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

Abstract

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 ...

Detection of human pathogenic bacteria in rectal DNA samples from Zalophus californianus in the Gulf of California, Mexico

“…In addition to these well-established pathogens, we detected several bacterial species of growing concern that are currently classified as “high priority pathogens” by the World Health Organization. In this context, Campylobacter jejuni is considered to be the main pathogen involved in human food-borne outbreaks worldwide 41 . Campylobacter jejuni is a Gram-negative, aerobic, pleomorphic, and mobile bacterium.…”

“…Campylobacter jejuni is a Gram-negative, aerobic, pleomorphic, and mobile bacterium. The taxonomy of the Campylobacter genus has changed dramatically since its discovery 41 , 42 . At present, this genus comprises 25 species, 2 candidates species, and 8 subspecies, many of which are of clinical and economic importance 41 .…”

“…The taxonomy of the Campylobacter genus has changed dramatically since its discovery 41 , 42 . At present, this genus comprises 25 species, 2 candidates species, and 8 subspecies, many of which are of clinical and economic importance 41 . Among them, C. jejuni is one of the most medically important species and has been recognized since 1970 as the predominant bacterium of gastroenteritis, although it is associated with miscarriages and involved in other diseases such as proctitis, septicaemia, and meningitis 41 , 43 .…”

“…At present, this genus comprises 25 species, 2 candidates species, and 8 subspecies, many of which are of clinical and economic importance 41 . Among them, C. jejuni is one of the most medically important species and has been recognized since 1970 as the predominant bacterium of gastroenteritis, although it is associated with miscarriages and involved in other diseases such as proctitis, septicaemia, and meningitis 41 , 43 . Notably, in several livestock species, such as chickens, dogs, pigs, and sheep, C. jejuni is considered to be commensal organism 44 .…”

The rise of antibiotic resistance in Campylobacter

“…Poultry, ruminants, and pigs are common hosts of Campylobacter [3], with undercooked meat, eggs, milk, and cross-contamination being the most common causes of transmission [2 ▪▪ ]. The World Health Organization (WHO) has declared Campylobacter a high-priority antibiotic-resistant pathogen due to a rapid rise in quinolone resistance [4]. The primary choice of antibiotics in the treatment of human Campylobacter infection are quinolones (ciprofloxacin) and macrolides (erythromycin and azithromycin) [5,6].…”