The Mitis group of streptococci includes an important human pathogen,
Streptococcus pneumoniae
(pneumococcus) and about 20 other related species with much lower pathogenicity. In clinical practice, ...some representatives of these species, especially
Streptococcus pseudopneumoniae
and
Streptococcus mitis
, are sometimes mistaken for
S. pneumoniae
based on the results of classical microbiological methods, such as optochin susceptibility and bile solubility. Several various molecular approaches that address the issue of correct identification of pneumococci and other Mitis streptococci have been proposed and are discussed in this review, including PCR- and gene sequencing-based tests as well as new developments in the genomic field that represents an important advance in our understanding of relationships within the Mitis group.
Vancomycin-resistant enterococci (VRE) are important nosocomial pathogens. Invasive VRE infections are difficult to treat since common therapeutic options including ampicillin and glycopeptides often ...fail. In vitro, most VRE remain susceptible to last-resort antibiotics such as linezolid, tigecycline and daptomycin. However, neither tigecycline nor linezolid act in a bactericidal manner, and daptomycin has proven activity only at high dosages licensed for treating enterococcal endocarditis. Despite these pharmacological and therapeutic limitations, reports on resistance to these last-resort drugs in VRE, and enterococci in general, have increased in recent years. In this review, we briefly recapitulate the current knowledge on the mode of action as well as the known and novel mechanisms of resistance and describe surveillance data on resistance to linezolid, tigecycline and daptomycin in enterococci. In addition, we also suggest a common nomenclature for designating enterococci and VRE with resistances to these important last-resort antibiotics.
Linezolid is considered a last resort drug in treatment of severe infections caused by Gram-positive pathogens, resistant to other antibiotics, such as vancomycin-resistant enterococci (VRE), ...methicillin-resistant staphylococci and multidrug resistant pneumococci. Although the vast majority of Gram-positive pathogenic bacteria remain susceptible to linezolid, resistant isolates of enterococci, staphylococci and streptococci have been reported worldwide. In these bacteria, apart from mutations, affecting mostly the 23S rRNA genes, acquisition of such genes as cfr, cfr(B), optrA and poxtA, often associated with mobile genetic elements (MGE), plays an important role for resistance. The purpose of this paper is to provide an overview on diversity and epidemiology of MGE carrying linezolid-resistance genes among clinically-relevant Gram-positive pathogens such as enterococci and streptococci.
•Linezolid resistance in Gram-positive bacteria is determined by various mechanisms.•Acquired linezolid resistance genes are often carried by MGE.•In enterococci, plasmids carrying linezolid resistance genes belong to various replicon types.•In Streptococcus suis linezolid resistance genes are plasmid-, phage- and ICE-located.
Coagulase-negative staphylococci, ubiquitous commensals of human skin, and mucous membranes represent important pathogens for immunocompromised patients and neonates. The increasing antibiotic ...resistance among
Staphylococcus epidermidis
is an emerging problem worldwide. In particular, the linezolid-resistant
S. epidermidis
(LRSE) strains are observed in Europe since 2014. The aim of our study was to genetically characterize 11 LRSE isolates, recovered mostly from blood in the University Children’s Hospital in Krakow, Poland, between 2015 and 2017. For identification of the isolates at the species level, we used 16S rRNA sequencing and RFLP of the
saoC
gene. Isolates were characterized phenotypically by determining their antimicrobial resistance patterns and using molecular methods such as PFGE, MLST, SCC
mec
typing, detection of the
ica
operon, and analysis of antimicrobial resistance determinants. All isolates were multidrug-resistant, including resistance to methicillin, and exhibited so-called PhLOPS
A
phenotype. In PFGE, all isolates (excluding one from a catheter) represented identical patterns, were identified as ST2, and harbored the
ica
operon, responsible for biofilm formation. Linezolid resistance was associated with acquisition of A157R mutation in the ribosomal protein L3 and the presence of
cfr
gene. All isolates revealed new SCC
mec
cassette element composition. Recently, pediatric patients with serious staphylococcal infections are often treated with linezolid. The increasing linezolid resistance in bacterial strains becomes a real threat for patients, and monitoring such infections combined with surveillance and infection prevention programs is very important to decrease number of linezolid-resistant staphylococcal strains.
Antimicrobial photodynamic therapy (APDT) is one of the promising tools for bacteria inactivation, which can be considered as an alternative to the common ways of treatment in the era of growing ...resistance to antibiotics. Presently applied phototherapeutic agents are often based on porphyrins. Porphycenes, isomers of porphyrin, exhibit even better spectral and photophysical properties regarding PDT and have therefore been proposed as photosensitizers in such applications as anticancer and antimicrobial PDT. We compare three different porphycenes in the study of photodestruction of commonly occurring bacteria: Enteroccocus faecalis, Staphylococcus aureus and Staphylococcus epidermidis. Special interest is drawn to the parent, unsubstituted porphycene, a compound which was not tested before in terms of its photosensitizing activity in the biological systems. The results show that two out of three investigated compounds, the parent porphycene and its quadruply substituted derivative, 2,7,12,17-tetrakis(β-methoxyethyl) exhibit very good ability of bacteria eradication and fulfill the criteria that are commonly required from the APDT photosensitizers. In contrast, 2,7,12,17-tetra-t-butylporphycene, of which the spectral and photophysical characteristics are very similar to those of the parent compound, is not photoactive. This is explained by its inability to penetrate into the bacteria cell. These results demonstrate extreme sensitivity of the photodestruction efficiency to minor structural variations in the photosensitizer.
•Ability of selected porphycenes to photoinactivate bacteria was demonstrated.•S. aureus, S. epidermidis, and E. faecalis were eradicated using red light.•Very similar porphycenes dramatically differ in bactericidal activity.
The success of Enterococcus faecium and E. faecalis evolving as multi-resistant nosocomial pathogens is associated with their ability to acquire and share adaptive traits, including antimicrobial ...resistance genes encoded by mobile genetic elements (MGEs). Here, we investigate this mobilome in successful hospital associated genetic lineages, E. faecium sequence type (ST)17 (n=10) and ST78 (n=10), E. faecalis ST6 (n=10) and ST40 (n=10) by DNA microarray analyses.
The hybridization patterns of 272 representative targets including plasmid backbones (n=85), transposable elements (n=85), resistance determinants (n=67), prophages (n=29) and clustered regularly interspaced short palindromic repeats (CRISPR)-cas sequences (n=6) separated the strains according to species, and for E. faecalis also according to STs. RCR-, Rep_3-, RepA_N- and Inc18-family plasmids were highly prevalent and with the exception of Rep_3, evenly distributed between the species. There was a considerable difference in the replicon profile, with rep 17/pRUM , rep 2/pRE25 , rep 14/EFNP1 and rep 20/pLG1 dominating in E. faecium and rep 9/pCF10 , rep 2/pRE25 and rep 7 in E. faecalis strains. We observed an overall high correlation between the presence and absence of genes coding for resistance towards antibiotics, metals, biocides and their corresponding MGEs as well as their phenotypic antimicrobial susceptibility pattern. Although most IS families were represented in both E. faecalis and E. faecium, specific IS elements within these families were distributed in only one species. The prevalence of IS256-, IS3-, ISL3-, IS200/IS605-, IS110-, IS982- and IS4-transposases was significantly higher in E. faecium than E. faecalis, and that of IS110-, IS982- and IS1182-transposases in E. faecalis ST6 compared to ST40. Notably, the transposases of IS981, ISEfm1 and IS1678 that have only been reported in few enterococcal isolates were well represented in the E. faecium strains. E. faecalis ST40 strains harboured possible functional CRISPR-Cas systems, and still resistance and prophage sequences were generally well represented.
The targeted MGEs were highly prevalent among the selected STs, underlining their potential importance in the evolution of hospital-adapted lineages of enterococci. Although the propensity of inter-species horizontal gene transfer (HGT) must be emphasized, the considerable species-specificity of these MGEs indicates a separate vertical evolution of MGEs within each species, and for E. faecalis within each ST.
Introduction
Increasing incidence of
Enterococcus faecium
resistant to key antimicrobials used in therapy of hospitalized patients is a worrisome phenomenon observed worldwide. Our aim was to ...characterize a tigecycline-, linezolid- and vancomycin-resistant
E. faecium
isolate with the
vanA
and
vanB
genes, originating from a hematoma of a patient hospitalized in an intensive care unit in Poland.
Methods
Antimicrobial susceptibility (a broad panel) was tested using gradient tests with predefined antibiotic concentrations. The complete genome sequence was obtained from a mixed assembly of Illumina MiSeq and Oxford Nanopore’s MinION reads. The genome was analyzed with appropriate tools available at the Center for Genomic Epidemiology, PubMLST and GenBank. Transferability of oxazolidinone, tigecycline and vancomycin resistance genes was investigated by conjugation, followed by PCR screen of transconjugants for antimicrobial resistance genes and plasmid
rep
genes characteristic for the donor and genomic sequencing of selected transconjugants.
Results
The isolate was resistant to most antimicrobials tested; susceptibility to daptomycin, erythromycin and chloramphenicol was significantly reduced, and only oritavancin retained the full activity. The isolate represented sequence type 18 (ST18) and carried
vanA
,
vanB
,
poxtA
,
fexB
,
tet
(L),
tet
(M),
aac(6')-aph(2''), ant(6)-Ia
and
ant(6')-Ii
. The
vanA
,
poxtA
and
tet
(M) genes located on ~ 40-kb plasmids were transferable by conjugation yielding transconjugants resistant to vancomycin, linezolid and tigecycline. The substitutions in LiaS, putative histidine kinase, SulP, putative sulfate transporter, RpoB and RpoC were potential determinants of an elevated daptomycin MIC. Comparative analyses of the studied isolate with
E. faecium
isolates from other countries revealed its similarity to ST18 isolates from Ireland and Uganda from human infections.
Conclusions
We provide the detailed characteristics of the genomic determinants of antimicrobial resistance of a clinical
E. faecium
demonstrating the concomitant presence of both
vanA
and
vanB
and resistance to vancomycin, linezolid, tigecycline and several other compounds and decreased daptomycin susceptibility. This isolate is a striking example of an accumulation of resistance determinants involving various mechanisms by a single hospital strain.
An increasing resistance to vancomycin among clinically relevant enterococci, such as Enterococcus faecalis and Enterococcus faecium is a cause of a great concern, as it seriously limits treatment ...options. The vanB operon is one of most common determinants of this type of resistance. Genes constituting the operon are located in conjugative transposons, such as Tn1549-type transposons or, more rarely, in ICEEfaV583-type structures. Such elements show differences in structure and size, and reside in various sites of bacterial chromosome or, in the case of Tn1549-type transposons, are also occasionally associated with plasmids of divergent replicon types. While conjugative transposition contributes to the acquisition of Tn1549-type transposons from anaerobic gut commensals by enterococci, chromosomal recombination and conjugal transfer of plasmids appear to represent main mechanisms responsible for horizontal dissemination of vanB determinants among hospital E. faecalis and E. faecium.
This review focuses on diversity of genetic elements harbouring vanB determinants in hospital-associated strains of E. faecium and E. faecalis, the mechanisms beyond vanB spread in populations of these bacteria, and provides an overview of the vanB-MGE distribution among other enterococci and Gram-positive bacteria as potential reservoirs of vanB genes.
•MGEs play an important role in the acquisition and spread of the VanB-type vancomycin resistance among hospital enterococci.•Tn1549-type conjugative transposons with vanB operons are acquired from anaerobic Gram-positive gut commensals.•Structural studies allowed to elucidate the mechanism of Tn1549 insertion into target site with a minimal sequence homology.•Conjugative plasmids and chromosomal recombination are involved in dissemination of vanB among hospital enterococci.•vanB genes are also present, albeit very rarely among streptococci and staphylococci.
Streptococcus suis, a zoonotic bacterial pathogen circulated through swine, can cause severe infections in humans. Because human S. suis infections are not notifiable in most countries, incidence is ...underestimated. We aimed to increase insight into the molecular epidemiology of human S. suis infections in Europe. To procure data, we surveyed 7 reference laboratories and performed a systematic review of the scientific literature. We identified 236 cases of human S. suis infection from those sources and an additional 87 by scanning gray literature. We performed whole-genome sequencing to type 46 zoonotic S. suis isolates and combined them with 28 publicly available genomes in a core-genome phylogeny. Clonal complex (CC) 1 isolates accounted for 87% of typed human infections; CC20, CC25, CC87, and CC94 also caused infections. Emergence of diverse zoonotic clades and notable severity of illness in humans support classifying S. suis infection as a notifiable condition.
The aim of our study was to investigate phenotypic and genotypic features of streptococci misidentified (misID) as
Streptococcus pneumoniae
, obtained over 20 years from hospital patients in Poland. ...Sixty-three isolates demonstrating microbiological features typical for pneumococci (optochin susceptibility and/or bile solubility) were investigated by phenotypic tests,
lytA
and 16S rRNA gene polymorphism and whole-genome sequencing (WGS). All isolates had a 6-bp deletion in the
lytA
3′ terminus, characteristic for Mitis streptococc and all but two isolates lacked the pneumococcal signature cytosine at nucleotide position 203 in the 16S rRNA genes. The counterparts of
psaA
and
ply
were present in 100% and 81.0% of isolates, respectively; the spn9802 and spn9828 loci were characteristic for 49.2% and 38.1% of isolates, respectively. Phylogenetic trees and networks, based on the multilocus sequence analysis (MLSA) scheme, ribosomal multilocus sequence typing (rMLST) scheme and core-genome analysis, clearly separated investigated isolates from
S. pneumoniae
and demonstrated the polyclonal character of misID streptococci, associated with the
Streptococcus pseudopneumoniae
and
Streptococcus mitis
groups. While the
S. pseudopneumoniae
clade was relatively well defined in all three analyses, only the core-genome analysis revealed the presence of another cluster comprising a fraction of misID streptococci and a strain proposed elsewhere as a representative of a novel species in the Mitis group. Our findings point to complex phylogenetic and taxonomic relationships among
S. mitis-
like bacteria and support the notion that this group may in fact consist of several distinct species.
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