1
|
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.
Collapse
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
| |
Collapse
|
2
|
Roth RS, Liden M, Huttner A. The urobiome in men and women: a clinical review. Clin Microbiol Infect 2023; 29:1242-1248. [PMID: 36028087 DOI: 10.1016/j.cmi.2022.08.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 08/12/2022] [Accepted: 08/13/2022] [Indexed: 11/15/2022]
Abstract
BACKGROUND Antibiotic therapy alone is unable to control recurrent urinary tract infection (UTI); uropathogens have become multiresistant, and alternative strategies are needed. Far from sterile, the urinary tract contains various low-biomass microbiota, some of whose members appear to protect against clinical UTI. OBJECTIVES This narrative review summarizes (a) the current knowledge of male and female urobiomes in healthy and diseased states, as well as their interplay among sexual partners and (b) clinical trials to date assessing probiotic and other nonantibiotic measures to reduce UTI. SOURCES We used the PubMed interface to search Ovid Medline for articles describing urogenital flora, UTI, UTI dysbiosis, the effects of sexual intercourse on urogenital flora, and clinical trials of probiotics as UTI prophylaxis. CONTENT The healthy urobiome of women contains several Lactobacillus species, some of which may impede Escherichia coli growth in the urinary tract. Although Lactobacilli have been found in male urethral microbiota, their presence in male bladder microbiota is less certain. Distal male urethral and vaginal microbiomes of male and sexual female partners influence one another, but more research is needed on the direct interplay of their full urobiomes. Clinical trials assessing the therapeutic potential of Lactobacilli have been largely underpowered and highly varied in tested formulations and routes and frequencies of administration; as such, they have failed to show a clear benefit. Faecal microbiota transplantation for recurrent Clostridium difficile infection was shown, in a retrospective study of seven patients, to reduce recurrent UTI as a side effect. IMPLICATIONS The urobiome in men and women is complex, variable, and still understudied. Although there is hope that Lactobacilli and faecal microbial transplantation could be future nonantibiotic options for recurrent UTI, both require more pharmacologic and clinical research to identify optimal preparations and routes of administration.
Collapse
Affiliation(s)
- Romain S Roth
- Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland
| | - Mia Liden
- University of Geneva, Faculty of Medicine, Geneva, Switzerland
| | - Angela Huttner
- Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland; University of Geneva, Faculty of Medicine, Geneva, Switzerland; Center for Clinical Research, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland.
| |
Collapse
|
3
|
Elankumaran P, Browning GF, Marenda MS, Reid CJ, Djordjevic SP. Close genetic linkage between human and companion animal extraintestinal pathogenic Escherichia coli ST127. CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 3:100106. [PMID: 35128493 PMCID: PMC8803956 DOI: 10.1016/j.crmicr.2022.100106] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Escherichia coli ST127, a recently emerged global pathogen noted for high virulence gene carriage, is a leading cause of urinary tract and blood stream infections. ST127 is frequently isolated from humans and companion animals; however, it is unclear if they are distinct or related populations of ST127. We performed a phylogenomic analysis of 299 E. coli ST127 of diverse epidemiological origin to characterize their population structure, genetic determinants of virulence, antimicrobial resistance, and repertoire of mobile genetic elements with a focus on plasmids. The core gene phylogeny was divided into 13 clusters, the largest of which (BAP4) contained the majority of human and companion animal origin isolates. This dominant cluster displayed genetic differences to the remainder of the phylogeny, most notably alternative gene alleles encoding important virulence factors including lipid A, flagella, and K capsule. Furthermore, numerous close genetic linkages (<30 SNPs) between human and companion animal isolates were observed within the cluster. Carriage of antimicrobial resistance genes in the collection was limited, but virulence gene carriage was extensive. We found evidence of pUTI89-like virulence plasmid carriage in over a third of isolates, localised to four of the major phylogenetic clusters. Our study supports global scale repetitive transfer of E. coli ST127 lineages between humans and companion animals, particularly within the dominant BAP4 cluster.
Collapse
Affiliation(s)
- Paarthiphan Elankumaran
- iThree Institute, School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW, Australia
| | - Glenn F. Browning
- Asia-Pacific Centre for Animal Health, Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville and Werribee, Victoria, Australia
| | - Marc S. Marenda
- Asia-Pacific Centre for Animal Health, Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville and Werribee, Victoria, Australia
| | - Cameron J. Reid
- iThree Institute, School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW, Australia
| | - Steven P. Djordjevic
- iThree Institute, School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW, Australia
| |
Collapse
|
4
|
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: 9] [Impact Index Per Article: 4.5] [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.
Collapse
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
| |
Collapse
|
5
|
Kuitunen I, Artama M, Haapanen M, Renko M. Urinary tract infections decreased in Finnish children during the COVID-19 pandemic. Eur J Pediatr 2022; 181:1979-1984. [PMID: 35098402 PMCID: PMC8801286 DOI: 10.1007/s00431-022-04389-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 09/01/2021] [Accepted: 01/22/2022] [Indexed: 11/05/2022]
Abstract
UNLABELLED Social restrictions reduced the rates of respiratory infections in 2020, but studies on the rates of urinary tract infections (UTIs) during lockdown have had conflicting results. This study aimed to report UTI incidence during the first and second waves of COVID-19 pandemic in Finland. We conducted a retrospective register-based cohort study. The whole Finnish pediatric population (children under the age of 15 years, N = 860,000) was included. The yearly and monthly incidences of UTIs per 100,000 children in 2020 were compared to that of three previous years (2017-2019) by incidence rate ratios (IRRs) with 95% confidence intervals (CIs). A total of 10,757 cystitis and 4873 pyelonephritis cases were included. The yearly incidence of cystitis was 12% lower (IRR 0.88, CI 0.83-0.94) among children aged 1-6 in 2020 and 11% (IRR 0.89, CI 0.83-0.95) lower among children aged 7-14 in 2020 compared with previous years. The yearly incidence of pyelonephritis was 16% lower (IRR 0.84, CI 0.76-0.94) among children aged 1-6. No significant decrease were observed among children aged < 1 and 7-14. CONCLUSION The incidence of cystitis and pyelonephritis during a period of social restrictions was lower than during 2017-2019, especially in children aged 1-6 years. These results raise the possibility of reducing the occurrence of urinary tract infections in children by improving hygiene measures. WHAT IS KNOWN • Social restrictions have reduced the rate of common respiratory infections globally. • Previous studies have presented a decreased or unchanged incidence of urinary tract infections during the COVID-19 pandemic. WHAT IS NEW • During the pandemic, there was a decrease in the incidence of urinary tract infections in Finnish children and the most prominent decrease was in daycare-aged children. • Improved hygiene measures and social restrictions may have influenced the transmission of uropathogens.
Collapse
Affiliation(s)
- Ilari Kuitunen
- Institute of Clinical Medicine, Department of Pediatrics, University of Eastern Finland, Kuopio, Finland. .,Department of Pediatrics, Mikkeli Central Hospital, Porrassalmenkatu 35-37, 50100, Mikkeli, Finland.
| | - Miia Artama
- grid.502801.e0000 0001 2314 6254Faculty of Social Sciences, Department of Epidemiology, Tampere University, Tampere, Finland ,grid.14758.3f0000 0001 1013 0499Finnish Institute of Health and Welfare, Tampere, Finland
| | - Marjut Haapanen
- grid.9668.10000 0001 0726 2490Institute of Clinical Medicine, Department of Pediatrics, University of Eastern Finland, Kuopio, Finland
| | - Marjo Renko
- grid.9668.10000 0001 0726 2490Institute of Clinical Medicine, Department of Pediatrics, University of Eastern Finland, Kuopio, Finland ,grid.410705.70000 0004 0628 207XDepartment of Pediatrics, Kuopio University Hospital, Kuopio, Finland ,grid.10858.340000 0001 0941 4873PEDEGO Research Unit, University of Oulu, Oulu, Finland
| |
Collapse
|
6
|
Toombs-Ruane LJ, Benschop J, French NP, Biggs PJ, Midwinter AC, Marshall JC, Chan M, Drinković D, Fayaz A, Baker MG, Douwes J, Roberts MG, Burgess SA. Carriage of Extended-Spectrum-Beta-Lactamase- and AmpC Beta-Lactamase-Producing Escherichia coli Strains from Humans and Pets in the Same Households. Appl Environ Microbiol 2020; 86:e01613-20. [PMID: 33036993 PMCID: PMC7688229 DOI: 10.1128/aem.01613-20] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 09/29/2020] [Indexed: 12/13/2022] Open
Abstract
Extended-spectrum-beta-lactamase (ESBL)- or AmpC beta-lactamase (ACBL)-producing Escherichia coli bacteria are the most common cause of community-acquired multidrug-resistant urinary tract infections (UTIs) in New Zealand. The carriage of antimicrobial-resistant bacteria has been found in both people and pets from the same household; thus, the home environment may be a place where antimicrobial-resistant bacteria are shared between humans and pets. In this study, we sought to determine whether members (pets and people) of the households of human index cases with a UTI caused by an ESBL- or ACBL-producing E. coli strain also carried an ESBL- or ACBL-producing Enterobacteriaceae strain and, if so, whether it was a clonal match to the index case clinical strain. Index cases with a community-acquired UTI were recruited based on antimicrobial susceptibility testing of urine isolates. Fecal samples were collected from 18 non-index case people and 36 pets across 27 households. Eleven of the 27 households screened had non-index case household members (8/18 people and 5/36 animals) positive for ESBL- and/or ACBL-producing E. coli strains. Whole-genome sequence analysis of 125 E. coli isolates (including the clinical urine isolates) from these 11 households showed that within seven households, the same strain of ESBL-/ACBL-producing E. coli was cultured from both the index case and another person (5/11 households) or pet dog (2/11 households). These results suggest that transmission within the household may contribute to the community spread of ESBL- or ACBL-producing E. coliIMPORTANCEEnterobacteriaceae that produce extended-spectrum beta-lactamases (ESBLs) and AmpC beta-lactamases (ACBLs) are important pathogens and can cause community-acquired illnesses, such as urinary tract infections (UTIs). Fecal carriage of these resistant bacteria by companion animals may pose a risk for transmission to humans. Our work evaluated the sharing of ESBL- and ACBL-producing E. coli isolates between humans and companion animals. We found that in some households, dogs carried the same strain of ESBL-producing E. coli as the household member with a UTI. This suggests that transmission events between humans and animals (or vice versa) are likely occurring within the home environment and, therefore, the community as a whole. This is significant from a health perspective, when considering measures to minimize community transmission, and highlights that in order to manage community spread, we need to consider interventions at the household level.
Collapse
Affiliation(s)
- Leah J Toombs-Ruane
- EpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Jackie Benschop
- EpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Nigel P French
- EpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Patrick J Biggs
- EpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Anne C Midwinter
- EpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Jonathan C Marshall
- EpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Maggie Chan
- EpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Dragana Drinković
- Microbiology Department, North Shore Hospital, Auckland, New Zealand
| | - Ahmed Fayaz
- EpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Michael G Baker
- Department of Public Health, University of Otago, Wellington, New Zealand
| | - Jeroen Douwes
- Centre for Public Health Research, Massey University, Wellington, New Zealand
| | - Mick G Roberts
- School of Natural and Mathematical Sciences, Massey University, Albany, New Zealand
| | - Sara A Burgess
- EpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| |
Collapse
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
Mfoutou Mapanguy CC, Adedoja A, Kecka LGV, Vouvoungui JC, Nguimbi E, Velavan TP, Ntoumi F. High prevalence of antibiotic-resistant Escherichia coli in Congolese students. Int J Infect Dis 2020; 103:119-123. [PMID: 33002618 DOI: 10.1016/j.ijid.2020.09.1441] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 09/19/2020] [Accepted: 09/22/2020] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Antimicrobial resistance (AMR) is of growing concern worldwide, and the AMR status in sub-Saharan Africa (SSA), including the Republic of the Congo, is largely undetermined due to a lack of real-time monitoring. As the incidence of multi-resistant Escherichia coli has been increasing in recent years, an investigation was performed to determine the antibiotic resistance of E. coli isolated from stool samples of Congolese students. Furthermore, factors associated with the carriage of resistant bacteria were investigated. METHODS A total of 339 stool samples from 339 high school students living in the Madibou area of Brazzaville, Republic of Congo, were tested for E. coli. Isolates obtained were tested for susceptibility to 10 antibiotics that are widely used in the region. RESULTS One hundred and seventy-three (51%) individuals were E. coli-positive in stool, with 61% being female students. Antimicrobial resistance was highest for ceftazidime (65%), followed by amoxicillin (57%), piperacillin-tazobactam (51%), ofloxacin (11%), azithromycin (8%), ciprofloxacin (4%), nalidixic acid (2%), and amoxicillin-clavulanic acid (1%). Antibiotic procurement from non-legalized local vendors had a significant impact on E. coli positivity and antibiotic resistance when compared to procurement from state-licensed pharmacies (p < 0.05). CONCLUSIONS The high prevalence of resistant commensal E. coli in the community justifies further investigation and urges the need for routine monitoring of antimicrobial susceptibility testing in the region.
Collapse
Affiliation(s)
- Claujens Chastel Mfoutou Mapanguy
- Fondation Congolaise pour la Recherche Médicale (FCRM), Brazzaville, Congo; Faculty of Sciences and Technology, University Marien Ngouabi, Brazzaville, Congo
| | - Ayodele Adedoja
- Fondation Congolaise pour la Recherche Médicale (FCRM), Brazzaville, Congo
| | | | | | - Etienne Nguimbi
- Faculty of Sciences and Technology, University Marien Ngouabi, Brazzaville, Congo
| | - Thirumalaisamy P Velavan
- Fondation Congolaise pour la Recherche Médicale (FCRM), Brazzaville, Congo; Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany; Faculty of Medicine, Duy Tan University, Da Nang, Viet Nam
| | - Francine Ntoumi
- Fondation Congolaise pour la Recherche Médicale (FCRM), Brazzaville, Congo; Faculty of Sciences and Technology, University Marien Ngouabi, Brazzaville, Congo; Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany.
| |
Collapse
|
9
|
Epidemiology and genotypic characterisation of dissemination patterns of uropathogenic Escherichia coli in a community. Epidemiol Infect 2020; 147:e148. [PMID: 30869058 PMCID: PMC6518783 DOI: 10.1017/s0950268819000426] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
To characterise the dissemination patterns of uropathogenic Escherichia coli (UPEC) in a community, we conducted a study utilising molecular and fundamental descriptive epidemiology. The subjects, consisted of women having community-acquired acute urinary tract infection (UTI), were enrolled in the study from 2011 to 2012. UPEC isolates were subjected to antibacterial-susceptibility testing, O serogrouping, phylotyping, multilocus-sequence typing with phylogenetic-tree analysis and pulsed-field-gel electrophoresis (PFGE). From the 209 unique positive urinary samples 166 UPEC were isolated, of which 129 were fully susceptible to the tested antibiotics. Of the 53 sequence types (STs), the four most prevalent STs (ST95, ST131, ST73 and ST357) accounted for 60% of all UPEC strains. Antimicrobial resistance was less frequently observed for ST95 and ST73 than for the others. A majority of rare STs and a few common STs constituted the diversity pattern within the population structure, which was composed of the two phylogenetically distinct clades. Eleven genetically closely related groups were determined by PFGE, which accounted for 42 of the 166 UPEC isolates, without overt geo-temporal clustering. Our results indicate that a few major lineages of UPEC, selected by unidentified factors, are disseminated in this community and contribute to a large fraction of acute UTIs.
Collapse
|
10
|
Mohammadzadeh M, Tavakoli M, Yaslianifard S, Asadi E, Golmohammadi R, Mirnejad R. Genetic diversity and antibiotic susceptibility of uropathogenic Escherichia coli isolates from kidney transplant recipients. Infect Drug Resist 2019; 12:1795-1803. [PMID: 31372004 PMCID: PMC6636430 DOI: 10.2147/idr.s200811] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 05/29/2019] [Indexed: 01/06/2023] Open
Abstract
Purpose Uropathogenic Escherichia coli (UPEC) strains are a common cause of transplant rejection, morbidity, and mortality among kidney transplant recipients. The virulence of UPEC strains differs based on their pathogenicity islands (PAIs) and susceptibility to antibiotics. The present study evaluates the clonal relationship and antibiotic susceptibility of UPEC PAI-genotypes among Escherichia coli (E. coli) isolates from kidney transplant patients. Patients and methods A total of 115 Escherichia coli (E. coli) isolates were collected from kidney transplant recipients with acute urinary tract infections (UTIs). Isolates were typed based on the presence of PAI-markers, and random amplified polymorphic DNA (RAPD). The disk diffusion method was performed for the antibiotic susceptibility pattern of isolates. Results According to the PAI-specific virulence markers, 69 (60%), 21 (18.3%), and 25 (21.7%) isolates were identified as genotypes related to UPEC 536, UPEC J96, and UPEC CFT073 strains, respectively. PAI III536 genotypes were the most prevalent genotype in this study. The findings showed a high-sensitivity to imipenem (93.9%) and nitrofurantoin (91.3%) and a low-sensitivity to trimethoprim/sulfamethoxazole (36.5%). Clonal association and similar antibiotic susceptibility pattern were seen in the PAI-related genotypes. Conclusion Due to a similar pattern of antibiotic susceptibility of these clonal groups and increased resistance to some important antibiotics such as trimethoprim/sulfamethoxazole in the treatment of urinary tract infections, especially in kidney transplant patients, the spread of these clones should be considered as a serious concern.
Collapse
Affiliation(s)
- Mohammad Mohammadzadeh
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Mahnaz Tavakoli
- Department of Medical Microbiology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Somayeh Yaslianifard
- Dietary Supplements and Probiotic Research Center, Alborz University of Medical Sciences, Alborz, Iran
| | - Ehsan Asadi
- Department of Microbiology, Faculty of Medical Sciences, Shahed University, Tehran, Iran
| | - Reza Golmohammadi
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Reza Mirnejad
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| |
Collapse
|
11
|
Flament-Simon SC, Duprilot M, Mayer N, García V, Alonso MP, Blanco J, Nicolas-Chanoine MH. Association Between Kinetics of Early Biofilm Formation and Clonal Lineage in Escherichia coli. Front Microbiol 2019; 10:1183. [PMID: 31214138 PMCID: PMC6555128 DOI: 10.3389/fmicb.2019.01183] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 05/09/2019] [Indexed: 01/27/2023] Open
Abstract
Background Escherichia coli biofilm formation has mostly been assessed in specific pathogenic E. coli groups. Here, we assessed the early biofilm formation (EBF), i.e., adhesion stage, using the BioFilm Ring Test® on 394 E. coli clinical isolates (EC) [196 consecutively isolated (CEC) in 2016 and 198 ESBL-producing E. coli (ESBLEC) isolated in 2015]. Then, biofilm-forming ability was contrasted with phylogroups, clonotypes (fumC-fimH), and sequence types (STs), all being used to define clones, virulence factors (VF), and FimB. Result According to both biofilm production levels at 2, 3, and 5 h, and EBF kinetics over 5 h, CEC and ESBLEC isolates segregated into three EBF groups: strong (G1), moderate (G2), and weak (G3) producers. At 2 h, strong producers were more frequent among CEC (n = 28; 14.3%) than among ESBLEC (n = 8; 4%) (P = 0.0004). As CEC and ESBLEC isolates showed similar individual EBF kinetics in each group, a comparison of isolate features between each group was applied to gathered CEC and ESBLEC isolates after 2 h of incubation, 2 h being the most representative time point of the CEC and ESBLEC isolate segregation into the three groups. Phylogroup B2 displayed by 51.3% of the 394 isolates was more frequent in G1 (77.8%) than in G3 (47.6%) (P = 0.0006). The 394 isolates displayed 153 clones, of which 31 included at least three isolates. B2-CH14-2-ST127, B2-CH40-22-ST131, B2-CH52-5/14-ST141, and E-CH100-96-ST362 clones were associated with G1 (P < 0.03) and accounted for 41.7% of G1 isolates. B2-CH40-30-ST131 clone was associated with G3 (P < 0.0001) and accounted for 25.5% of G3 isolates. VF mean was higher among G1 than among G3 isolates (P < 0.001). FimB-P2 variant was associated with G1 (P = 0.0011) and FimB-P1 variant was associated with G3 (P = 0.0023). Clone, some VF, and FimB were associated with EBF, with clonal lineage being able to explain 72% of the variability of EBF. Conclusion Among our 394 isolates, <10% are able to quickly and persistently produce high biofilm levels over 5 h. These isolates belong to a few clones previously described in various studies as dominant gut colonizers in mammalians and birds and comprised the B2-CH40-22-ST131 clone, i.e., the ancestor of the globally disseminated B2-CH40-30-ST131 clone that is the dominant clone among the weak biofilm producers.
Collapse
Affiliation(s)
- Saskia-Camille Flament-Simon
- Laboratorio de Referencia de Escherichia coli, Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | - Marion Duprilot
- Service de Microbiologie, Hôpital Beaujon, AP-HP, Clichy, France.,IAME, UMR 1137, INSERM, Université Paris Diderot, Paris, France
| | - Noémie Mayer
- Service de Microbiologie, Hôpital Beaujon, AP-HP, Clichy, France
| | - Vanesa García
- Laboratorio de Referencia de Escherichia coli, Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | - María Pilar Alonso
- Unidade de Microbioloxía, Hospital Universitario Lucus Augusti, Lugo, Spain
| | - Jorge Blanco
- Laboratorio de Referencia de Escherichia coli, Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | - Marie-Hélène Nicolas-Chanoine
- Service de Microbiologie, Hôpital Beaujon, AP-HP, Clichy, France.,IAME, UMR 1137, INSERM, Université Paris Diderot, Paris, France
| |
Collapse
|
12
|
Abstract
Extraintestinal pathogenic Escherichia coli (ExPEC) are important pathogens in humans and certain animals. Molecular epidemiological analyses of ExPEC are based on structured observations of E. coli strains as they occur in the wild. By assessing real-world phenomena as they occur in authentic contexts and hosts, they provide an important complement to experimental assessment. Fundamental to the success of molecular epidemiological studies are the careful selection of subjects and the use of appropriate typing methods and statistical analysis. To date, molecular epidemiological studies have yielded numerous important insights into putative virulence factors, host-pathogen relationships, phylogenetic background, reservoirs, antimicrobial-resistant strains, clinical diagnostics, and transmission pathways of ExPEC, and have delineated areas in which further study is needed. The rapid pace of discovery of new putative virulence factors and the increasing awareness of the importance of virulence factor regulation, expression, and molecular variation should stimulate many future molecular epidemiological investigations. The growing sophistication and availability of molecular typing methodologies, and of the new computational and statistical approaches that are being developed to address the huge amounts of data that whole genome sequencing generates, provide improved tools for such studies and allow new questions to be addressed.
Collapse
|
13
|
de Souza da-Silva AP, de Sousa VS, Martins N, da Silva Dias RC, Bonelli RR, Riley LW, Moreira BM. Escherichia coli sequence type 73 as a cause of community acquired urinary tract infection in men and women in Rio de Janeiro, Brazil. Diagn Microbiol Infect Dis 2017; 88:69-74. [PMID: 28214224 PMCID: PMC5392417 DOI: 10.1016/j.diagmicrobio.2017.01.024] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 01/25/2017] [Accepted: 01/31/2017] [Indexed: 12/22/2022]
Abstract
Escherichia coli clones ST131, ST69, ST95, and ST73 are frequent causes of urinary tract infections (UTI) and bloodstream infections. Specific clones and virulence profiles of E. coli causing UTI in men has been rarely described. The aim of this study was to characterize patient and clonal characteristics of community-acquired UTI caused by E. coli in men (n=12) and women (n=127) in Rio de Janeiro, Brazil, complementing a previous work. We characterized isolates in phylogenetic groups, ERIC2-PCR and PFGE types, MLST, genome similarity and virulence gene-profiles. UTI from men were more frequently caused by phylogenetic group B2 isolates (83% versus 42%, respectively, P = 0.01), a group with significantly higher virulence scores compared with women. ST73 was the predominant clone in men (50%) and the second most frequent in women (12%), with the highest virulence score (mean and median=9) among other clones. ST73 gnomes formed at least six clusters. E. coli from men carried significantly higher numbers of virulence genes, such as sfa/focDE (67% versus 27%), hlyA (58% versus 24%), cnf 1 (58% versus 16%), fyuA (100% versus 82%) and MalX (92% versus 44%), compared with isolates from women. These data suggest the predominance and spread of ST73 isolates likely relates to an abundance of virulence determinants.
Collapse
Affiliation(s)
| | - Viviane Santos de Sousa
- Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Rio de Janeiro, 21941-902, Brazil
| | - Natacha Martins
- Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Rio de Janeiro, 21941-902, Brazil
| | | | - Raquel Regina Bonelli
- Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Rio de Janeiro, 21941-902, Brazil
| | - Lee W Riley
- School of Public Health, University of California, Berkeley, CA
| | - Beatriz Meurer Moreira
- Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Rio de Janeiro, 21941-902, Brazil.
| |
Collapse
|
14
|
Johnson JR, Davis G, Clabots C, Johnston BD, Porter S, DebRoy C, Pomputius W, Ender PT, Cooperstock M, Slater BS, Banerjee R, Miller S, Kisiela D, Sokurenko EV, Aziz M, Price LB. Household Clustering of Escherichia coli Sequence Type 131 Clinical and Fecal Isolates According to Whole Genome Sequence Analysis. Open Forum Infect Dis 2016; 3:ofw129. [PMID: 27703993 PMCID: PMC5047392 DOI: 10.1093/ofid/ofw129] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 06/14/2016] [Indexed: 01/08/2023] Open
Abstract
In a whole genome-based phylogeny, clinical and fecal isolates of Escherichia coli sequence type 131 (H30R1 and H30Rx subclones) from six households formed household-specific clusters, interspersed among reference ST131 genomes. This supported the fecal-urethral hypothesis and confirmed within-household strain sharing. Background. Within-household sharing of strains from the resistance-associated H30R1 and H30Rx subclones of Escherichia coli sequence type 131 (ST131) has been inferred based on conventional typing data, but it has been assessed minimally using whole genome sequence (WGS) analysis. Methods. Thirty-three clinical and fecal isolates of ST131-H30R1 and ST131-H30Rx, from 20 humans and pets in 6 households, underwent WGS analysis for comparison with 52 published ST131 genomes. Phylogenetic relationships were inferred using a bootstrapped maximum likelihood tree based on core genome sequence polymorphisms. Accessory traits were compared between phylogenetically similar isolates. Results. In the WGS-based phylogeny, isolates clustered strictly by household, in clades that were distributed widely across the phylogeny, interspersed between H30R1 and H30Rx comparison genomes. For only 1 household did the core genome phylogeny place epidemiologically unlinked isolates together with household isolates, but even there multiple differences in accessory genome content clearly differentiated these 2 groups. The core genome phylogeny supported within-household strain sharing, fecal-urethral urinary tract infection pathogenesis (with the entire household potentially providing the fecal reservoir), and instances of host-specific microevolution. In 1 instance, the household's index strain persisted for 6 years before causing a new infection in a different household member. Conclusions. Within-household sharing of E coli ST131 strains was confirmed extensively at the genome level, as was long-term colonization and repeated infections due to an ST131-H30Rx strain. Future efforts toward surveillance and decolonization may need to address not just the affected patient but also other human and animal household members.
Collapse
Affiliation(s)
- James R Johnson
- Minneapolis Veterans Affairs Health Care System, Minnesota; University of Minnesota, Minneapolis
| | - Gregg Davis
- George Washington University , Washington, District of Columbia
| | - Connie Clabots
- Minneapolis Veterans Affairs Health Care System , Minnesota
| | - Brian D Johnston
- Minneapolis Veterans Affairs Health Care System, Minnesota; University of Minnesota, Minneapolis
| | - Stephen Porter
- Minneapolis Veterans Affairs Health Care System , Minnesota
| | | | | | - Peter T Ender
- St. Luke's University Hospital and Health Network , Bethlehem, Pennsylvania
| | | | | | | | | | | | | | - Maliha Aziz
- George Washington University , Washington, District of Columbia
| | - Lance B Price
- George Washington University , Washington, District of Columbia
| |
Collapse
|