Category Archives: AMR

Research – Monitoring AMR in Campylobacter jejuni from Italy in the last 10 years (2011–2021): Microbiological and WGS data risk assessment


Campylobacter jejuni is considered as the main pathogen in human food‐borne outbreaks worldwide. Over the past years, several studies have reported antimicrobial resistance (AMR) in C. jejuni strains. In Europe, the official monitoring of AMR comprises the testing of Campylobacter spp. from food‐producing animals because this microorganism is responsible for human infections and usually predominant in poultry. Food‐producing animals are considered to be a major source of campylobacteriosis through contamination of food products. Concerns are growing due to the current classification of C. jejuni by the WHO as a ‘high priority pathogen’ due to the emergence of resistance to multiple drugs such as those belonging to the fluoroquinolones, macrolides and other classes, which limits the treatment alternatives. Knowledge about the contributions of different food sources to gastrointestinal disease is fundamental to prioritise food safety interventions and to establish proper control strategies. Assessing the genetic diversity among Campylobacter species is essential to the understanding of their epidemiology and population structure. Using a population genetic approach and grouping the isolates into sequence types within different clonal complexes, it is possible to investigate the source of the human cases. The work programme was aimed for the fellow to assess the AMR of C. jejuni isolated from humans, poultry and birds from wild and urban Italian habitats. Given the public health concern represented by resistant pathogens in food‐producing animals and the paucity of data about this topic in Italy, the aim was to identify correlations between phenotypic and genotypic AMR and comparing the origin of the isolates. The work programme allowed the fellow to acquire knowledge, skills and competencies on the web‐based tools used by IZSAM to process the NGS data and perform bioinformatics analyses for the identification of epidemiological clusters, the study of AMR patterns in C. jejuni isolates, and the assessment of the human exposure to such AMR pathogens. Furthermore, the fellow became able to transfer the acquired knowledge through innovative web‐based didactical tools applied to WGS and clustering of specific food‐borne pathogens, with particular reference to C. jejuni. To achieve this objective, 2,734 C. jejuni strains isolated from domestic and wild animals and humans, during the period 2011–2021 were analysed. The resistance phenotypes of the isolates were determined using the microdilution method with EUCAST breakpoints, for the following antibiotics: nalidixic acid, ciprofloxacin, chloramphenicol, erythromycin, gentamicin, streptomycin, tetracycline. The data were complemented by WGS data for each strain, uploaded in the Italian information system for the collection and analysis of complete genome sequence of pathogens isolated from animal, food and environment (GENPAT) developed and maintained at IZSAM; information like clonal complex and sequence type to understand the phylogenetical distance between strains according to their origins were also considered. This work underlines that a better knowledge of the resistance levels of C. jejuni is necessary, and mandatory monitoring of Campylobacter species in the different animal productions is strongly suggested.

UK – Research – A survey of Salmonella, Escherichia coli (E. coli) and antimicrobial resistance in frozen, part-cooked, breaded or battered poultry products on retail sale in the United Kingdom


A survey of Salmonella, Escherichia coli (E. coli) and antimicrobial resistance in frozen, part-cooked, breaded or battered poultry products on retail sale in the United Kingdom

In this study we estimated how frequently Salmonella spp. were present in frozen, breaded or battered chicken products, intended to be cooked before consumption, on retail sale in the UK between April and July 2021.

Frozen, breaded, ready-to-cook chicken products have been implicated in outbreaks of salmonellosis. Some of these outbreaks can be large. For example, one outbreak of Salmonella Enteritidis involved 193 people in nine countries between 2018 and 2020, of which 122 cases were in the UK. These ready-to-cook products have a browned, cooked external appearance, which may be perceived as ready-to-eat, leading to mishandling or undercooking by consumers. Continuing concerns about these products led FSA to initiate a short-term (four month), cross-sectional surveillance study undertaken in 2021 to determine the prevalence of Salmonella spp., Escherichia coli and antimicrobial resistance (AMR) in frozen, breaded or battered chicken products on retail sale in the UK.

This study sought to obtain data on AMR levels in Salmonella and E. coli in these products, in line with a number of other FSA instigated studies of the incidence and nature of AMR in the UK food chain, for example, the systematic review (2016).

Between the beginning of April and the end of July 2021, 310 samples of frozen, breaded or battered chicken products containing either raw or partly cooked chicken, were collected using representative sampling of retailers in England, Wales, Scotland and Northern Ireland based on market share data. Samples included domestically produced and imported chicken products and were tested for E. coli (including extended-spectrum beta-lactamase (ESBL)-producing, colistin-resistant and carbapenem-resistant E. coli) and Salmonella spp. One isolate of each bacterial type from each contaminated sample was randomly selected for additional AMR testing to determine the minimum inhibitory concentration (MIC) for a range of antimicrobials. More detailed analysis based on Whole Genome Sequencing (WGS) data was used to further characterise Salmonella spp. isolates and allow the identification of potential links with human isolates.

Salmonella spp. were detected in 5 (1.6%) of the 310 samples and identified as Salmonella Infantis (in three samples) and S. Java (in two samples). One of the S. Infantis isolates fell into the same genetic cluster as S. Infantis isolates from three recent human cases of infection; the second fell into another cluster containing two recent cases of infection. Countries of origin recorded on the packaging of the five Salmonella contaminated samples were Hungary (n=1), Ireland (n=2) and the UK (n=2). One S. Infantis isolate was multi-drug resistant (i.e. resistant to three different classes of antimicrobials), while the other Salmonella isolates were each resistant to at least one of the classes of antimicrobials tested. E. coli was detected in 113 samples (36.4%), with counts ranging from ❤ to >1100 MPN (Most Probable Number)/g. Almost half of the E. coli isolates (44.5%) were susceptible to all antimicrobials tested. Multi-drug resistance was detected in 20.0% of E. coli isolates. E. coli isolates demonstrating the ESBL (but not AmpC) phenotype were detected in 15 of the 310 samples (4.8%) and the AmpC phenotype alone was detected in two of the 310 samples (0.6%) of chicken samples. Polymerase Chain Reaction (PCR) testing showed that five of the 15 (33.3%) ESBL-producing E. coli carried blaCTX-M genes (CTX-M-1, CTX-M-55 or CTX-M-15), which confer resistance to third generation cephalosporin antimicrobials. One E. coli isolate demonstrated resistance to colistin and was found to possess the mcr-1 gene.

The five Salmonella-positive samples recovered from this study, and 20 similar Salmonella-positive samples from a previous UKHSA (2020/2021) study (which had been stored frozen), were subjected to the cooking procedures described on the sample product packaging for fan assisted ovens. No Salmonella were detected in any of these 25 samples after cooking.

The current survey provides evidence of the presence of Salmonella in frozen, breaded and battered chicken products in the UK food chain, although at a considerably lower incidence than reported in an earlier (2020/2021) study carried out by PHE/UKHSA as part of an outbreak investigation where Salmonella prevalence was found to be 8.8%.

The current survey also provides data on the prevalence of specified AMR bacteria found in the tested chicken products on retail sale in the UK. It will contribute to monitoring trends in AMR prevalence over time within the UK, support comparisons with data from other countries, and provide a baseline against which to monitor the impact of future interventions. While AMR activity was observed in some of the E. coli and Salmonella spp. examined in this study, the risk of acquiring AMR bacteria from consumption of these processed chicken products is low if the products are cooked thoroughly and handled hygienically.

Research – New NARMS report shows rising resistance in Salmonella, Campylobacter


The latest data from a national surveillance system that monitors foodborne bacterial pathogens for antimicrobial resistance (AMR) shows some concerning changes in resistance patterns among serotypes of Salmonella.

The findings come from the National Antimicrobial Resistance Monitoring Systems (NARMS) 2019 Integrated Summary, which combines data from the Centers for Disease Control and Prevention (CDC), the Food and Drug Administration (FDA), and the US Department of Agriculture (USDA). The report provides a snapshot of resistance patterns found in bacteria isolated from humans, animals, raw meats from retail outlets (chicken, ground turkey, ground beef, and pork chops), and meat and poultry product samples collected at slaughtering facilities.

In addition to Salmonella, which causes an estimated 1.35 million illnesses and 26,500 hospitalizations each year, the NARMS report also includes resistance data on Campylobacter (1.5 million illnesses and 19,500 hospitalizations), Escherichia coli, and Enterococcus. NARMS monitors these bacteria to detect emerging resistance patterns to the antibiotics that are most important to human medicine, multidrug resistance, and specific resistance genes.

Increase in multidrug-resistant Salmonella serotype

Overall, the NARMS report shows that more than three fourths of the Salmonella isolates (78%) from humans were not resistant to any of the antibiotics tested, and that the overall level of resistance in humans remains relatively unchanged since 2018. However, the report also found rising resistance to ciprofloxacin—one of the three antibiotics used to treat severe Salmonella infections.

From 2018 to 2019, Salmonella with decreased susceptibility to ciprofloxacin increased from 9% to 11% in humans, from 18% to 31% in retail chicken, from 20% to 30% in chicken product samples, from 26% to 32% in chicken cecal content samples, and from 0% to 14% in retail pork samples.

The increase in resistance to ciprofloxacin among poultry isolates was primarily due to the increase in Salmonella Infantis, a multidrug-resistant (MDR) serotype that emerged in 2014.

The rise in Salmonella Infantis isolates was also behind an increase in MDR isolates found in retail chicken (from 20% to 32%) and in chicken product samples (22% to 29%). Up to 10 antimicrobial resistance (AMR) genes were found in some of the Salmonella Infantis isolates.

In addition, the NARMS report shows an increase in another MDR Salmonella serotype, I 4,[5],12:i:-, which is linked to pigs and has become an increasing public health concern in Europe and the United States. The percentage of MDR isolates from humans that are of the I 4,[5],12:i:- serotype rose from 7% in 2010 to 26% in 2019, and from 7% to 35% in swine samples.

NARMS data also show rising fluoroquinolone resistance in Campylobacter isolates. In humans, the proportion of ciprofloxacin-resistant Campylobacter isolates rose from 29% in 2018 to 34% in 2019 for Campylobacter jejuni and from 41% to 45% in C coli. Ciprofloxacin-resistant C jejuni isolated from chicken cecal contents (21% in 2018 to 26% in 2019) and chicken retail samples (20% to 22%) also rose.

Analysis of E coli isolates found increases in ceftriaxone resistance in sow cecal samples (3% in 2018 to 7% in 2019) and in retail pork (4% to 7%). Whole-genome sequencing of Salmonella and E coli from animals, animal products, and retail meats found that none harbored any of the MCR-1 through MCR-8 colistin-resistance genes.