scholarly journals Cluster analysis of resistance combinations in Escherichia coli from different human and animal populations in Germany 2014-2017

PLoS ONE ◽  
2021 ◽  
Vol 16 (1) ◽  
pp. e0244413
Author(s):  
Beneditta Suwono ◽  
Tim Eckmanns ◽  
Heike Kaspar ◽  
Roswitha Merle ◽  
Benedikt Zacher ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Cluster Analysis ◽  
One Health ◽  
Average Distance ◽  
Companion Animals ◽  
Clinical Isolates ◽  
Human Populations ◽  
Animal Populations ◽  
Routine Surveillance ◽  
Animal Isolates

Recent findings on Antibiotic Resistance (AR) have brought renewed attention to the comparison of data on AR from human and animal sectors. This is however a major challenge since the data is not harmonized. This study performs a comparative analysis of data on resistance combinations in Escherichia coli (E. coli) from different routine surveillance and monitoring systems for human and different animal populations in Germany. Data on E. coli isolates were collected between 2014 and 2017 from human clinical isolates, non-clinical animal isolates from food-producing animals and food, and clinical animal isolates from food-producing and companion animals from national routine surveillance and monitoring for AR in Germany. Sixteen possible resistance combinations to four antibiotics—ampicillin, cefotaxime, ciprofloxacin and gentamicin–for these populations were used for hierarchical clustering (Euclidian and average distance). All analyses were performed with the software R 3.5.1 (Rstudio 1.1.442). Data of 333,496 E. coli isolates and forty-one different human and animal populations were included in the cluster analysis. Three main clusters were detected. Within these three clusters, all human populations (intensive care unit (ICU), general ward and outpatient care) showed similar relative frequencies of the resistance combinations and clustered together. They demonstrated similarities with clinical isolates from different animal populations and most isolates from pigs from both non-clinical and clinical isolates. Isolates from healthy poultry demonstrated similarities in relative frequencies of resistance combinations and clustered together. However, they clustered separately from the human isolates. All isolates from different animal populations with low relative frequencies of resistance combinations clustered together. They also clustered separately from the human populations. Cluster analysis has been able to demonstrate the linkage among human isolates and isolates from various animal populations based on the resistance combinations. Further analyses based on these findings might support a better one-health approach for AR in Germany.

scholarly journals Cluster analysis of resistance combinations in Escherichia coli from different human and animal populations in Germany 2014-2017

2020 ◽  
Author(s):  
Beneditta Suwono ◽  
Tim Eckmanns ◽  
Heike Kaspar ◽  
Roswitha Merle ◽  
Benedikt Zacher ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Cluster Analysis ◽  
Average Distance ◽  
Companion Animals ◽  
Clinical Isolates ◽  
Human Populations ◽  
E Coli ◽  
Animal Populations ◽  
Routine Surveillance ◽  
Animal Isolates

Abstract Recent findings on Antibiotic Resistance (AR) have brought renewed attention to the comparison of data on AR from human and animal sectors. This is however, a major challenge since the data is not harmonized. This study performs a comparative analysis of data on resistance combinations in Escherichia coli (E. coli) from different routine surveillance and monitoring systems for human and different animal populations in Germany. Data on E. coli isolates were collected between 2014 and 2017 from human clinical isolates, non-clinical animal isolates from food-producing animals and food, and clinical animal isolates from food-producing and companion animals from national routine surveillance and monitoring for AR in Germany. Sixteen possible resistance combinations to four antibiotics - ampicillin, cefotaxime, ciprofloxacin and gentamicin – for these populations were used for hierarchical clustering (Euclidian and average distance). All analyses were performed with the software R 3.5.1 (Rstudio 1.1.442). Data of 333,496 E. coli isolates and forty-one different human and animal populations were included in the cluster analysis. Three main clusters were detected. Within these three clusters, all human populations (intensive care unit (ICU), general ward and outpatient care) showed similar relative frequencies of the resistance combinations and clustered together. They demonstrated similarities with clinical isolates from different animal populations and most isolates from pigs from both non-clinical and clinical isolates. Isolates from healthy poultry demonstrated similarities in relative frequencies of resistance combinations and clustered together. However, they clustered separately from the human isolates. All isolates from different animal populations with low relative frequencies of resistance combinations clustered together and likewise separately from the human populations. Cluster analysis has been able to demonstrate the linkage among human isolates and isolates from various animal populations based on the resistance combinations. Further analyses based on these findings might promote a better one-health approach for AR in Germany.

scholarly journals Cluster analysis of resistance combinations in Escherichia coli from different human and animal populations in Germany 2014-2017

2020 ◽  
Author(s):  
Beneditta Suwono ◽  
Tim Eckmanns ◽  
Heike Kaspar ◽  
Roswitha Merle ◽  
Benedikt Zacher ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Cluster Analysis ◽  
Average Distance ◽  
Companion Animals ◽  
Clinical Isolates ◽  
Human Populations ◽  
E Coli ◽  
Animal Populations ◽  
Routine Surveillance ◽  
Resistance Patterns

Abstract Background Recent findings on Antibiotic Resistance (AR) have brought renewed attention to the comparison of data on AR from human and animal sectors. This is however, a major challenge since the data is not harmonized. This study performs a comparative analysis of phenotypical AR data from different routine surveillance and monitoring systems in Germany. Escherichia coli data were used as a model to describe the similarities based on the resistance patterns in human and different animal populations in Germany. Method: Data on E. coli isolates were collected from 2014 to 2017 from human clinical isolates, non-clinical isolates from food-producing animals and food, and clinical isolates from food-producing and companion animals from national routine surveillance and monitoring for AR in Germany. Four antibiotics - ampicillin, cefotaxime, ciprofloxacin and gentamicin - were chosen for the analysis. Resistant isolates were defined according to EUCAST clinical breakpoints for humans. Based on the 16 possible resistance combinations to these four antibiotics, cluster analysis was performed using hierarchical clustering with Euclidian and average distance. All analyses were performed with the software “R”. Result Data of 333,496 E. coli isolates were included in this study. Forty-one different human and animal populations were included in the cluster analysis. Three main clusters were detected. Within these three clusters, all human populations (intensive care unit (ICU), general ward and outpatient care) showed similar relative frequencies of the resistance combinations and clustered together. They demonstrated similarities with clinical isolates from different animal populations and most isolates from pigs from both non-clinical and clinical isolates. Isolates from healthy poultry demonstrated similarities in relative frequencies of resistance combinations and clustered together. However, they clustered separately from the human isolates. All isolates from different animal populations with low relative frequencies of resistance combinations clustered together and likewise separately from the human populations. Conclusion Cluster analysis facilitated the comparison of phenotypical AR data across human and animal sectors. It indicated linkage among human isolates and with isolates from various animal populations based on the resistance combinations in E. coli. Further analyses based on these findings might promote a better one-health approach for AR in Germany.

scholarly journals An ecological approach to assessing the epidemiology of antimicrobial resistance in animal and human populations

2011 ◽  
Vol 279 (1733) ◽  
pp. 1630-1639 ◽  
Author(s):  
Alison E. Mather ◽  
Louise Matthews ◽  
Dominic J. Mellor ◽  
Richard Reeve ◽  
Matthew J. Denwood ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Ecological Approach ◽  
Human Populations ◽  
Ecological Diversity ◽  
Animal Population ◽  
Current Policy ◽  
Animal Populations ◽  
Two Populations ◽  
Animal Isolates

We examined long-term surveillance data on antimicrobial resistance (AMR) in Salmonella Typhimurium DT104 (DT104) isolates from concurrently sampled and sympatric human and animal populations in Scotland. Using novel ecological and epidemiological approaches to examine diversity, and phenotypic and temporal relatedness of the resistance profiles, we assessed the more probable source of resistance of these two populations. The ecological diversity of AMR phenotypes was significantly greater in human isolates than in animal isolates, at the resolution of both sample and population. Of 5200 isolates, there were 65 resistance phenotypes, 13 unique to animals, 30 unique to humans and 22 were common to both. Of these 22, 11 were identified first in the human isolates, whereas only five were identified first in the animal isolates. We conclude that, while ecologically connected, animals and humans have distinguishable DT104 communities, differing in prevalence, linkage and diversity. Furthermore, we infer that the sympatric animal population is unlikely to be the major source of resistance diversity for humans. This suggests that current policy emphasis on restricting antimicrobial use in domestic animals may be overly simplistic. While these conclusions pertain to DT104 in Scotland, this approach could be applied to AMR in other bacteria–host ecosystems.

scholarly journals A Shared Population of Epidemic Methicillin-Resistant Staphylococcus aureus 15 Circulates in Humans and Companion Animals

mBio ◽  
2014 ◽  
Vol 5 (3) ◽  
Author(s):  
Ewan M. Harrison ◽  
Lucy A. Weinert ◽  
Matthew T. G. Holden ◽  
John J. Welch ◽  
Katherine Wilson ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
United Kingdom ◽  
One Health ◽  
Companion Animals ◽  
Methicillin Resistant ◽  
Content Type ◽  
The United Kingdom ◽  
Animal Populations ◽  
The One ◽  
Veterinary Hospital

ABSTRACTMethicillin-resistantStaphylococcus aureus(MRSA) is a global human health problem causing infections in both hospitals and the community. Companion animals, such as cats, dogs, and horses, are also frequently colonized by MRSA and can become infected. We sequenced the genomes of 46 multilocus sequence type (ST) 22 MRSA isolates from cats and dogs in the United Kingdom and compared these to an extensive population framework of human isolates from the same lineage. Phylogenomic analyses showed that all companion animal isolates were interspersed throughout the epidemic MRSA-15 (EMRSA-15) pandemic clade and clustered with human isolates from the United Kingdom, with human isolates basal to those from companion animals, suggesting a human source for isolates infecting companion animals. A number of isolates from the same veterinary hospital clustered together, suggesting that as in human hospitals, EMRSA-15 isolates are readily transmitted in the veterinary hospital setting. Genome-wide association analysis did not identify any host-specific single nucleotide polymorphisms (SNPs) or virulence factors. However, isolates from companion animals were significantly less likely to harbor a plasmid encoding erythromycin resistance. When this plasmid was present in animal-associated isolates, it was more likely to contain mutations mediating resistance to clindamycin. This finding is consistent with the low levels of erythromycin and high levels of clindamycin used in veterinary medicine in the United Kingdom. This study furthers the “one health” view of infectious diseases that the pathogen pool of human and animal populations are intrinsically linked and provides evidence that antibiotic usage in animal medicine is shaping the population of a major human pathogen.IMPORTANCEMethicillin-resistantStaphylococcus aureus(MRSA) is major problem in human medicine. Companion animals, such as cats, dogs, and horses, can also become colonized and infected by MRSA. Here, we demonstrate that a shared population of an important and globally disseminated lineage of MRSA can infect both humans and companion animals without undergoing host adaptation. This suggests that companion animals might act as a reservoir for human infections. We also show that the isolates from companion animals have differences in the presence of certain antibiotic resistance genes. This study furthers the “one health” view of infectious diseases by demonstrating that the pool of MRSA isolates in the human and animal populations are shared and highlights how different antibiotic usage patterns between human and veterinary medicine can shape the population of bacterial pathogens.

scholarly journals Integrated veterinary-medical activity on characterization of shigatoxin producing Escherichia coli

2019 ◽  
Vol 29 (Supplement_4) ◽  
Author(s):  
B Bertasi ◽  
G Finazzi ◽  
R Colombo ◽  
C Vignati ◽  
A Dodaro ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Food Samples ◽  
Clinical Isolates ◽  
Health Concern ◽  
O157 Strain ◽  
Pathogenic Potential ◽  
Source Of Infection ◽  
Uremic Syndrome ◽  
Animal Isolates

Abstract Background Shiga toxin-producing Escherichia coli (STEC) are an important public health concern as they cause severe conditions (bloody diarrhea and hemolytic uremic syndrome - HUS) and have epidemic potential. Cattle are the main reservoir for the highly virulent STEC O157 strain, and other HUS-associated non-O157 strains. This study aimed to characterize strains from animals and humans and to compare their molecular profiles. Animal isolates were tested for the presence of virulence factors correlated to their pathogenic potential. Methods 74 STEC human isolates from 43 clinical cases (sporadic or epidemic) and 270 animal isolates from feces from 62 cattle farms were collected. Epidemiological investigation to collect environmental and suspected food samples was carried out for 22 cases. All isolates were typed with PFGE and their serotype was defined by Real-Time PCR. Animal isolates were also tested for the presence of subAB, saa, tia, cfk, adfO, hlyA, efaI1-lifA5’3’, and toxB virulence genes. Results O157 was detected in 44% of human cases, other relevant serogroups O26, O111, O103, O145 in 21, 9, 5 and 5% of cases, respectively. The source of infection was identified in one case (cheese contaminated by a O157 strain). Among animal isolates 2, 0.7, 0.7 and 0.3% were identified as O157, O11, O113, and O145, respectively. PFGE highlighted a high heterogeneicity among animal strains, however no pulsotype common to cattle and clinical isolates was found. adfO, cfk, efaI1-lifA5’3’ and toxB were found significantly correlated to eae (intimin). Conclusions Human and cattle strains were not correlated, however STEC diversity in cattle was very high and included some strains potentially pathogenic to humans. For this reason, upholding an integrated surveillance is very important. Key messages Serotypes relevant to human health were found in cattle in a small but not negligible frequence. No direct correlation was found between animal and clinical isolates.

scholarly journals Escherichia coli as Possible Agents of Spread of Multidrug Resistance in Port Harcourt, Rivers State.

2019 ◽  
Vol 4 (1) ◽  
pp. 16-21
Author(s):  
Kome Otokunefor ◽  
Victor Ogechi Osogho ◽  
Chijindu Precious Nwankwo
Keyword(s):  
Escherichia Coli ◽  
Antibiotic Resistance ◽  
Multidrug Resistance ◽  
Clinical Isolates ◽  
Human Populations ◽  
Plasmid Curing ◽  
Port Harcourt ◽  
Genes Encoding ◽  
Mar Index ◽  
High Level

AbstractMultidrug resistance (MDR) continues to be a growing global issue. The problem of MDR is fuelled in part by the spread of the genes encoding resistance horizontally which is linked particularly to conjugation involving plasmids. Studies have demonstrated the presence of plasmids in drug resistant isolates, few have shown a link between these plasmids and drug resistance via plasmid curing especially in our locale. This study set out to explore this link inEscherichia coliisolates from Port Harcourt, Nigeria. Plasmid curing was done on a selection of clinical and non-clinical bacteria using acridine orange and antibiotic susceptibility testing carried out on both cured and uncured variants. Data generated was analysed to ascertain the multiple antibiotic resistance (MAR) index and MDR of each isolate. Data was then compared to ascertain effects of plasmid curing on antibiotic resistance of the isolates. Results revealed a decrease in resistance to 7 of 8 antibiotics following plasmid curing. The highest change was noted in ceftazidime (40%), followed by ofloxacin (26.7%). Plasmid curing caused a shift in MAR index values of isolates from higher to lower indices. At MAR index values of ≤0.25 occurrence increased from 5% to 36.7% while at MAR index values ≥0.75, occurrence reduced from 29.9% to 10.0%. A reduction in the degree of MDR was noted (from 55% to 36.7%). Strikingly, the reduction in MDR level of non-clinical isolates was 30% as opposed to 3.4% in the clinical isolates. This study shows a link between plasmids and antibiotic resistance. For the non-clinical isolates, the high-level link between MDR and plasmid carriage could indicate a higher use of antimicrobials in non-clinical rather than clinical settings. Additionally, it could be an indicator for a higher risk of the transfer of MDR determinants from non-clinical sources to human populations in our locale.

scholarly journals Monitoring the patterns of submission and presence of tick-borne pathogens in Ixodes scapularis collected from humans and companion animals in Ontario, Canada (2011–2017)

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Mark P. Nelder ◽  
Curtis B. Russell ◽  
Antonia Dibernardo ◽  
Katie M. Clow ◽  
Steven Johnson ◽  
...  
Keyword(s):  
Borrelia Burgdorferi ◽  
Regression Models ◽  
Ixodes Scapularis ◽  
Companion Animals ◽  
Companion Animal ◽  
Babesia Microti ◽  
Blacklegged Tick ◽  
Host Type ◽  
Animal Populations ◽  
Pathogen Prevalence

Abstract Background The universal nature of the human–companion animal relationship and their shared ticks and tick-borne pathogens offers an opportunity for improving public and veterinary health surveillance. With this in mind, we describe the spatiotemporal trends for blacklegged tick (Ixodes scapularis) submissions from humans and companion animals in Ontario, along with pathogen prevalence. Methods We tested tick samples submitted through passive surveillance (2011–2017) from humans and companion animals for Borrelia burgdorferi, Borrelia miyamotoi, Anaplasma phagocytophilum and Babesia microti. We describe pathogen prevalence in ticks from humans and from companion animals and constructed univariable Poisson and negative binomial regression models to explore the spatiotemporal relationship between the rates of tick submissions by host type. Results During the study, there were 17,230 blacklegged tick samples submitted from humans and 4375 from companion animals. Tick submission rates from companion animals were higher than expected in several public health units (PHUs) lacking established tick populations, potentially indicating newly emerging populations. Pathogen prevalence in ticks was higher in PHUs where established blacklegged tick populations exist. Borrelia burgdorferi prevalence was higher in ticks collected from humans (maximum likelihood estimate, MLE = 17.5%; 95% confidence interval, CI 16.97–18.09%) than from companion animals (9.9%, 95% CI 9.15–10.78%). There was no difference in pathogen prevalence in ticks by host type for the remaining pathogens, which were found in less than 1% of tested ticks. The most common co-infection B. burgdorferi + B. miyamotoi occurred in 0.11% of blacklegged ticks from humans and animals combined. Borrelia burgdorferi prevalence was higher in unengorged (21.9%, 95% CI 21.12–22.65%) than engorged ticks (10.0%, 95% CI 9.45–10.56%). There were no consistent and significant spatiotemporal relationships detected via regression models between the annual rates of submission of each host type. Conclusions While B. burgdorferi has been present in blacklegged ticks in Ontario for several decades, other tick-borne pathogens are also present at low prevalence. Blacklegged tick and pathogen surveillance data can be used to monitor risk in human and companion animal populations, and efforts are under consideration to unite surveillance efforts for the different target populations. Graphic Abstract

scholarly journals Virulence Properties of mcr-1-Positive Escherichia coli Isolated from Retail Poultry Meat

2021 ◽  
Vol 9 (2) ◽  
pp. 308
Author(s):  
Michaela Kubelová ◽  
Ivana Koláčková ◽  
Tereza Gelbíčová ◽  
Martina Florianová ◽  
Alžběta Kalová ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Poultry Meat ◽  
Human Populations ◽  
E Coli ◽  
Antimicrobial Resistance Genes ◽  
Mlst Type ◽  
On Line ◽  
Sequence Types

The great plasticity and diversity of the Escherichia coli genome, together with the ubiquitous occurrence, make E. coli a bacterium of world-wide concern. Of particular interest are pathogenic strains and strains harboring antimicrobial resistance genes. Overlapping virulence-associated traits between avian-source E. coli and human extraintestinal pathogenic E. coli (ExPEC) suggest zoonotic potential and safety threat of poultry food products. We analyzed whole-genome sequencing (WGS) data of 46 mcr-1-positive E. coli strains isolated from retail raw meat purchased in the Czech Republic. The investigated strains were characterized by their phylogroup—B1 (43%), A (30%), D (11%), E (7%), F (4%), B2 (2%), C (2%), MLST type, and serotype. A total of 30 multilocus sequence types (STs), of which ST744 was the most common (11%), were identified, with O8 and O89 as the most prevalent serogroups. Using the VirulenceFinder tool, 3 to 26 virulence genes were detected in the examined strains and a total of 7 (15%) strains met the pathogenic criteria for ExPEC. Four strains were defined as UPEC (9%) and 18 (39%) E. coli strains could be classified as APEC. The WGS methods and available on-line tools for their evaluation enable a comprehensive approach to the diagnosis of virulent properties of E. coli strains and represent a suitable and comfortable platform for their detection. Our results show that poultry meat may serve as an important reservoir of strains carrying both virulence and antibiotic resistance genes for animal and human populations.

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