Loss of GdpP Function in Staphylococcus aureus Leads to ß-Lactam Tolerance and Enhanced Evolution of ß-Lactam Resistance.

Infections caused by Staphylococcus aureus are a leading cause of mortality. Treating infections caused by S. aureus is difficult due to resistance against most traditional antibiotics, including ß-lactams. We previously reported the presence of mutations in gdpP among S. aureus strains that were obtained by serial passaging in ß-lactam drugs. Similar mutations have recently been reported in natural S. aureus isolates that are either nonsusceptible or resistant to ß-lactam antibiotics. gdpP codes for a phosphodiesterase that cleaves cyclic-di-AMP (CDA), a newly discovered second messenger. In this study, we sought to identify the role of gdpP in ß-lactam resistance in S. aureus. Our results showed that gdpP-associated mutations caused loss of phosphodiesterase function, leading to increased CDA accumulation in the bacterial cytosol. Deletion of gdpP led to an enhanced ability of the bacteria to withstand a ß-lactam challenge (2 to 3 log increase in bacterial CFU) by promoting tolerance without enhancing MICs of ß-lactam antibiotics. Our results demonstrated that increased drug tolerance due to loss of GdpP function can provide a selective advantage in acquisition of high-level ß-lactam resistance. Loss of GdpP function thus increases tolerance to ß-lactams that can lead to its therapy failure and can permit ß-lactam resistance to occur more readily.

PBP4-mediated ß-lactam resistance among clinical strains of Staphylococcus aureus.

BACKGROUND: PBP4, a low-molecular-weight PBP in Staphylococcus aureus, is not considered to be a classical mediator of ß-lactam resistance. Previous studies carried out by our group with laboratory strains of S. aureus demonstrated the ability of PBP4 to produce ß-lactam resistance through mutations associated with the pbp4 promoter and/or gene. Recent studies of ß-lactam-resistant clinical isolates of S. aureus have reported similar mutations associated with pbp4. OBJECTIVES: To determine if pbp4-associated mutations reported among clinical strains of S. aureus mediate ß-lactam resistance. METHODS: The pbp4 promoters and genes bearing mutations from clinical isolates were cloned into a heterologous host. Reporter, growth and Bocillin assays were performed to assess their role in ß-lactam resistance. X-ray crystallography was used to obtain acyl-enzyme intermediate structures of the WT and mutant PBP4 with nafcillin and cefoxitin. RESULTS: Of the five strains that contained pbp4 promoter mutations, three strains exhibited enhanced expression of PBP4. The R200L mutation in pbp4 resulted in increased survival in the presence of the ß-lactams nafcillin and cefoxitin. Further, introduction of either a promoter or a gene mutation into the genome of a WT host increased the ability of the strains to resist the action of ß-lactams. The four high-resolution X-ray structures presented demonstrate the binding pose of the ß-lactams tested and provide hints for further drug development. CONCLUSIONS: Mutations associated with the pbp4 promoter and pbp4 gene altered protein activity and mediated ß-lactam resistance among the clinically isolated strains that were studied.

Large diversity of linezolid-resistant isolates discovered in food-producing animals through linezolid selective monitoring in Belgium in 2019.

BACKGROUND: Linezolid is a critically important antibiotic used to treat human infections caused by MRSA and VRE. While linezolid is not licensed for food-producing animals, linezolid-resistant (LR) isolates have been reported in European countries, including Belgium. OBJECTIVES: To: (i) assess LR occurrence in staphylococci and enterococci isolated from different Belgian food-producing animals in 2019 through selective monitoring; and (ii) investigate the genomes and relatedness of these isolates. METHODS: Faecal samples (n = 1325) and nasal swab samples (n = 148) were analysed with a protocol designed to select LR bacteria, including a 44-48 h incubation period. The presence of LR chromosomal mutations, transferable LR genes and their genetic organizations and other resistance genes, as well as LR isolate relatedness (from this study and the NCBI database) were assessed through WGS. RESULTS: The LR rate differed widely between animal host species, with the highest rates occurring in nasal samples from pigs and sows (25.7% and 20.5%, respectively) and faecal samples from veal calves (16.4%). WGS results showed that LR determinants are present in a large diversity of isolates circulating in the agricultural sector, with some isolates closely related to human isolates, posing a human health risk. CONCLUSIONS: LR dedicated monitoring with WGS analysis could help to better understand the spread of LR. Cross-selection of LR transferable genes through other antibiotic use should be considered in future action plans aimed at combatting antimicrobial resistance and in future objectives for the rational use of antibiotics in a One Health perspective.

Epidemiology of the Staphylococcus aureus CA-MRSA USA300 in Belgium.

The methicillin-resistant Staphylococcus aureus (MRSA) sequence type (ST) 8 Panton-Valentine toxin (PVL)-positive USA300 clone has a worldwide distribution. The USA300 North American (NA) variant, harbouring the arginine catabolic mobile element (ACME), is predominant in the USA while the Latin American (LV) variant is predominant in Northern South America. Both variants have failed to become endemic in Europe. We examined here the epidemiology of the USA300 clone in Belgium from 2006 to 2019. A total of 399 clonal complex 8 PVL-positive MRSA isolates received between 2006 and 2019 by the Belgian National Reference Laboratory for S. aureus were investigated for the presence of ACME. Selected ACME-positive (n=102) and ACME-negative (n=16) isolates were sequenced, characterized for the presence of several resistance and virulence molecular markers and subjected to phylogenetic analysis. A total of 300 isolates were USA300-NA (ACME-positive), while only 99 were ACME-negative. Most USA300-NA interspersed in the phylogeny analysis with isolates from other countries, suggesting multiple introductions. However, two big clades were maintained and spread over a decade, peaking between 2010 and 2017 to finally decrease. Few ACME-negative isolates, mainly related to trips to South America, were identified as USA300-LV. The remaining ACME-negative isolates were ST8 SCCmec IVb or ST923 SCCmec IVa (COL923). Two clades of the USA300-NA clone have successfully spread in Belgium, but seem to currently decrease. Related South American variants have been detected for the first time in Belgium, including the emerging COL923 clone.

Low specificity of Aspergillus spp. ELITe MGB assay, and potential risks in management of invasive aspergillosis.

Objectives: In recent years, commercial molecular tools for diagnosis of invasive aspergillosis have emerged, requiring evaluation to ensure quality. Here we assessed the specificity of Aspergillus spp.-ELITe MGB Assay a commercial assay tergeting 18S gene of Aspergillus spp. Design and methods: As part of a method validation, we evaluate the specificity of the Aspergillus spp.-ELITe MGB Assay by testing fourteen culture based samples of sequenced non-Aspergillus fungal species. The benefits of a pre-lysis treatment was evaluated in parallel on serial dilutions of an Aspergillus fumigatus strain. Results: Our findings revealed cross-reactivity in five strains using the 50 copies/mL cut-off recommended by the manufacturer, suggesting potential diagnostic errors and inappropriate management of patients. Pre-lysis treatment does not affect the limit of detection at serial dilution. Conclusions: In conclusion, the Aspergillus spp. ELITe MGB Assay exhibits limited specificity in culture-based samples, underscoring the importance of careful utilization in laboratories. Further studies are warranted to better comprehend of the impact of this cross-reactivity on clinical samples.

Identification of staphylococcal cassette chromosome mec in Staphylococcus aureus and non-aureus staphylococci from dairy cattle in Belgium: Comparison of multiplex PCR and whole genome sequencing.

The present study compared multiplex PCR (mPCR) and Whole Genome Sequencing (WGS) using the SCCmecFinder database to identify the Staphylococcal Cassette Chromosome (SCC) mec in five Staphylococcus aureus (SA) and nine non-aureus staphylococci (NAS) isolated from dairy cattle. mPCR identified an SCCmecIV in four SA and one NAS, but could not differentiate between SCCmecII and IV in the fifth SA, that all harbored the mecA gene and were phenotypically resistant to cefoxitin. SCCmecFinder confirmed the presence of an SCCmecIVc(2B) in four SA and of the SCCmecIVa(2B) in the fifth SA and the one NAS. Both methods also detected one untypeable SCCmec in another cefoxitin-resistant NAS harboring the mecA gene and a pseudo SCCmec in one cefoxitin-sensitive NAS harboring one mecC-related gene. No SCCmec elements were identified either in one cefoxitin-sensitive NAS harboring the mecA2 gene, or in five NAS (one resistant and four sensitive to cefoxitin) harboring the mecA1 gene. SCCmecFinder could even not identify the presence of any mecA1 gene in these five NAS, whose presence was nevertheless confirmed by ResFinder. The conclusions of this study are: (i) mPCR and WGS sequencing using SCCmecFinder are complementary methodologies to identify SCCmec; (ii) SCCmecFinder and ResFinder to a lesser extent cannot identify all mec gene allotypes; (iii) a specific classification of the SCCmec in NAS would be epidemiologically helpful; (iv) presence of a mecA gene and a complete SCCmec is linked to cefoxitin resistance, whereas presence of other mec genes and of pseudo or no SCCmec is not.

Comparison of the Staphylococcal Chromosome Cassette (SCC) mec in Methicillin-Resistant Staphylococcus aureus (MRSA) and Non-aureus Staphylococci (MRNAS) from Animals and Humans.

Methicillin-resistant Staphylococcus aureus (MRSA) and non-aureus staphylococci (MRNAS) cause different infections in animals, including mastitis, in livestock and humans. This study aimed to identify and compare the staphylococcal chromosome cassette mec (SCCmec) types of MRSA or MRNAS isolated from several animal species and humans in different countries. Of 1462 S. aureus and non-aureus staphylococci, 68 grew on Chrom MRSA ID® agar, were phenotypically resistant to cefoxitin and tested positive with the PCR for the mecA gene. These 60 MRSA and 8 MRNAS were isolated in Belgium mainly from cows (livestock-associated (LA) MRS) and humans (community-acquired (CA) MRS) and in Japan from dogs and cats. The SCCmec cassettes were identified by multiplex PCR in 52 MRSA and 7 MRNAS and by whole genome sequencing (WGS) in 8 additional MRSA. The SCCmec types IV and V were the most frequent in Belgian LA-MRS and CA-MRS, while the SCCmec type II was identified in four of the five Japanese MRSA. The remaining isolate was a bovine S. haemolyticus in which no SCCmec was identified. These results confirm the high prevalence of the SCCmec types IV and V in LA-MRS and CA-MRS in Belgium, emphasizing the possible public health hazard of the former, and the absence of SCCmec in some MRNAS.

Antibiotic Resistance, Biofilm Formation, and Intracellular Survival As Possible Determinants of Persistent or Recurrent Infections by Staphylococcus aureus in a Vietnamese Tertiary Hospital: Focus on Bacterial Response to Moxifloxacin.

Resistance is notoriously high in Asia but may not entirely explain therapeutic failures. Specific modes of bacterial life, such as biofilm or intracellular survival, may also contribute to the persistent and/or recurrent character of infections. Most Staphylococcus aureus isolates form biofilm and many survive and even thrive intracellularly. We collected 36 nonduplicate S. aureus isolates (including 18 methicillin-resistant S. aureus) from patients with clinical evidence of persistent or recurrent infections in a large tertiary Vietnamese hospital. We examined their antibiotic resistance profile (minimal inhibitory concentration determination) and clonal relatedness (spa and agr typing, pulsed field gel electrophoresis profiles). We then assessed the activity of moxifloxacin in both biofilms and infected phagocytes (moxifloxacin previously proved to be one of the most active antibiotics against reference strains in these models). spa-types t189 and t437 and agr group I were the most frequent. Among the 36 isolates, 30 were multidrug resistant but 30 were recovered from patients having received an active drug. All tested isolates produced biofilm and survived inside phagocytes. At its human Cmax, moxifloxacin was inactive on biofilms made by moxifloxacin-susceptible as well as moxifloxacin-resistant isolates. It caused only a modest intracellular colony-forming unit decrease against moxifloxacin-susceptible isolates and was inactive against those resistant to moxifloxacin. While our data confirm for this collection the high resistance levels and prevalence of endemic spa- or agr- types in Asia, they show that tolerance in both biofilm and phagocytes are correlated and markedly limit moxifloxacin activity, which goes in line with the suggested role of these modes of life in persistence or recurrence of infections.