Campylobacter species prevalence, characterisation of antimicrobial resistance and analysis of whole-genome sequence of isolates from livestock and humans, Latvia, 2008 to 2016

Abstract

Background Campylobacter is the main cause of bacterial gastroenteritis worldwide. The main transmission route is through consumption of food contaminated with Campylobacter species or contact with infected animals. In Latvia, the prevalence of campylobacteriosis is reported to be low (4.6 cases per 100,000 population in 2016). Aim To determine prevalence, species spectrum and antimicrobial resistance (AMR) of Campylobacter spp. in Latvia, using data from various livestock and human clinical samples. Methods We analysed data of Campylobacter microbiological monitoring and AMR (2008 and 2014–16) in Latvia. Data from broilers, poultry, pigs, calves and humans were used to determine prevalence of Campylobacter . Additionally, 45 different origin isolates (22 human) were sequenced on the Illumina MiSeq platform; for each isolate core genome multilocus sequence typing was used and relevant antimicrobial resistance mechanisms were identified. Results Overall, Campylobacter prevalence in was 83.3% in pigs, 50.2% in broilers, 16.1% in calves and 5.3% in humans; C. jejuni was the predominant species in all sources except pigs where C. coli was main species. High level of resistance in Campylobacter were observed against fluoroquinolones, tetracycline and streptomycin, in most of sequenced isolates genetic determinants of relevant AMR profiles were identified. Conclusions In Latvia, prevalence of Campylobacter in livestock is high, especially in pigs and broilers; prevalence in poultry and humans were lower than in other European countries. AMR analysis reveals increase of streptomycin and tetracycline resistant broiler origin C. jejuni strains. WGS demonstrates a high compliance between resistance phenotype and genotype for quinolones and tetracyclines.

Molecular determination of genetic diversity among Campylobacter jejuni and Campylobacter coli isolated from milk, water, and meat samples using enterobacterial repetitive intergenic consensus PCR (ERIC-PCR)

“…The finding also revealed that C. coli isolate recovered from aquatic milieu was closely related with those from other sources and this result corresponds with the report of [ 53 ]. Detection of genotypic relatedness among some C. coli and C. jejuni isolates recovered from aquatic milieu and meat sources confirmed that livestock and poultry are sources of environmental spread of Campylobacter species and these results is in accordance with the report of [ 54 ]. Genetic diversity is one of the different mechanisms that helps pathogens to thrive in unfriendly circumstances within the environment or in the host given them the ability to colonize multiple hosts [ 55 ].…”

Antimicrobial Resistance and Virulence-Associated Markers in Campylobacter Strains From Diarrheic and Non-diarrheic Humans in Poland

“…High concordance (97.5%) was shown to occur between the presence of AMR determinants in WGS data and phenotypic resistance among 528 C. jejuni and C. coli isolates from England and Wales (Painset et al, 2020). Similar results were recently reported from Latvia (Meistere et al, 2019).…”

“…Only a few Campylobacter isolates possessed genes associated with aminoglycoside (e.g., gentamicin or streptomycin) resistance (approximately 11% had aph(3')-III or aadE-Cc genes). However, previous studies have shown that the prediction of resistance against aminoglycosides is not always straightforward from WGS data using currently available tools (Meistere et al, 2019). In this study, the obtained phenotypic rate of resistance to gentamicin was slightly lower compared to the genotypic rate, confirmed in 2 out of 43 isolates (CI 95%: 1.3-15.5%).…”

The source attribution analysis revealed the prevalent role of poultry over cattle and wild birds in human campylobacteriosis cases in the Baltic States

“…The collection of C. jejuni isolates (n = 420) with assigned MLST genotype from human patients (n = 132), poultry (n = 139), cattle (n = 48) and wild birds (n = 101) were obtained from three previously published studies [5][6][7] (S1 File). Sources with less than 40 strains were discarded.…”

“…Multilocus sequence typing (MLST) data has been successfully used for attribution studies to determine potential links between the sources and clinical isolates [4]. Several overview studies have been recently published regarding epidemiology and MLST genotype diversity of C. jejuni in the Baltic countries by Mäesaar et al [5], Meistere et al [6] and Aksomaitiene et al [7]. Although the studies demonstrated overlap between C. jejuni MLST genotypes isolated from human patients and genotypes found in poultry and cattle, there has not been conducted source attribution analyses of clinical Baltic C. jejuni isolates.…”