Epidemiological cut-off values for Vibrio anguillarum MIC and disc diffusion data generated by standardised methods

This work aims to generate the data needed to set epidemiological cut-off values for minimum inhibitory concentration (MIC) and disc-diffusion zone measurements of Vibrio anguillarum. A total of 261 unique isolates were tested, applying standard methods specifying incubation at 28°C for 24-28 h. Aggregated MIC distributions for a total of 247 isolates were determined in 9 laboratories for 11 agents. Data aggregations of the disc zone for the 10 agents analysed contained between 157 and 218 observations made by 4 to 7 laboratories. Acceptable ranges for quality control (QC) reference strains were available for 7 agents and the related multi-laboratory aggregated data were censored, excluding the data of a laboratory that failed to meet QC requirements. Statistical methods were applied to calculate epidemiological cut-off values. Cut-off values for MIC data were calculated for florfenicol (≤1 µg ml-1), gentamicin (≤4 µg ml-1), oxytetracycline (≤0.25 µg ml-1) and trimethoprim/sulfamethoxazole (≤0.125/2.38 µg ml-1). The cut-off values for disc zone data were calculated for enrofloxacin (≥29 mm), florfenicol (≥27 mm), gentamicin (≥19 mm), oxolinic acid (≥24 mm), oxytetracycline (≥24 mm) and trimethoprim/sulfamethoxazole (≥26 mm). MIC and disc-diffusion zone data for the other agents where not supported by QC, thus yielding only provisional cut-off values (meropenem, ceftazidime). Regardless of whether QC is available, some of the aggregated MIC distributions (enrofloxacin, oxolinic acid), disc zone (sulfamethoxazole), and MIC and disc-diffusion distributions (ampicillin, chloramphenicol) did not meet the statistical requirements. The data produced will be submitted to the Clinical Laboratory Standards Institute for their consideration in setting international consensus epidemiological cut-off values.

A global genomic analysis of Salmonella Concord reveals lineages with high antimicrobial resistance in Ethiopia

Antimicrobial resistant Salmonella enterica serovar Concord (S. Concord) is known to cause severe gastrointestinal and bloodstream infections in patients from Ethiopia and Ethiopian adoptees, and occasional records exist of S. Concord linked to other countries. The evolution and geographical distribution of S. Concord remained unclear. Here, we provide a genomic overview of the population structure and antimicrobial resistance (AMR) of S. Concord by analysing genomes from 284 historical and contemporary isolates obtained between 1944 and 2022 across the globe. We demonstrate that S. Concord is a polyphyletic serovar distributed among three Salmonella super-lineages. Super-lineage A is composed of eight S. Concord lineages, of which four are associated with multiple countries and low levels of AMR. Other lineages are restricted to Ethiopia and horizontally acquired resistance to most antimicrobials used for treating invasive Salmonella infections in low- and middle-income countries. By reconstructing complete genomes for 10 representative strains, we demonstrate the presence of AMR markers integrated in structurally diverse IncHI2 and IncA/C2 plasmids, and/or the chromosome. Molecular surveillance of pathogens such as S. Concord supports the understanding of AMR and the multi-sector response to the global AMR threat. This study provides a comprehensive baseline data set essential for future molecular surveillance.

Implementation of WGS analysis of ESBL-producing Escherichia coli within EU AMR monitoring in livestock and meat

BACKGROUND

As WGS comes of age, changes in EU legislation implemented in 2021 allow its usage for systematic monitoring of ESBL-producing Escherichia coli from livestock and meat, replacing phenotypic testing. Presently, phenotypic testing correlates well with antimicrobial resistance predicted from WGS data. WGS has added value in the wealth of additional information that is present in the data.

OBJECTIVES

In this study we have detected the resistance phenotypes for a panel of antimicrobials while also analysing the molecular epidemiology of ESBL-producing E. coli.

METHODS

Susceptibility testing was performed with broth microdilution of selectively isolated E. coli. Short-read WGS was performed in parallel and phenotypes predicted based on the sequence data, which was also used to determine the phylogeny of the isolates.

RESULTS

The phenotypically determined resistance and the predicted resistance correlated 90%-100% for the different antimicrobial classes. Furthermore, clonal relationships were detected amongst ESBL-producing E. coli within livestock sectors and the meat produced by this sector.

CONCLUSIONS

Further implementation of WGS analysis of ESBL/AmpC-producing E. coli within the AMR monitoring programme of EU member states and global surveillance programmes will contribute to determining the attribution of livestock in the prevalence of ESBL/AmpC-encoding E. coli in humans.

Building an International One Health Strain Level Database to Characterise the Epidemiology of AMR Threats: ESBL—AmpC Producing E. coli as An Example—Challenges and Perspectives

Antimicrobial resistance (AMR) is one of the top public health threats nowadays. Among the most important AMR pathogens, Escherichia coli resistant to extended spectrum cephalosporins (ESC-EC) is a perfect example of the One Health problem due to its global distribution in animal, human, and environmental sources and its resistant phenotype, derived from the carriage of plasmid-borne extended-spectrum and AmpC β-lactamases, which limits the choice of effective antimicrobial therapies. The epidemiology of ESC-EC infection is complex as a result of the multiple possible sources involved in its transmission, and its study would require databases ideally comprising information from animal (livestock, companion, wildlife), human, and environmental sources. Here, we present the steps taken to assemble a database with phenotypic and genetic information on 10,763 ESC-EC isolates retrieved from multiple sources provided by 13 partners located in eight European countries, in the frame of the DiSCoVeR Joint Research project funded by the One Health European Joint Programme (OH-EJP), along with its strengths and limitations. This database represents a first step to help in the assessment of different geographical and temporal trends and transmission dynamics in animals and humans. The work performed highlights aspects that should be considered in future international efforts, such as the one presented here.

Antimicrobial resistance in Campylobacter fetus: emergence and genomic evolution

Campylobacter fetus is a pathogen, which is primarily associated with fertility problems in sheep and cattle. In humans, it can cause severe infections that require antimicrobial treatment. However, knowledge on the development of antimicrobial resistance in C. fetus is limited. Moreover, the lack of epidemiological cut-off values (ECOFFs) and clinical breakpoints for C. fetus hinders consistent reporting about wild-type and non-wild-type susceptibility. The aim of this study was to determine the phenotypic susceptibility pattern of C. fetus and to determine the C. fetus resistome [the collection of all antimicrobial resistance genes (ARGs) and their precursors] to describe the genomic basis of antimicrobial resistance in C. fetus isolates over time. Whole-genome sequences of 295 C. fetus isolates, including isolates that were isolated in the period 1939 till the mid 1940s, before the usage of non-synthetic antimicrobials, were analysed for the presence of resistance markers, and phenotypic antimicrobial susceptibility was obtained for a selection of 47 isolates. C. fetus subspecies fetus (Cff) isolates showed multiple phenotypic antimicrobial resistances compared to C. fetus subspecies venerealis (Cfv) isolates that were only intrinsic resistant to nalidixic acid and trimethoprim. Cff isolates showed elevated minimal inhibitory concentrations for cefotaxime and cefquinome that were observed in isolates from 1943 onwards, and Cff isolates contained gyrA substitutions, which conferred resistance to ciprofloxacin. Resistances to aminoglycosides, tetracycline and phenicols were linked to acquired ARGs on mobile genetic elements. A plasmid-derived tet(O) gene in a bovine Cff isolate in 1999 was the first mobile genetic element observed, followed by detection of mobile elements containing tet(O)-aph(3')-III and tet(44)-ant(6)-Ib genes, and a plasmid from a single human isolate in 2003, carrying aph(3')-III-ant(6)-Ib and a chloramphenicol resistance gene (cat). The presence of ARGs in multiple mobile elements distributed among different Cff lineages highlights the risk for spread and further emergence of AMR in C. fetus. Surveillance for these resistances requires the establishment of ECOFFs for C. fetus.

European-wide antimicrobial resistance monitoring in commensal Escherichia coli isolated from healthy food animals between 2004 and 2018

OBJECTIVES

To describe the susceptibility of Escherichia coli to medically important antibiotics, collected over four periods (2004-2006, 2008-2009, 2013-2014, 2017-2018), from food-producing animals at slaughter.

METHODS

Intestinal contents from cattle, pigs and broilers were randomly sampled (5-6 countries/host; ≥4 abattoirs/country; one sample/animal/farm) for isolation of Escherichia coli; antimicrobial susceptibilities were centrally determined by CLSI agar dilution. Clinical breakpoints (CLSI) and epidemiological cut-off values (EUCAST) were applied for data interpretation.

RESULTS

In total, 10 613 E. coli strains were recovered. In broilers, resistance percentages were the lowest (P ≤ 0.01) in the latest time period. A significant decrease in MDR over time was also observed for broilers and a tendency for a decrease for pigs. Resistance to meropenem and tigecycline was absent, and resistance to azithromycin was 0.2%-2.0%. Also, low resistance to third-generation cephalosporins (1.1%-7.4%) was detected in broilers. Resistance to colistin varied between 0.1%-4.8%. E. coli from broilers showed high resistance to ciprofloxacin (7.3%-23.3%), whereas for cattle and pigs this was 0.2%-2.5%. Low/moderate resistance to chloramphenicol (9.3%-21.3%) and gentamicin (0.9%-7.0%) was observed in pigs and broilers. The highest resistance was noted for ampicillin (32.7%-65.3%), tetracycline (41.3%-67.5%), trimethoprim (32.0%-35.7%) and trimethoprim/sulfamethoxazole (27.5%-49.7%) from pigs and broilers, with marked country differences. MDR peaked in pigs and broilers with 24 and 26 phenotypes, with 21.9%-26.2% and 18.7%-34.1% resistance, respectively.

CONCLUSIONS

In this pan-EU survey antibiotic susceptibility of commensal E. coli varied largely between antibiotics, animal species and countries. Resistance to critically important antibiotics for human medicine was absent or low, except for ciprofloxacin in broilers and ampicillin in pigs and broilers.

Harmonisation of in-silico next-generation sequencing based methods for diagnostics and surveillance

Improvements in cost and speed of next generation sequencing (NGS) have provided a new pathway for delivering disease diagnosis, molecular typing, and detection of antimicrobial resistance (AMR). Numerous published methods and protocols exist, but a lack of harmonisation has hampered meaningful comparisons between results produced by different methods/protocols vital for global genomic diagnostics and surveillance. As an exemplar, this study evaluated the sensitivity and specificity of five well-established in-silico AMR detection software where the genotype results produced from running a panel of 436 Escherichia coli were compared to their AMR phenotypes, with the latter used as gold-standard. The pipelines exploited previously known genotype–phenotype associations. No significant differences in software performance were observed. As a consequence, efforts to harmonise AMR predictions from sequence data should focus on: (1) establishing universal minimum to assess performance thresholds (e.g. a control isolate panel, minimum sensitivity/specificity thresholds); (2) standardising AMR gene identifiers in reference databases and gene nomenclature; (3) producing consistent genotype/phenotype correlations. The study also revealed limitations of in-silico technology on detecting resistance to certain antimicrobials due to lack of specific fine-tuning options in bioinformatics tool or a lack of representation of resistance mechanisms in reference databases. Lastly, we noted user friendliness of tools was also an important consideration. Therefore, our recommendations are timely for widespread standardisation of bioinformatics for genomic diagnostics and surveillance globally.

Succession in the caecal microbiota of developing broilers colonised by extended-spectrum β-lactamase-producing Escherichia coli

Background

Broilers are among the most common and dense poultry production systems, where antimicrobials have been used extensively to promote animal health and performance. The continuous usage of antimicrobials has contributed to the appearance of resistant bacteria, such as extended-spectrum β-lactamase-producing Escherichia coli (ESBL-Ec). Here, we studied the ESBL-Ec prevalence and successional dynamics of the caecal microbiota of developing broilers in a commercial flock during their production life cycle (0–35 days). Broilers were categorised as ESBL-Ec colonised (ESBL-Ec⁺) or ESBL-Ec non-colonised (ESBL-Ec⁻) by selective culturing. Using 16S rRNA gene sequencing, we i. compared the richness, evenness and composition of the caecal microbiota of both broilers’ groups and ii. assessed the combined role of age and ESBL-Ec status on the broilers’ caecal microbiota.

Results

From day two, we observed an increasing linear trend in the proportions of ESBL-Ec throughout the broilers' production life cycle, X² (1, N = 12) = 28.4, p < 0.001. Over time, the caecal microbiota richness was consistently higher in ESBL-Ec⁻ broilers, but significant differences between both broilers’ groups were found exclusively on day three (Wilcoxon rank-sum test, p = 0.016). Bray–Curtis distance-based RDA (BC-dbRDA) showed no explanatory power of ESBL-Ec status, while age explained 14% of the compositional variation of the caecal microbiota, F (2, 66) = 6.47, p = 0.001.

Conclusions

This study assessed the role of ESBL-Ec in the successional dynamics of the caecal microbiota in developing broilers and showed that the presence of ESBL-Ec is associated with mild but consistent reductions in alpha diversity and with transient bacterial compositional differences. We also reported the clonal spread of ESBL-Ec and pointed to the farm environment as a likely source for ESBLs.

Supplementary Information

The online version contains supplementary material available at 10.1186/s42523-022-00199-4.

Changes in Fecal Carriage of Extended-Spectrum β-Lactamase Producing Enterobacterales in Dutch Veal Calves by Clonal Spread of Klebsiella pneumoniae

This study aimed to characterize the changes in fecal carriage of Extended-Spectrum β-Lactamase (ESBL) producing Enterobacterales (ESBL-PE) in a single Dutch veal calves. During the rearing period at the Dutch veal farm, a decrease in fecal carriage of cefotaxime-resistant Escherichia coli isolates was observed after 2 weeks at the veal farm, while an increase of cefotaxime-resistant Klebsiella pneumoniae isolates was demonstrated. E. coli and K. pneumoniae were isolated from rectal swabs collected from 110 veal calves in week 2, 6, 10, 18, and 24 after their arrival at the farm. ESBL-PE isolates were selectively cultured and identified by MALDI-TOF. ESBL genes were characterized by RT-PCR, PCRs, and amplicon sequencing. A total of 80 E. coli and 174 K. pneumoniae strains were isolated from 104 out of 110 veal calves. The prevalence of ESBL-E. coli decreased from week 2 (61%) to week 6 (7%), while an unexpected increase in ESBL-K. pneumoniae colonization was detected in week 6 (80%). The predominant ESBL genes detected in E. coli isolates were bla_CTX-M-15 and the non-ESBL gene bla_TEM-1a, while in K. pneumoniae bla_CTX-M-14 gene was detected in all isolates. Four cefotaxime-resistant K. pneumoniae isolates were randomly selected and characterized in deep by transformation, PCR-based replicon typing, and whole-genome sequencing (WGS). The clonal relatedness of a subgroup of nine animals carrying K. pneumoniae ESBL genes was investigated by Multi Locus sequence typing (MLST). In four ESBL-K. pneumoniae isolates, bla_CTX-M-14 was located on IncFII_K and IncFII_NK plasmid replicons and the isolates were multi-drug resistant (MDR). MLST demonstrated a clonal spread of ESBL-K. pneumoniae ST107. To the best of our knowledge, this is the first study to report a change in fecal carriage of ESBL-PE over time in the same veal calf during the rearing period.

A Case of Persistent Diarrhea in a Man with the Molecular Detection of Various Campylobacter species and the First Isolation of candidatus Campylobacter infans

A man with a well-controlled HIV infection, previously diagnosed with lymphogranuloma venereum and treated for Hodgkin's lymphoma, was suffering from chronic diarrhea. He travelled to Indonesia in the month prior to the start of complaints. Over a 15-month period, sequences related to Campylobactertroglodytis/upsaliensis, C. pinnepediorum/mucosalis/concisus and C. hominis were detected by 16S rRNA qPCR-based assays in various stool samples and in a colon biopsy. Culture revealed the first isolation of "candidatus Campylobacter infans", a species identified recently by molecular methods only. The patient was treated with azithromycin, ciprofloxacin and tetracycline. To identify potential continuous exposure of the patient to Campylobacter, stool samples of the partner and the cat of the patient were analyzed and C. pinnepediorum/mucosalis/concisus and C. helveticus, respectively, were detected. The diversity in detected species in this immunocompromised patient with a lack of repeatedly consistent findings resulted in the conclusion that not any of the Campylobacter species was the primary cause of the clinical condition. This study shows the challenges in detection and interpretation of diagnostic results regarding Campylobacter.

Mobile colistin resistance gene mcr-1 detected on an IncI1 plasmid in Escherichia coli from meat

OBJECTIVES

Mobile colistin resistance (mcr) genes encoded on conjugative plasmids, although described only relatively recently, have been reported globally both in humans and livestock. The genes are often associated with the insertion sequence ISApl1 that can transpose the genes to novel genetic locations. Since its first report, multiple variants of mcr have been discovered in a variety of genetic locations in Escherichia coli, in plasmids and integrated into the chromosome.

METHODS

Using hybrid assembly of short-read and long-read whole-genome sequencing data, the presence ofmcr-1 was confirmed on an IncI1 plasmid in E. coli. In vitro conjugation assays were performed to determine the potential to transfer between strains. Genetic comparison with previously reported IncI1 plasmids was performed.

RESULTS

The genomic sequence identified thatmcr-1 is present on a complete IncI1 plasmid. Comparison with previously reported extended-spectrum β-lactamase (ESBL)-encoding plasmids from E. coli in the Netherlands from the same time period indicated a distinct lineage for this plasmid.

CONCLUSIONS

The observation ofmcr-1 on an IncI1 plasmid confirms that the genetic region of this gene is actively transposed between genetic locations. This active transposition has consequences for the study of the epidemiology of mcr in populations.

Validation of an antimicrobial susceptibility testing protocol for Brachyspira hyodysenteriae and Brachyspira pilosicoli in an international ring trial

Brachyspira hyodysenteriae and Brachyspira pilosicoli cause economically important enteric disease in pigs. Treatment of these infections often includes antimicrobial administration, which can be most effective when therapeutic options are informed by antimicrobial susceptibility testing data. Here we describe a method for broth dilution antimicrobial susceptibility testing of these bacteria, both of which are difficult to culture in vitro. The protocol was evaluated for its fitness for use in an inter-laboratory ring trial involving eight laboratories from seven countries, and employing eleven test strains (5 Brachyspira hyodysenteriae including the type strain B78^T and 6 Brachyspira pilosicoli) and six antibiotics. Overall intra- and inter-laboratory reproducibility of this method was very good (>90 % MICs at mode +/- 1 log₂). Whole genome sequencing revealed good correspondence between reduced susceptibility and the presence of previously defined antimicrobial resistance determinants. Interestingly, lnu(C) was identified in B. pilosicoli isolates with elevated MICs of lincomycin, whilst tva(B) was associated with elevated MICs of pleuromutilins in this species. We designated two new control strains with MICs lying within currently tested ranges, including for the pleuromutilins, in contrast to the control strain B. hyodysenteriae B78^T. These were deposited at the DSMZ-German Collection of Microorganisms and Cell Cultures GmbH. The validation of a standard protocol and identification of new control strains facilitates comparisons between studies, establishment of robust interpretative criteria, and ultimately contributes to rational antimicrobial use when treating infected livestock.

Molecular relatedness of ESBL/AmpC-producing Escherichia coli from humans, animals, food and the environment: a pooled analysis

Background

In recent years, ESBL/AmpC-producing Escherichia coli (ESBL/AmpC-EC) have been isolated with increasing frequency from animals, food, environmental sources and humans. With incomplete and scattered evidence, the contribution to the human carriage burden from these reservoirs remains unclear.

Objectives

To quantify molecular similarities between different reservoirs as a first step towards risk attribution.

Methods

Pooled data on ESBL/AmpC-EC isolates were recovered from 35 studies in the Netherlands comprising >27 000 samples, mostly obtained between 2005 and 2015. Frequency distributions of ESBL/AmpC genes from 5808 isolates and replicons of ESBL/AmpC-carrying plasmids from 812 isolates were compared across 22 reservoirs through proportional similarity indices (PSIs) and principal component analyses (PCAs).

Results

Predominant ESBL/AmpC genes were identified in each reservoir. PCAs and PSIs revealed close human-animal ESBL/AmpC gene similarity between human farming communities and their animals (broilers and pigs) (PSIs from 0.8 to 0.9). Isolates from people in the general population had higher similarities to those from human clinical settings, surface and sewage water and wild birds (0.7-0.8), while similarities to livestock or food reservoirs were lower (0.3-0.6). Based on rarefaction curves, people in the general population had more diversity in ESBL/AmpC genes and plasmid replicon types than those in other reservoirs.

Conclusions

Our 'One Health' approach provides an integrated evaluation of the molecular relatedness of ESBL/AmpC-EC from numerous sources. The analysis showed distinguishable ESBL/AmpC-EC transmission cycles in different hosts and failed to demonstrate a close epidemiological linkage of ESBL/AmpC genes and plasmid replicon types between livestock farms and people in the general population.

Diversity of Plasmids and Genes Encoding Resistance to Extended Spectrum Cephalosporins in Commensal Escherichia coli From Dutch Livestock in 2007-2017

Extended-spectrum β-lactamase (ESBL) and plasmid-mediated AmpC β-lactamase (pAmpC) genes confer resistance to extended spectrum cephalosporin’s. The spread of these genes is mostly facilitated by plasmid-mediated horizontal transfer. National surveillance activities to detect ESBL/pAmpC-producers in commensal bacteria from livestock are in place in the Netherlands since several years. This study aimed at reporting gene and plasmid diversity of commensal ESBL/pAmpC-producing Escherichia coli isolated from healthy animals during surveillance activities between 2007 and 2017. A collection of 2304 extended-spectrum cephalosporin-resistant (ESC-R) E. coli isolated from feces of broilers, dairy cattle, slaughter pigs, turkeys, ducks, and veal calves was investigated and ESBL/pAmpC genes were determined. Gene location of a selection of 473 E. coli isolates was determined and typing of plasmids linked to the ESBL/pAmpC genes was performed. Twenty-two different ESBL/pAmpC genes were identified with bla_CTX-M-1 being the most prevalent gene in livestock (43.7%), followed by bla_{CMY -2} and bla_{SHV -12}, independent of the animal source. Prevalence of typically human associated bla_CTX-M-15 was highest in cattle. Less than 10% E. coli isolates owed their ESC-R phenotype to promoter mutations of the chromosomal ampC gene. Majority (92%) of ESBL/pAmpC genes analyzed were plasmid located, with IncI1α being the most represented plasmid family in isolates from all animals, followed by IncF (veal calves, dairy cattle and slaughter pigs), IncK (broilers and laying hens), IncX1 in broilers, and emerging IncX3 in broilers and dairy cattle. Prevalence and molecular diversity of ESC-R E. coli isolated from livestock over an 11-year period revealed a composite scenario of gene-plasmid combinations.

En Route towards European Clinical Breakpoints for Veterinary Antimicrobial Susceptibility Testing: A Position Paper Explaining the VetCAST Approach

VetCAST is the EUCAST sub-committee for Veterinary Antimicrobial Susceptibility Testing. Its remit is to define clinical breakpoints (CBPs) for antimicrobial drugs (AMDs) used in veterinary medicine in Europe. This position paper outlines the procedures and reviews scientific options to solve challenges for the determination of specific CBPs for animal species, drug substances and disease conditions. VetCAST will adopt EUCAST approaches: the initial step will be data assessment; then procedures for decisions on the CBP; and finally the release of recommendations for CBP implementation. The principal challenges anticipated by VetCAST are those associated with the differing modalities of AMD administration, including mass medication, specific long-acting product formulations or local administration. Specific challenges comprise mastitis treatment in dairy cattle, the range of species and within species breed considerations and several other variable factors not relevant to human medicine. Each CBP will be based on consideration of: (i) an epidemiological cut-off value (ECOFF) - the highest MIC that defines the upper end of the wild-type MIC distribution; (ii) a PK/PD breakpoint obtained from pre-clinical pharmacokinetic data [this PK/PD break-point is the highest possible MIC for which a given percentage of animals in the target population achieves a critical value for the selected PK/PD index (fAUC/MIC or fT > MIC)] and (iii) when possible, a clinical cut-off, that is the relationship between MIC and clinical cure. For the latter, VetCAST acknowledges the paucity of such data in veterinary medicine. When a CBP cannot be established, VetCAST will recommend use of ECOFF as surrogate. For decision steps, VetCAST will follow EUCAST procedures involving transparency, consensus and independence. VetCAST will ensure freely available dissemination of information, concerning standards, guidelines, ECOFF, PK/PD breakpoints, CBPs and other relevant information for AST implementation. Finally, after establishing a CBP, VetCAST will promulgate expert comments and/or recommendations associated with CBPs to facilitate their sound implementation in a clinical setting.

Campylobacter in Broiler Chicken and Broiler Meat in Sri Lanka: Influence of Semi-Automated vs. Wet Market Processing on Campylobacter Contamination of Broiler Neck Skin Samples

Broiler meat can become contaminated with Campylobacter of intestinal origin during processing. The present study aimed to identify the prevalence of Campylobacter in broiler flocks and meat contamination at retail shops, and determine the influence of semi-automated and wet market processing on Campylobacter contamination of neck skin samples. Samples were collected from semi-automated plants (n = 102) and wet markets (n = 25). From each batch of broilers, pooled caecal samples and neck skin samples were tested for Campylobacter. Broiler meat purchased from retail outlets (n = 37) was also tested. The prevalence of Campylobacter colonized broiler flocks was 67%. The contamination of meat at retail was 59%. Both semi-automated and wet market processing resulted to contaminate the broiler neck skins to the levels of 27.4% and 48%, respectively. When Campylobacter-free broiler flocks were processed in semi-automated facilities 15% (5/33) of neck skin samples became contaminated by the end of processing whereas 25% (2/8) became contaminated after wet market processing. Characterization of isolates revealed a higher proportion of C. coli compared to C. jejuni. Higher proportions of isolates were resistant to important antimicrobials. This study shows the importance of Campylobacter in poultry industry in Sri Lanka and the need for controlling antimicrobial resistance.

Ten years later: still a high prevalence of MRSA in slaughter pigs despite a significant reduction in antimicrobial usage in pigs the Netherlands

OBJECTIVES

In 2005, 39% of pigs and 81% of the slaughter batches at Dutch slaughterhouses were MRSA positive. The objective of the present study was to investigate whether the 50% reduction of antimicrobial usage in finishing pigs in 2014 compared with 2009 in the Netherlands has led to a lower MRSA prevalence among Dutch slaughter pigs.

METHODS

Nasal swabs from eight slaughter batches of on average 10 animals at seven slaughterhouses were taken and cultured using method 1, which was used in 2005, and method 2, using high-salt pre-enrichment. Suspected isolates were confirmed by PCR for two Staphylococcus aureus-specific DNA fragments and the mecA gene. A subset of MRSA isolates were further investigated using spa typing, multiple-locus variable number of tandem repeat analysis (MLVA) and antimicrobial susceptibility testing.

RESULTS

Using methods 1 and 2, we found 461 of 558 (83%) and 552 of 558 (99%) of the pigs to carry MRSA in their nares, respectively. All 56 slaughter batches were MRSA positive. All MRSA isolates belonged to the livestock-associated MLVA complex 398, had a non-WT phenotype for tetracycline and spa type t011 predominated.

CONCLUSIONS

A very high prevalence of nasal MRSA carriage was found in Dutch slaughter pigs and therefore the reduction in antimicrobial usage at the national level has not yet had an effect on the MRSA carriage rate of pigs entering the slaughterhouse. Therefore, there is still an increased risk of MRSA carriage for personnel working at pig slaughterhouses, particularly those having contact with living animals. Method 2, using high salt pre-enrichment, detected more MRSA-positive pigs and is currently the preferred method for screening of MRSA in livestock in the Netherlands.

Investigations of Enterococcus faecalis-induced bacteraemia in brown layer pullets through different inoculation routes in relation to the production of arthritis

In the present aerosol experiment, assessment of the respiratory tract of 1-day-old birds as a natural route of infection for induction of Enterococcus faecalis bacteraemia and arthritis was performed. Second, the severity and type of arthritis produced through intramuscular infection in two different inoculation sites (musculus pectoralis versus musculus gastrocnemius) was studied. Third, the resulting bacteraemia was assessed qualitatively and quantitatively in relation to the occurrence of arthritis. Exposure of 1-day-old brown layer pullets to aerosolized E. faecalis with an estimated uptake of 10(4) to 10(5) colony forming units per chick resulted in bacteraemia; however, joint lesions were not induced. In contrast, 3/10 birds inoculated intratracheally with 10(8) colony forming units developed both bacteraemia and arthritis. This suggests the occurrence of a dose effect and a role for the respiratory tract as a natural infection route in young chickens. In both intramuscularly inoculated groups the incidence of arthritis was 10/10 birds and 9/10 birds, respectively. Birds inoculated in the m. pectoralis developed symmetric polyarthritis, which harmonizes with haematogenous colonization of joints. In contrast, m. gastrocnemius-inoculated chicks mostly had asymmetric (poly)arthritis of the injected leg and varus deformation of the contralateral leg, suggesting predominantly local spread. The qualitative and quantitative results of bacteriology of blood samples show that arthritis develops in those groups with the highest number of bacteraemic birds and the highest median bacterial colony forming units per millilitre of blood during the first 24 to 36 h after treatment.

[Multiresistant Brachyspira hyodysenteriae in a Dutch sow herd]

This case study describes the isolation ofa multiresistant strain ofBrachyspira hyodysenteriae in April 2007 in a Dutch sow herd with recurrent diarrhoea. Examination of faecal samples taken from 7-month-old breeding gilts with diarrhoea revealed the presence of resistance against tiamulin, lincomycin, tylosin, doxycycline, and tylvalosin (the active substance in Aivlosin) in four of five samples. Tiamulin resistance has not been reported in The Netherlands before. The repeated use of tiamulin on the affected farm was assumed to be the main cause of the development of resistance to the drug. The farmer was advised to adopt a medication strategy and to implement management practices that would prevent an ongoing cycle of infection on the farm. It is important that the Dutch swine industry appreciates that tiamulin-resistant strains of B. hyodysenteriae may be found on other farms as well. The appropriate and prudent use of antibiotics is essential in order to prevent the development of resistance against the last option left to cure B. hyodysenteriae infections: valnemulin.

[Antibiotic resistance in Escherichia coli O157 isolated between 1998 and 2003 in The Netherlands]

Little is known about the antibiotic resistance of E. coli O157 in The Netherlands. In this study, 218 human and 247 nonhuman samples, isolated between 1998 and 2003, were tested for antimicrobial resistance. About 5.5% of E. coli O157 isolates from human samples were resistant, as were about 4.00% of E. coli O157 isolates from non-human samples. These figures are lower than those reported in the literature. Class I integrons were found in six multiresistant isolates. This type of integron is also found in commensal E. coli in food animals and Salmonella spp. One of the integron-positive isolates contained the beta-lactamase bla(TEM-1b) and an extended spectrum beta-lactamase (ESBL), which belongs to the group 2 CTX-M enzymes. This is the first report of these beta-lactamases in E. coli O157 isolated from chicken.

External quality assurance system for antibiotic resistance in bacteria of animal origin in Europe (ARBAO-II), 2003

Initiated in 2003 by the European Union, ARBAO-II aims to establish a monitoring of antimicrobial susceptibility among the veterinary laboratories in all European countries based on validated methodologies. This includes an external quality control system for the most important bacterial pathogens. In 2003 two trials were performed. The first on Salmonella and Escherichia coli involved 31 laboratories in 18 countries and the second on Staphylococcus and Streptococcus included 22 laboratories in 15 countries. For the E. coli strains, 92.8% of the results complied with the reference MICs, for Salmonella 93.7%, for Streptococcus 80.4% and for Staphylococcus 93.1%. Most problems were observed when testing florfenicol (79.2% correct), gentamicin (84.2%) and amoxicillin + cl (84.9%) in E. coli; streptomycin in Salmonella (62.5%); gentamicin (56.7%), lincomycin (71.4%), clindamycin (75.4%), TMP + sulfonamides (75.7%) and chloramphenicol (78.5%) in Streptococcus; erythromycin (81.5%) and oxacillin (78.2.5%) in Staphylococcus. A few laboratories caused most deviations. However, there was no correlation between good performance for one bacterial group and good performance for other groups. This study showed that most laboratories are capable of performing correct susceptibility testing for E. coli and Salmonella, even though performance of some laboratories can be improved, and that some problems exist for Staphylococcus and Streptococcus. This clearly shows the need for continuous harmonisation of methodologies within the EU.

Quantitative susceptibility of Streptococcus suis strains isolated from diseased pigs in seven European countries to antimicrobial agents licenced in veterinary medicine

The susceptibility of Streptococcus suis strains (n=384) isolated from diseased pigs in seven European countries to 10 antimicrobial agents was determined. For that purpose a microbroth dilution method was used according to CLSI recommendations. The following antimicrobial agents were tested: ceftiofur, cefquinome, enrofloxacin, florfenicol, gentamicin, penicillin, spectinomycin, tetracycline, tilmicosin and trimethoprim/sulphamethoxazole. Using breakpoints established by CLSI for veterinary pathogens, all strains were susceptible to ceftiofur, florfenicol, enrofloxacin and penicillin. MIC-90 values of these antibiotics were < or = 0.03, 0.5, 2 and < or = 0.13 microg/mL, respectively. A low degree of resistance was observed for gentamicin (1.3%), spectinomycin (3.6%) and trimethoprim/sulphamethoxazole (6.0%). MIC-90 values of these antibiotics were 8, 16 and 2 microg/mL, respectively. A high level of resistance was observed for tetracycline (75.1%). A MIC-90 value of 64 microg/mL was found for this antibiotic. Serotype-associated differences in MIC-90 values were observed for tetracycline, tilmicosin and trimethoprim/suphamethoxazole.

Rapid selection of quinolone resistance in Campylobacter jejuni but not in Escherichia coli in individually housed broilers

OBJECTIVE

To determine the within-host population dynamics of Campylobacter jejuni and Escherichia coli in chickens during and after treatment with fluoroquinolones.

MATERIALS AND METHODS

Total and resistant faecal counts were determined from cloacal swabs during and after treatment with enrofloxacin. Chickens were housed individually to avoid confounding as a result of interaction between animals, and to be able to focus solely on the within-host dynamics. To determine the molecular basis of resistance, a number of isolates were checked for mutations in gyrA.

RESULTS

Treatment with enrofloxacin at doses routinely prescribed (50 ppm) rapidly reduced the faecal counts of E. coli below the detection limit and did not induce resistance. In C. jejuni, on the other hand, treatment with enrofloxacin quickly selected for high frequencies of fluoroquinolone-resistant strains. In all phenotypically resistant isolates, resistance was traced to mutations in the gyrA gene.

CONCLUSIONS

(1) A licensed dosage (50 ppm) of enrofloxacin in drinking water of chickens is effective (i.e. markedly reduced faecal counts) and is safe on a short time scale in E. coli (i.e. did not rapidly select for resistance), but is neither safe nor effective in C. jejuni. (2) The rapid emergence of resistance to quinolones in C. jejuni does not necessarily result from horizontal transmission of resistant strains among chickens, but could solely be the result of de novo selection of resistance in individual chickens.

Molecular epidemiology of unilateral amyloid arthropathy in broiler breeders associated with Enterococcus faecalis

Although symmetrical polyarticular amyloidosis has been described extensively in brown layers, spontaneous unilateral amyloid arthropathy has not been described previously in chickens. Birds from nine flocks of broiler parent stock (PS) had unilateral lameness associated with severe swelling of the left hock joint and the caudal aspect of the metatarsus. Gross pathology was restricted to the left hock joint and the left digital flexor tendons in almost all cases, suggesting an association with administration of Marek's disease vaccine. Amyloid deposits were found in 83% (25/30) of affected joints by histological examination of Congo red stained sections. Systemic amyloidosis, involving mainly the liver and spleen, was found in 59% (10/17) of birds. Enterococcus faecalis was isolated from joints in 77% (23/30) of cases and Staphylococcus aureus was isolated from the joint in one case (1/30). Thirty-five E. faecalis isolates from joints, tendons and blood samples from birds in five affected PS flocks were compared using pulsed-field gel electrophoresis (PFGE) to separate genomic fragments after digestion with SmaI. All but one isolate had identical or closely related restriction endonuclease digestion (RED) patterns that were very similar to a known arthropathic and amyloidogenic E. faecalis isolate. A further 30 E. faecalis isolates from seven grandparent stock (GPS) flocks and two isolates from two unaffected PS flocks of the same genetic background were analysed by PFGE. Among these isolates, 11 originating from four GPS flocks had RED patterns identical to or closely related to the reference amyloid-inducing strain. Moreover, one E. faecalis isolate from amyloidotic joints of brown layers housed in California, USA was included in the analysis and appeared to be identical to the reference strain. This study showed that the E. faecalis isolates involved in these outbreaks of unilateral amyloid arthropathy in broiler breeders belonged to the same clone as that responsible for outbreaks in brown layers.

Aerosol transmission of arthropathic and amyloidogenic Enterococcus faecalis

One-day-old brown layer chicks were exposed to an aerosol of an arthropathic and amyloidogenic Enterococcus faecalis strain alone or after being subjected to treatment with formaldehyde gas (100-200 ppm). Four-day-old chicks were also treated with the same aerosol but after treatment with a Newcastle disease vaccine virus (NDVV) aerosol or intramuscular injection with methylprednisolon at day 1. The same E. faecalis strain was inoculated intramuscularly in day-old chicks as positive control. Bacteremia with time showed that 24 hr after the aerosol the day-old exposed chicks had the highest rate of positive blood cultures (70%-80%). Lower numbers of bacteremic birds at this point in time were found in the chicks treated with E. faecalis aerosol at day 4 (3/10 in the methylprednisolon-treated group and 0/10 in the NDVV-treated group) and the E. faecalis intramuscular-injected group at day 1 (2/10). Formaldehyde gas treatment did not favor the occurrence of bacteremia. NDVV aerosol exposure or injection with corticosteroids did not favor the occurrence of bacteremia 24 hr after E. faecalis aerosol exposure at day 4 either, although 66 days after aerosol, one bird (1/14) treated with NDVV showed bacteremia. A few bacteremic birds were found 10 days after aerosol in the NDVV- and methylprednisolon-treated groups, whereas at 14 days after aerosol, one bacteremic bird was seen in the group subjected to E. faecalis aerosol at day 1, indicating the occurrence of chronic bacteremia. In contrast to the E. faecalis intramuscular-inoculated birds, no joint pathology was seen in the aerosol-exposed groups in spite of the occurrence of chronic bacteremia.

Epidemiology: Study on the vertical transmission of arthropathic and amyloidogenicEnterococcus faecalisin a flock of brown layer chickens

Enterococcus faecalis-related amyloid arthropathy was diagnosed in a sample of birds from a flock of brown layer parent chickens aged 57 weeks. E. faecalis was isolated from amyloidotic knee joints and from blood samples from lame birds. From this flock a smaller one was kept for production purposes to study the vertical transmission of arthropathic and amyloidogenic E. faecalis. Three batches of non-soiled and thoroughly disinfected eggs, to prevent egg-shell contamination, were collected for 6 weeks and submitted for incubation every 2 weeks. No joint pathology was found in the offspring chicks (n = 458) monitored for joint disease until 16 or 21 weeks of age. Fresh and candled eggs (infertiles and dead embryos) obtained at day 18 of the incubation period had negative results at bacteriological examination of the yolk sac, except one non-hatched egg (late embryonal death in shell) from which E. faecalis was isolated. Genotyping by pulsed-field gel electrophoresis (PFGE) of all E. faecalis isolates obtained from blood and joints (except one) of the parent birds and of the non-hatched egg after Sma I digestion showed that all isolates were genetically closely related or identical to a known arthropathic and amyloidogenic E. faecalis strain. In this study, vertical transmission of E. faecalis, although it may occur on a small scale as shown by PFGE, did not seem to play a significant role. Conversely, the chronicity of the condition and the development of an immune response may have affected the efficiency of its transmission.

[Preliminary results of antibiotic resistance monitoring in the Netherlands]

Qualitative tests are used to monitor antimicrobial resistance in bacteria of animal origin in the Netherlands. Quantitative information on trends in resistance is thus not obtained. Moreover, in general a limited panel of antibiotics is tested. The present study describes resistance in zoonotic food-borne pathogens Salmonella, Campylobacter, and Escherichia coli O157 isolated from human clinical cases and from faeces of healthy food animals in 1998 and 1999, as determined with quantitative susceptibility tests. The resistance of the indicator organisms E. coli and Enterococcus faecium isolated from faecal samples of broilers and pigs randomly sampled at slaughterhouses was also determined. For this end, faecal samples from veal calves were sampled in 1996 and 1997 at the three main Dutch veal calf slaughterhouses. In 1998 only a limited number of faecal samples of veal calves were taken at farms. For E. coli and Salmonella the following antibiotics were tested: amoxicillin, amoxicillin-clavulanic acid, piperacillin, cefotaxime, ceftazidime, imipenem, gentamicin, doxycycline, trimethoprim, trimethoprim/sulphamethoxazole, ciprofloxacin, chloramphenicol, florfenicol, carbadox, and flumequine. For E. faecium the following antibiotics were tested: amoxicillin, amoxicillin-clavulanic acid, chloramphenicol, doxycycline, erythromycin, vancomycin, teicoplanin, streptomycin ('high level' > 2000 mg/ml), gentamicin ('high level' > 500 mg/ml), ciprofloxacin, bacitracin, flavofosfolipol, salinomycin, quinupristin-dalfopristin, virginiamycin, tilmicosin, avilamycin, and everninomycin. For Campylobacter the following antibiotics were tested: erythromycin, doxycycline, gentamicin, carbadox, flavofosfolipol, ciprofloxacin, trimethoprim/sulphamethoxazole, amoxicillin, and metronidazole.

The effect of flavophospholipol (Flavomycin) and salinomycin sodium (Sacox) on the excretion of Clostridium perfringens, Salmonella enteritidis, and Campylobacter jejuni in broilers after experimental infection

Intestinal colonization and shedding of pathogenic bacteria in animal feces is an important factor in both human food safety and animal health. The effect of broiler feed additives flavophospholipol (FPL; Flavomycin, bambermycins) and salinomycin sodium (SAL; Sacox) given singly on the excretion of Salmonella enteritidis, Campylobacter jejuni, and Clostridium perfringens was studied following controlled infection. The incidence of shedding (number of birds with positive fecal cultures) and the degree of shedding (cfu per gram of feces in positive birds) were measured to determine the influence of these two common feed additive antibiotics on shedding rates of potential pathogens. A total of 216 Ross broiler chickens, housed in battery cages, were fed either an unmedicated feed (controls), feed containing FPL, or feed containing SAL. Feed treatment groups were subdivided into three bacterial challenge groups of 24 chicks, each receiving only one of the pathogens. Bacterial challenge was administered orally on Days 11 and 12 for Salmonella and Campylobacter and on Days 2 and 3 for Clostridium. Fecal samples were collected weekly up to 6 wk of age and cultured for presence of the target organism. The shedding rate was determined by decimal dilutions of the fecal samples. Feeding FPL resulted in a reduced (P < or = 0.05) degree and incidence of Salmonella and Clostridium shedding at 6 wk. Feeding SAL reduced (P < or = 0.05) the incidence of Salmonella shedding at 6 wk. Neither feed additive affected the incidence nor the degree of Campylobacter shedding. The results of this study indicate that these feed additives may reduce the incidence of these potential human and animal pathogens in preslaughter broilers.

Sensitivity testing of veterinary pathogens with a semi-automatic image analysis system compared with tablet diffusion and agar dilution tests

Recently a commercial computer-controlled image analysis system (IAS) was introduced to measure automatically the diameters of inhibition zones in the agar diffusion test. However, there is little information on the precision of this method. In the present study clinical isolates of Salmonella spp. (N = 104), Escherichia coli (N = 100), Pasteurella spp. (N = 99), Actinobacillus pleuropneumoniae (N = 85), porcine streptococci (N = 100), and Staphylococcus aureus (N = 95) were tested in the agar diffusion test, using nineteen different antibiotics in tablets. All inhibition zone diameters were first measured by a laboratory technician and then by the IAS. Although the zone diameters of all bacteria-antibiotic combinations measured by the IAS and those measured by the laboratory technician showed a significant positive correlation, the size of the inhibition zone diameters measured by the technician and the IAS differed significantly in 59% of the combinations. However, these differences were very small and may have no clinical relevance. The IAS was also used to calculate minimum inhibitory concentrations (MIC values) from the zone diameters. In 82% of the bacteria-antibiotic combinations MIC values calculated by the IAS showed a significant positive correlation with MIC values obtained with the reference agar dilution test. However, in 92% of the bacteria-antibiotic combinations, the calculated MIC values differed significantly from the reference values. In some cases these differences were so large that they could be of clinical relevance. The IAS was unable to measure the diameter of inhibition zones of porcine streptococci properly, due to poor contrast. We concluded that when tablets are used as antibiotic carriers the IAS accurately measures the diameter of inhibition zones for bacteria species that give good contrast between the agar and bacterial growth. MIC values determined with the IAS were only indicative of those determined with the reference agar dilution test.