Multidrug-Resistant and Clinically Relevant Gram-Negative Bacteria Are Present in German Surface Waters

Water is considered to play a role in the dissemination of antibiotic-resistant Gram-negative bacteria including those encoding Extended-spectrum beta-lactamases (ESBL) and carbapenemases. To investigate the role of water for their spread in more detail, we characterized ESBL/Carbapenemase-producing bacteria from surface water and sediment samples using phenotypic and genotypic approaches. ESBL/Carbapenemase-producing isolates were obtained from water/sediment samples. Species and antibiotic resistance were determined. A subset of these isolates (n = 33) was whole-genome-sequenced and analyzed for the presence of antibiotic resistance genes and virulence determinants. Their relatedness to isolates associated with human infections was investigated using multilocus sequence type and cgMLST-based analysis. Eighty-nine percent of the isolates comprised of clinically relevant species. Fifty-eight percent exhibited a multidrug-resistance phenotype. Two isolates harbored the mobile colistin resistance gene mcr-1. One carbapenemase-producing isolate identified as Enterobacter kobei harbored bla(VIM-)(1). Two Escherichia coli isolates had sequence types (ST) associated with human infections (ST131 and ST1485) and a Klebsiella pneumoniae isolate was classified as hypervirulent. A multidrug-resistant (MDR) Pseudomonas aeruginosa isolate encoding known virulence genes associated with severe lung infections in cystic fibrosis patients was also detected. The presence of MDR and clinically relevant isolates in recreational and surface water underlines the role of aquatic environments as both reservoirs and hot spots for MDR bacteria. Future assessment of water quality should include the examination of the multidrug resistance of clinically relevant bacterial species and thus provide an important link regarding the spread of MDR bacteria in a One Health context.Peer reviewe

Characterization of porphyrin nanorods on fluorine doped tin oxide glass sheet

Porphyrin nanorods (PNR) have been fabricated by electrostatic self-assembly of two oppositely charged porphyrin molecules. The free base meso-tetra-(4-phenylsulphonate) porphyrin (TPPS4)4) served as negatively charged counterpart for the positively charged metallo meso-tetra(4-NN-methylpyridyl) porphyrins (MTM’PyP) with either Sn, Co, Mn or In as central metal M. Films of PNR were prepared on fluorine doped tin oxide glass sheets (FTO) by using a drop-dry method. The electronic spectra revealed J-aggregation of the charged molecules for the colloid PNR as well as for the films. Transmission electron microscopy confirmed the formation of porphyrin nanorods. The laser microscope and scanning electron microscope (SEM) images of the PNR/FTO films showed the formation of three kinds of structures in the films which consist of differently branched or linear needles with their main axis grown in the direction of the solvent flow during preparation. During cyclic voltammetry either applying negative potentials from 0.0 V to -1.0 V or positive potentials from 0.0 V to ++2.2 V irreversible reduction or oxidation reactions were detected for the films. Consistently, SEM images taken following cyclic voltammetry showed the disintegration of the PNR on the films into smaller subunits. Spectroelectrochemical measurements showed the formation of porphyrin anionic radicals during oxidation by a decrease in the absorption intensities and broadening of spectra with an additional band appearing around 900 nm. A similar trend was observed when negative potentials were applied but in this case the cationic radical was produced. In both cases the decrease of the intensity of the J-aggregate confirms a loss of intermolecular coupling, again consistent with the smaller subunits observed in SEM analysis

Genome Analysis of a Historical Shigella dysenteriae Serotype 1 Strain Carrying a Conserved Stx Prophage Region

Shigella dysenteriae are significant agents of bacillary dysentery, accounting for a considerable number of illnesses with high morbidity worldwide. The Shiga toxin (Stx) encoded by a defective prophage is the key virulence factor of S. dysenteriae type 1 (SD1) strains. Here we present the full genome sequence of an SD1 strain HNCMB 20080 isolated in 1954, compare it to other sequenced SD1 genomes, and assess the diversity of Stx-prophages harbored by previously sequenced SD1 strains. The genome of HNCMB 20080 consists of a chromosome sized 4,393,622 bp containing 5,183 CDSs, as well as two small plasmids. Comparative genomic analysis revealed a high degree of uniformity among SD1 genomes, including the structure of Stx prophage regions, which we found to form two subgroups termed PT-I and PT-II. All PT-I strains are members of the sequence type (ST) 146 or ST260, while the only PT-II harboring strain, Sd1617 proved to be ST untypeable. In accordance with data from previous reports, the Stx1 prophage could not be induced from HNCMB 20080. Our cumulative data do not support the notion that stx-harboring phages in STEC are derived from historical SD1 isolates

Deep Transfer Learning Enables Robust Prediction of Antimicrobial Resistance for Novel Antibiotics

Antimicrobial resistance (AMR) has become one of the serious global health problems, threatening the effective treatment of a growing number of infections. Machine learning and deep learning show great potential in rapid and accurate AMR predictions. However, a large number of samples for the training of these models is essential. In particular, for novel antibiotics, limited training samples and data imbalance hinder the models’ generalization performance and overall accuracy. We propose a deep transfer learning model that can improve model performance for AMR prediction on small, imbalanced datasets. As our approach relies on transfer learning and secondary mutations, it is also applicable to novel antibiotics and emerging resistances in the future and enables quick diagnostics and personalized treatments

Cross-border emergence of clonal lineages of ST38 Escherichia coli producing the OXA-48-like carbapenemase OXA-244 in Germany and Switzerland

Background: Carbapenemase-producing Gram-negative bacteria cause infections that are difficult to treat and represent a rising threat to healthcare systems worldwide. This study analysed isolates of Escherichia coli (E. coli), a species associated with nosocomial-acquired and community-acquired infections, from hospitals in Germany and Switzerland exhibiting a slight decrease in susceptibility to carbapenems.Methods: E. coli strains from Germany and Switzerland, obtained mainly in 2019, were first screened for carbapenemase genes by PCR and subsequently whole-genome-sequenced and analysed for their clonal relationship using multilocus sequence typing, single nucleotide polymorphisms, virulence and antibiotic-resistance gene content.Results: The analysis revealed the presence of extended β-lactamase (ESBL)-producing E. coli clones producing OXA-244, a point- mutation derivative of OXA-48, with a predominance of isolates exhibiting the sequence type (ST) ST38 in both Germany and Switzerland. These clustered exclusively into two distinct lineages: one encoding CTX-M-27, a recently emerged extended-spectrum β-lactamase, and the other CTX-M-14b. All OXA244/CTX-M-27 ST38 isolates harboured the Dr adhesin operon and a representative isolate exhibited a diffuse adherence (DAEC) phenotype and was invasive for Hela cells.Conclusion: Clonal lineages of ST38 are members of E. coli phylogenetic group D commonly associated with extra-intestinal infections. Their increased isolation in two different European countries indicates ongoing spread of ST38 ESBL-producing and OXA-244- producing E. coli clonal lineages. It is possible that members of the multidrug-resistant DEAC ExPEC group have expanded globally, but that this is currently underreported because of the inherent difficulty in detecting isolates expressing the OXA-244 allele

Carbapenem-Resistant spp. as an Emerging Concern in the Hospital-Setting: Results From a Genome-Based Regional Surveillance Study.

The rise of Carbapenem-resistant Enterobacterales (CRE) represents an increasing threat to patient safety and healthcare systems worldwide. Citrobacter spp., long considered not to be a classical nosocomial pathogen, in contrast to Klebsiella pneumoniae and Escherichia coli, is fast gaining importance as a clinical multidrug-resistant pathogen. We analyzed the genomes of 512 isolates of 21 CRE species obtained from 61 hospitals within a three-year-period and found that Citrobacter spp. (C. freundii, C. portucalensis, C. europaeus, C. koseri and C. braakii) were increasingly detected (n=56) within the study period. The carbapenemase-groups detected in Citrobacter spp. were KPC, OXA-48/-like and MBL (VIM, NDM) accounting for 42%, 31% and 27% respectively, which is comparable to those of K. pneumoniae in the same study. They accounted for 10%, 17% and 14% of all carbapenemase-producing CRE detected in 2017, 2018 and 2019, respectively. The carbapenemase genes were almost exclusively located on plasmids. The high genomic diversity of C. freundii is represented by 22 ST-types. KPC-2 was the predominantly detected carbapenemase (n=19) and was located in 95% of cases on a highly-conserved multiple-drug-resistance-gene-carrying pMLST15 IncN plasmid. KPC-3 was rarely detected and was confined to a clonal outbreak of C. freundii ST18. OXA-48 carbapenemases were located on plasmids of the IncL/M (pOXA-48) type. About 50% of VIM-1 was located on different IncN plasmids (pMLST7, pMLST5). These results underline the increasing importance of the Citrobacter species as emerging carriers of carbapenemases and therefore as potential disseminators of Carbapenem- and multidrug-resistance in the hospital setting

Whole-Genome Sequences of Clinical Enterobacter bugandensis Isolates from Germany

Enterobacter bugandensis is the most pathogenic species of the genus Enterobacter and is a cause of life-threatening infections in neonates. Curiously, it was also detected in samples from the International Space Station. Here, we present complete closed genome sequences of two clinical E. bugandensis isolates recognized for the first time in Germany

Peripheral ligands as electron storage reservoirs and their role in enhancement of photocatalytic hydrogen generation

The contrasting early-time photodynamics of two related Ru/Pt photocatalysts with very different photocatalytic H2 generation capabilities are reported. Ultrafast equilibration (535 ± 17 fs) creates an electron reservoir on the peripheral ligands of the ester substituted complex, allowing a dramatic increase in photocatalytic performance. This insight opens the way towards a novel design strategy for H2 generating molecular photocatalysts

Vancomycin-resistant Enterococcus faecium colonizing patients on hospital admission in Germany: prevalence and molecular epidemiology

Objectives: To analyse the rectal carriage rate and the molecular epidemiology of vancomycin-resistant Enterococcus faecium (VREfm) recovered from patients upon hospital admission. Methods: Adult patients were screened at six German university hospitals from five different federal states upon hospital admission for rectal colonization with VREfm between 2014 and 2018. Molecular characterization of VREfm was performed by WGS followed by MLST and core-genome MLST analysis. Results: Of 16350 patients recruited, 263 were colonized with VREfm, with increasing prevalence rates during the 5year study period (from 0.8% to 2.6%). In total, 78.5% of the VREfm were vanB positive and 20.2% vanA positive, while 1.2% harboured both vanA and vanB. The predominant ST was ST117 (56.7%) followed by ST80 (15%), ST203 (10.9%), ST78 (5.7%) and ST17 (3.2%). ST117/vanB VREfm isolates formed a large cluster of 96 closely related isolates extending across all six study centres and four smaller clusters comprising 13, 5, 4 and 3 isolates each. In contrast, among the other STs inter-regional clonal relatedness was rarely observed. Conclusions: To our knowledge, this is the largest admission prevalence and molecular epidemiology study of VREfm. These data provide insight into the epidemiology of VREfm at six German university hospitals and demonstrate the remarkable inter-regional clonal expansion of the ST117/vanB VREfm clone

Resolving colistin resistance and heteroresistance in Enterobacter species

Taxonomical complexity has muddled the classification of clinically relevant Enterobacter species. Authors carry out a genome-based study on clinical isolates to investigate colistin resistance and heteroresistance in Enterobacter