Category Archives: ESBL

Research – Animal petting zoos as sources of Shiga toxin‐producing Escherichia coli, Salmonella and extended‐spectrum β‐lactamase (ESBL)‐producing Enterobacteriaceae

Wiley Online

Animal petting zoos and farm fairs provide the opportunity for children and adults to interact with animals, but contact with animals carries a risk of exposure to zoonotic pathogens and antimicrobial‐resistant bacteria. The aim of this study was to assess the occurrence of Shiga toxin‐producing Escherichia coli (STEC), Salmonella, extended‐spectrum β‐lactamase (ESBL)‐producing Enterobacteriaceae and methicillin‐resistant Staphylococcus aureus (MRSA) in animal faeces from six animal petting zoos and one farm fair in Switzerland. Furthermore, hygiene facilities on the venues were evaluated. Of 163 faecal samples, 75 contained stx1, stx2 or stx1/stx2 genes, indicating the presence of STEC. Samples included faeces from sika deer (100%), sheep (92%), goats (88%), mouflons (80%), camels (62%), llamas (50%), yaks (50%), pigs (29%) and donkeys (6%), whereas no stx genes were isolated from faeces of calves, guinea pigs, hens, ostriches, ponies, zebras or zebus. Salmonella enterica subsp. enterica serovar Stourbridge (S. Stourbridge) was detected in faecal samples from camels. A total of four ESBL‐producing E. coli strains were isolated from faeces of goats, camels and pigs. PCR and sequencing identified the presence of blaCTX‐M‐15 in three and blaCTX‐M‐65 in one Ecoli. Antimicrobial resistance profiling using the disk diffusion method revealed two multidrug‐resistant (MDR) E. coli with resistance to ciprofloxacin, gentamicin and azithromycin, all of which are critically important drugs for human medicine. Multilocus sequence typing identified E. coli ST162, E. coli ST2179, extraintestinal high‐risk E. coli ST410 and E. coli ST4553, which belongs to the emerging extraintestinal clonal complex (CC) 648. No MRSA was detected. On all animal petting venues, there were inadequacies with regard to access to hygiene information and handwashing hygiene facilities. This study provides data that underscore the importance of hygiene measures to minimize the risk of transmission of zoonotic pathogens and MDR, ESBL‐producing E. coli to visitors of animal petting venues.

Research – Bacteria Broadly-Resistant to Last Resort Antibiotics Detected in Commercial Chicken Farms


Resistance to last resort antibiotics in bacteria is an emerging threat to human and animal health. It is important to identify the source of these antimicrobial resistant (AMR) bacteria that are resistant to clinically important antibiotics and evaluate their potential transfer among bacteria. The objectives of this study were to (i) detect bacteria resistant to colistin, carbapenems, and β-lactams in commercial poultry farms, (ii) characterize phylogenetic and virulence markers of E. coli isolates to potentiate virulence risk, and (iii) assess potential transfer of AMR from these isolates via conjugation. Ceca contents from laying hens from conventional cage (CC) and cage-free (CF) farms at three maturity stages were randomly sampled and screened for extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae, carbapenem-resistant Acinetobacter (CRA), and colistin resistant Escherichia coli (CRE) using CHROMagar™ selective media. We found a wide-spread abundance of CRE in both CC and CF hens across all three maturity stages. Extraintestinal pathogenic Escherichia coli phylogenetic groups B2 and D, as well as plasmidic virulence markers iss and iutA, were widely associated with AMR E. coli isolates. ESBL-producing Enterobacteriaceae were uniquely detected in the early lay period of both CC and CF, while multidrug resistant (MDR) Acinetobacter were found in peak and late lay periods of both CC and CF. CRA was detected in CF hens only. blaCMY was detected in ESBL-producing E. coli in CC and CF and MDR Acinetobacter spp. in CC. Finally, the blaCMY was shown to be transferrable via an IncK/B plasmid in CC. The presence of MDR to the last-resort antibiotics that are transferable between bacteria in food-producing animals is alarming and warrants studies to develop strategies for their mitigation in the environment. View Full-Text

Research – Competitive Exclusion Prevents Colonization and Compartmentalization Reduces Transmission of ESBL-Producing Escherichia coli in Broilers


Image CDC

Extended spectrum beta-lactamase (ESBL)-producing bacteria are resistant to extended-spectrum cephalosporins and are common in broilers. Interventions are needed to reduce the prevalence of ESBL-producing bacteria in the broiler production pyramid. This study investigated two different interventions. The effect of a prolonged supply of competitive exclusion (CE) product and compartmentalization on colonization and transmission, after challenge with a low dose of ESBL-producing Escherichia coli, in broilers kept under semi-field conditions, were examined. One-day-old broilers (Ross 308) (n = 400) were housed in four experimental rooms, subdivided in one seeder (S/C1)-pen and eight contact (C2)-pens. In two rooms, CE product was supplied from day 0 to 7. At day 5, seeder-broilers were inoculated with E. coli strain carrying blaCTX–M–1 on plasmid IncI1 (CTX-M-1-E. coli). Presence of CTX-M-1-E. coli was determined using cloacal swabs (day 5–21 daily) and cecal samples (day 21). Time until colonization and cecal excretion (log10 CFU/g) were analyzed using survival analysis and linear regression. Transmission coefficients within and between pens were estimated using maximum likelihood. The microbiota composition was assessed by 16S ribosomal RNA gene amplicon sequencing in cecal content of broilers on days 5 and 21. None of the CE broilers was CTX-M-1-E. coli positive. In contrast, in the untreated rooms 187/200 of the broilers were CTX-M-1-E. coli positive at day 21. Broilers in C2-pens were colonized later than seeder-broilers (Time to event Ratio 3.53, 95% CI 3.14 to 3.93). The transmission coefficient between pens was lower than within pens (3.28 × 10–4 day–2, 95% CI 2.41 × 10–4 to 4.32 × 10–4 vs. 6.12 × 10–2 day–2, 95% CI 4.78 × 10–2 to 7.64 × 10–2). The alpha diversity of the cecal microbiota content was higher in CE broilers than in control broilers at days 5 and 21. The supply of a CE product from day 0 to 7 prevented colonization of CTX-M-1-E. coli after challenge at day 5, likely as a result of CE induced effects on the microbiota composition. Furthermore, compartmentalization reduced transmission rate between broilers. Therefore, a combination of compartmentalization and supply of a CE product may be a useful intervention to reduce transmission and prevent colonization of ESBL/pAmpC-producing bacteria in the broiler production pyramid.

Research – Netherlands – Surveillance zoonoses in broilers 2018-2019


Animals can carry pathogens that can cause disease in humans. The diseases which they cause are known as zoonoses. In 2018 and 2019 the National Institute for Public Health and the Environment (RIVM) and the Netherlands Food and Consumer Product Safety Authority [Netherlands Food and Consumer Product Safety Authority] (NVWA) investigated how often some of these pathogens occurred in broilers. This study involved broilers at 198 farms as well as 132 livestock farmers, family members and employees. RIVM assessed whether the same pathogens also occurred in these persons. Most of these pathogens usually cause diarrhoea, but the infections can sometimes be more severe. ESBL-producing bacteria were also assessed, as they are resistant to an important group of antibiotics.

A number of pathogens occur frequently in the investigated broilers. They are present in the animals’ intestines and therefore in the manure as well. Meat can become contaminated in the slaughterhouse if it comes into direct contact with the manure. People can prevent an infection by only eating chicken that has been thoroughly cooked. It is also important to prevent other food from coming into contact with raw meat.

Of the pathogens investigated, ESBL-producing bacteria were found most often, namely in the broilers on 36% of the farms. Among livestock farmers and family members, these bacteria were found in 7% of participants. This is comparable to the percentage in the general Dutch population.

Campylobacter was found on 32% of broiler farms. This is comparable to the numbers from Campylobacter surveillance conducted between 1999 and 2002. Campylobacter was also found in two of the human participants.

Salmonella surveillance is carried out on all broiler farms according to European legislation. Salmonella was reported in broilers from 11% of the farms. The types of Salmonella bacteria identified are those that can cause diarrhoea in people. Salmonella was also found in one human participant.

STEC and Listeria were found on very few broiler farms. These bacteria were detected on 1% (Listeria) or less (STEC) of the investigated farms.

Research – Assessing the microbiological quality of raw goats’ and ewes’ tank milk samples in Switzerland

Science Direct

In recent years, popularity of raw milk has increased in many industrialised countries.

This study (i) enumerated total viable counts (TVC) and Escherichia coli counts, (ii) assessed prevalence of Staphylococcus (S.aureusSalmonella spp. and STEC, (iii) screened for methicillin resistant S. aureus (MRSA) and extended-spectrum β-lactamases (ESBL)-producing Enterobacteriaceae in sheep and goat tank milk samples collected throughout Switzerland and (iv) provided further strain characteristics on isolated pathogens and MRSA. One hundred and twenty-three tank milk samples from 116 farms were analysed. The median TVC was 3.8 log cfu mL-1E. coli was detected in 16 (13.0%) and S. aureus in 18 (14.6%) samples. Polymerase chain reaction for stx genes was positive in 14 (11.4%) samples. MRSA were isolated from 4 (3.3%) samples. Salmonella spp. and ESBL-producing Enterobacteriaceae were not isolated.

Research – UK study: Food not likely source of drug resistant E coli.


CDC E.coli

Image CDC

A large genomic epidemiology study by scientists in the United Kingdom has found that most bloodstream infections caused by drug-resistant Escherichia coli involve human-associated strains of the pathogen, with little contribution from the food chain.

The study, published yesterday in The Lancet Infectious Diseases, found that the extended-spectrum beta-lactamase-producing (ESBL) E coli sequence type (ST) 131 was the predominant strain found in bloodstream isolates, as well as in samples collected from human feces and sewage, while isolates from meat, veterinary diagnostic samples, and farm runoff were dominated by other ESBL E coli sequence types. Few drug-resistant E coli strains were shared among the animal and human isolates.

The authors of the study say the findings suggest that while ESBL E coli strains are widespread in humans, animals, and the environment, there’s little crossover between these strains, and efforts to reduce invasive ESBL E coli infections should focus on limiting human transmission.

Research – Prevalence of Extended-Spectrum β-Lactamase–Producing Bacteria on Fresh Vegetables in Japan

Journal of Food Protection


Extended-spectrum β-lactamase (ESBL)–producing bacteria are spreading rapidly, posing a threat to human and animal health. Contamination of vegetables with antimicrobial-resistant bacteria or those harboring antimicrobial resistance genes or a combination of both presents a potential route of transmission to humans. Therefore, the aim of this study was to determine the prevalence of these bacteria in fresh vegetables in Japan. A total of 130 samples of fresh vegetables were collected from seven supermarkets in Japan. The predominant genus detected was Pseudomonas spp., including 10 ESBL-producing strains, isolated from 10 (7.7%) of the vegetable samples. Two ESBL genes were detected, blaTEM-116 (n = 7) and blaSHV-12 (n = 3), and some of these strains were resistant to multiple antibiotics. Because vegetables are often consumed raw, those contaminated with ESBL producers could represent an important route of transmission to humans in Japan. Thus, more stringent hygiene measures and monitoring are required to prevent transmission via this source.

  • Retail vegetables in Japan are not as frequently contaminated by animal feces.

  • ESBL-producing bacteria were isolated from vegetables (7.7%).

  • Two ESBL genes (blaTEM-116 and blaSHV-12) were detected in vegetables.

UK- Scotland – Levels of antimicrobial resistant E. coli in UK retail meat remain low


CDC E.coli


The Food Standards Agency (FSA) have published the Year Three results of an EU survey commissioned to assess the frequency of certain types of antimicrobial resistant (AMR) E. coli in raw UK retail pork and beef.

Year Three of the survey was carried out between January and December 2017 during which 314 beef and 310 pork samples were purchased from retail premises in England, Scotland, Wales and Northern Ireland and tested for specific types of AMR E. coli.

The survey generates baseline data on certain types of AMR E. coli found in retail meat in the UK, which informs assessment of the risks found, and steps needed be taken, in order to reduce exposure to AMR.

Overall, the results showed that less than 1% of the samples were positive for ESBL or AmpC E. coli, which are specific types of AMR. These results are similar to what was found in Year One of the survey. However, one beef sample was found to be contaminated with an E. coli containing the mcr-1 gene, which confers resistance to the antibiotic colistin.

[Source: FSA, 13 November 2018.…]

Research – Routine antibiotic therapy in dogs increases the detection of antimicrobial-resistant faecal Escherichia coli

Academic Oup



Antimicrobial resistance (AMR) is a critical health problem, with systemic antimicrobial therapy driving development of AMR across the host spectrum.


This study compares longitudinal carriage, at multiple timepoints, of AMR faecal Escherichia coli in dogs undergoing routine antimicrobial treatment.


Faecal samples (n =457) from dogs (n =127) were examined pretreatment, immediately after treatment and 1 month and 3 months post-treatment with one of five antimicrobials. Isolates were tested for susceptibility to a range of antimicrobials using disc diffusion for each treatment group at different timepoints; the presence/absence of corresponding resistance genes was investigated using PCR assays. The impact of treatment group/timepoint and other risk factors on the presence of resistance [MDR, fluoroquinolone resistance, third-generation cephalosporin resistance (3GCR) and ESBL and AmpC production] was investigated using multilevel modelling. Samples with at least one AMR E. coli from selective/non-selective agar were classed as positive. Resistance was also assessed at the isolate level, determining the abundance of AMR from non-selective culture.


Treatment with β-lactams or fluoroquinolones was significantly associated with the detection of 3GCR, AmpC-producing, MDR and/or fluoroquinolone-resistant E. coli, but not ESBL-producing E. coli, immediately after treatment. However, 1 month post-treatment, only amoxicillin/clavulanate was significantly associated with the detection of 3GCR; there was no significant difference at 3 months post-treatment for any antimicrobial compared with pretreatment samples.


Our findings demonstrated that β-lactam and fluoroquinolone antibiotic usage is associated with increased detection of important phenotypic and genotypic AMR faecal E. coli following routine therapy in vet-visiting dogs. This has important implications for veterinary and public health in terms of antimicrobial prescribing and biosecurity protocols, and dog waste disposal.

Research – Extended-spectrum beta-lactamase producing Enterobacteriaceae (ESBL-E) isolated from bean sprouts in the Netherlands

Plos One 


Community-acquired carriage and infections due to extended-spectrum beta-lactamase producing Enterobacteriaceae (ESBL-E) are increasing worldwide, resulting in increased morbidity, mortality and healthcare costs. The origins of community-acquired ESBL-E carriage and infections remain unclear. Bean sprouts are a potential source of Enterobacteriaceae for the community, as illustrated by outbreaks of pathogenic Enterobacteriaceae in the past. The current study focuses on contamination of retail bean sprouts with ESBL-E in the Netherlands. Of 131 bean sprout samples purchased between 2013 and 2016, 25 (19%) were contaminated with ESBL-E. The detected isolates were almost exclusively Klebsiella spp. and co-resistance to other antibiotics was observed frequently. Over time there was substantial genetic diversity between isolates. On the other hand, isolates from samples closely matched in time were frequently clonally related, indicative of batch contamination. Remarkably, no Escherichia coli was found. In conclusion, bean sprouts frequently harbor ESBL-E, which is a potential source for consumers.