Impact of species and antibiotic therapy of enterococcal peritonitis on 30-day mortality in critical care-an analysis of the OUTCOMEREA database.

INTRODUCTION: Enterococcus species are associated with an increased morbidity in intraabdominal infections (IAI). However, their impact on mortality remains uncertain. Moreover, the influence on outcome of the appropriate or inappropriate status of initial antimicrobial therapy (IAT) is subjected to debate, except in septic shock. The aim of our study was to evaluate whether an IAT that did not cover Enterococcus spp. was associated with 30-day mortality in ICU patients presenting with IAI growing with Enterococcus spp. MATERIAL AND METHODS: Retrospective analysis of French database OutcomeRea from 1997 to 2016. We included all patients with IAI with a peritoneal sample growing with Enterococcus. Primary endpoint was 30-day mortality. RESULTS: Of the 1017 patients with IAI, 76 (8%) patients were included. Thirty-day mortality in patients with inadequate IAT against Enterococcus was higher (7/18 (39%) vs 10/58 (17%), p = 0.05); however, the incidence of postoperative complications was similar. Presence of Enterococcus spp. other than E. faecalis alone was associated with a significantly higher mortality, even greater when IAT was inadequate. Main risk factors for having an Enterococcus other than E. faecalis alone were as follows: SAPS score on day 0, ICU-acquired IAI, and antimicrobial therapy within 3 months prior to IAI especially with third-generation cephalosporins. Univariate analysis found a higher hazard ratio of death with an Enterococcus other than E. faecalis alone that had an inadequate IAT (HR = 4.4 [1.3-15.3], p = 0.019) versus an adequate IAT (HR = 3.1 [1.0-10.0], p = 0.053). However, after adjusting for confounders (i.e., SAPS II and septic shock at IAI diagnosis, ICU-acquired peritonitis, and adequacy of IAT for other germs), the impact of the adequacy of IAT was no longer significant in multivariate analysis. Septic shock at diagnosis and ICU-acquired IAI were prognostic factors. CONCLUSION: An IAT which does not cover Enterococcus is associated with an increased 30-day mortality in ICU patients presenting with an IAI growing with Enterococcus, especially when it is not an E. faecalis alone. It seems reasonable to use an IAT active against Enterococcus in severe postoperative ICU-acquired IAI, especially when a third-generation cephalosporin has been used within 3 months.

Antiviral activity of SAFER®, a commercial acidifying desiccant powder, against African swine fever virus.

African swine fever (ASF) is one of the deadliest swine diseases, causing significant economic losses, threatening food security, and limiting pig production in affected countries. In the absence of an effective ASF vaccine, prevention and control of ASF depend mainly on effective biosecurity measures. In this study, the efficacy of SAFER®, a powdered disinfectant containing clay, an acid complex, and the active ingredient thyme essential oil, was tested against the ASF virus. The results showed that ASFV isolate (VNUA/HY/ASF1/Vietnam/2019) was inactivated by 3.5 and 5 Log10HAD50/ml after 20 and 120 min of treatment with SAFER®, respectively. When body fluids contaminated with ASFV, such as blood, saliva, urine, and feces, were treated with SAFER® for 20 min, the ASFV titer was reduced by 1.6, 2.2, 2.0, and 2.2 Log10HAD50/ml, respectively.

Characteristics and outcomes of SARS-COV 2 critically ill patients after emergence of the variant of concern 20H/501Y.V2: A comparative cohort study.

There are currently no data regarding characteristics of critically ill patients with Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variant of concern (VOC) 20H/501Y.V2. We therefore aimed to describe changes of characteristics in critically ill patients with Covid-19 between the first and the second wave when viral genome sequencing indicated that VOC was largely dominant in Mayotte Island (Indian Ocean). Consecutive patients with Covid-19 and over 18 years admitted in the unique intensive care unit (ICU) of Mayotte during wave 2 were compared with an historical cohort of patients admitted during wave 1. We performed a LR comparing wave 1 and wave 2 as outcomes. To complete analysis, we built a Random Forest model (RF), that is, a machine learning classification tool- using the same variable set as that of the LR. We included 156 patients, 41 (26.3%) and 115 (73.7%) belonging to the first and second waves respectively. Univariate analysis did not find difference in demographic data or in mortality. Our multivariate LR found that patients in wave 2 had less fever (absence of fever aOR 5.23, 95% confidence interval (CI) 1.89-14.48, p = .001) and a lower simplified acute physiology score (SAPS II) (aOR 0.95, 95% CI 0.91-0.99, p = .007) at admission; at 24 hours, the need of invasive mechanical ventilation was higher (aOR 3.49, 95% CI 0.98-12.51, p = .055) and pO2/FiO2 ratio was lower (aOR 0.99, 95 % CI 0.98-0.99, p = .03). Patients in wave 2 had also an increased risk of ventilator-associated pneumonia (VAP) (aOR 4.64, 95% CI 1.54-13.93, p = .006). Occurrence of VAP was also a key variable to classify patients between wave 1 and wave 2 in the variable importance plot of the RF model. Our data suggested that VOC 20H/501Y.V2 could be associated with a higher severity of respiratory failure at admission and a higher risk for developing VAP. We hypothesized that the expected gain in survival brought by recent improvements in critical care management could have been mitigated by increased transmissibility of the new lineage leading to admission of more severe patients. The immunological role of VOC 20H/501Y.V2 in the propensity for VAP requires further investigations.

Genetic diversity of Listeria monocytogenes recovered from infected persons and pork, seafood and dairy products on retail sale in France during 2000 and 2001.

Growth of the food-borne human pathogen Listeria monocytogenes to large numbers in ready-to-eat food products greatly increases the risk of disease for susceptible consumers. A better knowledge of the population structure of L. monocytogenes present in retailed food could allow better prevention strategies to be developed. We present the analysis of 450 L. monocytogenes isolates, 179 responsible for sporadic human cases of listeriosis and 271 isolated from foods collected from retailers. All isolates were investigated by multiplex PCR (food isolates), allowing serovar predictions, or serotyped (human isolates), and DNA macrorestriction patterns were determined. Isolates from different sources were significantly differently distributed into PCR groups. PCR group IIa, corresponding to serovars 1/2a and 3a, was predominant in food isolates (58%; OR=3.19; P<1 x 10(-7)). A larger proportion of human isolates belonged to PCR group IVb, corresponding to serovars 4b, 4d and 4e (44%; OR=5.69; P<1 x 10(-7)). DNA macrorestriction pattern analysis of PCR group IIa isolates showed that isolates from pork products had a very low diversity (ID=0.905) whereas isolates from humans were more diverse (ID=0.976). Furthermore, 78% of the pork product isolates belonging to PCR group IIa exhibited only two AscI profiles, a(1) and a(2), which were very similar (94%). DNA array analysis of representative isolates showed that isolates with a(1) and a(2) profiles constitute a homogeneous population, whereas isolates exhibiting non a(1)-a(2) profiles are more diverse. Six of the isolates with a(1) and a(2) profiles were selected and investigated for their gene content using a DNA array. With respect to 295 strains present in our data collection, a specific pattern of the presence and absence of 15 genes was identified. Five are predicted to encode internalins and cell surface proteins, and eight of the genes were missing in this group. They code for cell surface proteins, transcriptional regulators, an acylase, a sugar phosphorylase and proteins of unknown functions. The ability of strains to multiply in different niches may be determined by the presence or absence of these genes.

Multicenter validation of a multiplex PCR assay for differentiating the major Listeria monocytogenes serovars 1/2a, 1/2b, 1/2c, and 4b: toward an international standard.

The performance of a multiplex PCR assay that separates the four major serovars of the pathogenic Listeria monocytogenes into four distinct PCR groups was evaluated through a multicenter typing study. Identical panels of 90 Listeria isolates were distributed to five participating laboratories that were blind to the nature of the isolates. Isolates were characterized using the previously standardized protocol. Overall concordance was 96.6 to 100%, sufficient for the assay to be used as an alternative to serotyping and confidently applied in laboratories involved in L. monocytogenes typing.

Molecular analysis of resistance to streptogramin A compounds conferred by the Vga proteins of staphylococci.

The Vga and Msr resistance determinants, encoded by mobile genetic elements in various staphylococcal strains, belong to a family of ATP-binding cassette (ABC) proteins whose functions and structures are ill defined. Their amino acid sequences are similar to those of proteins involved in the immunity of streptomycetes to the macrolide-lincosamide-streptogramin antibiotics that they produce. Sequence analysis of the genomes of the gram-positive bacteria with low G+C contents revealed that Lmo0919 from Listeria monocytogenes is more closely related to Vga variants than to Msr variants. In the present study we compared the antibiotic resistance profiles conferred by the Vga-like proteins in two staphylococcal hosts. It was shown that Vga(A), the Vga(A) variant [Vga(A)v], and Lmo0919 can confer resistance to lincosamides and streptogramin A compounds, while only Vga(B) is able to increase the level of resistance to pristinamycin, a mixture of streptogramin A and streptogramin B compounds. By using polyclonal antibodies, we found that the Vga(A) protein colocalized with the beta subunit of the F(1)-F(0) ATPase in the membrane fractions of staphylococcal cells. In order to identify functional units in these atypical ABC proteins, such as regions that might be involved in substrate specificity and/or membrane targeting, we analyzed the resistance phenotypes conferred by various plasmids carrying parts or modified versions of the vga(A) gene and we determined the subcellular localization of the gene products. Only polypeptides composed of two ABC domains were detected in the cell membranes. No region of drug specificity was identified. Resistance properties were dependent on the integrities of both Walker B motifs.

Clonal diversity among streptogramin A-resistant Staphylococcus aureus isolates collected in French hospitals.

We analyzed 62 clinical isolates of streptogramin A-resistant (SGA(r)) Staphylococcus aureus collected between 1981 and 2001 in 14 hospitals located in seven French cities. These isolates, including five with decreased susceptibility to glycopeptides, were distributed into 45 antibiotypes and 38 SmaI genotypes. Each of these genotypes included between 1 and 11 isolates, the SmaI patterns of which differed by no more than three bands. Although numerous clones were identified, we observed the spread of monoclonal isolates either within the same hospital or within hospitals in distinct cities and at large time intervals. Hybridization with probes directed against 10 SGA(r) genes (vatA, vatB, vatC, vatD, vatE, vgaA, vgaB, vgaAv, vgbA, and vgbB) revealed six patterns: vgaAv (21 isolates), vatA-vgbA (24 isolates), vgaAv-vatB-vgaB (14 isolates), vgaAv-vatA-vgbA (1 isolate), vgaAv-vatA-vgbA-vatB-vgaB (1 isolate), and vgaA (1 isolate). We detected at least one SGA(r) determinant in all of the tested isolates. vgaAv, which is part of the recently characterized transposon Tn5406, was found in 59.7% of the tested isolates. Of the 16 streptogramin B-susceptible isolates, 14 carried vgaAv alone and were susceptible to the mixtures of streptogramins, whereas the 2 isolates carrying vgaAv-vatB-vgaB were resistant to these mixtures. vatA-vgbA was found on plasmids of the same apparent size in 26 (42%) of the tested clinical isolates from 18 unrelated SmaI genotypes. The possible dissemination of some of the multiple clones characterized in the present study with an expected increased selective pressure of streptogramins following the recent licensing of Synercid (quinupristin-dalfopristin) must be carefully monitored.

Characteristics of French methicillin-resistant Staphylococcus aureus isolates with decreased susceptibility or resistance to glycopeptides.

According to the French Society of Microbiology, Staphylococcus aureus isolates are suspected to have decreased susceptibility to glycopeptide(s) when at least one colony is able to grow from an inoculum of 10 microL of 2 McFarland bacterial suspension plated on Mueller-Hinton agar containing 5 mg/L teicoplanin and incubated for 48 h at 35-37 degrees C. We analysed 89 methicillin-resistant S. aureus isolates (MRSA), collected in 2000-2001 from 24 hospitals located in 18 French cities, which were able to grow on this selective medium. These isolates were distributed into six groups on the basis of their glycopeptide resistance phenotypes: (A) glycopeptide susceptible (GSSA, 21 isolates); (B) heterogeneous teicoplanin intermediately resistant (hetero-TISA, 24 isolates); (C) heterogeneous and intermediately resistant to both glycopeptides, teicoplanin and vancomycin (hetero-GISA, six isolates); (D) heterogeneous vancomycin intermediately resistant/teicoplanin intermediately resistant (hetero-VISA/TISA, 30 isolates); (E) GISA (four isolates); (F) TISA (four isolates). Despite the persistent decrease in gentamicin-resistant MRSA isolates in French hospitals since 1993, their prevalence is very high in groups D, E and F. Moreover, most of the group C, D and E isolates exhibiting decreased susceptibility to both glycopeptides belong to the same major SmaI genotype, which has been detected in Europe since at least 1989.

DNA macroarray for identification and typing of Staphylococcus aureus isolates.

A DNA macroarray containing 465 intragenic amplicons was designed to identify Staphylococcus aureus at the species level and to type S. aureus isolates. The genes selected included those encoding (i) S. aureus-specific proteins, (ii) staphylococcal and enterococcal proteins mediating antibiotic resistance and factors involved in their expression, (iii) putative virulence proteins and factors controlling their expression, and (iv) proteins produced by mobile elements. The macroarray was hybridized with the cellular DNAs of 80 S. aureus clinical isolates that were previously typed by analyses of their antibiograms and SmaI patterns. The set selected contained unrelated, endemic, and outbreak-related isolates belonging to 45 SmaI genotypes. In a gene content dendrogram, the 80 isolates were distributed into 52 clusters. The outbreak-related isolates were linked in the same or a closely related cluster(s). Clustering based on gene content provided a better discrimination than SmaI pattern analysis for the tested mecA(+) isolates that were endemic to Europe. All of the antibiotic resistance genes detected could be correlated with their corresponding phenotypes, except for one isolate which carried a mecA gene without being resistant. The 16 isolates responsible for bone infections were distinguishable from the 12 isolates from uninfected nasal carriers by a significantly higher prevalence of the sdrD gene coding for a putative SD (serine-aspartate) adhesin (in 15 and 7 isolates, respectively). In conclusion, the macroarray designed for this study offers an attractive and rapid typing method which has the advantage of providing additional information concerning the gene content of the isolate of interest.

Tracking adhesion factors in Staphylococcus caprae strains responsible for human bone infections following implantation of orthopaedic material.

Ten Staphylococcus caprae strains isolated from four patients and responsible for bone infections following implantation of orthopaedic material were compared to four S. caprae strains collected from milk samples of healthy goats. The following characteristics were investigated: Smal patterns, hybridization patterns with pBA2 (ribotypes), slime production, adhesion to matrix proteins (fibrinogen, fibronectin, collagen) and the staphylococcal adhesion genes (fnbA, clfA, cna, atlE, ica, fbe). None of the characteristics enabled us to distinguish the human strains from the goat strains. Slime was occasionally produced by S. caprae strains but all of them carried nucleotide sequences hybridizing at low stringency with the following genes: atlE encoding a S. epidermidis autolysin binding vitronectin and responsible for the primary adhesion to polystyrene, ica operon involved in the biosynthesis of a S. epidermidis extracellular polysaccharide, and the part of clfA encoding the serine-aspartate repeated region of a S. aureus cell-wall fibrinogen-binding protein.