drug overconsumption, anthropogenic activity, absence of wastewater infrastructure, and aquaculture on AMR, thus stressing the need for proper infrastructure and global regulations to combat this growing problem.
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Affiliation(s)
| | - Emily Lou LaMartina
- School of Freshwater Sciences, University of Wisconsin - Milwaukee, Milwaukee, WI, USA
| | - Jenna Rachel Lewis
- Department of Biological Sciences, University of Wisconsin - Milwaukee, Milwaukee, WI, USA
| | - Andrew James Dahl
- Department of Biomedical Sciences, University of Wisconsin - Milwaukee, Milwaukee, WI, USA
| | - Nischala Nadig
- Department of Biomedical Sciences, University of Wisconsin - Milwaukee, Milwaukee, WI, USA
| | - Aniko Szabo
- Division of Biostatistics, Institute for Health & Equity, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Ryan J Newton
- School of Freshwater Sciences, University of Wisconsin - Milwaukee, Milwaukee, WI, USA
| | - Troy A Skwor
- Department of Biomedical Sciences, University of Wisconsin - Milwaukee, Milwaukee, WI, USA.
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14
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Snaith AE, Dunn SJ, Moran RA, Newton PN, Dance DAB, Davong V, Kuenzli E, Kantele A, Corander J, McNally A. The highly diverse plasmid population found in Escherichia coli colonizing travellers to Laos and its role in antimicrobial resistance gene carriage. Microb Genom 2023; 9:mgen001000. [PMID: 37171860 PMCID: PMC10272864 DOI: 10.1099/mgen.0.001000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 02/24/2023] [Indexed: 05/13/2023] Open
Abstract
Increased colonization by antimicrobial-resistant organisms is closely associated with international travel. This study investigated the diversity of mobile genetic elements involved with antimicrobial resistance (AMR) gene carriage in extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli that colonized travellers to Laos. Long-read sequencing was used to reconstruct complete plasmid sequences from 48 isolates obtained from the daily stool samples of 23 travellers over a 3 week period. This method revealed a collection of 105 distinct plasmids, 38.1 % (n=40) of which carried AMR genes. The plasmids in this population were diverse, mostly unreported and included 38 replicon types, with F-type plasmids (n=23) the most prevalent amongst those carrying AMR genes. Fine-scale analysis of all plasmids identified numerous AMR gene contexts and emphasized the importance of IS elements, specifically members of the IS6/IS26 family, in the evolution of complex multidrug resistance regions. We found a concerning convergence of ESBL and colistin resistance determinants, with three plasmids from two different F-type lineages carrying bla CTX-M and mcr genes. The extensive diversity seen here highlights the worrying probability that stable new vehicles for AMR will evolve in E. coli populations that can disseminate internationally through travel networks.
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Affiliation(s)
- Ann E. Snaith
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Steven J. Dunn
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Robert A. Moran
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Paul N. Newton
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Rue Mahosot, Vientiane, Laos
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - David A. B. Dance
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Rue Mahosot, Vientiane, Laos
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Viengmon Davong
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Rue Mahosot, Vientiane, Laos
| | - Esther Kuenzli
- Department of Medicine, Swiss Tropical and Public Health Institute of Basel, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Anu Kantele
- Meilahti Infectious Diseases and Vaccine Research Center, MeVac, Biomedicum 1, Haartmaninkatu 8, Helsinki University Hospital and University of Helsinki, Helsinki 00290, Finland
- Multidisciplinary Center of Excellence in Antimicrobial Resistance Research, University of Helsinki, Helsinki, Finland
- Human Microbiome Research Program, Faculty of Medicine, Haartmaninkatu 4, 00014 University of Helsinki, Helsinki, Finland
| | - Jukka Corander
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Mathematics and Statistics, Helsinki Institute of Information Technology, University of Helsinki, Helsinki, Finland
| | - Alan McNally
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
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15
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Bengtsson RJ, Baker KS, Cunningham AA, Greig DR, John SK, Macgregor SK, Seilern-Moy K, Spiro S, Chong CC, De Silva PM, Jenkins C, Lawson B. The genomic epidemiology of Escherichia albertii infecting humans and birds in Great Britain. Nat Commun 2023; 14:1707. [PMID: 36973246 PMCID: PMC10043262 DOI: 10.1038/s41467-023-37312-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 03/13/2023] [Indexed: 03/29/2023] Open
Abstract
Escherichia albertii is a recently identified gastrointestinal bacterial pathogen of humans and animals which is typically misidentified as pathotypes of diarrhoeagenic Escherichia coli or Shigella species and is generally only detected during genomic surveillance of other Enterobacteriaceae. The incidence of E. albertii is likely underestimated, and its epidemiology and clinical relevance are poorly characterised. Here, we whole genome sequenced E. albertii isolates from humans (n = 83) and birds (n = 79) isolated in Great Britain between 2000 and 2021 and analysed these alongside a broader public dataset (n = 475) to address these gaps. We found human and avian isolates typically (90%; 148/164) belonged to host-associated monophyletic groups with distinct virulence and antimicrobial resistance profiles. Overlaid patient epidemiological data suggested that human infection was likely related to travel and possibly foodborne transmission. The Shiga toxin encoding stx2f gene was associated with clinical disease (OR = 10.27, 95% CI = 2.98-35.45 p = 0.0002) in finches. Our results suggest that improved future surveillance will further elucidate disease ecology and public and animal health risks associated with E. albertii.
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Affiliation(s)
- Rebecca J Bengtsson
- Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, The University of Liverpool, Liverpool, UK
| | - Kate S Baker
- Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, The University of Liverpool, Liverpool, UK.
| | - Andrew A Cunningham
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK
| | - David R Greig
- Gastrointestinal and Food Safety (One Health) Division, UK Health Security Agency, Colindale, London, UK
| | - Shinto K John
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK
| | - Shaheed K Macgregor
- Wildlife Health Services, Zoological Society of London, Regent's Park, London, NW1 4RY, UK
| | - Katharina Seilern-Moy
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK
| | - Simon Spiro
- Wildlife Health Services, Zoological Society of London, Regent's Park, London, NW1 4RY, UK
| | - Charlotte C Chong
- Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, The University of Liverpool, Liverpool, UK
| | - P Malaka De Silva
- Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, The University of Liverpool, Liverpool, UK
| | - Claire Jenkins
- Gastrointestinal and Food Safety (One Health) Division, UK Health Security Agency, Colindale, London, UK
| | - Becki Lawson
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK
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16
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Lee K, Raguideau S, Sirén K, Asnicar F, Cumbo F, Hildebrand F, Segata N, Cha CJ, Quince C. Population-level impacts of antibiotic usage on the human gut microbiome. Nat Commun 2023; 14:1191. [PMID: 36864029 PMCID: PMC9981903 DOI: 10.1038/s41467-023-36633-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 02/06/2023] [Indexed: 03/04/2023] Open
Abstract
The widespread usage of antimicrobials has driven the evolution of resistance in pathogenic microbes, both increased prevalence of antimicrobial resistance genes (ARGs) and their spread across species by horizontal gene transfer (HGT). However, the impact on the wider community of commensal microbes associated with the human body, the microbiome, is less well understood. Small-scale studies have determined the transient impacts of antibiotic consumption but we conduct an extensive survey of ARGs in 8972 metagenomes to determine the population-level impacts. Focusing on 3096 gut microbiomes from healthy individuals not taking antibiotics we demonstrate highly significant correlations between both the total ARG abundance and diversity and per capita antibiotic usage rates across ten countries spanning three continents. Samples from China were notable outliers. We use a collection of 154,723 human-associated metagenome assembled genomes (MAGs) to link these ARGs to taxa and detect HGT. This reveals that the correlations in ARG abundance are driven by multi-species mobile ARGs shared between pathogens and commensals, within a highly connected central component of the network of MAGs and ARGs. We also observe that individual human gut ARG profiles cluster into two types or resistotypes. The less frequent resistotype has higher overall ARG abundance, is associated with certain classes of resistance, and is linked to species-specific genes in the Proteobacteria on the periphery of the ARG network.
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Affiliation(s)
- Kihyun Lee
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, 17546, Republic of Korea
- CJ Bioscience, Seoul, 04527, Republic of Korea
| | | | - Kimmo Sirén
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Francesco Asnicar
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Fabio Cumbo
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Falk Hildebrand
- Organisms and Ecosystems, Earlham Institute, Norwich, NR4 7UZ, UK
- Gut Microbes and Health, Quadram Institute, Norwich, NR4 7UQ, UK
| | - Nicola Segata
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Chang-Jun Cha
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, 17546, Republic of Korea.
| | - Christopher Quince
- Organisms and Ecosystems, Earlham Institute, Norwich, NR4 7UZ, UK.
- Gut Microbes and Health, Quadram Institute, Norwich, NR4 7UQ, UK.
- Warwick Medical School, University of Warwick, Coventry, CV4 7HL, UK.
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17
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Toombs-Ruane LJ, Marshall JC, Benschop J, Drinković D, Midwinter AC, Biggs PJ, Grange Z, Baker MG, Douwes J, Roberts MG, French NP, Burgess SA. Extended-spectrum β-lactamase- and AmpC β-lactamase-producing Enterobacterales associated with urinary tract infections in the New Zealand community: a case-control study. Int J Infect Dis 2023; 128:325-334. [PMID: 36529370 DOI: 10.1016/j.ijid.2022.12.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 10/28/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022] Open
Abstract
OBJECTIVES To assess whether having a pet in the home is a risk factor for community-acquired urinary tract infections associated with extended-spectrum β-lactamase (ESBL)- or AmpC β-lactamase (ACBL)- producing Enterobacterales. METHODS An unmatched case-control study was conducted between August 2015 and September 2017. Cases (n = 141) were people with community-acquired urinary tract infection (UTI) caused by ESBL- or ACBL-producing Enterobacterales. Controls (n = 525) were recruited from the community. A telephone questionnaire on pet ownership and other factors was administered, and associations were assessed using logistic regression. RESULTS Pet ownership was not associated with ESBL- or ACBL-producing Enterobacterales-related human UTIs. A positive association was observed for recent antimicrobial treatment, travel to Asia in the previous year, and a doctor's visit in the last 6 months. Among isolates with an ESBL-/ACBL-producing phenotype, 126/134 (94%) were Escherichia coli, with sequence type 131 being the most common (47/126). CONCLUSIONS Companion animals in the home were not found to be associated with ESBL- or ACBL-producing Enterobacterales-related community-acquired UTIs in New Zealand. Risk factors included overseas travel, recent antibiotic use, and doctor visits.
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Affiliation(s)
- Leah J Toombs-Ruane
- (m)EpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Jonathan C Marshall
- (m)EpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand; School of Mathematical and Computational Sciences, Massey University, Palmerston North, New Zealand
| | - Jackie Benschop
- (m)EpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Dragana Drinković
- Microbiology Department, North Shore Hospital, Auckland, New Zealand
| | - Anne C Midwinter
- (m)EpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Patrick J Biggs
- (m)EpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand; School of Natural Sciences, Massey University, Palmerston North, New Zealand; New Zealand Food Safety Science and Research Centre, Massey University, Palmerston North, New Zealand
| | - Zoë Grange
- (m)EpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Michael G Baker
- Department of Public Health, University of Otago, Wellington, New Zealand
| | - Jeroen Douwes
- Research Centre for Hauora and Health, Massey University, Wellington, New Zealand
| | - Mick G Roberts
- New Zealand Institute for Advanced Study, Massey University, Auckland, New Zealand
| | - Nigel P French
- (m)EpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand; New Zealand Food Safety Science and Research Centre, Massey University, Palmerston North, New Zealand; Research Centre for Hauora and Health, Massey University, Wellington, New Zealand
| | - Sara A Burgess
- (m)EpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand.
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18
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Impact of international travel and diarrhea on gut microbiome and resistome dynamics. Nat Commun 2022; 13:7485. [PMID: 36470885 PMCID: PMC9722912 DOI: 10.1038/s41467-022-34862-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 11/08/2022] [Indexed: 12/11/2022] Open
Abstract
International travel contributes to the global spread of antimicrobial resistance. Travelers' diarrhea exacerbates the risk of acquiring multidrug-resistant organisms and can lead to persistent gastrointestinal disturbance post-travel. However, little is known about the impact of diarrhea on travelers' gut microbiomes, and the dynamics of these changes throughout travel. Here, we assembled a cohort of 159 international students visiting the Andean city of Cusco, Peru and applied next-generation sequencing techniques to 718 longitudinally-collected stool samples. We find that gut microbiome composition changed significantly throughout travel, but taxonomic diversity remained stable. However, diarrhea disrupted this stability and resulted in an increased abundance of antimicrobial resistance genes that can remain high for weeks. We also identified taxa differentially abundant between diarrheal and non-diarrheal samples, which were used to develop a classification model that distinguishes between these disease states. Additionally, we sequenced the genomes of 212 diarrheagenic Escherichia coli isolates and found those from travelers who experienced diarrhea encoded more antimicrobial resistance genes than those who did not. In this work, we find the gut microbiomes of international travelers' are resilient to dysbiosis; however, they are also susceptible to colonization by multidrug-resistant bacteria, a risk that is more pronounced in travelers with diarrhea.
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19
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Mäklin T, Thorpe HA, Pöntinen AK, Gladstone RA, Shao Y, Pesonen M, McNally A, Johnsen PJ, Samuelsen Ø, Lawley TD, Honkela A, Corander J. Strong pathogen competition in neonatal gut colonisation. Nat Commun 2022; 13:7417. [PMID: 36456554 PMCID: PMC9715557 DOI: 10.1038/s41467-022-35178-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 11/21/2022] [Indexed: 12/02/2022] Open
Abstract
Opportunistic bacterial pathogen species and their strains that colonise the human gut are generally understood to compete against both each other and the commensal species colonising this ecosystem. Currently we are lacking a population-wide quantification of strain-level colonisation dynamics and the relationship of colonisation potential to prevalence in disease, and how ecological factors might be modulating these. Here, using a combination of latest high-resolution metagenomics and strain-level genomic epidemiology methods we performed a characterisation of the competition and colonisation dynamics for a longitudinal cohort of neonatal gut microbiomes. We found strong inter- and intra-species competition dynamics in the gut colonisation process, but also a number of synergistic relationships among several species belonging to genus Klebsiella, which includes the prominent human pathogen Klebsiella pneumoniae. No evidence of preferential colonisation by hospital-adapted pathogen lineages in either vaginal or caesarean section birth groups was detected. Our analysis further enabled unbiased assessment of strain-level colonisation potential of extra-intestinal pathogenic Escherichia coli (ExPEC) in comparison with their propensity to cause bloodstream infections. Our study highlights the importance of systematic surveillance of bacterial gut pathogens, not only from disease but also from carriage state, to better inform therapies and preventive medicine in the future.
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Affiliation(s)
- Tommi Mäklin
- grid.7737.40000 0004 0410 2071Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Helsinki, Finland
| | - Harry A. Thorpe
- grid.5510.10000 0004 1936 8921Department of Biostatistics, University of Oslo, Oslo, Norway
| | - Anna K. Pöntinen
- grid.5510.10000 0004 1936 8921Department of Biostatistics, University of Oslo, Oslo, Norway ,grid.412244.50000 0004 4689 5540Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Rebecca A. Gladstone
- grid.5510.10000 0004 1936 8921Department of Biostatistics, University of Oslo, Oslo, Norway
| | - Yan Shao
- grid.10306.340000 0004 0606 5382Parasites and Microbes, Wellcome Sanger Institute, Hinxton, Cambridgeshire UK
| | - Maiju Pesonen
- grid.5510.10000 0004 1936 8921Department of Biostatistics, University of Oslo, Oslo, Norway
| | - Alan McNally
- grid.6572.60000 0004 1936 7486Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Pål J. Johnsen
- grid.10919.300000000122595234Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Ørjan Samuelsen
- grid.412244.50000 0004 4689 5540Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway ,grid.10919.300000000122595234Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Trevor D. Lawley
- grid.10306.340000 0004 0606 5382Parasites and Microbes, Wellcome Sanger Institute, Hinxton, Cambridgeshire UK
| | - Antti Honkela
- grid.7737.40000 0004 0410 2071Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Helsinki, Finland
| | - Jukka Corander
- grid.5510.10000 0004 1936 8921Department of Biostatistics, University of Oslo, Oslo, Norway ,grid.10306.340000 0004 0606 5382Parasites and Microbes, Wellcome Sanger Institute, Hinxton, Cambridgeshire UK ,grid.7737.40000 0004 0410 2071Helsinki Institute for Information Technology HIIT, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
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20
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Geurtsen J, de Been M, Weerdenburg E, Zomer A, McNally A, Poolman J. Genomics and pathotypes of the many faces of Escherichia coli. FEMS Microbiol Rev 2022; 46:6617594. [PMID: 35749579 PMCID: PMC9629502 DOI: 10.1093/femsre/fuac031] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 06/22/2022] [Indexed: 01/09/2023] Open
Abstract
Escherichia coli is the most researched microbial organism in the world. Its varied impact on human health, consisting of commensalism, gastrointestinal disease, or extraintestinal pathologies, has generated a separation of the species into at least eleven pathotypes (also known as pathovars). These are broadly split into two groups, intestinal pathogenic E. coli (InPEC) and extraintestinal pathogenic E. coli (ExPEC). However, components of E. coli's infinite open accessory genome are horizontally transferred with substantial frequency, creating pathogenic hybrid strains that defy a clear pathotype designation. Here, we take a birds-eye view of the E. coli species, characterizing it from historical, clinical, and genetic perspectives. We examine the wide spectrum of human disease caused by E. coli, the genome content of the bacterium, and its propensity to acquire, exchange, and maintain antibiotic resistance genes and virulence traits. Our portrayal of the species also discusses elements that have shaped its overall population structure and summarizes the current state of vaccine development targeted at the most frequent E. coli pathovars. In our conclusions, we advocate streamlining efforts for clinical reporting of ExPEC, and emphasize the pathogenic potential that exists throughout the entire species.
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Affiliation(s)
- Jeroen Geurtsen
- Janssen Vaccines and Prevention B.V., 2333 Leiden, the Netherlands
| | - Mark de Been
- Janssen Vaccines and Prevention B.V., 2333 Leiden, the Netherlands
| | | | - Aldert Zomer
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 Utrecht, the Netherlands
| | - Alan McNally
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, B15 2TT Birmingham, United Kingdom
| | - Jan Poolman
- Janssen Vaccines and Prevention B.V., 2333 Leiden, the Netherlands
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21
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Corneci D, Torsin LI, Filimon CR, Tănase NV, Moisă E, Negoiță SI. Individualized surgical antibiotic prophylaxis – why, when, and how? ROMANIAN JOURNAL OF MILITARY MEDICINE 2022. [DOI: 10.55453/rjmm.2022.125.4.4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
"Surgical site infections (SSI) greatly concern clinicians, as they are associated with significant morbidity and mortality, prolonged hospitalization, and costs. Antibiotic prophylaxis plays a pivotal role among the procedures that are usually employed for the prevention of surgical-related infections. This narrative review aims to cover some of the particular situations when the clinician might consider individualizing antibiotic prophylaxis for a patient. With the rising incidence of multi-drug resistant bacteria carriage among not only hospitalized or institutionalized patients but also patients from the community, there might be a tendency to use extended-spectrum antibiotics for longer periods for surgical infection prevention. However, the inappropriate use of antibiotics increases the selection pressure, thus favoring the spreading of resistant bacteria. Moreover, specific patient characteristics or pathologies might need to be considered to customize the type, dose, or length of administration of an antibiotic as surgical prophylaxis. Using prosthetic material or prolonged surgeries with large fluid shifts are other situations when individualized antibiotic prophylaxis might be thought of. Keeping in mind that it is of utmost importance that everyone adheres to the current guidelines for surgical antibiotic prophylaxis, customization of local protocols according to well-thought-out strategies might prove beneficial in SSI prevention."
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22
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Pyörälä E, Sepponen K, Lauhio A, Saastamoinen L. Outpatient Antibiotic Use and Costs in Adults: A Nationwide Register-Based Study in Finland 2008-2019. Antibiotics (Basel) 2022; 11:1453. [PMID: 36358108 PMCID: PMC9686641 DOI: 10.3390/antibiotics11111453] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 10/17/2022] [Accepted: 10/20/2022] [Indexed: 12/27/2023] Open
Abstract
The objective of this study was to describe the prevalence of outpatient use and costs for systemic antibacterials by age and sex among adults in Finland from 2008-2019. Data from the Finnish statistical database Kelasto, containing information concerning all reimbursed medicines for 18+-year-olds during 2008-2019, were analyzed. In addition to the decreased (26%) use of systemic antibiotics, decreased use was observed in all antibiotic categories, notably including several wide-spectrum antibiotics. The use of quinolones decreased by 49% and of tetracyclines by 39%. The 10 most frequently used antibiotics covered 89% of all adult antibiotic prescriptions. Antibiotic use also decreased in every age group during the study period. Although the overall yearly costs of outpatient antibiotics during the 10-year study period decreased from EUR 36.4 million to EUR 30.7 million, the cost per prescription increased slightly. In conclusion, according to the findings of this study, concerning adults and the results of our previous study concerning children and adolescents (2008-2016), there has been a decreasing trend of outpatient antibacterial use among the whole Finnish outpatient population over the duration of nearly one decade. However, during the same time period, there has been a specific increasing trend for the Gram-negative AMR threat regarding E. coli resistance. Therefore, based on our important findings in Finland, methods other than the restriction of antibiotic use, such as new anti-infective innovations, including antibacterials, are needed as soon as possible to tackle this major global health threat-a silent pandemic.
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Affiliation(s)
- Elisa Pyörälä
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Kati Sepponen
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Anneli Lauhio
- Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland
- Finnish Medicines Agency Fimea, 00300 Helsinki, Finland
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23
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Lewis JM, Mphasa M, Banda R, Beale MA, Heinz E, Mallewa J, Jewell C, Faragher B, Thomson NR, Feasey NA. Colonization dynamics of extended-spectrum beta-lactamase-producing Enterobacterales in the gut of Malawian adults. Nat Microbiol 2022; 7:1593-1604. [PMID: 36065064 PMCID: PMC9519460 DOI: 10.1038/s41564-022-01216-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 07/25/2022] [Indexed: 01/09/2023]
Abstract
Drug-resistant bacteria of the order Enterobacterales which produce extended-spectrum beta-lactamase enzymes (ESBL-Enterobacterales, ESBL-E) are global priority pathogens. Antimicrobial stewardship interventions proposed to curb their spread include shorter courses of antimicrobials to reduce selection pressure but individual-level acquisition and selection dynamics are poorly understood. We sampled stool of 425 adults (aged 16-76 years) in Blantyre, Malawi, over 6 months and used multistate modelling and whole-genome sequencing to understand colonization dynamics of ESBL-E. Models suggest a prolonged effect of antimicrobials such that truncating an antimicrobial course at 2 days has a limited effect in reducing colonization. Genomic analysis shows largely indistinguishable diversity of healthcare-associated and community-acquired isolates, hence some apparent acquisition of ESBL-E during hospitalization may instead represent selection from a patient's microbiota by antimicrobial exposure. Our approach could help guide stewardship protocols; interventions that aim to review and truncate courses of unneeded antimicrobials may be of limited use in preventing ESBL-E colonization.
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Affiliation(s)
- Joseph M Lewis
- Malawi-Liverpool Wellcome Clinical Research Programme, Blantyre, Malawi.
- Liverpool School of Tropical Medicine, Liverpool, UK.
- University of Liverpool, Liverpool, UK.
- Wellcome Sanger Institute, Hinxton, UK.
| | - Madalitso Mphasa
- Malawi-Liverpool Wellcome Clinical Research Programme, Blantyre, Malawi
| | - Rachel Banda
- Malawi-Liverpool Wellcome Clinical Research Programme, Blantyre, Malawi
| | | | - Eva Heinz
- Liverpool School of Tropical Medicine, Liverpool, UK
| | - Jane Mallewa
- Kamuzu University of Health Sciences, Blantyre, Malawi
| | | | | | - Nicholas R Thomson
- Wellcome Sanger Institute, Hinxton, UK
- London School of Hygiene and Tropical Medicine, London, UK
| | - Nicholas A Feasey
- Malawi-Liverpool Wellcome Clinical Research Programme, Blantyre, Malawi
- Liverpool School of Tropical Medicine, Liverpool, UK
- London School of Hygiene and Tropical Medicine, London, UK
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24
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Kajova M, Khawaja T, Kantele A. European hospitals as source of multidrug-resistant bacteria: analysis of travellers screened in Finland after hospitalization abroad. J Travel Med 2022; 29:6540946. [PMID: 35234907 PMCID: PMC9282090 DOI: 10.1093/jtm/taac022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 02/01/2022] [Accepted: 02/06/2022] [Indexed: 12/05/2022]
Abstract
BACKGROUND As hospitals have a high prevalence of multidrug-resistant organisms (MDRO), hospitalization abroad indicates for travellers an increased risk of acquiring MDRO-and carrying the strains home. Antimicrobial resistance (AMR) rates are highest in the (sub)tropics, whereas Europe is considered a lower risk region. Since AMR prevalences vary within Europe, we aimed to gather country-specific data on the risks for hospitalized travellers. METHODS At hospitals of the Helsinki and Uusimaa district in Finland, patients hospitalized abroad over the past 12 months are systematically screened for methicillin-resistant Staphylococcus aureus (MRSA), extended-spectrum beta-lactamase (ESBL)-producing Enterobacterales (ESBL-PE), carbapenemase-producing bacteria and vancomycin-resistant Enterococcus spp. (VRE). Among patients screened 2010-19, we selected those hospitalized in Europe, recorded their MDRO findings, infections and mortality, and analysed MDRO-associated risk factors. RESULTS Of the 1772 patients treated in 41 European countries, 16.6% (295) carried MDRO, 12.5% (221) ESBL-PE, 7.8% (138) solely ESBL-E. coli, 2.6% (46) MRSA, 2.2% (30) of those screened VRE and 2.2% (39) carbapenem-resistant Gram-negatives. Among those colonized, 9.8% (29) had symptomatic MDRO infections and 0.3% (one) died. Colonization was most frequently recorded for those treated in eastern and southern Europe, with Bulgaria, Cyprus and the Russian Federation scoring highest. MDRO colonization was associated with antibiotic treatment and showed a negative correlation with time from discharge to screening. CONCLUSIONS After hospitalization in European countries, ESBL-PE carriage was relatively common (12.5%), while other MDROs proved less frequent (<5%). Antibiotic treatment and short time since hospitalization abroad increased the risk of MDRO colonization. Clear differences between countries and regions were revealed, with highest rates in the east and the south.
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Affiliation(s)
- Mikael Kajova
- Department of Infectious Diseases, Inflammation Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Meilahti Infectious Diseases and Vaccine Research Center, MeiVac, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Multidisciplinary Center of Excellence in Antimicrobial Resistance Research, University of Helsinki, Helsinki, Finland
| | - Tamim Khawaja
- Department of Infectious Diseases, Inflammation Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Meilahti Infectious Diseases and Vaccine Research Center, MeiVac, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Multidisciplinary Center of Excellence in Antimicrobial Resistance Research, University of Helsinki, Helsinki, Finland
| | - Anu Kantele
- Department of Infectious Diseases, Inflammation Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Meilahti Infectious Diseases and Vaccine Research Center, MeiVac, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Multidisciplinary Center of Excellence in Antimicrobial Resistance Research, University of Helsinki, Helsinki, Finland.,Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
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25
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Monger XC, Saucier L, Gilbert AA, Vincent AT. Stabilization of swine faecal samples influences taxonomic and functional results in microbiome analyses. MethodsX 2022; 9:101716. [PMID: 35601955 PMCID: PMC9118172 DOI: 10.1016/j.mex.2022.101716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 04/22/2022] [Indexed: 11/23/2022] Open
Abstract
Stabilization of faecal samples improves the integrity of extracted DNA. Microbiome results are affected by sample stabilization. Results are similar for samples that were stabilized when frozen, to samples that were stabilized before freezing.
Studies on the microbiome of different species are on the rise, due to a growing interest in animal health and the safety of food products of animal origin. A challenge with studying animals’ microbiomes is to find methods that obtain a good representation of the microbial community of interest. Good unbiased sampling protocols are the basis for a solid experimental design, but may need to be done in environments where sample preservation could be difficult. In this study, we evaluate by shotgun sequencing the impact of stabilizing swine faeces samples using a commercial stabilizer (PERFORMAbiome • GUT | PB-200, DNA Genotek). Using stabilizer makes it possible to obtain DNA that is significantly less degraded than when the samples are not stabilized. Also, the results on the taxonomy and on the bacterial functions encoded in the microbiome are impacted by whether or not the samples are stabilized. Finally, the stabilization of samples that had already been frozen and stored at -80°C led to extraction and DNA quality results similar to those obtained from samples that were stabilized before freezing.
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26
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Isles NS, Mu A, Kwong JC, Howden BP, Stinear TP. Gut microbiome signatures and host colonization with multidrug-resistant bacteria. Trends Microbiol 2022; 30:853-865. [DOI: 10.1016/j.tim.2022.01.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 01/20/2022] [Accepted: 01/20/2022] [Indexed: 12/17/2022]
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27
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Kantele A, Lääveri T. Extended-spectrum beta-lactamase-producing strains among diarrhoeagenic Escherichia coli-prospective traveller study with literature review. J Travel Med 2022; 29:6217594. [PMID: 33834207 PMCID: PMC8763120 DOI: 10.1093/jtm/taab042] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 01/27/2020] [Accepted: 01/29/2020] [Indexed: 01/25/2023]
Abstract
BACKGROUND Antibiotics are no longer the primary approach for treating all travellers' diarrhoea (TD): most cases resolve without antibiotics and using them predisposes to colonization by multidrug-resistant bacteria. Data are accumulating on increasing resistance among TD pathogens, yet research into the most common agents, diarrhoeagenic Escherichia coli (DEC), remains limited. METHODS A total of 413 travellers to the (sub)tropics were analyzed for travel-acquired diarrhoeal pathogens and ESBL-PE. To identify ESBL-producing DEC, ESBL-producing E. coli (ESBL-EC) isolates were subjected to multiplex qPCR for various DEC pathotypes: enteroaggregative (EAEC), enteropathogenic (EPEC), enterotoxigenic (ETEC), enteroinvasive (EIEC) and enterohaemorrhagic (EHEC) E. coli.For a literature review, we screened studies among travellers and locals in low- and middle-income countries (LMICs) on the frequency of ESBL-producing DEC, and among travellers, also DEC with resistance to ciprofloxacin, azithromycin, and rifamycin derivatives. RESULTS Our rate of ESBL-EC among all DEC findings was 2.7% (13/475); among EAEC 5.7% (10/175), EPEC 1.1% (2/180), ETEC 1.3% (1/80) and EHEC (0/35) or EIEC 0% (0/5). The literature search yielded three studies reporting ESBL-EC frequency and thirteen exploring resistance to TD antibiotics among travel-acquired DEC. For EAEC and ETEC, the ESBL-EC rates were 10-13% and 14-15%, resistance to fluoroquinolones 0-42% and 0-40%, azithromycin 0-29% and 0-61%, and rifaximin 0% and 0-20%. The highest rates were from the most recent collections. Proportions of ESBL-producing DEC also appear to be increasing among locals in LMICs and even carbapenemase-producing DEC were reported. CONCLUSION ESBL producers are no longer rare among DEC, and the overall resistance to various antibiotics is increasing. The data predict decreasing efficacy of antibiotic treatment, threatening its benefits, for disadvantages still prevail when efficacy is lost.
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Affiliation(s)
- Anu Kantele
- To whom correspondence should be addressed. Professor Anu Kantele, Meilahti Vaccine Research Center MeVac, University of Helsinki and Helsinki University Hospital, Biomedicum 1, Haartmaninkatu 8, FI-00029 HUS, Finland; Tel: +358-50-309-7640;
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Nguyen Q, Nguyen TTN, Pham P, Chau V, Nguyen LPH, Nguyen TD, Ha TT, Le NTQ, Vu DT, Baker S, Thwaites GE, Rabaa MA, Pham DT. Genomic insights into the circulation of pandemic fluoroquinolone-resistant extra-intestinal pathogenic Escherichia coli ST1193 in Vietnam. Microb Genom 2021; 7. [PMID: 34904942 PMCID: PMC8767341 DOI: 10.1099/mgen.0.000733] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Extra-intestinal pathogenic Escherichia coli (ExPEC) ST1193, a globally emergent fluoroquinolone-resistant clone, has become an important cause of bloodstream infections (BSIs) associated with significant morbidity and mortality. Previous studies have reported the emergence of fluoroquinolone-resistant ExPEC ST1193 in Vietnam; however, limited data exist regarding the genetic structure, antimicrobial resistance (AMR) determinants and transmission dynamics of this pandemic clone. Here, we performed genomic and phylogenetic analyses of 46 ST1193 isolates obtained from BSIs and healthy individuals in Ho Chi Minh City, Vietnam, to investigate the pathogen population structure, molecular mechanisms of AMR and potential transmission patterns. We further examined the phylogenetic structure of ST1193 isolates in a global context. We found that the endemic E. coli ST1193 population was heterogeneous and highly dynamic, largely driven by multiple strain importations. Several well-supported phylogenetic clusters (C1-C6) were identified and associated with distinct bla CTX-M variants, including bla CTXM-27 (C1-C3, C5), bla CTXM-55 (C4) and bla CTXM-15 (C6). Most ST1193 isolates were multidrug-resistant and carried an extensive array of AMR genes. ST1193 isolates also exhibited the ability to acquire further resistance while circulating in Vietnam. There were phylogenetic links between ST1193 isolates from BSIs and healthy individuals, suggesting these organisms may both establish long-term colonization in the human intestinal tract and induce infections. Our study uncovers factors shaping the population structure and transmission dynamics of multidrug-resistant ST1193 in Vietnam, and highlights the urgent need for local One Health genomic surveillance to capture new emerging ExPEC clones and to better understand the origins and transmission patterns of these pathogens.
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Affiliation(s)
- Quynh Nguyen
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | - Phuong Pham
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Vinh Chau
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | | | - Tuyen Thanh Ha
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Nhi Thi Quynh Le
- The University of Medicine and Pharmacy, Ho Chi Minh City, Vietnam
| | | | - Stephen Baker
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
| | - Guy E Thwaites
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Maia A Rabaa
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Duy Thanh Pham
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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29
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Interplay between Bacterial Clones and Plasmids in the Spread of Antibiotic Resistance Genes in the Gut: Lessons from a Temporal Study in Veal Calves. Appl Environ Microbiol 2021; 87:e0135821. [PMID: 34613750 DOI: 10.1128/aem.01358-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Intestinal carriage of extended spectrum β-lactamase (ESBL)-producing Escherichia coli is a frequent, increasing, and worrying phenomenon, but little is known about the molecular scenario and the evolutionary forces at play. We screened 45 veal calves, known to have high prevalence of carriage, for ESBL-producing E. coli on 514 rectal swabs (one randomly selected colony per sample) collected over 6 months. We characterized the bacterial clones and plasmids carrying blaESBL genes with a combination of genotyping methods, whole genome sequencing, and conjugation assays. One hundred and seventy-three ESBL-producing E. coli isolates [blaCTX-M-1 (64.7%), blaCTX-M-14 (33.5%), or blaCTX-M-15 (1.8%)] were detected, belonging to 32 bacterial clones, mostly of phylogroup A. Calves were colonized successively by different clones with a trend in decreasing carriage. The persistence of a clone in a farm was significantly associated with the number of calves colonized. Despite a high diversity of E. coli clones and blaCTX-M-carrying plasmids, few blaCTX-M gene/plasmid/chromosomal background combinations dominated, due to (i) efficient colonization of bacterial clones and/or (ii) successful plasmid spread in various bacterial clones. The scenario "clone versus plasmid spread" depended on the farm. Thus, epistatic interactions between resistance genes, plasmids, and bacterial clones contribute to optimize fitness in specific environments. IMPORTANCE The gut microbiota is the epicenter of the emergence of resistance. Considerable amount of knowledge on the molecular mechanisms of resistance has been accumulated, but the ecological and evolutionary forces at play in nature are less studied. In this context, we performed a field work on temporal intestinal carriage of extended spectrum β-lactamase (ESBL)-producing Escherichia coli in veal farms. Veal calves are animals with one of the highest levels of ESBL producing E. coli fecal carriage, due to early high antibiotic exposure. We were able to show that calves were colonized successively by different ESBL-producing E. coli clones, and that two main scenarios were at play in the spread of blaCTX-M genes among calves: efficient colonization of several calves by a few bacterial clones and successful plasmid spread in various bacterial clones. Such knowledge should help develop new strategies to fight the emergence of antibiotic-resistance.
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30
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Chansamouth V, Mayxay M, Dance DA, Roberts T, Phetsouvanh R, Vannachone B, Vongsouvath M, Davong V, Inthavong P, Khounsy S, Keohavong B, Keoluangkhot V, Choumlivong K, Day NP, Turner P, Ashley EA, van Doorn HR, Newton PN. Antimicrobial use and resistance data in human and animal sectors in the Lao PDR: evidence to inform policy. BMJ Glob Health 2021; 6:e007009. [PMID: 34853032 PMCID: PMC8638151 DOI: 10.1136/bmjgh-2021-007009] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 10/23/2021] [Indexed: 11/17/2022] Open
Abstract
OBJECTIVES To review the scientific evidence base on antimicrobial use (AMU) and antimicrobial resistance (AMR) in human and animal sectors in the Lao PDR (Laos). METHODS We reviewed all publications from July 1994 (the first article describing AMR in Laos) to December 2020. Electronic searches were conducted using Google Scholar and PubMed with specific terms relating to AMR and AMU in Lao, French and English languages. FINDINGS We screened 1,357 peer-reviewed and grey reports by title and abstract and then full articles/reports. Of 80 included, 66 (83%) related to human health, nine (11%) to animal health, four (5%) to both animal and human health and one (1%) to the environment. Sixty-two (78%) were on AMR and 18 (22%) on AMU. Extended spectrum beta lactamase-producing Escherichia coli was the greatest concern identified; the proportion of isolates increased fivefold from 2004 to 2016 (2/28 (7%) to 27/78 (35%)) from blood cultures submitted to the Microbiology Laboratory, Mahosot Hospital, Vientiane. Carbapenem resistant Escherichia coli was first identified in 2015. Methicillin-resistant Staphylococcus aureus (MRSA) was uncommon, with 15 cases of MRSA from blood cultures between its first identification in 2017 and December 2020. AMR patterns of global antimicrobial resistance surveillance system (GLASS) target pathogens from livestock were less well documented. There were few data on AMU in human health and none on AMU in livestock. The first hospital AMU survey in Laos showed that 70% (1,386/1,981) of in-patients in five hospitals from 2017 to 2018 received antimicrobial(s). Antibiotic self-medication was common. CONCLUSION AMR in Laos is occurring at relatively low proportions for some GLASS pathogens, giving the country a window of opportunity to act quickly to implement strategies to protect the population from a worsening situation. Urgent interventions to roll out new guidelines with enhanced one-health antibiotic stewardship, reduce antibiotic use without prescriptions, enhance surveillance and improve understanding of AMU and AMR are needed.
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Affiliation(s)
- Vilada Chansamouth
- Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Mahosot Hospital, Vientiane, Lao People's Democratic Republic
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Mayfong Mayxay
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Mahosot Hospital, Vientiane, Lao People's Democratic Republic
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Faculty of Postgraduate Studies, University of Health Sciences, Vientiane, Lao People's Democratic Republic
| | - David Ab Dance
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Mahosot Hospital, Vientiane, Lao People's Democratic Republic
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Tamalee Roberts
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Mahosot Hospital, Vientiane, Lao People's Democratic Republic
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Rattanaxay Phetsouvanh
- Department of Communicable Disease Control, Ministry of Health, Vientiane, Lao People's Democratic Republic
| | - Bouakham Vannachone
- Department of Communicable Disease Control, Ministry of Health, Vientiane, Lao People's Democratic Republic
| | - Manivanh Vongsouvath
- Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Mahosot Hospital, Vientiane, Lao People's Democratic Republic
| | - Viengmon Davong
- Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Mahosot Hospital, Vientiane, Lao People's Democratic Republic
| | - Phout Inthavong
- Department of Livestock and Fisheries, Ministry of Agriculture, Vientiane, Lao People's Democratic Republic
| | - Syseng Khounsy
- Department of Livestock and Fisheries, Ministry of Agriculture, Vientiane, Lao People's Democratic Republic
| | - Bounxou Keohavong
- Department of Food and Drug, Ministry of Health, Vientiane, Lao People's Democratic Republic
| | - Valy Keoluangkhot
- Infectious Disease Center, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
| | | | - Nicholas Pj Day
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Mahidol Oxford Tropical Medicine Research Unit (MORU), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Paul Turner
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Cambodia Oxford Medical Research Unit, Siem Reap, Cambodia
| | - Elizabeth A Ashley
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Mahosot Hospital, Vientiane, Lao People's Democratic Republic
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - H Rogier van Doorn
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford University Clinical Research Unit, Hanoi, Viet Nam
| | - Paul N Newton
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Mahosot Hospital, Vientiane, Lao People's Democratic Republic
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
- Mahidol Oxford Tropical Medicine Research Unit (MORU), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
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Kajova M, Khawaja T, Kangas J, Mäkinen H, Kantele A. Import of multidrug-resistant bacteria from abroad through interhospital transfers, Finland, 2010-2019. ACTA ACUST UNITED AC 2021; 26. [PMID: 34596014 PMCID: PMC8485579 DOI: 10.2807/1560-7917.es.2021.26.39.2001360] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Background While 20–80% of regular visitors to (sub)tropical regions become colonised by extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-PE), those hospitalised abroad often also carry other multidrug-resistant (MDR) bacteria on return; the rates are presumed to be highest for interhospital transfers. Aim This observational study assessed MDR bacterial colonisation among patients transferred directly from hospitals abroad to Helsinki University Hospital. We investigated predisposing factors, clinical infections and associated fatalities. Methods Data were derived from screening and from diagnostic samples collected between 2010 and 2019. Risk factors of colonisation were identified by multivariable analysis. Microbiologically verified symptomatic infections and infection-related mortality were recorded during post-transfer hospitalisation. Results Colonisation rates proved highest for transfers from Asia (69/96; 71.9%) and lowest for those within Europe (99/524; 18.9%). Of all 698 patients, 208 (29.8%) were colonised; among those, 163 (78.4%) carried ESBL-PE, 28 (13.5%) MDR Acinetobacter species, 25 (12.0%) meticillin-resistant Staphylococcus aureus, 25 (12.0%) vancomycin-resistant Enterococcus, 14 (6.7%) carbapenemase-producing Enterobacteriaceae, and 12 (5.8%) MDR Pseudomonas aeruginosa; 46 strains tested carbapenemase gene-positive. In multivariable analysis, geographical region, intensive care unit (ICU) treatment and antibiotic use abroad proved to be risk factors for colonisation. Clinical MDR infections, two of them fatal (1.0%), were recorded for 22 of 208 (10.6%) MDR carriers. Conclusions Colonisation by MDR bacteria was common among patients transferred from foreign hospitals. Region of hospitalisation, ICU treatment and antibiotic use were identified as predisposing factors. Within 30 days after transfer, MDR colonisation manifested as clinical infection in more than 10% of the carriers.
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Affiliation(s)
- Mikael Kajova
- Inflammation Center, Department of Infectious Diseases, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Meilahti Infectious Diseases and Vaccine Research Center, MeiVac, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Tamim Khawaja
- Inflammation Center, Department of Infectious Diseases, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Meilahti Infectious Diseases and Vaccine Research Center, MeiVac, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Jonas Kangas
- Inflammation Center, Department of Infectious Diseases, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Meilahti Infectious Diseases and Vaccine Research Center, MeiVac, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Hilda Mäkinen
- Inflammation Center, Department of Infectious Diseases, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Meilahti Infectious Diseases and Vaccine Research Center, MeiVac, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Anu Kantele
- Inflammation Center, Department of Infectious Diseases, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
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Abstract
PURPOSE OF REVIEW Antimicrobial resistance (AMR) in bacteria poses a major risk to global public health, with many factors contributing to the observed increase in AMR. International travel is one recognized contributor. The purpose of this review is to summarize current knowledge regarding the acquisition, carriage and spread of AMR bacteria by international travelers. RECENT FINDINGS Recent studies have highlighted that travel is an important risk factor for the acquisition of AMR bacteria, with approximately 30% of studied travelers returning with an acquired AMR bacterium. Epidemiological studies have shown there are three major risk factors for acquisition: travel destination, antimicrobial usage and travelers' diarrhea (TD). Analyses have begun to illustrate the AMR genes that are acquired and spread by travelers, risk factors for acquisition and carriage of AMR bacteria, and local transmission of imported AMR organisms. SUMMARY International travel is a contributor to the acquisition and dissemination of AMR organisms globally. Efforts to reduce the burden of AMR organisms should include a focus on international travelers. Routine genomic surveillance would further elucidate the role of international travel in the global spread of AMR bacteria.
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Affiliation(s)
- Sushmita Sridhar
- Division of Infectious Diseases, Massachusetts General Hospital
- Department of Medicine, Harvard Medical School
| | - Sarah E. Turbett
- Division of Infectious Diseases, Massachusetts General Hospital
- Department of Medicine, Harvard Medical School
- Department of Pathology
| | - Jason B. Harris
- Division of Pediatric Global Health, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Regina C. LaRocque
- Division of Infectious Diseases, Massachusetts General Hospital
- Department of Medicine, Harvard Medical School
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Jarocki VM, Heß S, Anantanawat K, Berendonk TU, Djordjevic SP. Multidrug-Resistant Lineage of Enterotoxigenic Escherichia coli ST182 With Serotype O169:H41 in Airline Waste. Front Microbiol 2021; 12:731050. [PMID: 34557175 PMCID: PMC8454413 DOI: 10.3389/fmicb.2021.731050] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 07/21/2021] [Indexed: 12/30/2022] Open
Abstract
Enterotoxigenic Escherichia coli (ETEC) is the primary aetiologic agent of traveller’s diarrhoea and a significant cause of diarrhoeal disease and death in developing countries. ETEC O169:H41 strains are known to cause both traveller’s diarrhoea and foodborne outbreaks in developed countries and are cause for concern. Here, whole-genome sequencing (WGS) was used to assemble 46 O169:H41 (ST182) E. coli draft genomes derived from two airplane waste samples sourced from a German international airport. The ST182 genomes were compared with all 84 publicly available, geographically diverse ST182 genomes to construct a core genome-based phylogenetic tree. ST182 isolates were all phylogroup E, the majority serotype O169:H41 (n = 121, 93%) and formed five major clades. The airplane waste isolates differed by an average of 15 core SNPs (range 0–45) but their accessory genome content was diverse. While uncommon in other ST182 genomes, all airplane-derived ST182 isolates carried: (i) extended-spectrum β-lactamase gene blaCTX–M–15 notably lacking the typical adjacent ISEcp1; (ii) qnrS1 and the S83L mutation in gyrA, both conferring resistance to fluoroquinolones; and (iii) a class 1 integron structure (IS26-intI1Δ648-dfrA17-aadA5-qacEΔ1-sul1-ORF-srpC-padR-IS6100-mphR-mrx-mphA-IS26) identified previously in major extraintestinal pathogenic E. coli STs but not in ETEC. ST182 isolates carried ETEC-specific virulence factors STp + CS6. Adhesin/invasin tia was identified in 89% of aircraft ST182 isolates (vs 23%) and was located on a putative genomic island within a hotspot region for various insertions including PAI I536 and plasmid-associated transposons. The most common plasmid replicons in this collection were IncFII (100%; F2:A-:B-) and IncB/O/K/Z (89%). Our data suggest that potentially through travel, E. coli ST182 are evolving a multidrug-resistant profile through the acquisition of class 1 integrons and different plasmids.
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Affiliation(s)
- Veronica M Jarocki
- iThree Institute, University of Technology Sydney, Sydney, NSW, Australia
| | - Stefanie Heß
- Institute of Microbiology, Technische Universität Dresden, Dresden, Germany
| | - Kay Anantanawat
- iThree Institute, University of Technology Sydney, Sydney, NSW, Australia
| | - Thomas U Berendonk
- Institute of Hydrobiology, Technische Universität Dresden, Dresden, Germany
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Sasse M, Reinhardt F, Lübbert C. [Traveler's Diarrhea]. Dtsch Med Wochenschr 2021; 146:1258-1264. [PMID: 34553350 DOI: 10.1055/a-1582-2544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Travelers' diarrhea is the most common infectious disease in travel medicine. This article deals with epidemiology, diagnostics, prophylaxis and therapy. The causative pathogens, important differential diagnoses and indications for extended diagnostic measures are discussed in detail. Furthermore, aspects of travel medicine advice as well as the possibilities and limits of infection prevention are presented.
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Affiliation(s)
- Melanie Sasse
- Medizinische Klinik II (Bereich Infektiologie und Tropenmedizin) des Universitätsklinikums Leipzig
| | - Fabian Reinhardt
- Medizinische Klinik II (Bereich Infektiologie und Tropenmedizin) des Universitätsklinikums Leipzig
| | - Christoph Lübbert
- Medizinische Klinik II (Bereich Infektiologie und Tropenmedizin) des Universitätsklinikums Leipzig
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