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Musicha P, Morse T, Cocker D, Mugisha L, Jewell CP, Feasey NA. Time to define One Health approaches to tackling antimicrobial resistance. Nat Commun 2024; 15:8782. [PMID: 39389965 PMCID: PMC11467174 DOI: 10.1038/s41467-024-53057-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: 11/16/2023] [Accepted: 09/26/2024] [Indexed: 10/12/2024] Open
Abstract
Antimicrobial resistance is a One Health problem that impacts humans, animals, and the environment. In this Comment, the authors discuss evidence for antimicrobial resistance transmission to humans, highlighting contrasting pictures between high- and low/middle-income settings.
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Affiliation(s)
- Patrick Musicha
- Malawi Liverpool Wellcome Programme, Blantyre, Malawi.
- Liverpool School of Tropical Medicine, Liverpool, UK.
| | | | - Derek Cocker
- Malawi Liverpool Wellcome Programme, Blantyre, Malawi
- University of Liverpool, Liverpool, UK
| | - Lawrence Mugisha
- Makerere University, College of Veterinary Medicine, Animal Resources and Biosecurity, Kampala, Uganda
| | | | - Nicholas A Feasey
- Malawi Liverpool Wellcome Programme, Blantyre, Malawi
- Liverpool School of Tropical Medicine, Liverpool, UK
- University of St. Andrews, St. Andrews, UK
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Fuhrmeister ER, Kim S, Mairal SA, McCormack C, Chieng B, Swarthout JM, Harvey Paulos A, Njenga SM, Pickering AJ. Context-Seq: CRISPR-Cas9 Targeted Nanopore Sequencing for Transmission Dynamics of Antimicrobial Resistance. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.12.612745. [PMID: 39314343 PMCID: PMC11419053 DOI: 10.1101/2024.09.12.612745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
Antimicrobial resistance (AMR) aligns with a One Health framework in that resistant bacteria and antibiotic resistance genes (ARGs) can be transmitted between humans, animals, and the environment. However, there is a critical need to more precisely understand how and to what extent AMR is exchanged between animals and humans. Metagenomic sequencing has low detection for rare targets such as ARGs, while whole genome sequencing of isolates is burdensome and misses exchange between uncultured bacterial species. We developed a novel, targeted sequencing assay using CRISPR-Cas9 to selectively sequence ARGs and their genomic context with long-read sequencing. Using this method, termed Context-Seq, we investigated overlapping AMR elements containing the ARGs bla CTX-M and bla TEM between adults, children, poultry, and dogs in animal-owning households in Nairobi, Kenya. We identified 22 genetically distinct clusters (> 80%ID over ≥ 3000 bp) containing bla TEM and one cluster containing bla CTX-M that were shared within and between households. Half of the clusters were shared between humans and animals, while the other half were shared only between animals (poultry-poultry, dog-dog, and dog-poultry). We identified potentially pathogenic hosts of ARGs including Escherichia coli, Klebsiella pneumonia, and Haemophilus influenzae across sample types. Context-Seq complements conventional methods to obtain an additional view of bacterial and mammalian hosts in the proliferation of AMR.
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Affiliation(s)
- Erica R. Fuhrmeister
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, Washington, USA
- Department of Civil and Environmental Engineering, University of California, Berkeley, CA, USA
| | - Sooyeol Kim
- Department of Civil and Environmental Engineering, University of California, Berkeley, CA, USA
| | - Shruteek A. Mairal
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA
| | - Caroline McCormack
- Department of Civil and Environmental Engineering, University of California, Berkeley, CA, USA
| | - Benard Chieng
- Eastern and Southern Africa Centre of International Parasite Control, Kenya Medical Research Institute, Nairobi, Kenya
| | - Jenna M. Swarthout
- Department of Civil and Environmental Engineering, Tufts University, Medford, MA, USA
| | - Abigail Harvey Paulos
- Department of Civil and Environmental Engineering, University of California, Berkeley, CA, USA
| | - Sammy M. Njenga
- Eastern and Southern Africa Centre of International Parasite Control, Kenya Medical Research Institute, Nairobi, Kenya
| | - Amy J. Pickering
- Department of Civil and Environmental Engineering, University of California, Berkeley, CA, USA
- Blum Center for Developing Economies, University of California, Berkeley, CA, USA
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Kara A, Massaro C, Giammanco GM, Alduina R, Boussoualim N. Phylogenetic Diversity, Antibiotic Resistance, and Virulence of Escherichia coli Strains from Urinary Tract Infections in Algeria. Antibiotics (Basel) 2024; 13:773. [PMID: 39200073 PMCID: PMC11350822 DOI: 10.3390/antibiotics13080773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 07/23/2024] [Accepted: 08/08/2024] [Indexed: 09/01/2024] Open
Abstract
Urinary tract infections (UTIs) caused by Escherichia coli represent a significant public health concern due to the high virulence and antimicrobial resistance exhibited by these pathogens. This study aimed to analyze the phylogenetic diversity and antibiotic resistance profiles of Uropathogenic E. coli (UPEC) strains isolated from UTI patients in Algeria, focusing on virulence factors such as extended β-lactamase (ESBL) production, biofilm formation, and hemolytic activity. Phylogenetic grouping of 86 clinical imipenem resistant E. coli isolates showed the prevalence of group B2 (48.9%), followed by groups E (22.1%), unknown (12.8%), A (8.1%), and B1 (4.7%), and Clade I, D, Clade I, or Clade II (1.2%). The highest resistance rates were observed towards amoxicillin (86.04%), ticarcillin (82.55%), piperacillin (73.25%), nitrofurantoin (84.88%), and trimethoprim-sulfamethoxazole (51.16%). Notably, 69.8% of UPEC strains were multidrug-resistant (MDR) and 23.2% were extensively drug-resistant (XDR). Additionally, 48.9%, 42%, and 71% of strains demonstrated ESBL production, hemolytic activity, and weak biofilm production, respectively. Continuous monitoring and characterization of UPEC strains are essential to track the spread of the most resistant and virulent phylogenetic groups over time, facilitating rapid therapeutic decisions to treat infections and prevent the emergence of new resistant organisms, helping choose the most effective antibiotics and reducing treatment failure.
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Affiliation(s)
- Anfal Kara
- Laboratory of Applied Biochemistry, Faculty of Nature and Life Sciences, University Ferhat Abbas of Setif 1, Setif 19000, Algeria; (A.K.); (N.B.)
| | - Chiara Massaro
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Viale delle Scienze, Bldg. 16, 90128 Palermo, Italy;
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties “G. D’Alessandro”, University of Palermo, 90127 Palermo, Italy;
| | - Giovanni M. Giammanco
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties “G. D’Alessandro”, University of Palermo, 90127 Palermo, Italy;
| | - Rosa Alduina
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Viale delle Scienze, Bldg. 16, 90128 Palermo, Italy;
- NBFC, National Biodiversity Future Center, Piazza Marina 61, 90133 Palermo, Italy
| | - Naouel Boussoualim
- Laboratory of Applied Biochemistry, Faculty of Nature and Life Sciences, University Ferhat Abbas of Setif 1, Setif 19000, Algeria; (A.K.); (N.B.)
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Abeni BA, Frank-Peterside N, Otokunefor K. Comparative analysis of virulence gene profiles of Escherichia coli from human and non-human sources in Rivers State, Nigeria. Access Microbiol 2024; 6:000776.v6. [PMID: 39130738 PMCID: PMC11316598 DOI: 10.1099/acmi.0.000776.v6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 07/10/2024] [Indexed: 08/13/2024] Open
Abstract
Traditionally, the presence of virulence features has been thought to be a key factor in differentiating pathogenic from commensal strains. An understanding of the virulence potential of Escherichia coli isolates from various sources is essential to shed light on potential contamination/transmission rates between the various sources. This study was therefore aimed at exploring the occurrence of specific virulence genes and gene profiles associated with E. coli from human and non-human sources in Rivers State, Nigeria. Two hundred samples from human (urine and faeces) and non-human (soil and poultry droppings) sources (50 each) were analysed using standard microbiological procedures. DNA was extracted from isolates presumptively identified as E. coli using the Presto Mini gDNA Bacteria-Kit Quick protocol following the manufacturer's instructions. Isolate identities were confirmed using E. coli-specific 16S rRNA primers, and confirmed isolates were screened for the presence of six virulence genes [afimbriae binding adhesin (afa), type 1 fimbriae (fimH) and P-fimbrial usher protein (papC)], iron acquisition systems: aerobactin (aer), cytotoxic necrotizing factor I (cnf1) and alpha-hemolysin (hly). Results showed that all isolates harboured at least one of the tested virulence genes, with fimH (97%) as the most prevalent virulence gene and papC the least commonly occurring (35%). A higher occurrence of virulence genes was noted in non-human isolates, though hly and cnf were not detected at all in any of the isolates studied (0%). Ten different profiles were observed with the afaCc-aer-fimH profile the most commonly occurring virulence gene profile being in general (33.3%). For non-human isolates, however, aer-afaCc-fimH-papC was the most commonly occurring profile (42.9%). This study shows that the test E. coli from human and non-human sources do not carry distinct virulence gene profiles. Studies on a larger subset of isolates would however be necessary to determine if the virulence genes tested in this study really cannot be used to tell whether an isolate is from a human source or not in the South-South of Nigeria.
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Affiliation(s)
- Barira Azeez Abeni
- Department of Microbiology, Faculty of Science, University of Port Harcourt, Port Harcourt, Nigeria
| | - Nnenna Frank-Peterside
- Department of Microbiology, Faculty of Science, University of Port Harcourt, Port Harcourt, Nigeria
| | - Kome Otokunefor
- Department of Microbiology, Faculty of Science, University of Port Harcourt, Port Harcourt, Nigeria
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Hu H, Zhang P, Liu F, Pan S. Regulations of Citrus Pectin Oligosaccharide on Cholesterol Metabolism: Insights from Integrative Analysis of Gut Microbiota and Metabolites. Nutrients 2024; 16:2002. [PMID: 38999750 PMCID: PMC11243408 DOI: 10.3390/nu16132002] [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: 03/21/2024] [Revised: 04/25/2024] [Accepted: 05/04/2024] [Indexed: 07/14/2024] Open
Abstract
(1) Background: Recently, academic studies are demonstrating that the cholesterol-lowering effects of pectin oligosaccharides (POSs) are correlated to intestinal flora. However, the mechanisms of POS on cholesterol metabolisms are limited, and the observations of intestinal flora are lacking integrative analyses. (2) Aim and methods: To reveal the regulatory mechanisms of POS on cholesterol metabolism via an integrative analysis of the gut microbiota, the changes in gut microbiota structure and metabolite composition after POS addition were investigated using Illumina MiSeq sequencing and non-targeted metabolomics through in vitro gut microbiota fermentation. (3) Results: The composition of fecal gut flora was adjusted positively by POS. POS increased the abundances of the cholesterol-related bacterial groups Bacteroidetes, Bifidobacterium and Lactobacillus, while it decreased conditional pathogenic Escherichia coli and Enterococcus, showing good prebiotic activities. POS changed the composition of gut microbiota fermentation metabolites (P24), causing significant changes in 221 species of fermentation metabolites in a non-targeted metabolomics analysis and promoting the production of short-chain fatty acids. The abundances of four types of cholesterol metabolism-related metabolites (adenosine monophosphate, cyclic adenosine monophosphate, guanosine and butyrate) were significantly higher in the P24 group than those in the control group without POS addition. (4) Conclusion: The abovementioned results may explain the hypocholesterolemic effects of POS and promotion effects on cholesterol efflux of P24. These findings indicated that the potential regulatory mechanisms of citrus POS on cholesterol metabolism are modulated by cholesterol-related gut microbiota and specific metabolites.
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Affiliation(s)
- Haijuan Hu
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Peipei Zhang
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Fengxia Liu
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Siyi Pan
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
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Garzon A, Basbas C, Schlesener C, Silva-del-Rio N, Karle BM, Lima FS, Weimer BC, Pereira RV. WGS of intrauterine E. coli from cows with early postpartum uterine infection reveals a non-uterine specific genotype and virulence factors. mBio 2024; 15:e0102724. [PMID: 38742889 PMCID: PMC11237492 DOI: 10.1128/mbio.01027-24] [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: 04/08/2024] [Accepted: 04/09/2024] [Indexed: 05/16/2024] Open
Abstract
Escherichia coli has been attributed to playing a major role in a cascade of events that affect the prevalence and severity of uterine disease in cattle. The objectives of this project were to (i) define the association between the prevalence of specific antimicrobial resistance and virulence factor genes in E. coli with the clinical status related to uterine infection, (ii) identify the genetic relationship between E. coli isolates from cows with diarrhea, with mastitis, and with and without metritis, and (iii) determine the association between the phenotypic and genotypic antimicrobial resistance identified on the E. coli isolated from postpartum cattle. Bacterial isolates (n = 148) were obtained from a larger cross-sectional study. Cows were categorized into one of three clinical groups before enrollment: metritis, cows with purulent discharge, and control cows. For genomic comparison, public genomes (n = 130) from cows with diarrhea, mastitis, and metritis were included in a genome-wide association study, to evaluate differences between the drug classes or the virulence factor category among clinical groups. A distinct E. coli genotype associated with metritis could not be identified. Instead, a high genetic diversity among the isolates from uterine sources was present. A virulence factor previously associated with metritis (fimH) using PCR was not associated with metritis. There was moderate accuracy for whole-genome sequencing to predict phenotypic resistance, which varied depending on the antimicrobial tested. Findings from this study contradict the traditional pathotype classification and the unique intrauterine E. coli genotype associated with metritis in dairy cows.IMPORTANCEMetritis is a common infectious disease in dairy cattle and the second most common reason for treating a cow with antimicrobials. The pathophysiology of the disease is complex and is not completely understood. Specific endometrial pathogenic Escherichia coli have been reported to be adapted to the endometrium and sometimes lead to uterine disease. Unfortunately, the specific genomic details of the endometrial-adapted isolates have not been investigated using enough genomes to represent the genomic diversity of this organism to identify specific virulence genes that are consistently associated with disease development and severity. Results from this study provide key microbial ecological advances by elucidating and challenging accepted concepts for the role of Intrauterine E. coli in metritis in dairy cattle, especially contradicting the existence of a unique intrauterine E. coli genotype associated with metritis in dairy cows, which was not found in our study.
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Affiliation(s)
- Adriana Garzon
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, California, USA
| | - Carl Basbas
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, California, USA
| | - Cory Schlesener
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, California, USA
- Department of Population Health and Reproduction, 100K Pathogen Genome Project, School of Veterinary Medicine, University of California, Davis, California, USA
| | - Noelia Silva-del-Rio
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, California, USA
- Veterinary Medicine Teaching and Research Center, School of Veterinary Medicine, University of California, Tulare, California, USA
| | - Betsy M. Karle
- Cooperative Extension, Division of Agriculture and Natural Resources, University of California, Orland, California, USA
| | - Fabio S. Lima
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, California, USA
| | - Bart C. Weimer
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, California, USA
- Department of Population Health and Reproduction, 100K Pathogen Genome Project, School of Veterinary Medicine, University of California, Davis, California, USA
| | - Richard V. Pereira
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, California, USA
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Flatgard BM, Williams AD, Amin MB, Hobman JL, Stekel DJ, Rousham EK, Islam MA. Tracking antimicrobial resistance transmission in urban and rural communities in Bangladesh: a One Health study of genomic diversity of ESBL-producing and carbapenem-resistant Escherichia coli. Microbiol Spectr 2024; 12:e0395623. [PMID: 38700359 PMCID: PMC11237648 DOI: 10.1128/spectrum.03956-23] [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: 11/16/2023] [Accepted: 04/05/2024] [Indexed: 05/05/2024] Open
Abstract
Antimicrobial resistance (AMR) poses a significant threat to global health and sustainable development goals, especially in low- and middle-income countries (LMICs). This study aimed to understand the transmission of AMR between poultry, humans, and the environment in Bangladesh using a One Health approach. We analyzed the whole genome sequences (WGS) of 117 extended-spectrum β-lactamase-producing Escherichia coli (ESBL-Ec) isolates, with 46 being carbapenem resistant. These isolates were obtained from human (n = 20) and poultry feces (n = 12), as well as proximal environments (wastewater) (n = 85) of three different study sites, including rural households (n = 48), rural poultry farms (n = 20), and urban wet markets (n = 49). The WGS of ESBL-Ec isolates were compared with 58 clinical isolates from global databases. No significant differences in antibiotic resistance genes (ARGs) were observed in ESBL-Ec isolated from humans with and without exposure to poultry. Environmental isolates showed higher ARG diversity than human and poultry isolates. No clonal transmission between poultry and human isolates was found, but wastewater was a reservoir for ESBL-Ec for both. Except for one human isolate, all ESBL-Ec isolates were distinct from clinical isolates. Most isolates (77.8%) carried at least one plasmid replicon type, with IncFII being the most prevalent. IncFIA was predominant in human isolates, while IncFII, Col(MG828), and p0111 were common in poultry. We observed putative sharing of ARG-carrying plasmids among isolates, mainly from wastewater. However, in most cases, bacterial isolates sharing plasmids were also clonally related, suggesting clonal spread was more probable than just plasmid transfer. IMPORTANCE Our study underscores that wastewater discharged from households and wet markets carries antibiotic-resistant organisms from both human and animal sources. Thus, direct disposal of wastewater into the environment not only threatens human health but also endangers food safety by facilitating the spread of antimicrobial resistance (AMR) to surface water, crops, vegetables, and subsequently to food-producing animals. In regions with intensive poultry production heavily reliant on the prophylactic use of antibiotics, compounded by inadequate waste management systems, such as Bangladesh, the ramifications are particularly pronounced. Wastewater serves as a pivotal juncture for the dissemination of antibiotic-resistant organisms and functions as a pathway through which strains of human and animal origin can infiltrate the environment and potentially colonize new hosts. Further research is needed to thoroughly characterize wastewater isolates/populations and understand their potential impact on interconnected environments, communities, and wildlife.
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Affiliation(s)
- Brandon M. Flatgard
- Paul G. Allen School for Global Health, Washington State University, Pullman, Washington, USA
| | - Alexander D. Williams
- Laboratory of Data Discovery for Health Ltd, Hong Kong Science and Technology Park, Tai Po, Hong Kong, China
- School of Public Health, University of Hong Kong, Pok Fu Lam, Hong Kong, China
| | | | - Jon L. Hobman
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Leicestershire, United Kingdom
| | - Dov J. Stekel
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Leicestershire, United Kingdom
- Department of Mathematics and Applied Mathematics, University of Johannesburg, Johannesburg, South Africa
| | - Emily K. Rousham
- School of Sport, Exercise and Health Sciences, Loughborough University, Loughborough, United Kingdom
| | - Mohammad Aminul Islam
- Paul G. Allen School for Global Health, Washington State University, Pullman, Washington, USA
- Laboratory of Food Safety and One Health, icddr,b, Dhaka, Bangladesh
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Agbemavor WSK, Buys EM. Dynamic Interactions between Diarrhoeagenic Enteroaggregative Escherichia coli and Presumptive Probiotic Bacteria: Implications for Gastrointestinal Health. Microorganisms 2023; 11:2942. [PMID: 38138086 PMCID: PMC10745617 DOI: 10.3390/microorganisms11122942] [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: 10/29/2023] [Revised: 11/30/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023] Open
Abstract
This study delves into the temporal dynamics of bacterial interactions in the gastrointestinal tract, focusing on how probiotic strains and pathogenic bacteria influence each other and human health. This research explores adhesion, competitive exclusion, displacement, and inhibition of selected diarrhoeagenic Escherichia coli (D-EAEC) and potential probiotic strains under various conditions. Key findings reveal that adhesion is time-dependent, with both D-EAEC K2 and probiotic L. plantarum FS2 showing increased adhesion over time. Surprisingly, L. plantarum FS2 outperformed D-EAEC K2 in adhesion and exhibited competitive exclusion and displacement, with inhibition of adhesion surpassing competitive exclusion. This highlights probiotics' potential to slow pathogen attachment when not in competition. Pre-infecting with L. plantarum FS2 before pathogenic infection effectively inhibited adhesion, indicating probiotics' ability to prevent pathogen attachment. Additionally, adhesion correlated strongly with interleukin-8 (IL-8) secretion, linking it to the host's inflammatory response. Conversely, IL-8 secretion negatively correlated with trans-epithelial electrical resistance (TEER), suggesting a connection between tight junction disruption and increased inflammation. These insights offer valuable knowledge about the temporal dynamics of gut bacteria interactions and highlight probiotics' potential in competitive exclusion and inhibiting pathogenic bacteria, contributing to strategies for maintaining gastrointestinal health and preventing infections.
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Affiliation(s)
- Wisdom Selorm Kofi Agbemavor
- Department of Consumer and Food Sciences, University of Pretoria, Private Bag X20, Pretoria 0028, South Africa
- Radiation Technology Centre, Biotechnology and Nuclear Agriculture Research Institute, Ghana Atomic Energy Commission, Legon, Accra P.O. Box LG 80, Ghana
| | - Elna Maria Buys
- Department of Consumer and Food Sciences, University of Pretoria, Private Bag X20, Pretoria 0028, South Africa
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Wang J, Huang Y, Guan C, Li J, Yang H, Zhao G, Liu C, Ma J, Tang B. Characterization of an Escherichia coli Isolate Coharboring the Virulence Gene astA and Tigecycline Resistance Gene tet(X4) from a Dead Piglet. Pathogens 2023; 12:903. [PMID: 37513750 PMCID: PMC10385434 DOI: 10.3390/pathogens12070903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 06/27/2023] [Accepted: 06/29/2023] [Indexed: 07/30/2023] Open
Abstract
tet(X4) is the critical resistance gene for tigecycline degradation that has been continually reported in recent years. In particular, pathogenic bacteria carrying tet(X4) are a severe threat to human health. However, information describing Escherichia coli coharboring tet(X4) with virulence genes is limited. Here, we isolated an E. coli strain coharboring tet(X4) and the heat-stable toxin gene astA from a dead piglet. The strain named 812A1-131 belongs to ST10. The genome was sequenced using the Nanopore and Illumina platforms. The virulence genes astA and tet(X4) are located on the chromosome and in the IncHI1-type plasmid p812A1-tetX4-193K, respectively. The plasmid could be conjugatively transferred to recipient E. coli J53 with high frequency. In vivo experiments showed that strain 812A1-131 is pathogenic to Galleria mellonella and could colonize the intestines of mice. In summary, pathogenic E. coli could receive a plasmid harboring the tet(X4) gene, which can increase the difficulty of treatment. The prevalence and transmission mechanisms of pathogenic bacteria coharboring the tet(X4) gene need more attention.
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Affiliation(s)
- Jianmei Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products & Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Yuting Huang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products & Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
- School of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Chunjiu Guan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products & Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
- School of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Jie Li
- College of Life Science, Liaocheng University, Liaocheng 252000, China
| | - Hua Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products & Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Guoping Zhao
- School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Canying Liu
- School of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Jiangang Ma
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products & Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Biao Tang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products & Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
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Delago J, Miller EA, Flores-Figueroa C, Munoz-Aguayo J, Cardona C, Smith AH, Johnson TJ. Survey of clinical and commensal Escherichia coli from commercial broilers and turkeys, with emphasis on high-risk clones using APECTyper. Poult Sci 2023; 102:102712. [PMID: 37156077 DOI: 10.1016/j.psj.2023.102712] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 04/09/2023] [Indexed: 05/10/2023] Open
Abstract
Molecular characterization of avian pathogenic Escherichia coli (APEC) is challenging due to the complex nature of its associated disease, colibacillosis, in poultry. Numerous efforts have been made toward defining APEC, and it is becoming clear that certain clonal backgrounds are predictive of an avian E. coli isolate's virulence potential. Thus, APEC can be further differentiated as high-risk APEC based upon their clonal background's virulence potential. However, less clear is the degree of overlap between clinical isolates of differing bird type, and between clinical and gastrointestinal isolates. This study aimed to determine genomic similarities and differences between such populations, comparing commercial broiler vs. turkey isolates, and clinical vs. gastrointestinal isolates. Differences were observed in Clermont phylogenetic groups between isolate populations, with B2 as the dominant group in turkey clinical isolates and G as the dominant group in broiler clinical isolates. Nearly all clinical isolates were classified as APEC using a traditional gene-based typing scheme, whereas 53.4% and 44.1% of broiler and turkey gastrointestinal isolates were classified as APEC, respectively. High-risk APEC were identified among 31.0% and 46.9% of broiler and turkey clinical isolates, compared with 5.7% and 2.9% of broiler and turkey gastrointestinal isolates. As found in previous studies, no specific known virulence or fitness gene sets were identified which universally differentiate between clinical and gastrointestinal isolates. This study further demonstrates the utility of a hybrid APEC typing approach, considering both plasmid content and clonal background, for the identification of dominant and highly virulent APEC clones in poultry production.
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Affiliation(s)
- Jodi Delago
- Arm and Hammer Animal and Food Production, Waukesha, WI, 53186, USA
| | - Elizabeth A Miller
- Department of Veterinary and Biomedical Sciences, University of Minnesota, St. Paul, MN, USA
| | | | | | - Carol Cardona
- Department of Veterinary and Biomedical Sciences, University of Minnesota, St. Paul, MN, USA
| | | | - Timothy J Johnson
- Department of Veterinary and Biomedical Sciences, University of Minnesota, St. Paul, MN, USA; Mid-Central Research and Outreach Center, University of Minnesota, Willmar, MN, USA.
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11
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Holcomb DA, Quist AJL, Engel LS. Exposure to industrial hog and poultry operations and urinary tract infections in North Carolina, USA. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 853:158749. [PMID: 36108846 PMCID: PMC9613609 DOI: 10.1016/j.scitotenv.2022.158749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 09/08/2022] [Accepted: 09/09/2022] [Indexed: 06/15/2023]
Abstract
An increasing share of urinary tract infections (UTIs) are caused by extraintestinal pathogenic Escherichia coli (ExPEC) lineages that have also been identified in poultry and hogs with high genetic similarity to human clinical isolates. We investigated industrial food animal production as a source of uropathogen transmission by examining relationships of hog and poultry density with emergency department (ED) visits for UTIs in North Carolina (NC). ED visits for UTI in 2016-2019 were identified by ICD-10 code from NC's ZIP code-level syndromic surveillance system and livestock counts were obtained from permit data and aerial imagery. We calculated separate hog and poultry spatial densities (animals/km2) by Census block with a 5 km buffer on the block perimeter and weighted by block population to estimate mean ZIP code densities. Associations between livestock density and UTI incidence were estimated using a reparameterized Besag-York-Mollié (BYM2) model with ZIP code population offsets to account for spatial autocorrelation. We excluded metropolitan and offshore ZIP codes and assessed effect measure modification by calendar year, ZIP code rurality, and patient sex, age, race/ethnicity, and health insurance status. In single-animal models, hog exposure was associated with increased UTI incidence (rate ratio [RR]: 1.21, 95 % CI: 1.07-1.37 in the highest hog-density tertile), but poultry exposure was associated with reduced UTI rates (RR: 0.86, 95 % CI: 0.81-0.91). However, the reference group for single-animal poultry models included ZIP codes with only hogs, which had some of the highest UTI rates; when compared with ZIP codes without any hogs or poultry, there was no association between poultry exposure and UTI incidence. Hog exposure was associated with increased UTI incidence in areas that also had medium to high poultry density, but not in areas with low poultry density, suggesting that intense hog production may contribute to increased UTI incidence in neighboring communities.
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Affiliation(s)
- David A Holcomb
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Arbor J L Quist
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Lawrence S Engel
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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12
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Amin MB, Talukdar PK, Asaduzzaman M, Roy S, Flatgard BM, Islam MR, Saha SR, Sharker Y, Mahmud ZH, Navab-Daneshmand T, Kile ML, Levy K, Julian TR, Islam MA. Effects of chronic exposure to arsenic on the fecal carriage of antibiotic-resistant Escherichia coli among people in rural Bangladesh. PLoS Pathog 2022; 18:e1010952. [PMID: 36480516 PMCID: PMC9731454 DOI: 10.1371/journal.ppat.1010952] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 10/26/2022] [Indexed: 12/13/2022] Open
Abstract
Antibiotic resistance is a leading cause of hospitalization and death worldwide. Heavy metals such as arsenic have been shown to drive co-selection of antibiotic resistance, suggesting arsenic-contaminated drinking water is a risk factor for antibiotic resistance carriage. This study aimed to determine the prevalence and abundance of antibiotic-resistant Escherichia coli (AR-Ec) among people and drinking water in high (Hajiganj, >100 μg/L) and low arsenic-contaminated (Matlab, <20 μg/L) areas in Bangladesh. Drinking water and stool from mothers and their children (<1 year) were collected from 50 households per area. AR-Ec was detected via selective culture plating and isolates were tested for antibiotic resistance, arsenic resistance, and diarrheagenic genes by PCR. Whole-genome sequencing (WGS) analysis was done for 30 E. coli isolates from 10 households. Prevalence of AR-Ec was significantly higher in water in Hajiganj (48%) compared to water in Matlab (22%, p <0.05) and among children in Hajiganj (94%) compared to children in Matlab (76%, p <0.05), but not among mothers. A significantly higher proportion of E. coli isolates from Hajiganj were multidrug-resistant (83%) compared to isolates from Matlab (71%, p <0.05). Co-resistance to arsenic and multiple antibiotics (MAR index >0.2) was observed in a higher proportion of water (78%) and child stool (100%) isolates in Hajiganj than in water (57%) and children (89%) in Matlab (p <0.05). The odds of arsenic-resistant bacteria being resistant to third-generation cephalosporin antibiotics were higher compared to arsenic-sensitive bacteria (odds ratios, OR 1.2-7.0, p <0.01). WGS-based phylogenetic analysis of E. coli isolates did not reveal any clustering based on arsenic exposure and no significant difference in resistome was found among the isolates between the two areas. The positive association detected between arsenic exposure and antibiotic resistance carriage among children in arsenic-affected areas in Bangladesh is an important public health concern that warrants redoubling efforts to reduce arsenic exposure.
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Affiliation(s)
- Mohammed Badrul Amin
- Laboratory of Food Safety and One Health, Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Prabhat Kumar Talukdar
- Paul G. Allen School for Global Health, Washington State University, Pullman, Washington, United States of America
| | - Muhammad Asaduzzaman
- Laboratory of Food Safety and One Health, Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
- Department of Community Medicine and Global Health, Institute of Health and Society, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Subarna Roy
- Laboratory of Food Safety and One Health, Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Brandon M. Flatgard
- Paul G. Allen School for Global Health, Washington State University, Pullman, Washington, United States of America
| | - Md. Rayhanul Islam
- Laboratory of Food Safety and One Health, Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Sumita Rani Saha
- Laboratory of Food Safety and One Health, Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Yushuf Sharker
- Center for Data Research and Analytics LLC, Bethesda, Maryland, United States of America
| | - Zahid Hayat Mahmud
- Laboratory of Environmental Health, Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Tala Navab-Daneshmand
- School of Chemical, Biological, and Environmental Engineering, Oregon State University, Corvallis, Oregon, United States of America
| | - Molly L. Kile
- School of Biological and Population Health Sciences, Oregon State University, Corvallis, Oregon, United States of America
| | - Karen Levy
- Department of Environmental and Occupational Health Sciences, University of Washington, Washington, United States of America
| | - Timothy R. Julian
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Mohammad Aminul Islam
- Laboratory of Food Safety and One Health, Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
- Paul G. Allen School for Global Health, Washington State University, Pullman, Washington, United States of America
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13
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Swarthout JM, Chan EMG, Garcia D, Nadimpalli ML, Pickering AJ. Human Colonization with Antibiotic-Resistant Bacteria from Nonoccupational Exposure to Domesticated Animals in Low- and Middle-Income Countries: A Critical Review. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:14875-14890. [PMID: 35947446 DOI: 10.1021/acs.est.2c01494] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Data on community-acquired antibiotic-resistant bacterial infections are particularly sparse in low- and middle-income countries (LMICs). Limited surveillance and oversight of antibiotic use in food-producing animals, inadequate access to safe drinking water, and insufficient sanitation and hygiene infrastructure in LMICs could exacerbate the risk of zoonotic antibiotic resistance transmission. This critical review compiles evidence of zoonotic exchange of antibiotic-resistant bacteria (ARB) or antibiotic resistance genes (ARGs) within households and backyard farms in LMICs, as well as assesses transmission mechanisms, risk factors, and environmental transmission pathways. Overall, substantial evidence exists for exchange of antibiotic resistance between domesticated animals and in-contact humans. Whole bacteria transmission and horizontal gene transfer between humans and animals were demonstrated within and between households and backyard farms. Further, we identified water, soil, and animal food products as environmental transmission pathways for exchange of ARB and ARGs between animals and humans, although directionality of transmission is poorly understood. Herein we propose study designs, methods, and topical considerations for priority incorporation into future One Health research to inform effective interventions and policies to disrupt zoonotic antibiotic resistance exchange in low-income communities.
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Affiliation(s)
- Jenna M Swarthout
- Department of Civil and Environmental Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - Elana M G Chan
- Department of Civil and Environmental Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - Denise Garcia
- Department of Civil and Environmental Engineering, University of California, Berkeley, Berkeley, California 94720, United States
| | - Maya L Nadimpalli
- Department of Civil and Environmental Engineering, Tufts University, Medford, Massachusetts 02155, United States
- Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance, Tufts University, Boston, Massachusetts 02111, United States
| | - Amy J Pickering
- Department of Civil and Environmental Engineering, Tufts University, Medford, Massachusetts 02155, United States
- Department of Civil and Environmental Engineering, University of California, Berkeley, Berkeley, California 94720, United States
- Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance, Tufts University, Boston, Massachusetts 02111, United States
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14
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Molecular Study to Detect Escherichia coli in Diarrheic Children and its Antibiotic Resistance. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2022. [DOI: 10.22207/jpam.16.2.49] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Diarrheal diseases can lead to infections and cause morbidity and mortality in children. Diarrheagenic Escherichia coli (DEC) is an etiological agent, which is considered the major causative agent of diarrhea in children in some developing countries. The aims of this work were to estimate Escherichia coli (E. coli) causing diarrhea in children less than 5 years old, and to detect some biofilm virulence factors and the effect of some antibiotics. For the methodology, a total of 112 specimens were collected from children from two health centers, Al-Zahraa Teaching Hospital and Public Health Laboratory (located in Al-Kut city/ and the Wasit province in Iraq). All specimens were grown on simple and rich media. A total of 43 (38.4%) E. coli isolates were identified using different traditional methods, such as biochemical tests and 16S rRNA sequencing. Polymerase chain reaction (PCR) testing was used to detect some virulence factor genes that play an important role in the pathogenesis of diarrheic E. coli e.g., 16S rRNA, bfpA, and eaeA. In this study, several antibiotics were used to estimate the sensitivity and resistivity of E. coli isolates. A total of 43 isolates were fully identified as E. coli. These samples were used to detect the virulence factor genes, and 31 (72.1%) and 29 (29.4%) isolates carried bfpA and eaeA, respectively. The preponderance of E. coli isolates were completely resistant to penicillin 43 (100%). Additionally, 33 (76.7%) and 27 (62.8%) isolates were resistant to cephalothin and amoxycillin-clavulanic acid, respectively. Furthermore, the isolates of E. coli isolates showed different levels of sensitivity to antibiotics, including polymyxin B 40 (93%), norfloxacin 38 (88.4%), gentamycin 26 (60.4%), and meropenem 22 (51.2%). In conclusion, diarrheagenic E. coli isolates were the prevalent among diarrheic children. Most isolates showed varying results for the presence of virulence factors. In addition, all isolates were resistant to penicillin and sensitive to polymyxin B.
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15
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Nadimpalli ML, Lanza VF, Montealegre MC, Sultana S, Fuhrmeister ER, Worby CJ, Teichmann L, Caduff L, Swarthout JM, Crider YS, Earl AM, Brown J, Luby SP, Islam MA, Julian TR, Pickering AJ. Drinking water chlorination has minor effects on the intestinal flora and resistomes of Bangladeshi children. Nat Microbiol 2022; 7:620-629. [PMID: 35422497 PMCID: PMC9249080 DOI: 10.1038/s41564-022-01101-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 02/24/2022] [Indexed: 02/07/2023]
Abstract
Healthy development of the gut microbiome provides long-term health benefits. Children raised in countries with high infectious disease burdens are frequently exposed to diarrhoeal pathogens and antibiotics, which perturb gut microbiome assembly. A recent cluster-randomized trial leveraging >4,000 child observations in Dhaka, Bangladesh, found that automated water chlorination of shared taps effectively reduced child diarrhoea and antibiotic use. In this substudy, we leveraged stool samples collected from 130 children 1 year after chlorine doser installation to examine differences between treatment and control children's gut microbiota. Water chlorination was associated with increased abundance of several bacterial genera previously linked to improved gut health; however, we observed no effects on the overall richness or diversity of taxa. Several clinically relevant antibiotic resistance genes were relatively more abundant in the gut microbiome of treatment children, possibly due to increases in Enterobacteriaceae. While further studies on the long-term health impacts of drinking chlorinated water would be valuable, we conclude that access to chlorinated water did not substantially impact child gut microbiome development in this setting, supporting the use of chlorination to increase global access to safe drinking water.
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Affiliation(s)
- Maya L. Nadimpalli
- Department of Civil and Environmental Engineering, Tufts University, Medford, MA, USA,Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance (Levy CIMAR), Tufts University, Boston, MA, USA
| | - Val F. Lanza
- Bioinformatics Unit, Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain,Network Research Center for Infectious Diseases (CIBERINFEC), Spain
| | | | - Sonia Sultana
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Erica R. Fuhrmeister
- Department of Civil and Environmental Engineering, Tufts University, Medford, MA, USA
| | - Colin J. Worby
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA
| | - Lisa Teichmann
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Lea Caduff
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Jenna M. Swarthout
- Department of Civil and Environmental Engineering, Tufts University, Medford, MA, USA
| | - Yoshika S. Crider
- Energy and Resources Group, University of California Berkeley, Berkeley, CA, USA,King Center on Global Development, Stanford University, Stanford, CA, USA
| | - Ashlee M. Earl
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA
| | - Joe Brown
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Stephen P. Luby
- Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, USA
| | - Mohammad Aminul Islam
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland,Paul G. Allen School for Global Health, Washington State University, Pullman, WA, USA
| | - Timothy R. Julian
- Network Research Center for Infectious Diseases (CIBERINFEC), Spain,Swiss Tropical and Public Health Institute, Basel, Switzerland,University of Basel, Basel, Switzerland
| | - 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,Correspondence and requests for materials should be addressed to Dr. Amy Pickering () and Dr. Tim Julian ()
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16
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Amin MB, Hoque KI, Roy S, Saha SR, Islam MR, Julian TR, Islam MA. Identifying the Sources of Intestinal Colonization With Extended-Spectrum β-Lactamase-Producing Escherichia coli in Healthy Infants in the Community. Front Microbiol 2022; 13:803043. [PMID: 35432268 PMCID: PMC9008759 DOI: 10.3389/fmicb.2022.803043] [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: 10/27/2021] [Accepted: 01/31/2022] [Indexed: 11/13/2022] Open
Abstract
The prevalence of fecal colonization with extended-spectrum β-lactamase-producing Escherichia coli (ESBL-Ec) among children in low- and middle-income countries is alarmingly high. This study aimed to identify the sources of ESBL-Ec colonization in children < 1 year old through comparative analysis of E. coli isolates from child stool, child’s mother stool, and point-of-use drinking water from 46 rural households in Bangladesh. The pairwise similarity in antibiotic susceptibility of E. coli from all three sources was evaluated, followed by phylogenetic clustering using enterobacterial repetitive intergenic consensus polymerase chain reaction and whole-genome sequence analysis of the isolates. Matching antibiotic susceptibility and enterobacterial repetitive intergenic consensus polymerase chain reaction patterns were found among ESBL-Ec isolates from child–mother dyads of 24 and 11 households, respectively, from child–water dyads of 5 and 4 households, respectively, and from child–mother–water triads of 3 and 4 households, respectively. Whole-genome sequence analysis of 30 isolates from 10 households revealed that ESBL-Ec from children in five households (50%) was clonally related to ESBL-Ec either from their mothers (2 households), drinking water sources (2 households), or both mother and drinking-water sources (1 household) based on serotype, phylogroup, sequence type, antibiotic resistance genes, mobile genetic elements, core single-nucleotide polymorphisms, and whole-genome multilocus sequence typing. Overall, this study provides empirical evidence that ESBL-Ec colonization in children is linked to the colonization status of mothers and exposure to the household environments contaminated with ESBL-Ec. Interventions such as improved hygiene practices and a safe drinking water supply may help reduce the transmission of ESBL-Ec at the household level.
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Affiliation(s)
- Mohammed Badrul Amin
- Laboratory of Food Safety and One Health, Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr, b), Dhaka, Bangladesh
- *Correspondence: Mohammed Badrul Amin,
| | - Kazi Injamamul Hoque
- Laboratory of Food Safety and One Health, Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr, b), Dhaka, Bangladesh
| | - Subarna Roy
- Laboratory of Food Safety and One Health, Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr, b), Dhaka, Bangladesh
| | - Sumita Rani Saha
- Laboratory of Food Safety and One Health, Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr, b), Dhaka, Bangladesh
| | - Md. Rayhanul Islam
- Laboratory of Food Safety and One Health, Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr, b), Dhaka, Bangladesh
| | - Timothy R. Julian
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Mohammad Aminul Islam
- Laboratory of Food Safety and One Health, Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr, b), Dhaka, Bangladesh
- Paul G. Allen School for Global Health, Washington State University, Pullman, DC, United States
- Mohammad Aminul Islam,
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17
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A longitudinal study of dominant E. coli lineages and antimicrobial Resistance in the gut of children living in an upper middle-income country. J Glob Antimicrob Resist 2022; 29:136-140. [PMID: 35283334 PMCID: PMC9232985 DOI: 10.1016/j.jgar.2022.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 03/07/2022] [Indexed: 11/24/2022] Open
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18
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Mounsey O, Schubert H, Findlay J, Morley K, Puddy EF, Gould VC, North P, Bowker KE, Williams OM, Williams PB, Barrett DC, Cogan TA, Turner KM, MacGowan AP, Reyher KK, Avison MB. Limited phylogenetic overlap between fluoroquinolone-resistant Escherichia coli isolated on dairy farms and those causing bacteriuria in humans living in the same geographical region. J Antimicrob Chemother 2021; 76:3144-3150. [PMID: 34450630 PMCID: PMC8598280 DOI: 10.1093/jac/dkab310] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 08/03/2021] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Our primary aim was to test whether cattle-associated fluoroquinolone-resistant (FQ-R) Escherichia coli found on dairy farms are closely phylogenetically related to those causing bacteriuria in humans living in the same 50 × 50 km geographical region suggestive of farm-human sharing. Another aim was to identify risk factors for the presence of FQ-R E. coli on dairy farms. METHODS FQ-R E. coli were isolated during 2017-18 from 42 dairy farms and from community urine samples. Forty-two cattle and 489 human urinary isolates were subjected to WGS, allowing phylogenetic comparisons. Risk factors were identified using a Bayesian regularization approach. RESULTS Of 489 FQ-R human isolates, 255 were also third-generation-cephalosporin-resistant, with strong genetic linkage between aac(6')Ib-cr and blaCTX-M-15. We identified possible farm-human sharing for pairs of ST744 and ST162 isolates, but minimal core genome SNP distances were larger between farm-human pairs of ST744 and ST162 isolates (71 and 63 SNPs, respectively) than between pairs of isolates from different farms (7 and 3 SNPs, respectively). Total farm fluoroquinolone use showed a positive association with the odds of isolating FQ-R E. coli, while total dry cow therapy use showed a negative association. CONCLUSIONS This work suggests that FQ-R E. coli found on dairy farms have a limited impact on community bacteriuria within the local human population. Reducing fluoroquinolone use may reduce the on-farm prevalence of FQ-R E. coli and this reduction may be greater when dry cow therapy is targeted to the ecology of resistant E. coli on the farm.
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Affiliation(s)
- Oliver Mounsey
- School of Cellular & Molecular Medicine, University of Bristol, Bristol, UK
| | - Hannah Schubert
- Bristol Veterinary School, University of Bristol, Bristol, UK
| | - Jacqueline Findlay
- School of Cellular & Molecular Medicine, University of Bristol, Bristol, UK
| | - Katy Morley
- Bristol Veterinary School, University of Bristol, Bristol, UK
| | - Emma F Puddy
- School of Cellular & Molecular Medicine, University of Bristol, Bristol, UK
- Bristol Veterinary School, University of Bristol, Bristol, UK
| | - Virginia C Gould
- School of Cellular & Molecular Medicine, University of Bristol, Bristol, UK
- Bristol Veterinary School, University of Bristol, Bristol, UK
| | - Paul North
- Department of Microbiology, Infection Sciences, Southmead Hospital, North Bristol NHS Trust, Bristol, UK
| | - Karen E Bowker
- Department of Microbiology, Infection Sciences, Southmead Hospital, North Bristol NHS Trust, Bristol, UK
| | - O Martin Williams
- Bristol Royal Infirmary, University Hospitals Bristol and Weston NHS Foundation Trust, Bristol, UK
| | - Philip B Williams
- Bristol Royal Infirmary, University Hospitals Bristol and Weston NHS Foundation Trust, Bristol, UK
| | - David C Barrett
- Bristol Veterinary School, University of Bristol, Bristol, UK
| | - Tristan A Cogan
- Bristol Veterinary School, University of Bristol, Bristol, UK
| | - Katy M Turner
- Bristol Veterinary School, University of Bristol, Bristol, UK
| | - Alasdair P MacGowan
- Department of Microbiology, Infection Sciences, Southmead Hospital, North Bristol NHS Trust, Bristol, UK
| | | | - Matthew B Avison
- School of Cellular & Molecular Medicine, University of Bristol, Bristol, UK
- Corresponding author. E-mail:
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19
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Webale MK, Guyah B, Wanjala C, Nyanga PL, Webale SK, Abonyo C, Kitungulu N, Kiboi N, Bowen N. Phenotypic and Genotypic Antibiotic Resistant diarrheagenic Escherichia coli pathotypes isolated from Children with Diarrhea in Nairobi City, Kenya. Ethiop J Health Sci 2021; 30:881-890. [PMID: 33883832 PMCID: PMC8047252 DOI: 10.4314/ejhs.v30i6.5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Background The marked genome plasticity of diarrheagenic Escherichia coli promotes emergence of pathotypes displaying unique phenotypic and genotypic resistance. This study examined phenotypic and genotypic antibiotic resistant diarrheagenic Escherichia coli pathotypes among children in Nairobi City, Kenya. Methods In a cross-sectional study, diarrheagenic Escherichia coli pathotypes were isolated from stool samples and their phenotypic and genotypic resistance against eight antimicrobial agents assayed. Results Diarrheagenic Escherichia coli was detected in 136(36.4%) children. Most of diarrheagenic Escherichia coli that were resistant to ampicillin, ceftriaxone, streptomycin, gentamycin, ciprofloxacin, chloramphenicol, erythromycin and tetracycline, harbored citm, bla CMY, aadA1, aac(3)-IV, qnr, catA, ere(A) and tet(A) corresponding resistant genes. Conclusion Antimicrobial-resistant genes are highly prevalent among phenotypic resistant ETEC pathotypes indicating a possibility of horizontal gene transfer in spreading antibiotic resistant genes among E. coli pathotypes.
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Affiliation(s)
| | | | - Christine Wanjala
- School of Public Health, Masinde Muliro University of Science and Technology, Kakamega, Kenya Unit, Ministry of Health, Nairobi city, Kenya
| | | | | | - Collins Abonyo
- School of Public Health, Masinde Muliro University of Science and Technology, Kakamega, Kenya Unit, Ministry of Health, Nairobi city, Kenya
| | - Nicholas Kitungulu
- School of Natural Sciences, Masinde Muliro University of Science and Technology, Kenya
| | - Nathan Kiboi
- School of Pure and Applied Sciences, Kenyatta University, Kenya
| | - Nancy Bowen
- National Public health Laboratories, Ministry of Health, Nairobi city, Kenya
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20
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Abstract
PURPOSE OF REVIEW Several types of Escherichia coli cause acute diarrhea in humans and are responsible for a large burden of disease globally. The purpose of this review is to summarize diarrheagenic Escherichia coli (DEC) pathotype definitions and discuss existing and emerging molecular, genomic, and gut microbiome methods to detect, define, and study DEC pathotypes. RECENT FINDINGS DEC pathotypes are currently diagnosed by molecular detection of unique virulence genes. However, some pathotypes have defied coherent molecular definitions because of imperfect gene targets, and pathotype categories are complicated by hybrid strains and isolation of pathotypes from asymptomatic individuals. Recent progress toward more efficient, sensitive, and multiplex DEC pathotype detection has been made using emerging PCR-based technologies. Genomics and gut microbiome detection methods continue to advance rapidly and are contributing to a better understanding of DEC pathotype diversity and functional potential. SUMMARY DEC pathotype categorizations and detection methods are useful but imperfect. The implementation of molecular and sequence-based methods and well designed epidemiological studies will continue to advance understanding of DEC pathotypes. Additional emphasis is needed on sequencing DEC genomes from regions of the world where they cause the most disease and from the pathotypes that cause the greatest burden of disease globally.
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21
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Munhoz DD, Santos FF, Mitsunari T, Schüroff PA, Elias WP, Carvalho E, Piazza RMF. Hybrid Atypical Enteropathogenic and Extraintestinal Escherichia coli (aEPEC/ExPEC) BA1250 Strain: A Draft Genome. Pathogens 2021; 10:475. [PMID: 33919948 PMCID: PMC8070890 DOI: 10.3390/pathogens10040475] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 04/07/2021] [Accepted: 04/09/2021] [Indexed: 01/02/2023] Open
Abstract
Diarrheagenic Escherichia coli is the major bacterial etiological agent of severe diarrhea and a major concern of public health. These pathogens have acquired genetic characteristics from other pathotypes, leading to unusual and singular genetic combinations, known as hybrid strains and may be more virulent due to a set of virulence factors from more than one pathotype. One of the possible combinations is with extraintestinal E. coli (ExPEC), a leading cause of urinary tract infection, often lethal after entering the bloodstream and atypical enteropathogenic E. coli (aEPEC), responsible for death of thousands of people every year, mainly children under five years old. Here we report the draft genome of a strain originally classified as aEPEC (BA1250) isolated from feces of a child with acute diarrhea. Phylogenetic analysis indicates that BA1250 genome content is genetically closer to E. coli strains that cause extraintestinal infections, other than intestinal infections. A deeper analysis showed that in fact this is a hybrid strain, due to the presence of a set of genes typically characteristic of ExPEC. These genomic findings expand our knowledge about aEPEC heterogeneity allowing further studies concerning E. coli pathogenicity and may be a source for future comparative studies, virulence characteristics, and evolutionary biology.
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Affiliation(s)
- Danielle D. Munhoz
- Laboratório de Bacteriologia, Instituto Butantan, São Paulo 05503-900, Brazil; (T.M.); (P.A.S.); (W.P.E.); (E.C.)
| | - Fernanda F. Santos
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo 04023-062, Brazil;
| | - Thais Mitsunari
- Laboratório de Bacteriologia, Instituto Butantan, São Paulo 05503-900, Brazil; (T.M.); (P.A.S.); (W.P.E.); (E.C.)
| | - Paulo A. Schüroff
- Laboratório de Bacteriologia, Instituto Butantan, São Paulo 05503-900, Brazil; (T.M.); (P.A.S.); (W.P.E.); (E.C.)
| | - Waldir P. Elias
- Laboratório de Bacteriologia, Instituto Butantan, São Paulo 05503-900, Brazil; (T.M.); (P.A.S.); (W.P.E.); (E.C.)
| | - Eneas Carvalho
- Laboratório de Bacteriologia, Instituto Butantan, São Paulo 05503-900, Brazil; (T.M.); (P.A.S.); (W.P.E.); (E.C.)
| | - Roxane M. F. Piazza
- Laboratório de Bacteriologia, Instituto Butantan, São Paulo 05503-900, Brazil; (T.M.); (P.A.S.); (W.P.E.); (E.C.)
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22
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Gharpure R, Mor SM, Viney M, Hodobo T, Lello J, Siwila J, Dube K, Robertson RC, Mutasa K, Berger CN, Hirai M, Brown T, Ntozini R, Evans C, Hoto P, Smith LE, Tavengwa NV, Joyeux M, Humphrey JH, Berendes D, Prendergast AJ. A One Health Approach to Child Stunting: Evidence and Research Agenda. Am J Trop Med Hyg 2021; 104:1620-1624. [PMID: 33684062 PMCID: PMC8103449 DOI: 10.4269/ajtmh.20-1129] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 10/19/2020] [Indexed: 12/18/2022] Open
Abstract
Stunting (low height for age) affects approximately one-quarter of children aged < 5 years worldwide. Given the limited impact of current interventions for stunting, new multisectoral evidence-based approaches are needed to decrease the burden of stunting in low- and middle-income countries (LMICs). Recognizing that the health of people, animals, and the environment are connected, we present the rationale and research agenda for considering a One Health approach to child stunting. We contend that a One Health strategy may uncover new approaches to tackling child stunting by addressing several interdependent factors that prevent children from thriving in LMICs, and that coordinated interventions among human health, animal health, and environmental health sectors may have a synergistic effect in stunting reduction.
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Affiliation(s)
- Radhika Gharpure
- Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Siobhan M. Mor
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- International Livestock Research Institute, Addis Ababa, Ethiopia
| | - Mark Viney
- Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | | | - Joanne Lello
- College of Biomedical and Life Sciences, Cardiff University, Cardiff, United Kingdom
| | - Joyce Siwila
- School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - Kululeko Dube
- Food and Agriculture Organization of the United Nations, Harare, Zimbabwe
| | | | - Kuda Mutasa
- Zvitambo Institute for Maternal and Child Health Research, Harare, Zimbabwe
| | - Cedric N. Berger
- College of Biomedical and Life Sciences, Cardiff University, Cardiff, United Kingdom
| | | | - Tim Brown
- School of Geography, Queen Mary University of London, London, United Kingdom
| | - Robert Ntozini
- Zvitambo Institute for Maternal and Child Health Research, Harare, Zimbabwe
| | - Ceri Evans
- Blizard Institute, Queen Mary University of London, London, United Kingdom
- Zvitambo Institute for Maternal and Child Health Research, Harare, Zimbabwe
| | - Patience Hoto
- Food and Agriculture Organization of the United Nations, Harare, Zimbabwe
| | - Laura E. Smith
- Zvitambo Institute for Maternal and Child Health Research, Harare, Zimbabwe
- Department of Epidemiology and Environmental Health, University at Buffalo, Buffalo, New York
| | - Naume V. Tavengwa
- Zvitambo Institute for Maternal and Child Health Research, Harare, Zimbabwe
| | | | - Jean H. Humphrey
- Zvitambo Institute for Maternal and Child Health Research, Harare, Zimbabwe
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - David Berendes
- Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Andrew J. Prendergast
- Blizard Institute, Queen Mary University of London, London, United Kingdom
- Zvitambo Institute for Maternal and Child Health Research, Harare, Zimbabwe
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
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23
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Rousham EK, Asaduzzaman M, Mozmader TAU, Amin MB, Rahman M, Hossain MI, Islam MR, Mahmud ZH, Unicomb L, Islam MA. Human Colonization with Extended-Spectrum Beta-Lactamase-Producing E. coli in Relation to Animal and Environmental Exposures in Bangladesh: An Observational One Health Study. ENVIRONMENTAL HEALTH PERSPECTIVES 2021; 129:37001. [PMID: 33656920 PMCID: PMC7929562 DOI: 10.1289/ehp7670] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 12/07/2020] [Accepted: 01/27/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Human exposure to intensively farmed livestock is a potential risk for transmission of antibiotic-resistant bacteria (ARB) but few studies have assessed the relative role of animal vs. environmental sources of ARB in low-resource community settings. OBJECTIVES We conducted an observational study to compare ARB colonization and antibiotic-resistant gene prevalence and abundance in humans with high or low exposure to poultry in rural households, commercial poultry farms, and urban markets in Bangladesh. METHODS Extended-spectrum β-lactamase (ESBL)-producing and carbapenem-resistant E. coli were quantified in feces from adults with high or low poultry exposure (n=100, respectively), poultry (n=200), drinking water (n=120), and wastewater (n=120) from 40 rural households, 40 poultry farms, and 40 urban markets. RESULTS ESBL-producing E. coli (ESBL-EC) prevalence was 67.5% (95% CI: 61.0, 74.0) in samples from adults, 68.0% (95% CI: 61.5, 74.5) in samples from poultry, and 92.5% (95% CI: 87.7, 97.3) in wastewater samples. Carbapenem-resistant E. coli prevalence was high in market wastewaters [30% (95% CI: 15.0, 45.0)] but low in humans (1%) and poultry (1%). Human, poultry, and wastewater isolates shared common resistance genes: blaCTX-M-1, qnr, and blaTEM. Human colonization was not significantly associated with exposure to poultry or setting (rural, farm, or market). Ninety-five percent of commercial poultry farms routinely administered antibiotics. Susceptibility tests were significantly different in household vs. farm and market poultry isolates for four of seven antibiotic classes. In human isolates, there were no differences except aminoglycoside resistance (16.4% high vs. 4.4% low exposure, p=0.02). Urban market wastewaters and poultry samples had significantly higher concentrations of ESBL-EC (p<0.001) and blaCTX-M-1 (p<0.001) compared with samples from farms and rural households. DISCUSSION ESBL-EC colonization was high in humans but not significantly associated with exposure to poultry. Bidirectional transmission of antibiotic resistance is likely between humans, poultry, and the environment in these community settings, underlining the importance of One Health mitigation strategies. https://doi.org/10.1289/EHP7670.
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Affiliation(s)
- Emily K. Rousham
- Centre for Global Health and Human Development, School of Sport, Exercise and Health Sciences, Loughborough University, Loughborough, UK
| | - Muhammad Asaduzzaman
- Centre for Global Health, Institute of Health and Society, Faculty of Medicine, Oslo University, Norway
| | | | - Mohammed Badrul Amin
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Mahdia Rahman
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | | | - Md. Rayhanul Islam
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Zahid Hayat Mahmud
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Leanne Unicomb
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Mohammad Aminul Islam
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, Washington, USA
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24
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Nowicki S, deLaurent ZR, de Villiers EP, Githinji G, Charles KJ. The utility of Escherichia coli as a contamination indicator for rural drinking water: Evidence from whole genome sequencing. PLoS One 2021; 16:e0245910. [PMID: 33481909 PMCID: PMC7822521 DOI: 10.1371/journal.pone.0245910] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 01/09/2021] [Indexed: 12/12/2022] Open
Abstract
Across the water sector, Escherichia coli is the preferred microbial water quality indicator and current guidance upholds that it indicates recent faecal contamination. This has been challenged, however, by research demonstrating growth of E. coli in the environment. In this study, we used whole genome sequencing to investigate the links between E. coli and recent faecal contamination in drinking water. We sequenced 103 E. coli isolates sampled from 9 water supplies in rural Kitui County, Kenya, including points of collection (n = 14) and use (n = 30). Biomarkers for definitive source tracking remain elusive, so we analysed the phylogenetic grouping, multi-locus sequence types (MLSTs), allelic diversity, and virulence and antimicrobial resistance (AMR) genes of the isolates for insight into their likely source. Phylogroup B1, which is generally better adapted to water environments, is dominant in our samples (n = 69) and allelic diversity differences (z = 2.12, p = 0.03) suggest that naturalised populations may be particularly relevant at collection points with lower E. coli concentrations (<50 / 100mL). The strains that are more likely to have originated from human and/or recent faecal contamination (n = 50), were found at poorly protected collection points (4 sites) or at points of use (12 sites). We discuss the difficulty of interpreting health risk from E. coli grab samples, especially at household level, and our findings support the use of E. coli risk categories and encourage monitoring that accounts for sanitary conditions and temporal variability.
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Affiliation(s)
- Saskia Nowicki
- School of Geography and the Environment, University of Oxford, Oxford, United Kingdom
| | - Zaydah R. deLaurent
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
| | - Etienne P. de Villiers
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
- Department of Public Health, Pwani University, Kilifi, Kenya
| | - George Githinji
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
| | - Katrina J. Charles
- School of Geography and the Environment, University of Oxford, Oxford, United Kingdom
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25
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Puvača N, de Llanos Frutos R. Antimicrobial Resistance in Escherichia coli Strains Isolated from Humans and Pet Animals. Antibiotics (Basel) 2021; 10:69. [PMID: 33450827 PMCID: PMC7828219 DOI: 10.3390/antibiotics10010069] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/06/2021] [Accepted: 01/12/2021] [Indexed: 12/12/2022] Open
Abstract
Throughout scientific literature, we can find evidence that antimicrobial resistance has become a big problem in the recent years on a global scale. Public healthcare systems all over the world are faced with a great challenge in this respect. Obviously, there are many bacteria that can cause infections in humans and animals alike, but somehow it seems that the greatest threat nowadays comes from the Enterobacteriaceae members, especially Escherichia coli. Namely, we are witnesses to the fact that the systems that these bacteria developed to fight off antibiotics are the strongest and most diverse in Enterobacteriaceae. Our great advantage is in understanding the systems that bacteria developed to fight off antibiotics, so these can help us understand the connection between these microorganisms and the occurrence of antibiotic-resistance both in humans and their pets. Furthermore, unfavorable conditions related to the ease of E. coli transmission via the fecal-oral route among humans, environmental sources, and animals only add to the problem. For all the above stated reasons, it is evident that the epidemiology of E. coli strains and resistance mechanisms they have developed over time are extremely significant topics and all scientific findings in this area will be of vital importance in the fight against infections caused by these bacteria.
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Affiliation(s)
- Nikola Puvača
- Faculty of Biomedical and Health Sciences, Jaume I University, Avinguda de Vicent Sos Baynat, s/n, 12071 Castelló de la Plana, Spain;
- Department of Engineering Management in Biotechnology, Faculty of Economics and Engineering Management in Novi Sad, University Business Academy in Novi Sad, Cvećarska 2, 21000 Novi Sad, Serbia
| | - Rosa de Llanos Frutos
- Faculty of Biomedical and Health Sciences, Jaume I University, Avinguda de Vicent Sos Baynat, s/n, 12071 Castelló de la Plana, Spain;
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26
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Brukner I, Oughton M. A Fundamental Change in Antibiotic Susceptibility Testing Would Better Prevent Therapeutic Failure: From Individual to Population-Based Analysis. Front Microbiol 2020; 11:1820. [PMID: 32973694 PMCID: PMC7461948 DOI: 10.3389/fmicb.2020.01820] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 07/10/2020] [Indexed: 11/16/2022] Open
Affiliation(s)
- Ivan Brukner
- Department of Diagnostic Medicine, Jewish General Hospital, Montreal, QC, Canada.,Molecular and Regenerative Medicine, Lady Davis Institute for Medical Research, Montreal, QC, Canada.,Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - Matthew Oughton
- Department of Diagnostic Medicine, Jewish General Hospital, Montreal, QC, Canada.,Molecular and Regenerative Medicine, Lady Davis Institute for Medical Research, Montreal, QC, Canada.,Faculty of Medicine, McGill University, Montreal, QC, Canada
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27
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Schierack P, Heiden SE, Khan MM, Nikolaus L, Kolenda R, Stubbe M, Lkhagvasuren D, Rödiger S, Guenther S, Schaufler K. Genomic and Phenotypic Analysis of an ESBL-Producing E. coli ST1159 Clonal Lineage From Wild Birds in Mongolia. Front Microbiol 2020; 11:1699. [PMID: 32793163 PMCID: PMC7385280 DOI: 10.3389/fmicb.2020.01699] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 06/29/2020] [Indexed: 12/05/2022] Open
Abstract
Background In addition to the broad dissemination of pathogenic extended-spectrum beta-lactamase (ESBL)-producing Escherichia (E.) coli in human and veterinary medicine and the community, their occurrence in wildlife and the environment is a growing concern. Wild birds in particular often carry clinically relevant ESBL-producing E. coli. Objectives We analyzed ESBL-producing and non-ESBL-producing E. coli obtained from wild birds in Mongolia to identify phylogenetic and functional characteristics that would explain the predominance of a particular E. coli clonal lineage in this area. Methods We investigated ESBL-producing E. coli using whole-genome sequencing and phylogenetics to describe the population structure, resistance and virulence features and performed phenotypic experiments like biofilm formation and adhesion to epithelial cells. We compared the phenotypic characteristics to non-ESBL-producing E. coli from the same background (Mongolian wild birds) and genomic results to publicly available genomes. Results and Conclusion We found ESBL-producing E. coli sequence type (ST) 1159 among wild birds in Mongolia. This clonal lineage carried virulence features typical for extra-intestinal pathogenic or enterotoxigenic E. coli. Comparative functional experiments suggested no burden of resistance in the ST1159 isolates, which is despite their carriage of ESBL-plasmids. Wild birds will likely disseminate these antibiotic-resistant pathogens further during migration.
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Affiliation(s)
- Peter Schierack
- Multiparametric Diagnostics, Brandenburg University of Technology Cottbus - Senftenberg, Senftenberg, Germany
| | - Stefan E Heiden
- Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Muhammad Moman Khan
- Multiparametric Diagnostics, Brandenburg University of Technology Cottbus - Senftenberg, Senftenberg, Germany
| | - Lena Nikolaus
- Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Rafal Kolenda
- Multiparametric Diagnostics, Brandenburg University of Technology Cottbus - Senftenberg, Senftenberg, Germany
| | - Michael Stubbe
- Institute of Biology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Davaa Lkhagvasuren
- Department of Biology, National University of Mongolia, Ulaanbaatar, Mongolia
| | - Stefan Rödiger
- Multiparametric Diagnostics, Brandenburg University of Technology Cottbus - Senftenberg, Senftenberg, Germany.,Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus - Senftenberg, The Brandenburg Medical School Theodor Fontane and the University of Potsdam, Senftenberg, Germany
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28
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Digital multiplex ligation assay for highly multiplexed screening of β-lactamase-encoding genes in bacterial isolates. Commun Biol 2020; 3:264. [PMID: 32451431 PMCID: PMC7248093 DOI: 10.1038/s42003-020-0980-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 04/30/2020] [Indexed: 11/21/2022] Open
Abstract
Increasing incidence of antibiotic resistance in clinical and environmental settings calls for increased scalability in their surveillance. Current screening technologies are limited by the number of samples and genes that can easily be screened. We demonstrate here digital multiplex ligation assay (dMLA) as a low-cost targeted genomic detection workflow capable of highly-parallel screening of bacterial isolates for multiple target gene regions simultaneously. Here, dMLA is used for simultaneous detection of 1187 β-lactamase-encoding genes, including extended spectrum β-lactamase (ESBL) genes, in 74 bacterial isolates. We demonstrate dMLA as a light-weight and cost-efficient workflow which provides a highly scalable tool for antimicrobial resistance surveillance and is also adaptable to genetic screening applications beyond antibiotic resistance. Tamminen et al. develop a digital multiplex ligation assay (dMLA) that enables the detection of bacterial isolates using probe hybridization and ligation-based assays with next-generation sequencing. Their method can be applied in high-throughput and affordable screening for antibiotic resistance.
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