Abstract
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.
Summary
The objective of this study was to analyse the occurrence of methicillin‐resistant Staphylococcus aureus (MRSA) in three dairy herds in the southwest of Germany that had experienced ...individual cases of clinical and subclinical mastitis associated with MRSA. The herds were identified by the detection of MRSA during routine resistance testing of mastitis pathogens. All quarters of all cows in the herds that were positive on California Mastitis Test were sampled for bacteriological analysis on two occasions. Bulk tank milk samples were also tested. Furthermore, nasal swabs were collected from people working on the farms and from cattle. Environmental samples were collected from associated pig holdings. Isolates were characterized using spa‐typing and testing for antimicrobial resistance. Our results revealed a substantial spread of MRSA in the three dairy herds. In the first of the two investigations carried out on all cows in the three herds, milk samples of 5.1–16.7% of dairy cows were found positive for MRSA. The respective proportions in the second herd level investigation were 1.4–10.0%. Quarters harbouring MRSA had higher somatic cell counts than quarters that were negative on culture. Methicillin‐resistant Staphylococcus aureus were also detected in nasal swabs of staff (7/9), cows (7/15) and calves (4/7), bulk tank milk samples (3/3) and environmental samples from pig premises (4/5) on the farm. Herds B and C had no contact to herd A. However, in all three herds MRSA of spa‐type t011 were detected in milk samples. Results show that MRSA of spa‐type t011 is a problem in dairy farms that needs urgent attention.
is an important pathogen for both humans and animals. It can infect livestock, as well as pets and wild animals. During recent years, a number of reports have described the isolation of
from zoo ...animals, mainly birds and mammals, for which the infection was mostly lethal. Between 2005 and 2019, there were at least 17 cases of deceased mammals, belonging to five different species, which suffered from a
infection at the Zoo Wuppertal, Germany. Since only scarce information exists on the properties of
from zoo animals, we characterized eight isolates, covering all infected species, in detail. All isolates were members of biotype 1, but belonged to five serotypes, five sequence types (STs), and seven core-genome multilocus sequence types (cgMLSTs). Using pulsed-field gel electrophoresis (PFGE) analysis and whole-genome sequencing (WGS), the seven isolates could be discriminated from each other. They differed significantly regarding their virulence genes and mobile genetic elements. While the virulence plasmid pYV existed in all serotypes (five isolates), a complete high-pathogenicity island (HPI) was detected only in the serotypes O:1a, O:1b, and O:13 (four isolates), but not in O:2a and O:2b. Similarly, the content of other plasmids and prophages varied greatly between the isolates. The data demonstrate that the deceased mammals were infected by seven individual isolates and not by a single type predominating in the zoo animals.
A few reports indicate that livestock might represent a new reservoir for carbapenemase-producing Enterobacteriaceae (CPE). In 2015, VIM-1-producing
Escherichia coli
were detected at slaughter in ...colon contents of animals from a German fattening pig farm within the national monitoring on ESBL-producing
E. coli.
In this study, pooled faces samples from pigs, as well as samples from the barn surrounding environment of this fattening farm were taken, to evaluate the dissemination of CPEs. Several modifications of the culture-dependent detection procedure were investigated for their potential to improve the sensitivity of the CPE isolation method. The current reference procedure was adapted by adding a real-time PCR pre-screening and additional enrichment steps. It was possible to isolate 32 VIM-1-producing
E. coli
from four fecal samples of three different barns using two serial enrichment steps in combination with real-time PCR and selective agar plates. By genetic typing, we confirmed the presence of two
E. coli
clonal lineages circulating on this particular farm: one was harboring the
bla
VIM–
1
on an IncHI2 plasmid while the second lineage carried the gene on the chromosome. Despite its different locations, the
bla
VIM–
1
gene was harbored on a class 1 integron in both clonal lineages. Whole-genome sequencing revealed that the VIM-1-carrying plasmids exhibited only slight variability in its compositions and sizes. We assume that the prevalence of CPEs in animal production in Germany and other European countries might be underestimated and there is a concern of further spread of VIM-1-producing bacteria in German livestock and food.
Contamination of food during processing is recognized as a main transmission route of
To prevent microbial contamination, biocides are widely applied as disinfectants in food processing plants. ...However, there are concerns about the development of antimicrobial resistance in foodborne pathogens due to widespread biocide usage. In our study, 93
isolates from German food production facilities were (i) tested for biocide and antibiotic susceptibility using broth microdilution assays, (ii) analyzed for links between reduced biocide susceptibility and antibiotic resistance, and (iii) characterized by whole-genome sequencing, including the detection of genes coding for biocide tolerance, antibiotic resistance, and other virulence factors. Fifteen
isolates were tolerant to benzalkonium chloride (BAC), and genes conferring BAC tolerance were found in 13 of them. Antibiotic resistance was not associated with biocide tolerance. BAC-tolerant isolates were assigned to 6 multilocus sequence type (MLST) clonal complexes, and most of them harbored internalin A pseudogenes with premature stop codons or deletions (
= 9). Our study demonstrated a high genetic diversity among the investigated isolates including genotypes that are frequently involved in human infections. Although
adaptation studies to biocides have raised concerns about increasing cross-resistance to antibiotics, our results do not provide evidence for this phenomenon in field isolates.
Foodborne pathogens such as
can persist in food production environments for a long time, causing perennial outbreaks. Hence, bacterial pathogens are able to survive cleaning and disinfection procedures. Accordingly, they may be repeatedly exposed to sublethal concentrations of disinfectants, which might result in bacterial adaptation to these biocides. Furthermore, antibiotic coresistance and cross-resistance are known to evolve under biocide selection pressure
Hence, antimicrobial tolerance seems to play a crucial role in the resilience and persistence of foodborne pathogens in the food chain and might reduce therapeutic options in infectious diseases.
During recent years, the animal-associated methicillin-resistant Staphylococcus aureus clone ST398 has extensively been studied. The DNA of these isolates turned out to be refractory to SmaI ...restriction, and consequently, SmaI is unsuitable for subtyping this clone by standard pulsed-field gel electrophoresis (PFGE). Very recently, ST398 DNA was shown to be digested by Cfr9I, a neoschizomer of SmaI. In the present study, we employed Cfr9I PFGE on 100 German and 5 Dutch ST398 isolates and compared their PFGE profiles, protein A gene variable repeat regions (spa types), and types of the staphylococcal cassette chromosome mec (SCCmec). The isolates (from healthy carrier pigs, clinical samples from pigs, dust from farms, milk, and meat) were assigned to 35 profiles, which were correlated to the SCCmec type. A dendrogram with the Cfr9I patterns assigned all profiles to two clusters. Cluster A grouped nearly all isolates with SCCmec type V, and cluster B comprised all SCCmec type IVa and V* (a type V variant first identified as III) carriers plus one isolate with SCCmec type V. Both clusters also grouped methicillin-susceptible S. aureus isolates. The association of the majority of isolates with SCCmec type V in one large cluster indicated the presence of a successful subclone within the clonal complex CC398 from pigs, which has diversified. In general, the combination of Cfr9I PFGE with spa and SCCmec typing demonstrated the heterogeneity of the series analyzed and can be further used for outbreak investigations and traceability studies of the MRSA ST398 emerging clone.
Abstract
The large number of non-coding RNAs (ncRNAs) and their breadth of functionalities has fuelled many studies on their roles in cancer. We previously linked four microRNAs to breast cancer ...prognosis. One of these microRNAs,
hsa-miR-7
, was found to be regulated by another type of ncRNA, the circular non-coding RNA (circRNA)
CDR1-AS
, which contains multiple
hsa-miR-7
binding sites. Based on this finding, we studied the potential clinical value of this circRNA on breast cancer prognosis in a cohort based on a cohort that was previously analysed for
hsa-miR-7
and in an adjuvant hormone-naïve cohort for 1
st
-line tamoxifen treatment outcomes, in which we also analysed
hsa-miR-7
. A negative correlation was observed between
hsa-miR-7
and
CDR1-AS
in both cohorts. Despite associations with various clinical metrics (e.g., tumour grade, tumour size, and relapse location),
CDR1-AS
was neither prognostic nor predictive of relevant outcomes in our cohorts. However, we did observe stromal
CDR1-AS
expression, suggesting a possible cell-type specific interaction. Next to the known association of
hsa-miR-7
expression with poor prognosis in primary breast cancer, we found that high
hsa-miR-7
expression was predictive of an adverse response to tamoxifen therapy and poor progression-free and post-relapse overall survival in patients with recurrent disease.
An increasing number of reported detections of methicillin‐resistant Staphylococcus aureus (MRSA) in food animals since 2007 has led to the assumption that there is an emerging zoonotic problem with ...livestock associated (la)MRSA potentially aggravating the MRSA problem in humans. It was the objective of the study to investigate, whether MRSA was present in clinical specimens of pigs collected at post‐mortem since 2004 and to further characterize these isolates. We studied 138 isolates of S. aureus collected between 2004 and 2007 from various pathological lesions of pigs at necropsy. Potential MRSA were identified by growth on selective chromogenic media. Isolates were confirmed as MRSA using multiplex PCR. Confirmed isolates were spa‐ and SCCmec‐typed and were tested for antimicrobial resistance. Overall, 60 (43%) S. aureus isolates were identified as MRSA. The majority (57/60) of the MRSA isolates found in the altered porcine tissues were spa‐types associated with MRSA ST398. Three MRSA were ST97 isolates, a type that has not been described as an MRSA in pigs before. Other clonal complexes (ST9, ST30) dominated among the methicillin‐sensitive S. aureus. MRSA were found in similar frequency in all 4 years. We assume that MRSA in pigs may have occurred earlier than 2004 and might be not really ‘emerging', but rather have been overlooked until recently. The potentially causative role of the MRSA in the lesions warrants further investigation.
This work generates the data needed to set epidemiological cut-off values for disc-diffusion zone measurements of Vibrio cholerae. The susceptibility of 147 European isolates of non-O1/non-O139 V. ...cholerae to 19 antibiotics was established using a standardised disc diffusion method which specified incubation of Mueller Hinton agar plates at 35°C. Epidemiological cut-off values were calculated by analysis of the zone size data with the statistically based normalised resistance interpretation method. Cut-off values for 17 agents were calculated by analysis of the aggregated data from all 4 laboratories participating in this study. The cut-off values calculated were ≥18 mm for amoxicillin/clavulanate, ≥18 mm for amikacin, ≥19 mm for ampicillin, ≥27 mm for cefepime, ≥31 mm for cefotaxime, ≥24 mm for ceftazidime, ≥24 mm for chloramphenicol, ≥31 mm for ciprofloxacin, ≥16 mm for erythromycin, ≥ 27 mm for florfenicol, ≥16 mm for gentamicin, ≥23 mm for imipenem, ≥25 mm for meropenem, ≥29 mm for nalidixic acid, ≥28 mm for norfloxacin, ≥13 mm for streptomycin and ≥23 mm for tetracycline. For the other 2 agents the data from 1 laboratory was excluded from the censored aggregation because the data from that laboratory was considered excessively imprecise. The cut-off values for these 2 agents calculated for the aggregation of the data from 3 laboratories were ≥23 mm for trimethoprim and ≥24 mm for trimethoprim/sulfamethoxazole. These zone size data will be submitted to the Clinical Laboratory Standards Institute (CLSI) and European Committee for Antimicrobial Susceptibility Testing (EUCAST) for their consideration in setting international consensus epidemiological cut-off values for non O1/non-O139 V. cholerae.
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