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1.
Artículo en Inglés | MEDLINE | ID: mdl-38240650

RESUMEN

A novel, Gram-positive, facultative anaerobe, coccoid and non-motile bacterium, designated as CoE-012-22T was isolated from dried beef sausage (the original name in Montenegro is Govedji Kulen) manufactured in the municipality of Rozaje (Montenegro) in 2021. Cells of this strain were oxidase- and catalase-negative. Growth occurred at 4-50 °C, at pH 5.0-8.0 and with 0-6.5 % (w/v) NaCl in diverse growth media. MALDI-TOF analysis identified the strain as Enterococcus canintestini (log score 2). Phylogenetic analysis of the 16S rRNA gene and whole genome sequences assigned the strain to the genus Enterococcus. The closest relatives were E. canintestini DSM 21207T and E. dispar ATCC 51266T with 16S rRNA gene sequence pairwise similarities of 99.34 and 98.59 %, respectively. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between isolate CoE-012-22T and other enterococci species were below the thresholds for species delineation thresholds (95.0 % ANI; 70.0 % dDDH) with maximum identities of 84.13 % (ANIb), 86.43 % (ANIm) and 28.4 % (dDDH) to E. saigonensis JCM 31193T and 70.97 % (ANIb), 88.99 % (ANIm) and 32.4 % (dDDH) to E. malodoratus ATCC 43197T. Two unknown Enterococcus isolates, Enterococcus sp. MJM12 and Enterococcus SMC-9, showed identities of 99.87 and 99.94 % (16S rRNA), 98.57 and 98.65 % (ANIb), 98.93 and 99.02 % (ANIm), and 89.8 and 90.0 % (dDDH) to strain CoE-012-22T and can therefore be regarded as the same species. Based on the characterization results, strain CoE-012-22T was considered to represent a novel species, for which the name Enterococcus montenegrensis sp. nov. is proposed. The type strain is CoE-012-22T (=DSM 115843T=NCIMB 15468T).


Asunto(s)
Enterococcus , Ácidos Grasos , Animales , Bovinos , Ácidos Grasos/química , Técnicas de Tipificación Bacteriana , Análisis de Secuencia de ADN , Filogenia , ARN Ribosómico 16S/genética , ADN Bacteriano/genética , Composición de Base , Fosfolípidos
2.
Infection ; 2024 Mar 06.
Artículo en Inglés | MEDLINE | ID: mdl-38446279

RESUMEN

BACKGROUND: Listeria monocytogenes is a bacterial pathogen known for causing listeriosis, a foodborne illness with a wide spectrum of clinical presentations ranging from mild gastroenteritis to severe invasive disease, particularly affecting immunocompromised individuals, pregnant women, newborns, and the elderly. Successful treatment of patients with recurring listeria episodes due to colonised foreign material is often challenging, typically requiring a combination of antimicrobial treatment and surgical removal. CASE PRESENTATION: Here, we present a particularly complex case of chronic invasive listeriosis with a total of six relapses. After extensive investigations, the patient's ICD device was identified as the focus of infection. CONCLUSION: The confirmation of relapses through cgMLST analysis highlights the persistence of Listeria monocytogenes and the potential for recurrence even after apparent resolution of symptoms in patients with foreign material. It emphasises the necessity for a comprehensive assessment to identify and mitigate the risk of relapses, thereby ensuring optimal management and outcomes.

3.
J Clin Microbiol ; 61(4): e0163122, 2023 04 20.
Artículo en Inglés | MEDLINE | ID: mdl-36988494

RESUMEN

Next-generation whole-genome sequencing is essential for high-resolution surveillance of bacterial pathogens, for example, during outbreak investigations or for source tracking and escape variant analysis. However, current global sequencing and bioinformatic bottlenecks and a long time to result with standard technologies demand new approaches. In this study, we investigated whether novel nanopore Q20+ long-read chemistry enables standardized and easily accessible high-resolution typing combined with core genome multilocus sequence typing (cgMLST). We set high requirements for discriminatory power by using the slowly evolving bacterium Bordetella pertussis as a model pathogen. Our results show that the increased raw read accuracy enables the description of epidemiological scenarios and phylogenetic linkages at the level of gold-standard short reads. The same was true for our variant analysis of vaccine antigens, resistance genes, and virulence factors, demonstrating that nanopore sequencing is a legitimate competitor in the area of next-generation sequencing (NGS)-based high-resolution bacterial typing. Furthermore, we evaluated the parameters for the fastest possible analysis of the data. By combining the optimized processing pipeline with real-time basecalling, we established a workflow that allows for highly accurate and extremely fast high-resolution typing of bacterial pathogens while sequencing is still in progress. Along with advantages such as low costs and portability, the approach suggested here might democratize modern bacterial typing, enabling more efficient infection control globally.


Asunto(s)
Bacterias , Genoma Bacteriano , Técnicas de Genotipaje , Tipificación de Secuencias Multilocus , Secuenciación de Nanoporos , Antígenos Bacterianos/genética , Bacterias/genética , Bacterias/aislamiento & purificación , Bacterias/patogenicidad , Vacunas Bacterianas/genética , Bordetella pertussis/genética , Bordetella pertussis/aislamiento & purificación , Bordetella pertussis/patogenicidad , Farmacorresistencia Bacteriana/genética , Monitoreo del Ambiente , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Tipificación de Secuencias Multilocus/métodos , Secuenciación de Nanoporos/métodos , Filogenia , Reproducibilidad de los Resultados , Factores de Virulencia/genética
4.
Int J Mol Sci ; 23(19)2022 Sep 24.
Artículo en Inglés | MEDLINE | ID: mdl-36232576

RESUMEN

Antimicrobial resistance (AMR) is a public health issue attributed to the misuse of antibiotics in human and veterinary medicine. Since AMR surveillance requires a One Health approach, we sampled nine interconnected compartments at a hydrological open-air lab (HOAL) in Austria to obtain six bacterial species included in the WHO priority list of antibiotic-resistant bacteria (ARB). Whole genome sequencing-based typing included core genome multilocus sequence typing (cgMLST). Genetic and phenotypic characterization of AMR was performed for all isolates. Eighty-nine clinically-relevant bacteria were obtained from eight compartments including 49 E. coli, 27 E. faecalis, 7 K. pneumoniae and 6 E. faecium. Clusters of isolates from the same species obtained in different sample collection dates were detected. Of the isolates, 29.2% were resistant to at least one antimicrobial. E. coli and E. faecalis isolates from different compartments had acquired antimicrobial resistance genes (ARGs) associated with veterinary drugs such as aminoglycosides and tetracyclines, some of which were carried in conjugative and mobilizable plasmids. Three multidrug resistant (MDR) E. coli isolates were found in samples from field drainage and wastewater. Early detection of ARGs and ARB in natural and farm-related environments can identify hotspots of AMR and help prevent its emergence and dissemination along the food/feed chain.


Asunto(s)
Antibacterianos , Drogas Veterinarias , Aminoglicósidos , Antagonistas de Receptores de Angiotensina , Inhibidores de la Enzima Convertidora de Angiotensina , Animales , Antibacterianos/farmacología , Austria , Bacterias/genética , Farmacorresistencia Bacteriana/genética , Farmacorresistencia Bacteriana Múltiple/genética , Escherichia coli/genética , Humanos , Pruebas de Sensibilidad Microbiana , Tetraciclinas , Aguas Residuales , Secuenciación Completa del Genoma
5.
Emerg Infect Dis ; 27(3): 862-871, 2021 03.
Artículo en Inglés | MEDLINE | ID: mdl-33622477

RESUMEN

Pertussis is a vaccine-preventable disease, and its recent resurgence might be attributable to the emergence of strains that differ genetically from the vaccine strain. We describe a novel pertussis isolate-based surveillance system and a core genome multilocus sequence typing scheme to assess Bordetella pertussis genetic variability and investigate the increased incidence of pertussis in Austria. During 2018-2020, we obtained 123 B. pertussis isolates and typed them with the new scheme (2,983 targets and preliminary cluster threshold of <6 alleles). B. pertussis isolates in Austria differed genetically from the vaccine strain, both in their core genomes and in their vaccine antigen genes; 31.7% of the isolates were pertactin-deficient. We detected 8 clusters, 1 of them with pertactin-deficient isolates and possibly part of a local outbreak. National expansion of the isolate-based surveillance system is needed to implement pertussis-control strategies.


Asunto(s)
Bordetella pertussis , Tos Ferina , Alelos , Austria , Proteínas de la Membrana Bacteriana Externa/genética , Bordetella pertussis/genética , Humanos , Vacuna contra la Tos Ferina , Factores de Virulencia de Bordetella
6.
Int J Mol Sci ; 22(11)2021 May 31.
Artículo en Inglés | MEDLINE | ID: mdl-34072783

RESUMEN

Marine mammals have been described as sentinels of the health of marine ecosystems. Therefore, the aim of this study was to investigate (i) the presence of extended-spectrum ß-lactamase (ESBL)- and AmpC-producing Enterobacterales, which comprise several bacterial families important to the healthcare sector, as well as (ii) the presence of Salmonella in these coastal animals. The antimicrobial resistance pheno- and genotypes, as well as biocide susceptibility of Enterobacterales isolated from stranded marine mammals, were determined prior to their rehabilitation. All E. coli isolates (n = 27) were screened for virulence genes via DNA-based microarray, and twelve selected E. coli isolates were analyzed by whole-genome sequencing. Seventy-one percent of the Enterobacterales isolates exhibited a multidrug-resistant (MDR) pheno- and genotype. The gene blaCMY (n = 51) was the predominant ß-lactamase gene. In addition, blaTEM-1 (n = 38), blaSHV-33 (n = 8), blaCTX-M-15 (n = 7), blaOXA-1 (n = 7), blaSHV-11 (n = 3), and blaDHA-1 (n = 2) were detected. The most prevalent non-ß-lactamase genes were sul2 (n = 38), strA (n = 34), strB (n = 34), and tet(A) (n = 34). Escherichia coli isolates belonging to the pandemic sequence types (STs) ST38, ST167, and ST648 were identified. Among Salmonella isolates (n = 18), S. Havana was the most prevalent serotype. The present study revealed a high prevalence of MDR bacteria and the presence of pandemic high-risk clones, both of which are indicators of anthropogenic antimicrobial pollution, in marine mammals.


Asunto(s)
Organismos Acuáticos/microbiología , Enterobacter/enzimología , Mamíferos/microbiología , Salmonella/enzimología , beta-Lactamasas/biosíntesis , Animales , Antibacterianos/farmacología , Proteínas Bacterianas/genética , Técnicas de Tipificación Bacteriana , Farmacorresistencia Bacteriana , Enterobacter/efectos de los fármacos , Enterobacter/genética , Enterobacter/aislamiento & purificación , Genotipo , Pruebas de Sensibilidad Microbiana , Salmonella/efectos de los fármacos , Salmonella/genética , Salmonella/aislamiento & purificación , Factores de Virulencia/genética , beta-Lactamasas/genética
7.
Euro Surveill ; 24(39)2019 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-31576804

RESUMEN

In late December 2018, an outbreak of listeriosis occurred after a group of 32 individuals celebrated in a tavern in Styria, Austria; traditional Austrian food (e.g. meat, meat products and cheese) was served. After the celebration, 11 individuals developed gastrointestinal symptoms, including one case with severe sepsis. Cases had consumed mixed platters with several meat products and pâtés originating from a local production facility (company X). Human, food and environmental samples taken from the tavern and company X were tested for L. monocytogenes. Whole genome sequence-based typing detected a novel L. monocytogenes strain of serotype IVb, sequence type 4 and CT7652 in 15 samples; 12 human, two food and one environmental sample from company X with an allelic difference of 0 to 1. Active case finding identified two further cases who had not visited the tavern but tested positive for the outbreak strain. In total, 13 cases (seven females and six males; age range: 4-84 years) were identified. Liver pâté produced by company X was identified as the likely source of the outbreak. Control measures were implemented and since the end of December 2018, no more cases were detected.


Asunto(s)
Brotes de Enfermedades/estadística & datos numéricos , Listeria monocytogenes/genética , Listeriosis/epidemiología , Hígado/microbiología , Productos de la Carne/microbiología , Adolescente , Adulto , Anciano , Anciano de 80 o más Años , Austria/epidemiología , Niño , Preescolar , Femenino , Humanos , Listeria monocytogenes/aislamiento & purificación , Masculino , Persona de Mediana Edad
8.
Microb Ecol ; 76(3): 801-813, 2018 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-29445826

RESUMEN

Infections due to Clostridioides difficile (previously known as Clostridium difficile) are a major problem in hospitals, where cases can be caused by community-acquired strains as well as by nosocomial spread. Whole genome sequences from clinical samples contain a lot of information but that needs to be analyzed and compared in such a way that the outcome is useful for clinicians or epidemiologists. Here, we compare 663 public available complete genome sequences of C. difficile using average amino acid identity (AAI) scores. This analysis revealed that most of these genomes (640, 96.5%) clearly belong to the same species, while the remaining 23 genomes produce four distinct clusters within the Clostridioides genus. The main C. difficile cluster can be further divided into sub-clusters, depending on the chosen cutoff. We demonstrate that MLST, either based on partial or full gene-length, results in biased estimates of genetic differences and does not capture the true degree of similarity or differences of complete genomes. Presence of genes coding for C. difficile toxins A and B (ToxA/B), as well as the binary C. difficile toxin (CDT), was deduced from their unique PfamA domain architectures. Out of the 663 C. difficile genomes, 535 (80.7%) contained at least one copy of ToxA or ToxB, while these genes were missing from 128 genomes. Although some clusters were enriched for toxin presence, these genes are variably present in a given genetic background. The CDT genes were found in 191 genomes, which were restricted to a few clusters only, and only one cluster lacked the toxin A/B genes consistently. A total of 310 genomes contained ToxA/B without CDT (47%). Further, published metagenomic data from stools were used to assess the presence of C. difficile sequences in blinded cases of C. difficile infection (CDI) and controls, to test if metagenomic analysis is sensitive enough to detect the pathogen, and to establish strain relationships between cases from the same hospital. We conclude that metagenomics can contribute to the identification of CDI and can assist in characterization of the most probable causative strain in CDI patients.


Asunto(s)
Clostridioides difficile/genética , Clostridioides difficile/aislamiento & purificación , Genoma Bacteriano , Secuencia de Aminoácidos , Proteínas Bacterianas/química , Proteínas Bacterianas/genética , Toxinas Bacterianas/metabolismo , Clostridioides difficile/química , Clostridioides difficile/clasificación , Infecciones por Clostridium/microbiología , Dosificación de Gen , Humanos , Datos de Secuencia Molecular , Tipificación de Secuencias Multilocus , Filogenia , Homología de Secuencia de Aminoácido
10.
Microbiol Immunol ; 59(8): 433-42, 2015 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-26085084

RESUMEN

Cattle are reservoirs of enterohemorrhagic Escherichia coli; however, their role in the epidemiology of other pathogenic E. coli remains undefined. A new set of quantitative real-time PCR assays for the direct detection and quantification of nine virulence-associated genes (VAGs) characteristic of the most important human E. coli pathotypes and four serotype-related genes (wzxO104 , fliCH4 , rbfO157 , fliCH7 ) that can be used as a surveillance tool for detection of pathogenic strains was developed. A total of 970 cattle fecal samples were collected in slaughterhouses in Germany and Spain, pooled into 134 samples and analyzed with this tool. stx1, eae and invA were more prevalent in Spanish samples whereas bfpA, stx2, ehxA, elt, est and the rbfO157 /fliCH7 combination were observed in similar proportions in both countries. Genes characteristic of the hybrid O104:H4 strain of the 2011 German outbreak (stx2/aggR/wzxO104 /fliCH4 ) were simultaneously detected in six fecal pools from one German abattoir located near the outbreak epicenter. Although no isolate harboring the full stx2/aggR/wzxO104 /fliCH4 combination was cultured, sequencing of the aggR positive PCR products revealed 100% homology to the aggR from the outbreak strain. Concomitant detection by this direct approach of VAGs from a novel human pathogenic E. coli strain in cattle samples implies that the E. coli gene pool in these animals can be implicated in de novo formation of such highly-virulent strains. The application of this set of qPCRs in surveillance studies could be an efficient early-warning tool for the emergence of zoonotic E. coli in livestock.


Asunto(s)
Enfermedades de los Bovinos/microbiología , Escherichia coli Enterohemorrágica/genética , Infecciones por Escherichia coli/veterinaria , Escherichia coli/genética , Factores de Virulencia/genética , Mataderos , Animales , Bovinos , Escherichia coli Enterohemorrágica/aislamiento & purificación , Monitoreo Epidemiológico , Escherichia coli/aislamiento & purificación , Infecciones por Escherichia coli/microbiología , Heces/microbiología , Genotipo , Alemania , Reacción en Cadena en Tiempo Real de la Polimerasa , Serogrupo , España
11.
BMC Microbiol ; 14: 21, 2014 Feb 03.
Artículo en Inglés | MEDLINE | ID: mdl-24491224

RESUMEN

BACKGROUND: Different polymorphisms have been described as markers to classify the lineages of the Mycobacterium tuberculosis complex. The analysis of nine single nucleotide polymorphisms (SNPs) was used to describe seven SNPs cluster groups (SCGs). We attempted to classify those strains that could not been categorized into lineages by the genotyping methods used in the routine testing. RESULTS: The M. tuberculosis complex isolates collected in 2010 in our region were analysed. A new method based on multiplex-PCRs and pyrosequencing to analyse these SNPs was designed. For the pyrosequencing assay nine SNPs that defined the seven SCGs were selected from the literature: 1977, 74092, 105139, 232574, 311613, 913274, 2460626, 3352929 and gyrA95. In addition, SNPs in katG(463), mgtC(182), Ag85C(103) and RD(Rio) deletion were detected. CONCLUSIONS: This work has permitted to achieve a better classification of Aragonian strains into SCGs and in some cases, to assign strains to its certain lineage. Besides, the description of a new pattern shared by two isolates "SCG-6c" reinforces the interest of SNPs to follow the evolution of M. tuberculosis complex.


Asunto(s)
Análisis por Conglomerados , Tipificación Molecular/métodos , Mycobacterium tuberculosis/clasificación , Mycobacterium tuberculosis/genética , Filogenia , Polimorfismo de Nucleótido Simple , Humanos , Reacción en Cadena de la Polimerasa Multiplex , Análisis de Secuencia de ADN , España , Tuberculosis/microbiología
12.
Microbiol Resour Announc ; 13(4): e0003524, 2024 Apr 11.
Artículo en Inglés | MEDLINE | ID: mdl-38451213

RESUMEN

Microbacterium plantarum (M. plantarum) was recently described as a new species isolated from copper globemallow (Sphaeralcea angustifolia). Here, we report the complete genome of M. plantarum CoE-159-22, which was obtained from traditionally produced Montenegrin cheese.

13.
Microbiol Resour Announc ; 10(31): e0054621, 2021 Aug 05.
Artículo en Inglés | MEDLINE | ID: mdl-34351226

RESUMEN

Lactococcus garvieae and Lactococcus petauri cause lactococcosis in fish. Both species have also been isolated from various food products and are considered emerging zoonotic pathogens. Here, we report the genomes of L. garvieae INF126 and L. petauri INF110, obtained from traditional Montenegrin brine cheeses.

14.
Microorganisms ; 9(8)2021 Jul 28.
Artículo en Inglés | MEDLINE | ID: mdl-34442691

RESUMEN

In many dairy products, Leuconostoc spp. is a natural part of non-starter lactic acid bacteria (NSLAB) accounting for flavor development. However, data on the genomic diversity of Leuconostoc spp. isolates obtained from cheese are still scarce. The focus of this study was the genomic characterization of Leuconostoc spp. obtained from different traditional Montenegrin brine cheeses with the aim to explore their diversity and provide genetic information as a basis for the selection of strains for future cheese production. In 2019, sixteen Leuconostoc spp. isolates were obtained from white brine cheeses from nine different producers located in three municipalities in the northern region of Montenegro. All isolates were identified as Ln. mesenteroides. Classical multilocus sequence tying (MLST) and core genome (cg) MLST revealed a high diversity of the Montenegrin Ln. mesenteroides cheese isolates. All isolates carried genes of the bacteriocin biosynthetic gene clusters, eight out of 16 strains carried the citCDEFG operon, 14 carried butA, and all 16 isolates carried alsS and ilv, genes involved in forming important aromas and flavor compounds. Safety evaluation indicated that isolates carried no pathogenic factors and no virulence factors. In conclusion, Ln. mesenteroides isolates from Montenegrin traditional cheeses displayed a high genetic diversity and were unrelated to strains deposited in GenBank.

15.
Microbiol Resour Announc ; 10(37): e0076221, 2021 Sep 16.
Artículo en Inglés | MEDLINE | ID: mdl-34528819

RESUMEN

Extraintestinal Escherichia coli sequence type 1193 (ST1193) is an important source of fluoroquinolone resistance, which has emerged in recent years. We report the first draft genome sequence and annotation of a multidrug-resistant E. coli ST1193 strain obtained from a wastewater treatment plant in Austria.

16.
Antibiotics (Basel) ; 10(9)2021 Sep 03.
Artículo en Inglés | MEDLINE | ID: mdl-34572647

RESUMEN

The aim of this study was continuous monitoring of the presence of mcr-1 to mcr-5 genes in Enterobacterales isolated from cattle, pigs, and domestic poultry at intensive breeding facilities in Northern Vojvodina, Serbia, from 1 January 1 to 1 October 2020. Out of 2167 examined samples, mcr-1 was observed in five E. coli isolates originating from healthy turkeys. Four isolates belonged to the phylogenetic group B1, and one isolate to the phylogenetic group A. Detected E. coli serogenotypes (somatic O and flagellar H antigens) were O8:H25 and O29:H25. Core-genome multi-locus sequence typing (cgMLST) revealed three ST58 isolates clustering together in Clonal Complex (CC) 155 and two singletons of ST641-CC86 and ST410-CC23, respectively. Clonotyping revealed CH4-32 (n = 3), CH6-53 (n = 1) and CH4-24 (n = 1). In all isolates, the mcr-1 gene was located on a large IncX4 replicon type plasmid. Eight virulence-associated genes (VAGs) typical of avian pathogenic E. coli (APEC) (fyuA, fimH, hlyF, iss, ompT, sitA, traT, iroN) were detected in four isolates. These isolates were investigated for susceptibility to four biocides and revealed MIC values of 0.125% for glutardialdehyde, of 0.00003-0.00006% for chlorohexidine, of 4-6% for isopropanol and of 0.001-0.002% for benzalkonium chloride. All obtained MIC values of the tested biocides were comparable to the reference strain, with no indication of possible resistance. This is the first report of mcr-1.1-carrying E. coli from Serbia. Although only samples from turkeys were mcr-positive in this study, continuous monitoring of livestock samples is advised to prevent a spill-over from animals to humans.

17.
Front Microbiol ; 10: 2282, 2019.
Artículo en Inglés | MEDLINE | ID: mdl-31632381

RESUMEN

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.

18.
Artículo en Inglés | MEDLINE | ID: mdl-31516698

RESUMEN

Background: Enterococcus faecium is part of the human gastrointestinal flora but may act as opportunistic pathogen. Environmental persistence, high colonization capability and diverse intrinsic and acquired resistance mechanisms make it especially successful in nosocomial high-risk settings. In March 2014, an outbreak of Linezolid resistant Enterococcus faecium (LREfm) was observed at the hematooncology department of a tertiary care center in Upper Austria. Methods: We report on the outbreak investigation together with the whole genome sequencing (WGS)-based typing results including also non-outbreak LREfm and susceptible isolates. Results: The 54 investigated isolates could be divided in six clusters based on cgMLST. Cluster one comprised LREfm isolates of genotype ST117 and CT24, which was identified as the causative clone of the outbreak. In addition, the detection of four other clusters comprising isolates originating from hematooncology patients but also at other hospitals, pointed to LREfm transmission between local healthcare facilities. LREfm patients (n = 36) were typically at risk for acquisition of nosocomial pathogens because of immunosuppression, frequent hospitalization and antibiotic therapies. Seven of these 36 patients developed LREfm infection but were successfully treated. After termination of the initial outbreak, sporadic cases occurred despite a bundle of applied outbreak control interventions. Conclusions: WGS proved to be an effective tool to differentiate several LREfm clusters in an outbreak. Active screening for LREfm is important in a high-risk setting such as hematooncology, where multiple introductions are possible and occur despite intensified infection control measures.


Asunto(s)
Infección Hospitalaria/epidemiología , Brotes de Enfermedades , Farmacorresistencia Bacteriana , Enterococcus faecium/aislamiento & purificación , Infecciones por Bacterias Grampositivas/epidemiología , Adulto , Anciano , Anciano de 80 o más Años , Austria , Infección Hospitalaria/microbiología , Infección Hospitalaria/transmisión , Enterococcus faecium/clasificación , Enterococcus faecium/efectos de los fármacos , Femenino , Genoma Bacteriano , Infecciones por Bacterias Grampositivas/microbiología , Infecciones por Bacterias Grampositivas/transmisión , Humanos , Linezolid , Masculino , Persona de Mediana Edad , Tipificación Molecular , Filogenia , Centros de Atención Terciaria , Secuenciación Completa del Genoma , Adulto Joven
19.
Travel Med Infect Dis ; 31: 101362, 2019.
Artículo en Inglés | MEDLINE | ID: mdl-30609386

RESUMEN

BACKGROUND: We studied geographic distribution of diarrhoeagenic Escherichia coli virulence genes (DEC VGs) acquisition in travellers and investigated if they acquired highly virulent EAEC/STEC hybrid strains. METHODS: From the prospective, multicentre COMBAT study among 2001 Dutch travellers, 491 travellers were selected based on travel destination to 7 subregions. Faecal samples taken directly before and after travel were screened for nine DEC VGs with real-time PCR. Incidence proportions and rates were calculated for each gene and subregion. RESULTS: 479 travellers were analysed. 21.8% acquired aggR (EAEC), with highest acquisition rates in Northern and Western Africa and 15.3% acquired eae (STEC/EPEC) with highest rates in travellers to Western and Eastern Africa. ETEC (elt or est gene) was acquired by 4.2% of travellers and acquisition of est was associated with traveller's diarrhoea. Overall, the risk of acquiring DEC VGs was low in Southern Africa and South America. Although the combination of aggR (EAEC) and stx1/2 (STEC) was acquired by 3 travellers, these genes could not be detected together in a single E. coli strain. CONCLUSIONS: The risk of acquisition of DEC VGs strongly depends on the travel destination, with those travelling to Africa - except Southern Africa - having a higher risk.


Asunto(s)
Infecciones por Escherichia coli/microbiología , Escherichia coli/genética , Escherichia coli/patogenicidad , Viaje , Factores de Virulencia/genética , Heces/microbiología , Transferencia de Gen Horizontal , Humanos , Países Bajos , Estudios Prospectivos , Riesgo
20.
Microbiologyopen ; 6(3)2017 06.
Artículo en Inglés | MEDLINE | ID: mdl-28213899

RESUMEN

Cattle are the main reservoirs for Shiga-toxin-producing Escherichia coli (STEC), the only known zoonotic intestinal E. coli pathotype. However, there are other intestinal pathotypes that can cause disease in humans, whose presence has been seldom investigated. Thus, our aim was to identify the effects of anthropic pressure and of wild and domestic ungulate abundance on the distribution and diversity of the main human E. coli pathotypes and nine of their representative virulence genes (VGs). We used a quantitative real-time PCR (qPCR) for the direct detection and quantification of the genus-specific gene uidA, nine E. coli VGs (stx1, sxt2, eae, ehxA, aggR, est, elt, bfpA, invA), as well as four genes related to O157:H7 (rfbO157 , fliCH7 ) and O104:H4 (wzxO104 , fliCH4 ) serotypes in animals (feces from deer, cattle, and wild boar) and water samples collected in three areas of Doñana National Park (DNP), Spain. Eight of the nine VGs were detected, being invA, eae, and stx2 followed by stx1, aggR, and ehxA the most abundant ones. In quantitative terms (gene copies per mg of sample), stx1 and stx2 gave the highest values. Significant differences were seen regarding VGs in the three animal species in the three sampled areas. The serotype-related genes were found in all but one sample types. In general, VGs were more diverse and abundant in the northern part of the Park, where the surface waters are more contaminated by human waste and farms. In the current study, we demonstrated that human influence is more relevant than host species in shaping the E. coli VGs spatial pattern and diversity in DNP. In addition, wildlife could be potential reservoirs for other pathotypes different from STEC, however further isolation steps would be needed to completely characterize those E. coli.


Asunto(s)
Ecosistema , Infecciones por Escherichia coli/veterinaria , Escherichia coli O157/genética , Evolución Molecular , Genotipo , Factores de Virulencia/genética , Animales , Animales Domésticos , Animales Salvajes , Bovinos , Ciervos , Infecciones por Escherichia coli/microbiología , Escherichia coli O157/clasificación , Escherichia coli O157/aislamiento & purificación , Heces/microbiología , Reacción en Cadena en Tiempo Real de la Polimerasa , España , Sus scrofa , Microbiología del Agua
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