species complex: From wastewater to the environment.

plays a significant role in nosocomial infections and spreading antibiotic resistance, and therefore forms a major threat to public health. In this study, we investigated the role of the wastewater pathway in the spread of pathogenic bacteria and more specifically, in the spread of antibiotic resistant subspecies. Whole-genome sequencing was performed of 185  isolates collected from hospital, nursing home, and community wastewater, the receiving wastewater treatment plant (WWTP), and clinical isolates from the investigated hospital.

Targeted phage hunting to specific clinical isolates is an efficient antibiotic resistance and infection control strategy.

is one of the most threatening multi-drug-resistant pathogens today, with phage therapy being a promising alternative for personalized treatments. However, the intrinsic capsule diversity in spp. poses a substantial barrier to the phage host range, complicating the development of broad-spectrum phage-based treatments.

Corrigendum: Phenotypic and molecular characterization of IMP-producing Enterobacterales in Spain: predominance of IMP-8 in and IMP-22 in .

[This corrects the article DOI: 10.3389/fmicb.2022.

An increase in erythromycin resistance in methicillin-susceptible from blood correlates with the use of macrolide/lincosamide/streptogramin antibiotics. EARS-Net Spain (2004-2020).

Objectives: To describe and analyse erythromycin resistance trends in blood isolates of (EARS-Net Spain, 2004-2020) and the association of these trends with the consumption of macrolide, lincosamide, and streptogramin B (MLS) antibiotics. To assess molecular changes that could be involved in erythromycin resistance trends by whole genome analysis of representative isolates.

Materials And Methods: We collected antibiotic susceptibility data for all first-blood isolates in patients from 47 Spanish hospitals according to EARS-Net criteria.

Widespread Detection of Yersiniabactin Gene Cluster and Its Encoding Integrative Conjugative Elements (ICE) among Nonoutbreak OXA-48-Producing Clinical Isolates from Spain and the Netherlands.

In this study, we determined the presence of virulence factors in nonoutbreak, high-risk clones and other isolates belonging to less common sequence types associated with the spread of OXA-48-producing Klebsiella pneumoniae clinical isolates from The Netherlands ( = 61) and Spain ( = 53). Most isolates shared a chromosomally encoded core of virulence factors, including the enterobactin gene cluster, fimbrial and gene clusters, and urea metabolism genes (). We observed a high diversity of K-Locus and K/O loci combinations, KL17 and KL24 (both 16%), and the O1/O2v1 locus (51%) being the most prevalent in our study.

Carbapenemase-Producing in COVID-19 Intensive Care Patients: Identification of IncL-VIM-1 Plasmid in Previously Non-Predominant Sequence Types.

During the COVID-19 pandemic, intensive care units (ICUs) operated at or above capacity, and the number of ICU patients coinfected by nosocomial microorganisms increased. Here, we characterize the population structure and resistance mechanisms of carbapenemase-producing (CP-Kpn) from COVID-19 ICU patients and compare them to pre-pandemic populations of CP-Kpn. We analyzed 84 CP-Kpn isolates obtained during the pandemic and 74 CP-Kpn isolates obtained during the pre-pandemic period (2019) by whole genome sequencing, core genome multilocus sequence typing, plasmid reconstruction, and antibiotic susceptibility tests.

Staphylococcus aureus populations from the gut and the blood are not distinguished by virulence traits-a critical role of host barrier integrity.

Background: The opportunistic pathogen Staphylococcus aureus is an asymptomatically carried member of the microbiome of about one third of the human population at any given point in time. Body sites known to harbor S. aureus are the skin, nasopharynx, and gut.

Phenotypic and molecular characterization of IMP-producing Enterobacterales in Spain: Predominance of IMP-8 in and IMP-22 in .

Objectives: Little is known about IMP-producing Enterobacterales (IMP-Ent) in Europe. We analyzed at genomic and phenotypic level IMP-Ent isolates circulating in Spain in a 9-year period.

Materials And Methods: IMP-Ent isolates submitted to our reference laboratory were included.

Effects of Clinical Wastewater on the Bacterial Community Structure from Sewage to the Environment.

This study pertains to measure differences in bacterial communities along the wastewater pathway, from sewage sources through the environment. Our main focus was on taxa which include pathogenic genera, and genera harboring antibiotic resistance (henceforth referred to as "target taxa"). Our objective was to measure the relative abundance of these taxa in clinical wastewaters compared to non-clinical wastewaters, and to investigate what changes can be detected along the wastewater pathway.

Predominance of CTX-M-15-producing ST131 strains among ESBL-producing Escherichia coli isolated from asylum seekers in the Netherlands.

Objectives: Numerous studies show increased prevalence of MDR bacteria amongst asylum seekers, but data on the molecular profiles of such strains are limited. We aimed to evaluate the molecular profiles of ESBL-producing Escherichia coli (ESBL-E. coli) strains isolated from asylum seekers and investigate their phylogenetic relatedness.

Farm dust resistomes and bacterial microbiomes in European poultry and pig farms.

Background: Livestock farms are a reservoir of antimicrobial resistant bacteria from feces. Airborne dust-bound bacteria can spread across the barn and to the outdoor environment. Therefore, exposure to farm dust may be of concern for animals, farmers and neighboring residents.

Description and determinants of the faecal resistome and microbiome of farmers and slaughterhouse workers: A metagenome-wide cross-sectional study.

Background: By studying the entire human faecal resistome and associated microbiome, the diversity and abundance of faecal antimicrobial resistance genes (ARGs) can be comprehensively characterized. Prior culture-based studies have shown associations between occupational exposure to livestock and carriage of specific antimicrobial resistant bacteria. Using shotgun metagenomics, the present study investigated 194 faecal resistomes and bacteriomes from humans occupationally exposed to ARGs in livestock (i.

Decreasing prevalence of contamination with extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-E) in retail chicken meat in the Netherlands.

Retail chicken meat is a potential source of extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-E). In the past decade, vast national efforts were undertaken to decrease the antibiotic use in the veterinary sector, resulting in a 58% decrease in antibiotic sales in the sector between 2009 and 2014. This decrease in antibiotic use was followed by a decrease in ESBL-E prevalence in broilers.

Revealing the Virulence Potential of Clinical and Environmental Isolates Using Whole-Genome Sequencing.

is considered a common causative agent of human fungal infections. A restricted number of virulence factors have been described, and none of them lead to a differentiation in the virulence level among different strains. Variations in the virulence phenotype depending on the isolate origin, measured as survival percentage in animal infection models, have been previously reported.

Abundance and Antimicrobial Resistance of Three Bacterial Species along a Complete Wastewater Pathway.

After consumption, antibiotic residues and exposed bacteria end up via the feces in wastewater, and therefore wastewater is believed to play an important role in the spread of antimicrobial resistance (AMR). We investigated the abundance and AMR profiles of three different species over a complete wastewater pathway during a one-year sampling campaign, as well as including antimicrobial consumption and antimicrobial concentrations analysis. A total of 2886 isolates (997 , 863 spp.

Extended-spectrum beta-lactamase producing Enterobacteriaceae (ESBL-E) isolated from bean sprouts in the Netherlands.

Community-acquired carriage and infections due to extended-spectrum beta-lactamase producing Enterobacteriaceae (ESBL-E) are increasing worldwide, resulting in increased morbidity, mortality and healthcare costs. The origins of community-acquired ESBL-E carriage and infections remain unclear. Bean sprouts are a potential source of Enterobacteriaceae for the community, as illustrated by outbreaks of pathogenic Enterobacteriaceae in the past.

Detection of in Water from Hospital Dental Chair Units and Molecular Characterization by Whole-Genome Sequencing.

This study aims to assess contamination with spp. in water from dental chair units (DCUs) of a hospital dental ward and to perform its molecular characterization by whole-genome sequencing (WGS). We collect eight water samples (250 mL) from four DCUs (sink and water-syringe).

Epidemiology of Extended-Spectrum β-Lactamase-Producing and Vancomycin-Resistant Enterococci in the Northern Dutch-German Cross-Border Region.

To reveal the prevalence and epidemiology of extended-spectrum β-lactamase (ESBL)- and/or plasmid AmpC (pAmpC)- and carbapenemase (CP) producing and vancomycin-resistant enterococci (VRE) across the Northern Dutch-German border region. A point-prevalence study on ESBL/pAmpC/CP producing and VRE was carried out in hospitalized patients in the Northern Netherlands ( = 445, 2012-2013) and Germany ( = 242, 2012). Healthy individuals from the Dutch community ( = 400, 2010-2012) were also screened.

Reprint of "Application of next generation sequencing in clinical microbiology and infection prevention".

Current molecular diagnostics of human pathogens provide limited information that is often not sufficient for outbreak and transmission investigation. Next generation sequencing (NGS) determines the DNA sequence of a complete bacterial genome in a single sequence run, and from these data, information on resistance and virulence, as well as information for typing is obtained, useful for outbreak investigation. The obtained genome data can be further used for the development of an outbreak-specific screening test.

Application of next generation sequencing in clinical microbiology and infection prevention.

Current molecular diagnostics of human pathogens provide limited information that is often not sufficient for outbreak and transmission investigation. Next generation sequencing (NGS) determines the DNA sequence of a complete bacterial genome in a single sequence run, and from these data, information on resistance and virulence, as well as information for typing is obtained, useful for outbreak investigation. The obtained genome data can be further used for the development of an outbreak-specific screening test.

Phylogeny, resistome and mobile genetic elements of emergent OXA-48 and OXA-245 Klebsiella pneumoniae clones circulating in Spain.

Objectives: The global emergence of OXA-48-producing Klebsiella pneumoniae clones is a significant threat to public health. We used WGS and phylogenetic analysis of Spanish isolates to investigate the population structure of blaOXA-48-like-expressing K. pneumoniae ST11 and ST405 and to determine the distribution of resistance genes and plasmids encoding blaOXA-48-like carbapenemases.

Molecular Typing of Enterobacteriaceae from Pig Holdings in North-Western Germany Reveals Extended- Spectrum and AmpC β-Lactamases Producing but no Carbapenem Resistant Ones.

The increase of extended- spectrum β-lactamase-producing Enterobacteriaceae (ESBL-E) in humans and in food-producing animals is of public health concern. The latter could contribute to spreading of these bacteria or their resistance genes to humans. Several studies have reported the isolation of third generation cephalosporin resistant bacteria in livestock animals.

Frequent carriage of resistance mechanisms to β-lactams and biofilm formation in Haemophilus influenzae causing treatment failure and recurrent otitis media in young children.

Objectives: Non-typeable Haemophilus influenzae are a major cause of acute otitis media (AOM), including chronic and recurrent otitis in young children. The objective of this study was to determine whether non-typeable H. influenzae isolates causing these infections produce biofilms and carry resistance mechanisms to β-lactams.