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Clabots C, Thuras P, Johnson JR. Longitudinal molecular analysis of clinical and fecal Escherichia coli isolates at a Veterans Affairs Medical Center in Minnesota, USA, 2012-2019. Front Microbiol 2024; 15:1409272. [PMID: 38887718 PMCID: PMC11180817 DOI: 10.3389/fmicb.2024.1409272] [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: 03/29/2024] [Accepted: 04/26/2024] [Indexed: 06/20/2024] Open
Abstract
Introduction Extraintestinal Escherichia coli infections represent a growing public health threat, However, current studies often overlook important factors such as temporal patterns of infection, phylogenetic and clonal background, or the host gut E. coli population, despite their likely significance. Methods In this study, we analyzed >7000 clinical E. coli isolates from patients at the Minneapolis Veterans Affairs Health Care System (2012-2019), and concurrent fecal E. coli from uninfected veterans. We assessed phylogenetic group distribution, membership in selected sequence types (STs), and subsets thereof-including the pandemic, resistance-associated ST131-H30R, and ST1193 lineages-and strain type, as defined by pulsed-field gel electrophoresis. We then analyzed these features alongside the temporal patterns of infection in individual hosts. Results The H30R lineage emerged as the leading lineage, both overall and among fluoroquinolone-resistant isolates, with ST1193 following among fluoroquinolone-resistant isolates. Recurrences were common, occurring in 31% of subjects and 41% of episodes, and often multiple and delayed/prolonged (up to 23 episodes per subject; up to 2655d post-index). Remarkably, these recurrences typically involved the subject's index strain (63% of recurrences), even when affecting extra-urinary sites. ST131, H30R, ST1193, and fluoroquinolone-resistant strains generally caused significantly more recurrences than did other strains, despite similar recurrence intervals. ST131 strain types shifted significantly over the study period. Infection-causing strains were commonly detectable in host feces at times other than during an infection episode; the likelihood of detection varied with surveillance intensity and proximity to the infection. H30R and ST1193 were prominent causes of fecal-clinical clonal overlap. Discussion These findings provide novel insights into the temporal and clonal characteristics of E. coli infections in veterans and support efforts to develop anti-colonization interventions.
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Affiliation(s)
- Connie Clabots
- Minneapolis VA Health Care System, Minneapolis, MN, United States
| | - Paul Thuras
- Minneapolis VA Health Care System, Minneapolis, MN, United States
- Department of Psychiatry, University of Minnesota, Minneapolis, MN, United States
| | - James R. Johnson
- Minneapolis VA Health Care System, Minneapolis, MN, United States
- Department of Medicine, University of Minnesota, Minneapolis, MN, United States
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Johnston BD, Clabots C, Bender T, Porter SB, van den Dobbelsteen G, Poolman J, Thuras P, Johnson JR. Colonization with Escherichia coli ST131- H30R ( H30R) Corresponds with Increased Serum Anti-O25 IgG Levels and Decreased TNFα and IL-10 Responsiveness to H30R. Pathogens 2023; 12:pathogens12040603. [PMID: 37111489 PMCID: PMC10142592 DOI: 10.3390/pathogens12040603] [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: 02/28/2023] [Revised: 04/04/2023] [Accepted: 04/11/2023] [Indexed: 04/29/2023] Open
Abstract
An exceptional gut-colonizing ability may underlie the dramatic epidemiological success of the multidrug-resistant H30R subclone of Escherichia coli sequence type 131 (O25b:K+:H4). In order to inform the development of colonization-preventing measures, we studied systemic immune correlates of H30R intestinal colonization. Human volunteers' fecal samples were screened for H30R by selective culture and PCR. Subjects were assessed by enzyme immunoassay for serum levels of anti-O25 IgG (representing H30R) and anti-O6 IgG (representing non-H30 E. coli generally), initially and for up to 14 months. Whole blood was tested for the antigen-stimulated release of IFNγ, TNFα, IL-4, IL-10, and IL-17 after incubation with E. coli strains JJ1886 (H30R; O25b:K+:H4) or CFT073 (non-H30; O6:K2:H1). Three main findings were obtained. First, H30R-colonized subjects had significantly higher anti-O25 IgG levels than controls, but similar anti-O6 IgG levels, suggesting an IgG response to H30R colonization. Second, anti-O25 and anti-O6 IgG levels were stable over time. Third, H30R-colonized subjects exhibited a lower TNFα and IL-10 release than controls in response to strain JJ1886 (H30R) relative to strain CFT073 (non-H30R), consistent with TNFα hypo-responsiveness to H30R possibly predisposing to H30R colonization. Thus, H30R-colonized hosts exhibit a sustained serum anti-O25 IgG response and an underlying deficit in TNFα responsiveness to H30R that could potentially be addressed for colonization prevention.
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Affiliation(s)
- Brian D Johnston
- Departments of Medicine and Psychiatry, University of Minnesota, Minneapolis 55455, MN, USA
| | - Connie Clabots
- Infectious Diseases (111F), Minneapolis VA Health Care System, Minneapolis 55417, MN, USA
| | - Tricia Bender
- Infectious Diseases (111F), Minneapolis VA Health Care System, Minneapolis 55417, MN, USA
| | - Stephen B Porter
- Infectious Diseases (111F), Minneapolis VA Health Care System, Minneapolis 55417, MN, USA
| | | | - Jan Poolman
- Janssen Vaccines & Prevention B.V., 2333 CN Leiden, The Netherlands
| | - Paul Thuras
- Departments of Medicine and Psychiatry, University of Minnesota, Minneapolis 55455, MN, USA
- Infectious Diseases (111F), Minneapolis VA Health Care System, Minneapolis 55417, MN, USA
| | - James R Johnson
- Departments of Medicine and Psychiatry, University of Minnesota, Minneapolis 55455, MN, USA
- Infectious Diseases (111F), Minneapolis VA Health Care System, Minneapolis 55417, MN, USA
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3
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Zou Z, Potter RF, McCoy WH, Wildenthal JA, Katumba GL, Mucha PJ, Dantas G, Henderson JP. E. coli catheter-associated urinary tract infections are associated with distinctive virulence and biofilm gene determinants. JCI Insight 2023; 8:e161461. [PMID: 36512427 PMCID: PMC9977300 DOI: 10.1172/jci.insight.161461] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 12/07/2022] [Indexed: 12/15/2022] Open
Abstract
Urinary catheterization facilitates urinary tract colonization by E. coli and increases infection risk. Here, we aimed to identify strain-specific characteristics associated with the transition from colonization to infection in catheterized patients. In a single-site study population, we compared E. coli isolates from patients with catheter-associated asymptomatic bacteriuria (CAASB) to those with catheter-associated urinary tract infection (CAUTI). CAUTI isolates were dominated by a phylotype B2 subclade containing the multidrug-resistant ST131 lineage relative to CAASB isolates, which were phylogenetically more diverse. A distinctive combination of virulence-associated genes was present in the CAUTI-associated B2 subclade. Catheter-associated biofilm formation was widespread among isolates and did not distinguish CAUTI from CAASB strains. Preincubation with CAASB strains could inhibit catheter colonization by multiple ST131 CAUTI isolates. Comparative genomic analysis identified a group of variable genes associated with high catheter biofilm formation present in both CAUTI and CAASB strains. Among these, ferric citrate transport (Fec) system genes were experimentally associated with enhanced catheter biofilm formation using reporter and fecA deletion strains. These results are consistent with a variable role for catheter biofilm formation in promoting CAUTI by ST131-like strains or resisting CAUTI by lower-risk strains that engage in niche exclusion.
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Affiliation(s)
- Zongsen Zou
- Center for Women’s Infectious Diseases Research
- Department of Internal Medicine, Division of Infectious Diseases
| | - Robert F. Potter
- The Edison Family Center for Genome Sciences and Systems Biology
- Department of Pathology and Immunology, and
| | - William H. McCoy
- Center for Women’s Infectious Diseases Research
- Department of Internal Medicine, Division of Dermatology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - John A. Wildenthal
- Center for Women’s Infectious Diseases Research
- Department of Internal Medicine, Division of Infectious Diseases
| | - George L. Katumba
- Center for Women’s Infectious Diseases Research
- Department of Internal Medicine, Division of Infectious Diseases
| | - Peter J. Mucha
- Department of Mathematics, Dartmouth College, Hanover, New Hampshire, USA
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences and Systems Biology
- Department of Pathology and Immunology, and
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Biomedical Engineering, Washington University in St. Louis, Missouri, USA
| | - Jeffrey P. Henderson
- Center for Women’s Infectious Diseases Research
- Department of Internal Medicine, Division of Infectious Diseases
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4
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Salamanca-Rivera E, López-Cerero L, Rodríguez-Martínez JM, Pascual A, Rodríguez-Baño J. Prevalence, Incidence, and Risk Factors for Intestinal Colonization Due to Fluoroquinolone-Resistant ST131 Escherichia coli: a Longitudinal Study in Highly Dependent, Long-Term Care Facility Residents. Microbiol Spectr 2022; 10:e0167322. [PMID: 35943257 PMCID: PMC9431526 DOI: 10.1128/spectrum.01673-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/13/2022] [Indexed: 11/20/2022] Open
Abstract
Escherichia coli ST131 clade C is an important driver for fluoroquinolone resistance (FQ-R). We conducted a prospective observational study in residents from two long-term care facilities (LTCFs) in Seville, Spain, in 2018. Fecal swabs and environmental samples were obtained. E. coli isolates were screened for clade C, FQ-R ST131 by PCR, and molecular typing by PFGE; representatives from pulsotypes were studied by whole-genome-sequencing (WGS) and assigned to lineages (cgSTs). Prevalence of colonization at each time point, incidence density, and risk factors for acquisition were studied. Seventy-six FQ-R ST131 E. coli isolates belonging to 34 cgSTs were obtained; 24 belonging to subclade C1 (116 isolates, 65.9%) and 10 to C2 (60, 34.1%). C1 lineages showed lower virulence scores than C2 (median [IQR], 19 [18 to 20] versus 21 [20 to 21.5], P = 0.001) and higher number of plasmids (4 [3 to 5] versus 2 [2 to 3], P = 0.01). aac(6')-Ib-cr and blaOXA-1 were less frequent in C1 than C2 (2 [8.3%] versus 6 [60%], P = 0.003 for both); ESBL genes were detected in eight (33.3%) C1 (5 blaCTX-M-27) and three (30%) C2 (all blaCTX-M-15). Of the 82 residents studied, 49 were colonized at some point (59.7%), with a pooled prevalence of 38.6%. Incidence density of new lineage acquisition was 2.22 per 100 resident weeks (1.28 and 0.93 C1 and C2 subclades, respectively). Independent risk factors for acquisitions were having a colonized roommate (HR = 4.21; 95% CI = 1.71 to 10.36; P = 0.002) and urinary or fecal incontinence (HR = 2.82; 95% CI = 1.21 to 6.56; P = 0.01). LTCFs are important reservoirs of clade C ST131 E. coli. The risk factors found suggest that cross-transmission is the most relevant transmission mechanisms. IMPORTANCE We aimed at investigating the microbiological and epidemiological features of clade C fluoroquinolone-resistant ST131 E. coli isolates colonizing highly dependent residents in long-term care facilities (LTCFs) during 40 weeks and the risk factors of acquisition. Isolates from C1 and C2 subclades were characterized in this environment. The clonality of the isolates was characterized and they were assigned to lineages (cgSTs), Resistance genes, virulence factors, and plasmids were also described. This study suggests that cross-transmission is the most relevant transmission mechanisms; however, environmental colonization might also play a role. We believe the data provide useful information to depict the epidemiology of these bacteria by merging detailed microbiological and epidemiological information.
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Affiliation(s)
- Elena Salamanca-Rivera
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen Macarena, Seville, Spain
- Instituto de Biomedicina de Sevilla and CSIC, Seville, Spain
- Centro de Investigación en Red en Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Lorena López-Cerero
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen Macarena, Seville, Spain
- Instituto de Biomedicina de Sevilla and CSIC, Seville, Spain
- Departamento de Microbiología, Universidad de Sevilla, Seville, Spain
- Centro de Investigación en Red en Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Jose Manuel Rodríguez-Martínez
- Instituto de Biomedicina de Sevilla and CSIC, Seville, Spain
- Departamento de Microbiología, Universidad de Sevilla, Seville, Spain
- Centro de Investigación en Red en Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Alvaro Pascual
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen Macarena, Seville, Spain
- Instituto de Biomedicina de Sevilla and CSIC, Seville, Spain
- Departamento de Microbiología, Universidad de Sevilla, Seville, Spain
- Centro de Investigación en Red en Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Jesús Rodríguez-Baño
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen Macarena, Seville, Spain
- Instituto de Biomedicina de Sevilla and CSIC, Seville, Spain
- Departamento de Medicina, Universidad de Sevilla, Seville, Spain
- Centro de Investigación en Red en Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
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Liu X, Li X, Yang AW, Tang B, Jian ZJ, Zhong YM, Li HL, Li YM, Yan Q, Liang XH, Liu WE. Community Fecal Carriage and Molecular Epidemiology of Extended-Spectrum β-Lactamase- and Carbapenemase-Producing Escherichia coli from Healthy Children in the Central South China. Infect Drug Resist 2022; 15:1601-1611. [PMID: 35418762 PMCID: PMC8995156 DOI: 10.2147/idr.s357090] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 03/26/2022] [Indexed: 12/25/2022] Open
Affiliation(s)
- Xuan Liu
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, People's Republic of China
| | - Xin Li
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, People's Republic of China
| | - A-Wen Yang
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, People's Republic of China
| | - Bin Tang
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, People's Republic of China
| | - Zi-Juan Jian
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, People's Republic of China
| | - Yi-Ming Zhong
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, People's Republic of China
| | - Hong-Ling Li
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, People's Republic of China
| | - Yan-Ming Li
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, People's Republic of China
| | - Qun Yan
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, People's Republic of China
| | - Xiang-Hui Liang
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, People's Republic of China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, People's Republic of China
| | - Wen-En Liu
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, People's Republic of China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, People's Republic of China
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Population genomics of Escherichia coli in livestock-keeping households across a rapidly developing urban landscape. Nat Microbiol 2022; 7:581-589. [PMID: 35288654 PMCID: PMC8975746 DOI: 10.1038/s41564-022-01079-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 02/03/2022] [Indexed: 12/12/2022]
Abstract
Quantitative evidence for the risk of zoonoses and the spread of antimicrobial resistance remains lacking. Here, as part of the UrbanZoo project, we sampled Escherichia coli from humans, livestock and peri-domestic wildlife in 99 households across Nairobi, Kenya, to investigate its distribution among host species in this rapidly developing urban landscape. We performed whole-genome sequencing of 1,338 E. coli isolates and found that the diversity and sharing patterns of E. coli were heavily structured by household and strongly shaped by host type. We also found evidence for inter-household and inter-host sharing and, importantly, between humans and animals, although this occurs much less frequently. Resistome similarity was differently distributed across host and household, consistent with being driven by shared exposure to antimicrobials. Our results indicate that a large, epidemiologically structured sampling framework combined with WGS is needed to uncover strain-sharing events among different host populations in complex environments and the major contributing pathways that could ultimately drive the emergence of zoonoses and the spread of antimicrobial resistance. Phylogeography and phylogenomic analyses of E. coli isolates collected from humans and domesticated and wild animals across 99 households in Nairobi reveal strong intra-household, and lower but detectable inter-household and inter-host, strain-sharing patterns.
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Johnson JR, Clabots C, Porter SB, Bender T, Johnston BD, Thuras P. Intestinal Persistence of Colonizing Escherichia coli Strains, Especially ST131-H30, in Relation to Bacterial and Host Factors. J Infect Dis 2022; 225:2197-2207. [PMID: 34979558 PMCID: PMC9200155 DOI: 10.1093/infdis/jiab638] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 12/30/2021] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Superior gut colonization may underlie the pandemic emergence of the resistance-associated H30 subclone of Escherichia coli sequence type 131 (ST131-H30). Little is known about the associated host and bacterial characteristics, or the comparative persistence of non-ST131 intestinal E. coli. METHODS Generic and fluoroquinolone-resistant E. coli isolates from volunteers' serial fecal samples underwent clonal analysis and extensive polymerase chain reaction (PCR)-based characterization (phylogroup, selected sequence types, virulence genes). Kaplan-Meier survival analysis and Cox proportional hazards survival analysis using penalized regression (a machine-learning method) were used to identify correlates of strain persistence. RESULTS Screening of 2005 subjects at the Minneapolis VA Medical Center identified 222 subjects (117 veterans, 105 human and animal household members) for longitudinal fecal surveillance. Analysis of their 585 unique-by-subject fecal E. coli strains identified multiple epidemiological, ecological, and bacterial correlates of strain persistence. ST131-H30, a strong univariable correlate of persistence, was superseded in multivariable analysis by outpatient status, fluoroquinolone resistance, and diverse (predominantly iron uptake-related) virulence genes. CONCLUSIONS ST131-H30 exhibits exceptional intestinal persistence, possibly due to a combination of fluoroquinolone resistance and virulence factors, which may be primarily colonization factors. This identifies both likely contributors to the ST131-H30 pandemic and potential targets for interventions against it.
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Affiliation(s)
- James R Johnson
- Correspondence: James R. Johnson, MD, Infectious Diseases (111F), VA Medical Center, 1 Veterans Drive, Minneapolis, MN 55417 ()
| | - Connie Clabots
- Minneapolis Veterans Affairs Medical Center, Minneapolis, Minnesota, USA
| | - Stephen B Porter
- Minneapolis Veterans Affairs Medical Center, Minneapolis, Minnesota, USA
| | - Tricia Bender
- Minneapolis Veterans Affairs Medical Center, Minneapolis, Minnesota, USA
| | - Brian D Johnston
- Minneapolis Veterans Affairs Medical Center, Minneapolis, Minnesota, USA,University of Minnesota, Minneapolis, Minnesota, USA
| | - Paul Thuras
- Minneapolis Veterans Affairs Medical Center, Minneapolis, Minnesota, USA,University of Minnesota, Minneapolis, Minnesota, USA
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López-Cerero L, Salamanca E, Delgado-Valverde M, Rodríguez-Martínez JM, Rodríguez-Baño J, Pascual Á. Higher prevalence of CTX-M-27-producing Escherichia coli belonging to ST131 clade C1 among residents of two long-term care facilities in Southern Spain. Eur J Clin Microbiol Infect Dis 2021; 41:335-338. [PMID: 34787750 DOI: 10.1007/s10096-021-04380-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 11/11/2021] [Indexed: 12/14/2022]
Abstract
Recently, the emergence of an international lineage of the CTX-M-27-producing clade C1 of Escherichia coli ST131 is being observed. The aim is to see if this strain has also been introduced in our area. Twenty-eight (33%) out of 86 individuals from two LTCFs in Seville were found to be colonized with fluoroquinolone-resistant E. coli ST131 and 46% isolates were ESBL/pAmpC producers. C1 isolates were more common than C2 and more frequently produced blaESBL/pAmpC genes (53% vs 33%). Strain sharing was observed in 6 groups of 2-5 cases (61%). A differentiated cluster of 5 C1-CTX-M-27 isolates was found which lacked the M27PP1 region.
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Affiliation(s)
- Lorena López-Cerero
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario, Virgen Macarena, Sevilla, Spain. .,Departamento de Microbiología, Universidad de Sevilla, Sevilla, Spain.
| | - Elena Salamanca
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario, Virgen Macarena, Sevilla, Spain
| | - Mercedes Delgado-Valverde
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario, Virgen Macarena, Sevilla, Spain
| | | | - Jesús Rodríguez-Baño
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario, Virgen Macarena, Sevilla, Spain.,Departamento de Medicina, Universidad de Sevilla, Sevilla, Spain
| | - Álvaro Pascual
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario, Virgen Macarena, Sevilla, Spain.,Departamento de Microbiología, Universidad de Sevilla, Sevilla, Spain
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9
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Molecular Characteristics, Ecology, and Zoonotic Potential of Escherichia coli Strains That Cause Hemorrhagic Pneumonia in Animals. Appl Environ Microbiol 2021; 87:e0147121. [PMID: 34550758 DOI: 10.1128/aem.01471-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Hemorrhagic pneumonia (HP) is a rare but highly lethal disease, mainly of dogs and cats, caused by hemolytic Escherichia coli strains that contain cnf1 (encoding cytotoxic necrotizing factor 1). After encountering fatal HP in two dogs, we used contemporary molecular methods, including multilocus sequence typing and whole-genome sequencing, to compare the corresponding case isolates with published HP clinical isolates and newly obtained fecal E. coli isolates from 20 humans and animals in the index HP case household. We also compared the aggregated HP clinical isolates, which represented 13 discrete strains, by pulsotype with a large, private pulsotype library of diverse-source E. coli. The HP clinical isolates represented a narrow range of phylogenetic group B2 lineages (mainly sequence types 12 and 127), O types (mainly O4 and O6), and H types (mainly H5 and H31), but diverse fimH alleles (type-1 fimbriae adhesin). Their extensive, highly conserved virulence genotypes, which qualified as extraintestinal pathogenic E. coli (ExPEC), encoded diverse adhesins, toxins, iron uptake systems, and protectins. Household surveillance identified multiple HP-like fecal strains, plus abundant between-host strain sharing, including of the household's index HP strain. The pulsotype library search identified, for five HP clinical strains, same-pulsotype human and animal fecal and clinical (predominantly urine) isolates, from diverse locales and time periods. Thus, E. coli strains that cause HP derive from a narrow range of ExPEC lineages within phylogroup B2, contain multiple virulence genes other than cnf1, are shared extensively between hosts, and likely function in nature mainly as intestinal colonizers and uropathogens. IMPORTANCE This study clarifies the clonal background and extensive virulence genotypes of the E. coli strains that cause hemorrhagic pneumonia in domestic animals (mainly dogs and cats), shows that such strains circulate among animals and humans, identifies a substantial intestinal colonization component to their lifestyle, and extends their known clinical manifestations to include bacteremia and urinary tract infection. The findings place these strains better into context vis-à-vis current understandings of E. coli phylogeny, ecology, and pathogenesis; identify questions for future research; and may prove relevant for surveillance and prevention efforts.
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10
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Fox TC, Clabots C, Porter SB, Bender T, Thuras P, Colpan A, Boettcher J, Johnson JR. Bacterial "Virulence" Traits and Host Demographics Predict Escherichia coli Colonization Behaviors Within Households. Open Forum Infect Dis 2020; 7:ofaa495. [PMID: 33241068 PMCID: PMC7676507 DOI: 10.1093/ofid/ofaa495] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 10/18/2020] [Indexed: 12/22/2022] Open
Abstract
Background Although intestinal colonization precedes most extraintestinal Escherichia coli infections, colonization-promoting factors are incompletely understood. We compared within-household E. coli colonization patterns with host and bacterial traits. Methods Twenty-two veterans with a clinical E. coli isolate and their 46 human and animal household members underwent longitudinal fecal sampling. Distinct E. coli strains were characterized for phylogenetic background, virulence genes, antibiotic resistance, and colonization behaviors. Host and bacterial traits were assessed statistically as predictors of colonization behaviors. Results Among the 139 unique-by-household fecal E. coli strains, univariable predictors of colonization behavior included (i) host demographics, (ii) matching the index clinical isolate, and (iii) bacterial characteristics (2 phylogroups, 5 clonal lineages, 18 virulence genes, and molecular extraintestinal pathogenic E. coli status). Multivariable predictors of colonization behavior included veteran host, spouse host, matching the index clinical isolate, phylogroup F, ST73, hlyD (alpha hemolysin), hlyF (variant hemolysin), H7 fliC (flagellar variant), vat (vacuolating toxin), and iha (adhesin-siderophore). Conclusions Host demographics, multiple bacterial “virulence” traits, and matching the index clinical isolate predicted E. coli fecal colonization behaviors. Thus, certain bacterial characteristics may promote both colonization and pathogenicity. Future interventions directed toward such traits might prevent E. coli infections both directly and by disrupting antecedent colonization.
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Affiliation(s)
- Teresa C Fox
- Infectious Diseases, University of Minnesota, Minneapolis, Minnesota, USA
| | - Connie Clabots
- Infectious Diseases, Veterans Affairs Medical Center, Minneapolis, Minnesota, USA
| | - Stephen B Porter
- Infectious Diseases, Veterans Affairs Medical Center, Minneapolis, Minnesota, USA
| | - Tricia Bender
- Infectious Diseases, Veterans Affairs Medical Center, Minneapolis, Minnesota, USA
| | - Paul Thuras
- Mental Health Patient Service Line, Veterans Affairs Medical Center, Minneapolis, Minnesota, USA.,Department of Psychiatry, University of Minnesota Minneapolis, Minnesota, USA
| | - Aylin Colpan
- Infectious Diseases, University of Minnesota, Minneapolis, Minnesota, USA
| | - Jessica Boettcher
- Infectious Diseases, University of Minnesota, Minneapolis, Minnesota, USA
| | - James R Johnson
- Infectious Diseases, Veterans Affairs Medical Center, Minneapolis, Minnesota, USA.,Infectious Diseases, University of Minnesota Minneapolis, Minnesota, USA
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