scholarly journals Genomic Characterisation of Campylobacter jejuni Isolates Recovered During Commercial Broiler Production

2021 ◽  
Vol 12 ◽  
Author(s):  
Brendha Truccollo ◽  
Paul Whyte ◽  
Catherine M. Burgess ◽  
Declan J. Bolton

Background:Campylobacter is commonly transmitted to humans from chickens. Campylobacter jejuni is the species most frequently associated with human illness, and the most prevalent species recovered from poultry.Objective: The objective of this study was to analyse a sub-population of C. jejuni from two broiler flocks on the farm and at slaughter using whole-genome sequencing to gain insights into the changes in the Campylobacter population during broiler production, including changes in virulence and antimicrobial resistance profiles.Methods: In this study, ten composite faecal samples (n=10), obtained by pooling ten fresh faecal samples (n=10), were collected in the broiler house on two farms on days 14, 21, 28, and 34 (n=80) and ten composite (n=10) caecal samples were collected at the time of slaughter for each flock (n=20). These were tested for C. jejuni using the ISO 10272-2:2016 method. Seven isolates were randomly selected from each of the nine Campylobacter-positive sampling points (n=63) and were subjected to antimicrobial susceptibility tests. Their genomes were sequenced and the data obtained was used to characterise the population structure, virulence, antimicrobial resistance determinants and inter-strain variation.Results: The Farm 1 isolates had three MLST types (ST257-257, ST814-661 and ST48-48) while those on Farm 2 were ST6209-464 and ST9401. Interestingly, only the MLST types positive for most of the virulence genes tested in this study persisted throughout the production cycle, and the detection of antimicrobial resistance determinants (gyrA T86I and tetO) increased after thinning and at slaughter, with the detection of new strains.Conclusion: The persistence of the most virulent strains detected in this study throughout the production cycle has important implications for the risk to consumers and requires further investigation. The detection of new strains within the population corresponding with the time of thinning and transportation reflects previous reports and provides further evidence that these activities pose a risk of introducing new Campylobacter strains to broiler batches.

2018 ◽  
Vol 2018 ◽  
pp. 1-7 ◽  
Author(s):  
Fanta Gashe ◽  
Eshetu Mulisa ◽  
Mekidim Mekonnen ◽  
Gemechu Zeleke

Background. Drug resistant microorganisms lead to an increase in morbidity and mortality as they boost the risk of inappropriate therapy. Hence, data on antimicrobial resistance help define the best possible treatment for individual patients. Therefore, this study aimed to screen the antimicrobial resistant profile of 3rd generation cephalosporin drugs in Jimma University Specialized Teaching Hospital. Methods. A hospital based prospective cross-sectional study was conducted in Jimma University Specialized Hospital (JUSH) from April to August 2016. The clinical samples such as wound swab, urine, sputum, and stool were collected from hospitalized patients. Then, bacterial species were isolated and identified as per the standard microbiological methods. Antimicrobial susceptibility tests were carried out using various antimicrobial discs by Kirby–Bauer disc diffusion method. Results. Totally, 248 bacterial isolates were obtained from 154 (62.1%) male and 94 (37.9%) female patients. Escherichia coli (25.4%) and Staphylococcus aureus (19.0 %) were the predominant organisms isolated from specimens. About 140 (56.5%) and 149 (60.1%) of the total bacterial isolates were found to be resistant to ceftriaxone and ceftazidime, respectively. The majority of Escherichia coli isolates 46 (73%) were resistant to ceftriaxone and 41 (65%) of them were resistant to ceftazidime. Staphylococcus aureus, which accounted 19% of the total bacterial isolates, showed 23.4% and 34% resistance to ceftriaxone and ceftazidime, respectively. Among the bacterial strains revealing resistant to ceftriazone and ceftazidime, about 109 (44%) and 108 (43.5%) of them were resistant to two, three, or four other drugs, respectively. Conclusion. Bacterial resistance towards third-generation cephalosporin (ceftriaxone and ceftazidime) is escalating as more than half of the isolated strains demonstrated resistance to these drugs. Moreover, these strains also revealed multidrug resistance mainly against clinically used drugs which could render therapy unsuccessful. Therefore, in clinical use appropriate medications should be selected based on the data obtained from antimicrobial susceptibility tests.


2016 ◽  
Vol 82 (8) ◽  
pp. 2347-2355 ◽  
Author(s):  
A. B. Vidal ◽  
F. M. Colles ◽  
J. D. Rodgers ◽  
N. D. McCarthy ◽  
R. H. Davies ◽  
...  

ABSTRACTThe genetic diversity ofCampylobacter jejuniandCampylobacter coliisolates from commercial broiler farms was examined by multilocus sequence typing (MLST), with an assessment of the impact of the sample type and laboratory method on the genotypes ofCampylobacterisolated. A total of 645C. jejuniand 106C. coliisolates were obtained from 32 flocks and 17 farms, with 47 sequence types (STs) identified. TheCampylobacter jejuniisolates obtained by different sampling approaches and laboratory methods were very similar, with the same STs identified at similar frequencies, and had no major effect on the genetic profile ofCampylobacterpopulation in broiler flocks at the farm level. ForC. coli, the results were more equivocal. While some STs were widely distributed within and among farms and flocks, analysis of molecular variance (AMOVA) revealed a high degree of genetic diversity among farms forC. jejuni, where farm effects accounted for 70.5% of variance, and among flocks from the same farm (9.9% of variance forC. jejuniand 64.1% forC. coli). These results show the complexity of the population structure ofCampylobacterin broiler production and that commercial broiler farms provide an ecological niche for a wide diversity of genotypes. The genetic diversity ofC. jejuniisolates among broiler farms should be taken into account when designing studies to understandCampylobacterpopulations in broiler production and the impact of interventions. We provide evidence that supports synthesis of studies onC. jejunipopulations even when laboratory and sampling methods are not identical.


Author(s):  
Yuiko Takebayashi ◽  
Jacqueline Findlay ◽  
Kate J Heesom ◽  
Philip J Warburton ◽  
Matthew B Avison ◽  
...  

Abstract Objectives To measure the variability in carbapenem susceptibility conferred by different OxaAb variants, characterize the molecular evolution of oxaAb and elucidate the contribution of OxaAb and other possible carbapenem resistance factors in the clinical isolates using WGS and LC–MS/MS. Methods Antimicrobial susceptibility tests were performed on 10 clinical Acinetobacter baumannii isolates. Carbapenem MICs were evaluated for all oxaAb variants cloned into A. baumannii CIP70.10 and BM4547, with and without their natural promoters. Molecular evolution analysis of the oxaAb variants was performed using FastTree and SplitsTree4. Resistance determinants were studied in the clinical isolates using WGS and LC–MS/MS. Results Only the OxaAb variants with I129L and L167V substitutions, OxaAb(82), OxaAb(83), OxaAb(107) and OxaAb(110) increased carbapenem MICs when expressed in susceptible A. baumannii backgrounds without an upstream IS element. Carbapenem resistance was conferred with the addition of their natural upstream ISAba1 promoter. LC–MS/MS analysis on the original clinical isolates confirmed overexpression of the four I129L and L167V variants. No other differences in expression levels of proteins commonly associated with carbapenem resistance were detected. Conclusions Elevated carbapenem MICs were observed by expression of OxaAb variants carrying clinically prevalent substitutions I129L and L167V. To drive carbapenem resistance, these variants required overexpression by their upstream ISAba1 promoter. This study clearly demonstrates that a combination of IS-driven overexpression of oxaAb and the presence of particular amino acid substitutions in the active site to improve carbapenem capture is key in conferring carbapenem resistance in A. baumannii and other mechanisms are not required.


2019 ◽  
Vol 29 (Supplement_4) ◽  
Author(s):  
M Barchitta ◽  
A Quattrocchi ◽  
A Maugeri ◽  
M C La Rosa ◽  
C La Mastra ◽  
...  

Abstract Background Antimicrobial resistance (AMR) is one of the ten threats identified by the WHO in 2019. In order to face this issue and in the framework of the National Action Plan on Antimicrobial Resistance (PNCAR) 2017-2020, the Sicilian Health Authority has implemented a surveillance system of antibiotic consumption in the hospital sector and in the community and of antibiotic resistance in the Sicilian hospitals. The aim of the present work is to report the results of three-year surveillance. Methods From 2015 to 2017, data on antibiotic consumption have been collected from pharmacies of participating hospitals. AMR data on seven bacterial pathogens isolated in blood and cerebrospinal fluid have been collected from hospital laboratories, using routine clinical antimicrobial susceptibility tests. Antibiotic consumption was expressed as Defined Daily Dose (DDD) per 100 patient-days. Antibiotic resistance rates (RRs) were calculated as the number of non-susceptible isolates divided by the total number of isolates multiplied by 100. Results The most commonly consumed antibiotics in participating hospitals were fluoroquinolones in 2015, penicillins in 2016, and beta-lactams in 2017, respectively. RRs of Klebsiella pneumoniae significantly increased for all antimicrobial classes (p < 0.001), but carbapenems. By contrast, RRs of Escherichia coli resistant to third-generation cephalosporins and carbapenems showed significant decreasing trends (p < 0.001). Conclusions The implementation of the Sicilian surveillance system provides Sicilian reference data to monitor trends and target interventions and policies for reducing the threat of AMR. Recently, using toolkits of the ECDC-EAAD initiative adapted with regional surveillance data, an educational campaign “Obiettivo Antibiotico” - https://www.obiettivoantibiotico.it/ - was designed and launched to raise awareness of prudent use of antibiotics in the general public and in healthcare professionals in Sicily. Key messages Inappropriate antimicrobial consumption observed in Sicilian hospitals contributes to the emergence and selection of AMR. Surveillance system of antimicrobial consumption and AMR can help identify strategies for preventing spread of multi-drug resistant microorganisms.


2020 ◽  
Vol 9 (1) ◽  
pp. 66
Author(s):  
Jurgita Aksomaitiene ◽  
Aleksandr Novoslavskij ◽  
Egle Kudirkiene ◽  
Ausra Gabinaitiene ◽  
Mindaugas Malakauskas

Spread of antibiotic resistance via mobile genetic elements associates with transfer of genes providing resistance against multiple antibiotics. Use of various comparative genomics analysis techniques enables to find intrinsic and acquired genes associated with phenotypic antimicrobial resistance (AMR) in Campylobacter jejuni genome sequences with exceptionally high-level multidrug resistance. In this study, we used whole genome sequences of seven C. jejuni to identify isolate-specific genomic features associated with resistance and virulence determinants and their role in multidrug resistance (MDR). All isolates were phenotypically highly resistant to tetracycline, ciprofloxacin, and ceftriaxone (MIC range from 64 to ≥256 µg/mL). Besides, two C. jejuni isolates were resistant to gentamicin, and one was resistant to erythromycin. The extensive drug-resistance profiles were confirmed for the two C. jejuni isolates assigned to ST-4447 (CC179). The most occurring genetic antimicrobial-resistance determinants were tetO, beta-lactamase, and multidrug efflux pumps. In this study, mobile genetic elements (MGEs) were detected in genomic islands carrying genes that confer resistance to MDR, underline their importance for disseminating antibiotic resistance in C. jejuni. The genomic approach showed a diverse distribution of virulence markers, including both plasmids and phage sequences that serve as horizontal gene transfer tools. The study findings describe in silico prediction of AMR and virulence genetics determinants combined with phenotypic AMR detection in multidrug-resistant C. jejuni isolates from Lithuania.


Author(s):  
Dominic Poulin-Laprade ◽  
Jean-Simon Brouard ◽  
Nathalie Gagnon ◽  
Annie Turcotte ◽  
Alexandra Langlois ◽  
...  

Pigs are major reservoirs of resistant Enterobacteriaceae that can reach humans through consumption of contaminated meat or vegetables grown in manure-fertilized soil. Samples were collected from sows during lactation and their piglets at five time points spanning the production cycle. Cefotaxime-resistant bacteria were quantified and isolated from feed, feces, manures and carcasses of pigs reared with penicillin-using or antibiotic-free husbandries. The isolates were characterized by antibiotic susceptibility testing, whole genome sequencing and conjugation assays. The extended spectrum β-lactamase (ESBL) phenotype was more frequent in isolates originating from antibiotic-free animals, while the bacteria isolated from penicillin-using animals were on average resistant to a greater number of antibiotics. The ESBL-encoding genes identified were blaCTX-M-1, blaCTX-M-15 and blaCMY-2 and they co-localised on plasmids with various genes encoding resistance to ß-lactams, co-trimoxazole, phenicols and tetracycline, all antibiotics used in pig production. Groups of genes conferring the observed resistance and the mobile elements disseminating multidrug resistance were determined. The observed resistance to ß-lactams was mainly due to the complementary actions of penicillin-binding proteins, an efflux pump and ß-lactamases. Most resistance determinants were shared by animals raised with or without antimicrobials. This suggests a key contribution of indigenous enterobacteria maternally transmitted along the sow lineage, regardless of antimicrobial use. It is unclear if the antimicrobial resistance observed in the enterobacteria populations of the commercial pig herds studied were present before the use of antibiotics, or the extent to which historical antimicrobial use exerted a selective pressure defining the resistant bacterial populations in farms using penicillin prophylaxis. Importance: Antimicrobial resistance is a global threat that needs to be fought on numerous fronts along the One Health continuum. Vast quantities of antimicrobials are used in agriculture to ensure animal welfare and productivity, and are arguably a driving force for the persistence of environmental and food-borne resistant bacteria. This study evaluated the impact of conventional, organic and other antibiotic-free husbandry practices on the frequency and nature of antimicrobial resistance genes and multidrug resistant enterobacteria. It provides knowledge about the relative contribution of specific resistance determinants to observed antibiotic resistance. It also showed the clear co-selection of genes coding for extended-spectrum beta-lactamases and genes coding for the resistance to antibiotics commonly used for prophylaxis or in curative treatments in pig operations.


2020 ◽  
Vol 64 (2) ◽  
pp. 263-268
Author(s):  
Lingling Wei ◽  
Cheng Yang ◽  
Wangfeng Shao ◽  
Tongzheng Sun ◽  
Jianyu Wang ◽  
...  

AbstractIntroductionSalmonellosis is a zoonotic disease, and Salmonella spp. can sometimes be found in dogs and cats, posing a risk to human health. In this study, the prevalence and antimicrobial susceptibility of faecal Salmonella were investigated in pet dogs and cats in Xuzhou, Jiangsu Province, China.Material and MethodsFaecal samples from 243 dogs and 113 cats, at seven pet clinics, were tested between March 2018 and May 2019. Each Salmonella isolate was characterised using serotyping and antimicrobial susceptibility tests.ResultsThe prevalence of Salmonella was 9.47% in dogs and 1.77% in cats. Among the 25 isolates, eight serotypes of Salmonella enterica subsp. enterica were detected, S. Kentucky (n = 11), S. Indiana (n = 5), and S. Typhimurium (n = 4) predominating. S. Derby, S. Toucra, S. Sandiego, S. Newport, and S. Saintpaul all occurred singly. The 23 Salmonella strains found in dogs were from seven different serovars, while the two strains in cats were from two. The highest resistance rates were found for tetracycline (92%), azithromycin (88%), cefazolin (84%), nalidixic acid (80%), ampicillin (80%), ceftriaxone (80%), and streptomycin (76%). Resistance to three or more antimicrobial agents was detected in 24 (96%) isolates. Most of the S. Kentucky and S. Indiana isolates were multi-drug resistant to more than 11 agents.ConclusionThe carriage rate was far higher in dogs than in cats from Xuzhou. Some isolated strains were highly resistant to antimicrobials used to treat infections in humans and pets, which may raise the risk of humans being infected with multi-drug resistant Salmonella via close contact with pets.


2021 ◽  
Author(s):  
◽  
Richard Musoke ◽  
Nathan Musisi Lubowa

Background: Wound infections are associated with increased morbidity and mortality. Etiologic agents of wound infections vary with geographical locations. Pathogens that infect wounds can be part of normal flora or acquired from the hospital environment. This study aimed to determine the prevalence of wound infections, investigate the profile of pathogens cultured from an infected wound and determine their antimicrobial resistance pattern to commonly prescribed antibiotics.  Methodology: A prospective cross-sectional study was conducted at Uganda Martyrs’ Hospital Lubaga from March 2020 to May 2020. Swabs from different types of wounds were processed to investigate etiologic agents using the standard microbiological technique. Antimicrobial susceptibility tests were done using a simple disc diffusion technique.  Results: Out of 210 wound swab samples analyzed, 125(59.5%) were culture positive. 20(16%) of the culture had mixed infections and a total of 238 bacteria were isolated from 205 cases. Staphylococcus aureus was the most frequently isolated pathogen which accounted for 94 (75.2%) of isolates followed by Proteus 11 (8.8%). The sensitivity rates of Ciprofloxacin, ceftriaxone, and gentamicin were 80.6%, 80.6%, and 74.2% respectively.  Conclusions and recommendation: S. aureus and Proteus were the predominant causes of wound infections. Ciprofloxacin, ceftriaxone, and Gentamicin were the most effective drugs. Periodic surveillance of the species of bacteria involved in wound infection and determination of their antimicrobial resistance is recommended for empirical treatment.


PLoS ONE ◽  
2021 ◽  
Vol 16 (3) ◽  
pp. e0246843
Author(s):  
Brendha Truccollo ◽  
Paul Whyte ◽  
Catherine Burgess ◽  
Declan Bolton

Campylobacter spp. is a significant and prevalent public health hazard globally. Campylobacter jejuni is the most frequently recovered species from human cases and poultry are considered the most important reservoir for its transmission to humans. In this study, 30 Campylobacter jejuni isolates were selected from clinical (n = 15) and broiler (n = 15) sources from a larger cohort, based on source, virulence, and antimicrobial resistance profiles. The objective of this study was to further characterise the genomes of these isolates including MLST types, population structure, pan-genome, as well as virulence and antimicrobial resistance determinants. A total of 18 sequence types and 12 clonal complexes were identified. The most common clonal complex was ST-45, which was found in both clinical and broiler samples. We characterised the biological functions that were associated with the core and accessory genomes of the isolates in this study. No significant difference in the prevalence of virulence or antimicrobial resistance determinants was observed between clinical and broiler isolates, although genes associated with severe illness such as neuABC, wlaN and cstIII were only detected in clinical isolates. The ubiquity of virulence factors associated with motility, invasion and cytolethal distending toxin (CDT) synthesis in both clinical and broiler C. jejuni genomes and genetic similarities between groups of broiler and clinical C. jejuni reaffirm that C. jejuni from poultry remains a significant threat to public health.


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