Category Archives: ESBL

Research – Sink survey to investigate multidrug resistance pattern of common foodborne bacteria from wholesale chicken markets in Dhaka city of Bangladesh

Antimicrobial resistance (AMR) among foodborne bacteria is a well-known public health problem. A sink survey was conducted to determine the AMR pattern of common foodborne bacteria in cloacal swab of broiler chickens and sewage samples from five wholesale chicken markets of Dhaka city in Bangladesh. Bacteria were identified by culture-based and molecular methods, and subjected to antimicrobial susceptibility testing. Resistance genes were identified by multiplex PCR and sequencing. Multidrug resistance (MDR) was observed in 93.2% of E. coli, 100% of Salmonella spp., and 97.2% of S. aureus from cloacal swab samples. For sewage samples, 80% of E. coli, and 100% of Salmonella and S. aureus showed MDR. Noteworthy, 8.3% of S. aureus from cloacal swab samples showed possible extensively drug resistance. Antimicrobial resistance genes (beta-lactamase—blaTEM, blaSHV; quinolone resistance gene—qnrS) were detected in a number of E. coli and Salmonella isolates from cloacal swab and sewage samples. The methicillin resistance gene (mecA) was detected in 47.2% and 25% S. aureus from cloacal swab and sewage samples, respectively. The findings envisage the potential public health risk and environmental health hazard through spillover of common foodborne MDR bacteria.

Research – Salmonella and Campylobacter continue to show high levels of antibiotic resistance


Antibiotic resistance in Salmonella and Campylobacter bacteria is still high, says a report released today by the European Centre for Disease Prevention and Control (ECDC) and the European Food Safety Authority (EFSA).

Campylobacteriosis was the most reported zoonosis in the EU in 2020 and the most frequently reported cause of foodborne illness. Campylobacter bacteria from humans and poultry continues to show very high resistance to ciprofloxacin, a fluoroquinolone antibiotic, that is commonly used to treat some types of bacterial human infection.

Increasing trends of resistance against the fluoroquinolone class of antibiotics has been observed in humans and broilers for Campylobacter jejuni. In Salmonella Enteritidis, the most common type of Salmonella in humans, increasing trends of resistance to the quinolone/fluoroquinolone class of antibiotics were observed. In animals, resistance to these antibiotics in Campylobacter jejuni and Salmonella Enteritidis were generally moderate to high.

However, despite the increasing trends of resistance against certain antibiotics, simultaneous resistance to two critically important antibiotics – remains low for E. coliSalmonella and Campylobacter in bacteria from both humans and food-producing animals.

A decline in resistance to tetracyclines and ampicillin in Salmonella from humans was observed in nine and ten countries, respectively, over the period 2016-2020, and this was particularly evident in Salmonella Typhimurium. Despite the decline, resistance to these antibiotics still remains high in bacteria from both humans and animals.

Furthermore, in more than half of the European Union countries, a statistically significant decreasing trend in the prevalence of extended-spectrum β-lactamase (ESBL)-producing E. coli was observed in food-producing animals. This is an important finding as particular strains of ESBL-producing E. coli are responsible for serious infections in humans.

Carbapenem resistance remains extremely rare in E. coli and Salmonella from food-producing animals. Carbapenems are a class of last resort antibiotics and any findings showing resistance to these in zoonotic bacteria are concerning.

Although findings and trends are consistent with data reported in previous years, the COVID-19 pandemic had an impact on the amount of data reported, particularly with regards to public health.

An interactive data visualisation tool shows resistance levels in humans, animals and food, country-by-country in 2019 and 2020.

Additionally, the human food and waterborne antibiotic resistance data is published in ECDC’s Surveillance Atlas of Infectious Diseases (under the diseases campylobacteriosis, salmonellosis and shigellosis, respectively).

Research – First report on the molecular characterization and the occurrence of extended-spectrum β-lactamase producing Enterobacteriaceae in unpasteurized bovine’s buttermilk

Wiley Online

The dairy products have been reported as a source of extended-spectrum β-lactamase (ESBL)-producing bacteria. The aim of this study is to determine the potential transfer of ESBL Enterobacteriaceae to humans due to the consumption of buttermilk made from raw, unpasteurized milk collected in Batna province (Northeast of Algeria) as well as to identify isolates and genes encoding resistance in these isolates. Two hundred and forty-three samples of buttermilk made from raw, unpasteurized milk were collected and screened for the presence of ceftazidime-resistant Enterobacteriaceae. The suspected isolates were identified by molecular methods. Enterobacteriaceae isolates were subjected to antimicrobial susceptibility testing and were examined phenotypically for ESBL production and confirmed by using PCR assay and DNA sequencing. Thirteen ceftazidime-resistant Enterobacteriaceae were observed at a rate of 5.76% including Escherichia coli (n = 4), Klebsiella pneumoniae (n = 4), Klebsiella oxytoca (n = 1), Hafnia paralvei (n = 3), and Citrobacter freundii (n = 1). Eight Enterobacteriaceae (61.53%, 8) revealed multidrug resistance, while (61.53%, 8) were confirmed as ESBL-producing Enterobacteriaceae. Polymerase chain reaction assay revealed that blaTEM (87.5%, 7) was the most common gene, followed by the blaCTX-M gene (75%, 6) and finally the blaSHV gene (50%, 4). The sequencing of genes identified blaTEM-1DblaSHV-1, and blaSHV-11. Our findings signified that buttermilk made from raw, unpasteurized milk could be the reservoir for the prevalence of ESBL-producing Enterobacteriaceae and the potential source of transmission for the consumer. Pasteurization of buttermilk is critical to reduce the risk associated with ESBL-producing isolates.

Research – Risk evaluation of E. coli ST 131 as a foodborne pathogen in Switzerland


Within recent years, the topic of multidrug-resistant, uropathogenic Escherichia coli strains has seen a rise in occurrence as foodborne pathogens. At the core of this topic is the specific clonal group referred to as Escherichia coli O25b:H4 sequence type 131 (ST 131). It is an extended-spectrum β-lactamase (ESBL) producing E. coli strain, postulated to be responsible for the spread of ESBL-encoding genes world-wide.
This literature review aimed to evaluate ST 131 as a foodborne pathogen in Switzerland, in order to assess the risk it poses for food producers in Switzerland specifically. On a global scale, ST 131 has been identified on all continents. It is mostly associated with chicken and poultry meat, and has been isolated from retail products many times.
Not exclusive to chicken, it was rarely identified from fish guts and gills. In all other meat products, ST 131 was found only in faecal matter, not in the product itself. Besides meat, the pathogen was not identified from any sources such as dairy, fruit and vegetables.
The situation is similar in Switzerland, where it was isolated frequently from chicken, rarely from fish and a complete absence of the pathogen in all other food product groups. The risk, ST 131 poses towards Swiss food producers has been evaluated as a medium risk factor for both chicken and fish products, and a low risk factor for any other products. Despite ST 131 being evaluated as a medium-to-low risk factor, depending on the product, it is still recommended to perform further research on the topic. Especially looking towards prevalence in Swiss food, in chicken and poultry meat, but also in fish.
Specifically fish designated for raw consumption (Sushi, Sashimi). Moreover, the spread of afore-mentioned ESBL-encoding genes is hypothesized to occur also during infection of humans. This leads to the recommendation, that ST 131 should be considered a food-safety risk in all products, in order to eliminate said spread. Whether this consideration as a food-safety risk is feasible, cannot be said without further analysis of products and viable treatment options.

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.