Whole-genome sequencing (WGS) has emerged today as an ultimate typing tool to characterize Listeria monocytogenes outbreaks. However, data analysis and interlaboratory comparability of WGS data are ...still challenging for most public health laboratories. Therefore, we have developed and evaluated a new L. monocytogenes typing scheme based on genome-wide gene-by-gene comparisons (core genome multilocus the sequence typing cgMLST) to allow for a unique typing nomenclature. Initially, we determined the breadth of the L. monocytogenes population based on MLST data with a Bayesian approach. Based on the genome sequence data of representative isolates for the whole population, cgMLST target genes were defined and reappraised with 67 L. monocytogenes isolates from two outbreaks and serotype reference strains. The Bayesian population analysis generated five L. monocytogenes groups. Using all available NCBI RefSeq genomes (n = 36) and six additionally sequenced strains, all genetic groups were covered. Pairwise comparisons of these 42 genome sequences resulted in 1,701 cgMLST targets present in all 42 genomes with 100% overlap and ≥90% sequence similarity. Overall, ≥99.1% of the cgMLST targets were present in 67 outbreak and serotype reference strains, underlining the representativeness of the cgMLST scheme. Moreover, cgMLST enabled clustering of outbreak isolates with ≤10 alleles difference and unambiguous separation from unrelated outgroup isolates. In conclusion, the novel cgMLST scheme not only improves outbreak investigations but also enables, due to the availability of the automatically curated cgMLST nomenclature, interlaboratory exchange of data that are crucial, especially for rapid responses during transsectorial outbreaks.
In 2009, the European Society of Clinical Microbiology and Infectious Diseases (ESCMID) published the first treatment guidance document for Clostridioides difficile infection (CDI). This document was ...updated in 2014. The growing literature on CDI antimicrobial treatment and novel treatment approaches, such as faecal microbiota transplantation (FMT) and toxin-binding monoclonal antibodies, prompted the ESCMID study group on C. difficile (ESGCD) to update the 2014 treatment guidance document for CDI in adults.
Key questions on CDI treatment were formulated by the guideline committee and included: What is the best treatment for initial, severe, severe-complicated, refractory, recurrent and multiple recurrent CDI? What is the best treatment when no oral therapy is possible? Can prognostic factors identify patients at risk for severe and recurrent CDI and is there a place for CDI prophylaxis? Outcome measures for treatment strategy were: clinical cure, recurrence and sustained cure. For studies on surgical interventions and severe-complicated CDI the outcome was mortality. Appraisal of available literature and drafting of recommendations was performed by the guideline drafting group. The total body of evidence for the recommendations on CDI treatment consists of the literature described in the previous guidelines, supplemented with a systematic literature search on randomized clinical trials and observational studies from 2012 and onwards. The Grades of Recommendation Assessment, Development and Evaluation (GRADE) system was used to grade the strength of our recommendations and the quality of the evidence. The guideline committee was invited to comment on the recommendations. The guideline draft was sent to external experts and a patients' representative for review. Full ESCMID endorsement was obtained after a public consultation procedure.
Important changes compared with previous guideline include but are not limited to: metronidazole is no longer recommended for treatment of CDI when fidaxomicin or vancomycin are available, fidaxomicin is the preferred agent for treatment of initial CDI and the first recurrence of CDI when available and feasible, FMT or bezlotoxumab in addition to standard of care antibiotics (SoC) are preferred for treatment of a second or further recurrence of CDI, bezlotoxumab in addition to SoC is recommended for the first recurrence of CDI when fidaxomicin was used to manage the initial CDI episode, and bezlotoxumab is considered as an ancillary treatment to vancomycin for a CDI episode with high risk of recurrence when fidaxomicin is not available. Contrary to the previous guideline, in the current guideline emphasis is placed on risk for recurrence as a factor that determines treatment strategy for the individual patient, rather than the disease severity.
Extended Spectrum β-lactamase (ESBL)-producing Enterobacteriaceae are of major concern as they are implicated in multidrug resistant nosocomial infections. They are listed on a recently published ...global priority list of antibiotic-resistant bacteria by the World Health Organization which raises concern in both healthcare and community settings. This study aimed at determining the frequency of ESBL genes in multidrug resistant human clinical Enterobacteriaceae isolates from Edo state Nigeria and to characterize the resistance mechanisms using whole genome sequencing. A total of 217 consecutive clinical isolates of Enterobacteriaceae, selection based on inclusion criteria, were collected from March-May 2015 from three medical microbiology laboratories of hospitals in Edo state Nigeria. All isolates were analyzed using matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry. Antibiotic susceptibility testing was performed by Kirby-Bauer method and minimum inhibitory concentration (MIC) determination by E-test method. Double disc synergy test was used to screen for the production of ESBL. Whole genome sequencing (WGS) was performed for isolate characterization and identification of resistance determinants. Out of 217 consecutive clinical Enterobacteriaceae isolates, 148 (68.2%) were multi-drug resistant. Of these multi-drug resistant isolates, 60 (40.5%) were positive for the ESBL phenotypic test and carried ESBL genes. CTX-M-15 was the predominant ESBL found, among 93.3% (n = 56/60). Thirty-two plasmid incompatibility groups and 28 known and two new sequence types were identified among the ESBL isolates. The high occurrence of CTX-M-15 with associated resistant determinants in multidrug resistant Enterobacteriaceae harboring different plasmid incompatibility groups and sequence types calls for the need of continuous monitoring of this resistance threat to reduce its public health impact. To our knowledge, this study presents the first genomic characterization of ESBL production mediated by blaCTX-M-15 in human clinical isolates of Enterobacter hormaechei, Citrobacter werkmanii and Atlantibacter hermannii from Nigeria.
In 2016, the Austrian Agency for Health and Food Safety started a pilot project to investigate antimicrobial resistance in surface water. Here we report on the characterisation of carbapenem ...resistant and ESBL-producing K. pneumoniae isolates from Austrian river water samples compared to 95 clinical isolates recently obtained in Austrian hospitals.
Ten water samples were taken from four main rivers, collected upstream and downstream of major cities in 2016. For subtyping and comparison, public core genome multi locus sequence typing (cgMLST) schemes were used. The presence of AMR genes, virulence genes and plasmids was extracted from whole genome sequence (WGS) data.
In total three ESBL-producing strains and two carbapenem resistant strains were isolated. WGS based comparison of these five water isolates to 95 clinical isolates identified three clusters. Cluster 1 (ST11) and cluster 2 (ST985) consisted of doublets of carbapenem resistant strains (one water and one clinical isolate each). Cluster 3 (ST405) consisted of three ESBL-producing strains isolated from one water sample and two clinical specimens. The cities, in which patient isolates of cluster 2 and 3 were collected, were in concordance with the water sampling locations downstream from these cities. The genetic concordance between isolates from river water samples and patient isolates raises concerns regarding the release of wastewater treatment plant effluents into surface water. From a public health perspective these findings demand attention and strategies are required to minimize the spread of multiresistant strains to the environment.
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•Detection of ESBL-, carbapenemase-producing K. pneumoniae in Austrian river water•Relatedness of clinical and water isolates identified using WGS.•Accordance of hospital wastewater effluent and water sampling location•Evidence of anthropogenic pollution of river water in urban areas in Austria
There is a link between antibiotic resistance in humans, livestock and the environment. This study was carried out to characterize antibiotic resistant bovine and environmental
isolates from Edo ...state, Nigeria. A total of 109 consecutive isolates of
were isolated from March-May 2015 from 150 fecal samples of healthy bovine animals from three farms at slaughter in Edo state Nigeria. Similarly, 43
isolates were also obtained from a total of 100 environmental samples from different sources. Isolates were recovered and identified from samples using standard microbiological techniques. Recovered isolates were pre-identified by the Microbact Gram-Negative identification system and confirmed with Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry and ribosomal multilocus sequence typing (rMLST). Antibiotic susceptibility testing was carried out by Kirby-Bauer method for 14 antibiotics. Whole genome sequencing (WGS) was carried out for isolate characterization and identification of resistance determinants. Out of 109 animal and 43 environmental
isolates, 18 (17%) and 8 (19%) isolates based on selection criteria showed antibiotic resistance and were further investigated by whole genome sequencing (WGS). Resistance genes were detected in all (100%) of the resistant bovine and environmental
isolates. The resistance determinants included β-lactamase genes, aminoglycoside modifying enzymes,
genes, sulfonamide, tetracycline and trimethoprim resistance genes, respectively. Out of the 18 and 8 resistant animal and environmental isolates 3 (17%) and 2 (25%) were multidrug resistant (MDR) and had resistance determinants which included efflux genes, regulatory systems modulating antibiotic efflux and antibiotic target alteration genes. Our study shows the dissemination of antibiotic resistance especially MDR strains among Nigerian bovine and environmental
isolates. The presence of these resistant strains in animals and the environment constitute a serious health concern indicated by the difficult treatment options of the infections caused by these organisms. To the best of our knowledge we report the first detailed genomic characterization of antibiotic resistance in bovine and environmental
isolates for Nigeria.
Listeria monocytogenes
(
L. monocytogenes
) is a ubiquitous organism that can easily enter the food chain. Infection with
L. monocytogenes
can cause invasive listeriosis. Since 2014, in Austria,
L. ...monocytogenes
isolates from human and food/food-associated samples have been provided on a mandatory basis by food producers and laboratories to the National Reference Laboratory. Since 2017, isolates undergo routinely whole genome sequencing (WGS) and core genome Multilocus Sequence Typing (cgMLST) for cluster analyses. Aims of this study were to characterize isolates and clusters of 2017 by using WGS data and to assess the usefulness of this isolate-based surveillance for generating hypotheses on sources of invasive listeriosis in real-time. WGS data from 31 human and 1744 non-human isolates originating from 2017, were eligible for the study. A cgMLST-cluster was defined as two or more isolates differing by ≤10 alleles. We extracted the sequence types (STs) from the WGS data and analyzed the food subcategories meat, fish, vegetable and diary for associations with the ten most prevalent STs among food, through calculating prevalence ratios (PR) with 95% confidence intervals (CI). The three most frequent STs among the human isolates were ST1 (7/31; 22.6%), ST155 (4/31; 12.9%) and ST451 (3/31; 9.7%) and among the non-human isolates ST451 (614/1744; 35.2%), ST8 (173/1744, 10.0%) and ST9 (117/1744; 6.7%). We found ST21 associated with vegetables (PR: 11.39, 95% CI: 8.32–15.59), ST121 and ST155 with fish (PR: 7.05, 95% CI: 4.88–10.17, PR: 3.29, 95% CI: 1.86–5.82), and ST511, ST7 and ST451 with dairy products (PR: 8.55, 95% CI: 6.65–10.99; PR: 5.05, 95% CI: 3.83–6.66, PR: 3.03, 95% CI: 2.02–4.55). We identified 132 cgMLST-clusters. Six clusters contained human isolates (ST155, ST1, ST101, ST177, ST37 and ST7) and for five of those cgMLST-based cluster analyses solely was able to hypothesize the source: an Austrian meat processing company, two Austrian cheese manufacturers and two vegetable processing companies, one based in Austria and the other in Belgium. Determining routinely STs in food isolates by WGS allows to associate STs with food products. Real-time WGS of
L. monocytogenes
isolates provided mandatorily, proved to be useful in promptly generating hypotheses on sources of invasive listeriosis.
Cronobacter sakazakii has been documented as a cause of life-threating infections, predominantly in neonates. We conducted a multicenter study to assess the occurrence of C. sakazakii across Europe ...and the extent of clonality for outbreak detection. National coordinators representing 24 countries in Europe were requested to submit all human C. sakazakii isolates collected during 2017 to a study center in Austria. Testing at the center included species identification by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, subtyping by whole-genome sequencing (WGS), and determination of antimicrobial resistance. Eleven countries sent 77 isolates, including 36 isolates from 2017 and 41 historical isolates. Fifty-nine isolates were confirmed as C. sakazakii by WGS, highlighting the challenge of correctly identifying Cronobacter spp. WGS-based typing revealed high strain diversity, indicating absence of multinational outbreaks in 2017, but identified 4 previously unpublished historical outbreaks. WGS is the recommended method for accurate identification, typing, and detection of this pathogen.
Invasive listeriosis is a severe foodborne infection in humans and is difficult to control. Listeriosis incidence is increasing worldwide, but some countries have implemented molecular surveillance ...programs to improve recognition and management of listeriosis outbreaks. In Germany, routine whole-genome sequencing, core genome multilocus sequence typing, and single nucleotide polymorphism calling are used for subtyping of Listeria monocytogenes isolates from listeriosis cases and suspected foods. During 2018-2019, an unusually large cluster of L. monocytogenes isolates was identified, including 134 highly clonal, benzalkonium-resistant sequence type 6 isolates collected from 112 notified listeriosis cases. The outbreak was one of the largest reported in Europe during the past 25 years. Epidemiologic investigations identified blood sausage contaminated with L. monocytogenes highly related to clinical isolates; withdrawal of the product from the market ended the outbreak. We describe how epidemiologic investigations and complementary molecular typing of food isolates helped identify the outbreak vehicle.
We investigated genomic determinants of antimicrobial resistance in 1,318 Neisseria gonorrhoeae strains isolated in Austria during 2016–2020. Sequence type (ST) 9363 and ST11422 isolates had high ...rates of azithromycin resistance, and ST7363 isolates correlated with cephalosporin resistance. These results underline the benefit of genomic surveillance for antimicrobial resistance monitoring.
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