Category Archives: ESBL

Research – Microbiological Quality and Safety of Fresh Turkey Meat at Retail Level, Including the Presence of ESBL-Producing Enterobacteriaceae and Methicillin-Resistant S. aureus



The aim of this work was to study the microbiological safety and quality of marketed fresh turkey meat, with special emphasis on methicillin-resistant S. aureus, ESBL-producing E. coli, and K. pneumoniae. A total of 51 fresh turkey meat samples were collected at retail level in Spain. Mesophile, Pseudomonas spp., enterococci, Enterobacteriaceae, and staphylococci counts were 5.10 ± 1.36, 3.17 ± 0.87, 2.03 ± 0.58, 3.18 ± 1.00, and 2.52 ± 0.96 log CFU/g, respectively. Neither Campylobacter spp. nor Clostridium perfringens was detected in any sample. ESBL-producing K. pneumoniae and E. coli were detected in 22 (43.14%), and three (5.88%) samples, respectively, all of which were multi-resistant. Resistance to antimicrobials of category A (monobactams, and glycilcyclines) and category B (cephalosporins of third or fourth generation, polymixins, and quinolones), according to the European Medicine Agency classification, was found among the Enterobacteriaceae isolates. S. aureus and methicillin-resistant S. aureus were detected in nine (17.65%) and four samples (7.84%), respectively. Resistance to antimicrobials of category A (mupirocin, linezolid, rifampicin, and vancomycin) and category B (cephalosporins of third- or fourth generation) was found among S. aureus, coagulase-negative staphylococci, and M. caseolyticus isolates.

Research – ESBL- and Carbapenemase-Producing Escherichia coli and Klebsiella pneumoniae among Bivalves from Portuguese Shellfish Production Areas



Bivalves are filter-feeding organisms and biomarkers of bacterial pollution. Our study aimed to analyze the occurrence and characteristics of extended-spectrum β-lactamase (ESBL)- and carbapenemase-producing Escherichia coli among bivalves. A total of 522 bivalve samples were collected along Portuguese shellfish production areas. Homogenized samples were screened for E. coli contamination on corresponding selective plates, allowing for concomitant growth of Klebsiella pneumoniaeE. coli growth was observed in 39% of the samples. Subsequent selective screening identified nine samples (4.4%) contaminated with ESBL producers, corresponding to E. coli (n = 7) and K. pneumoniae (n = 2), while a single carbapenemase-producing K. pneumoniae (0.5%) was identified. ESBLs were all CTX-M-types commonly identified in human isolates, i.e., CTX-M-32 (n = 4), CTX-M-15 (n = 4), and CTX-M-14 (n = 1). The carbapenemase producer harbored the blaGES-5 gene located on a ColE plasmid. Clonality was evaluated by multilocus sequence typing, identifying E. coli backgrounds as ST10, ST23, ST540, ST617, ST746, SLV206, and SLV2325, commonly identified among environmental and human strains. The K. pneumoniae isolates belonged to ST834, ST15, and DLV644. The occurrence of ESBL- and carbapenemase-producing Enterobacteriaceae in bivalves reveals how the marine environment constitutes a reservoir of critical bacterial pathogens, thus potentially representing a risk to human health.

Research – Insights into the Bacterial Diversity and Detection of Opportunistic Pathogens in Mexican Chili Powder


Chili powder is the most frequently consumed spice in Mexican diets. Thus, the dissemination of microorganisms associated with chili powder derived from Capsicum annuum L. is significant during microbial quality analysis, with special attention on detection of potential pathogens. The results presented here describe the initial characterization of bacterial community structure in commercial chili powder samples. Our results demonstrate that, within the domain Bacteria, the most abundant family was Bacillaceae, with a relative abundance of 99% in 71.4% of chili powder samples, while 28.6% of samples showed an average relative abundance of 60% for the Enterobacteriaceae family. Bacterial load for aerobic mesophilic bacteria (AMB) ranged from 104 to 106 cfu/g, while for sporulated mesophilic bacteria (SMB), the count ranged from 102 to 105 cfu/g. Bacillus cereus sensu lato (s.l.) was observed at ca. ˂600 cfu/g, while the count for Enterobacteriaceae ranged from 103 to 106 cfu/g, Escherichia coli and Salmonella were not detected. Fungal and yeast counts ranged from 102 to 105 cfu/g. Further analysis of the opportunistic pathogens isolated, such as B. cereus s.l. and Kosakonia cowanii, using antibiotic-resistance profiles and toxinogenic characteristics, revealed the presence of extended-spectrum β-lactamases (ESBLs) and Metallo-β-lactamases (MBLs) in these organisms. These results extend our knowledge of bacterial diversity and the presence of opportunistic pathogens associated with Mexican chili powder and highlight the potential health risks posed by its use through the spread of antibiotic-resistance and the production of various toxins. Our findings may be useful in developing procedures for microbial control during chili powder production. View Full-Text

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.