ABSTRACT
Objective: To compare the long-term effects on immune parameters, inflammation, and HIV-1 reservoir after switching to a two-drug (2DR) versus maintaining an integrase inhibitor (InSTI)-based three-drug regimen (3DR). Methods: Cross-sectional study in which HIV-1 treatment-naïve people started and maintained an InSTI-based 3DR or, at different times, switched to 2DR (dolutegravir or darunavir/cobicistat + lamivudine). CD4+ and CD8+ T-cell activation and exhaustion, plasma concentrations of hs-CRP, D-dimer, P-selectin, IL-1ß, IL-6, TNF-α, IFN-γ, IP-10, sTNFR-I/II, MIP-1α/ß, I-FABP, LBP, sCD14, sCD163, MCP-1, and cellular-associated HIV-1-DNA and -RNA were quantified by flow cytometry, different immunoassays, and droplet digital PCR, respectively. The U de Mann-Whitney test evaluated differences between 3DR and 2DR. Immune recovery was evaluated using a general linear model for repeated measures adjusted for different co-variables. Results: Fifty participants per group were included. The median time on 3DR was 82 months for the 3DR group and 30 months for the 2DR group, after which it switched to 2DR for a median of 57 months. We did not find differences between both groups in any of the parameters analyzed. Specifically, some values in 3DR and 2DR were hs-CRP, 0.92 mg/L (0.45-2.23) vs. 1.23 (0.61-2.38); D-dimer, 190.0 µg/L (150.0-370.0) vs. 190.0 (150.0-397.5); IL-6, 2.8 pg/mL (1.3-5.3) vs. 3.2 (2.1-4.7); sCD14, 4.5 ng/mL (3.3-6.2) vs. 5.0 (3.6-6.1), respectively, all p ≥ 0.399. Conclusion: In the long term, switching to 2DR does not negatively affect immunologic parameters, inflammatory markers, or HIV-1 reservoir. Clinical trial registration: identifier NCT04076423.
Subject(s)
Biomarkers , HIV Infections , HIV Integrase Inhibitors , HIV-1 , Humans , HIV Infections/drug therapy , HIV Infections/immunology , HIV Infections/virology , HIV Infections/blood , Male , HIV-1/drug effects , HIV-1/immunology , Female , Biomarkers/blood , Adult , Cross-Sectional Studies , HIV Integrase Inhibitors/therapeutic use , Middle Aged , Viral Load , Inflammation/immunology , CD8-Positive T-Lymphocytes/immunology , CD4-Positive T-Lymphocytes/immunology , Oxazines/therapeutic useABSTRACT
Linezolid resistance in Enterococcus spp. is increasingly considered critically important and a public health threat which mandates the need to understand their genomic contents and dissemination patterns. Here, we used whole-genome sequencing to characterize the resistome, virulome and mobile genetic elements of nine linezolid-resistant (LZDR) enterococci (seven optrA-E. faecalis, one poxtA-E. faecium and one optrA-E. casseliflavus) previously obtained from the nares of healthy dogs, pigs, pig farmers and tracheal samples of nestling storks in Spain. Also, the relatedness of the isolates with publicly available genomes was accessed by core-genome single nucleotide polymorphism (SNP) analysis. The optrA gene of the E. faecalis and E. casseliflavus isolates was located downstream of the fexA gene. The optrA gene in the E. casseliflavus isolate was carried in a plasmid (pURX4962), while those in the seven E. faecalis isolates were chromosomally located. The OptrA proteins were mostly variants of wild type (DP-2: Y176D/T481P; RDK: I104R/Y176D/E256K; DD-3: Y176D/G393D; and EDD: K3E/Y176D/G393D), except two that were wild type (one E. faecalis and one E. casseliflavus). The poxtA gene in the E. faecium isolate was found alone within its contig. The cfrD was upstream of ermB gene in the E. casseliflavus isolate and flanked by ISNCY and IS1216. All the LZDR enterococci carried plasmid rep genes (2-3) containing tetracycline, chloramphenicol and aminoglycoside resistance genes. All isolates except E. casseliflavus carried at least one intact prophage, of which E. faecalis-ST330 (X4957) from a pig carried the highest (n = 5). Tn6260 was associated with lnuG in E. faecalis-ST330 while Tn554 was with fexA in E. feaecalis-ST59 isolates. All except E. casseliflavus (n = 0) carried at least two metal resistance genes (MRGs), of which poxtA-carrying E. faecium-ST1739 isolate contained the most (arsA, copA, fief, ziaA, znuA, zosA, zupT, and zur). SNP-based analyses identified closely related optrA-E. faecalis isolates from a pig and a pig farmer on the same farm (SNP = 4). Moreover, optrA- carrying E. faecalis-ST32, -ST59, and -ST474 isolates from pigs were related to those previously described from humans (sick and healthy) and cattle in Spain, Belgium, and Switzerland (SNP range 43-86). These findings strongly suggest the transmission of LZDR-E. faecalis between a pig and a pig farmer and potential inter-country dissemination. These highlight the need to strengthen molecular surveillance of LZDR enterococci in all ecological niches and body parts to direct appropriate control strategies.
Subject(s)
Anti-Bacterial Agents , Drug Resistance, Bacterial , Enterococcus , Genome, Bacterial , Linezolid , Phylogeny , Animals , Linezolid/pharmacology , Swine/microbiology , Drug Resistance, Bacterial/genetics , Dogs , Anti-Bacterial Agents/pharmacology , Enterococcus/genetics , Enterococcus/drug effects , Enterococcus/isolation & purification , Enterococcus/classification , Gram-Positive Bacterial Infections/microbiology , Gram-Positive Bacterial Infections/transmission , Gram-Positive Bacterial Infections/veterinary , Humans , Whole Genome Sequencing , Spain , Polymorphism, Single Nucleotide , Microbial Sensitivity Tests , Bacterial Proteins/genetics , Genomics , Plasmids/geneticsABSTRACT
Pseudomonas aeruginosa isolates were recovered from surface river water samples in La Rioja region (Spain) to characterise their antibiotic resistance, molecular typing and virulence mechanisms. Fifty-two P. aeruginosa isolates were isolated from 15 different water samples (45.4%) and belonged to 23 different pulsed-field electrophoresis (PFGE) patterns. All isolates were susceptible to all antibiotics tested, except one carbapenem-resistant P. aeruginosa that showed a premature stop codon in OprD porin. Twenty-two sequence types (STs) (six new ones) were detected among 29 selected P. aeruginosa (one strain with a different PFGE pattern per sample), with ST274 (14%) being the most frequent one. O:6 and O:3 were the predominant serotypes (31%). Seven virulotypes were detected, being 59% exoS-exoY-exoT-exoA-lasA-lasB-lasI-lasR-rhlAB-rhlI-rhlR-aprA-positive P. aeruginosa. It is noteworthy that the exlA gene was identified in three strains (10.3%), and the exoU gene in seven (24.1%), exoS in 18 (62.1%), and both exoS and exoU genes in one strain. High motility ranges were found in these strains. Twenty-seven per cent of strains produced more biofilm biomass, 90% more pyorubin, 83% more pyocyanin and 65.5% more than twice the elastase activity compared with the PAO1 strain. These results highlight the importance of rivers as temporary reservoirs and sources of P. aeruginosa transmission, and show the importance of their epidemiological surveillance in the environment.
Subject(s)
Pseudomonas Infections , Pseudomonas aeruginosa , Humans , Pseudomonas aeruginosa/genetics , Virulence/genetics , Anti-Bacterial Agents/pharmacology , Rivers , Bacterial Proteins/genetics , Drug Resistance, Bacterial/genetics , Molecular Typing , Virulence Factors/genetics , WaterABSTRACT
Coagulase-negative staphylococci (CoNS) species in healthy dogs and their owners could be transferred between these hosts and carry diverse antimicrobial resistance (AMR) genes of public health concern. This study determined the frequency, diversity, and AMR genes of nasal CoNS from healthy dogs and in-contact people as well as the rate of intra-household (between healthy dogs and dog-owners) transmission of CoNS. Nasal samples were collected and processed from 34 dogs and 41 humans from 27 households, and CoNS identification was done by MALDI-TOF-MS. The AMR determinants and genetic lineages were determined by PCR/sequencing. A total of 216 CoNS isolates were initially obtained and identified, and the AMR phenotypes were determined. From these, 130 non-repetitive CoNS were selected (one isolate of each species per sample or more than one if they presented different AMR phenotypes) and further characterized. The predominant species from dog carriers were S. epidermidis (26.5%), S. hominis (8.8%), and S. cohnii (8.8%), whereas in the human carriers, the predominant ones were S. epidermidis (80.4%), S. lugdunensis (9.8%), and S. hominis (9.8%). Intra-host species diversity (>one CoNS species) was detected in 37.5% of dogs and 21.6% of dog-owners. Conversely, 50% of dogs and 70.3% of dog-owners had intra-species AMR diversity (2-4 AMR-CoNS profiles). About 20% were susceptible to all antimicrobial agents tested, 31.5% displayed a multidrug resistance phenotype, and 17.4% were mecA-positive, located in SCCmec type V (24.2%), III (18.1%), IVc (12.1%), and II (6.1%). The other mec-A positive CoNS isolates (39.5%) had non-typeable SCCmec. The highest AMR rates were found against erythromycin (32.3%/mph(C), msr(A)) and mupirocin (20.8%/mupA), but the resistance rates for other antimicrobial agents were <10% each. Remarkably, one linezolid-resistant S. epidermidis-ST35 isolate was identified and mediated by four amino acid substitutions in L3 and one in L4 ribosomal proteins. Dogs and dog-owners as carriers of S. epidermidis with similar AMR patterns and genetic lineages (ST59, ST61, ST166 and ST278) were detected in four households (14.8%). Diverse CoNS carriage and moderate level of AMR were obtained from this study. The detection of CoNS carrying diverse SCCmec elements and intra-species AMR diversity highlights the roles of dog ownership in the potential transmission of antimicrobial-resistant CoNS in either direction.
Subject(s)
Critical Illness , Respiration, Artificial , Humans , Suction , Critical Illness/therapy , Intubation, Intratracheal , Critical CareABSTRACT
OBJECTIVES: This study characterized the resistome, mobilome and phylogenomic relatedness of Staphylococcus aureus strains previously obtained from healthy nestling storks (HNS), pigs (HP) and pig farmers (HPF) to analyse possible transmission pathways of S. aureus with implications for the spread of antimicrobial resistance. METHODS: The genomic contents of 52 S. aureus strains obtained from the nasal cavity of HNS, HP and HPF in Spain were sequenced using the Illumina NextSeq platform to characterize their resistome, virulome and mobile genetic elements. The relatedness of strains was assessed by core-genome single nucleotide polymorphisms (SNPs). RESULTS: The frequencies of multidrug-resistance phenotype and transposons were significantly lower in strains from HNS than in those from HP and HPF (P < 0.005). However, the presence of human immune evasion cluster genes in S. aureus strains from HNS was significantly higher than in those from HP and HPF (P < 0.005). Interestingly, the frequencies of plasmids and phages were not significantly associated with the host (P > 0.05). The phylogenetic analysis identified a cluster of all the MSSA-CC398 strains carrying φSa3 and ermT on rep13 separately from the two MRSA-CC398 strains (carrying ermT on repUS18). Highly related MRSA-CC398 strains were detected in some pigs and related farmers (<10 SNPs). CONCLUSION: This study confirms high-level antibiotic selection in S. aureus in HP and HPF in comparison to HNS. Furthermore, our findings highlight the continuous transmission of MRSA-CC398 in the pig-to-human interface and MSSA-CC398 with human adaptation markers in HNS. Molecular surveillance of S. aureus using the One Health model is required to establish appropriate control strategies.
Subject(s)
Methicillin-Resistant Staphylococcus aureus , Staphylococcal Infections , Animals , Humans , Swine , Staphylococcus aureus/genetics , Anti-Bacterial Agents/pharmacology , Farms , Methicillin-Resistant Staphylococcus aureus/genetics , Host Adaptation , Phylogeny , Staphylococcal Infections/veterinary , Staphylococcal Infections/epidemiology , Birds , GenomicsABSTRACT
This study determined the nasal staphylococci diversity and characterized their resistome, with a focus on the mobilome of methicillin-susceptible Staphylococcus aureus (MSSA)-CC398 subclade from healthy adults in La Rioja (northern Spain). Nasal staphylococci recovered from 57 healthy individuals (HI) were identified (MALDI-TOF-MS) and their antimicrobial resistance, virulence determinants and genetic lineages were studied. The relatedness of MSSA-CC398 isolates was assessed by core-genome single-nucleotide-polymorphisms (SNPs). One-hundred-forty-three non-repetitive staphylococci were obtained from most HI (98.2%), of which S. epidermidis (87.7%) and S. aureus (36.8%) were the predominant species. About 15% of the 27 S. aureus and 30.1% of the 116 coagulase-negative staphylococci (CoNS) isolates presented a multidrug resistance (MDR) phenotype. All S. aureus isolates were MSSA but 30.2% of CoNS isolates were mecA-positive and carried SCCmec types III, IV, and V. The highest non-beta-lactam resistance (frequency/genes) in S. aureus and CoNS were: erythromycin-clindamycin-inducible (25.9%/ermT, ermC) and mupirocin (30.1%/mupA), respectively. About 85% of S. aureus isolates carried relevant virulence genes. Eight clonal complexes (CCs) of MSSA were identified, of which CC398 was the predominant (33.3%). About 78% of the CC398 isolates harboured rep13-bound ermT gene, however, one carried a rep10-bound ermC gene. Only the ermT-positive MSSA-CC398 isolates were closely related (<50 SNPs) and carried the φSa3. Diverse MDR-S. epidermidis isolates were identified which included the lineages ST59 and ST210. The high rate of toxigenic S. aureus and of MSSA-CC398 subclade highlight the ability of HI to carry and transmit virulent isolates. Moreover, the high frequency of MDR-CoNS, often linked with SCCmec, needs to be monitored for their potential human health implications.
Subject(s)
Methicillin-Resistant Staphylococcus aureus , Staphylococcal Infections , Adult , Humans , Staphylococcus aureus/genetics , Staphylococcus/genetics , Methicillin-Resistant Staphylococcus aureus/genetics , Spain/epidemiology , Anti-Bacterial Agents/pharmacology , Staphylococcal Infections/epidemiology , Microbial Sensitivity TestsABSTRACT
The ecology and diversity of resistome in coagulase-negative staphylococci (CoNS) from healthy pigs and pig farmers are rarely available as most studies focused on the livestock-associated methicillin-resistant S. aureus. This study aims to characterize the antimicrobial resistance (AMR) mechanisms, intra-host species diversity (more than one species in a host), and intra-species AMR diversity (same species with more than one AMR profile) in CoNS recovered from the nasal cavities of healthy pigs and pig farmers. One-hundred-and-one CoNS strains previously recovered from 40 pigs and 10 pig farmers from four Spanish pig farms were tested to determine their AMR profiles. Non-repetitive strains were selected (n = 75) and their AMR genes, SCCmec types, and genetic lineages were analyzed by PCR/sequencing. Of the non-repetitive strains, 92% showed a multidrug resistance (MDR) phenotype, and 52% were mecA-positive, which were associated with SCCmec types V (46.2%), IVb (20.5%), and IVc (5.1%). A total of 28% of the pigs and pig farmers had intra-host species diversity, while 26% had intra-species AMR diversity. High repertoires of AMR genes were detected, including unusual ones such as tetO, ermT, erm43, and cfr. Most important was the detection of cfr (in S. saprophyticus and S. epidermidis-ST16) in pigs and pig farmers; whereas MDR-S. borealis strains were identified in pig farmers. Pig-to-pig transmission of CoNS with similar AMR genes and SCCmec types was detected in 42.5% of pigs. The high level of multidrug, within-host, and intra-species resistome diversity in the nasal CoNS highlights their ability to be AMR gene reservoirs in healthy pigs and pig farmers. The detection of MDR-S. borealis and linezolid-resistant strains underscore the need for comprehensive and continuous surveillance of MDR-CoNS at the pig farm level.
ABSTRACT
BACKGROUND: Bacteriocins (of different origins) have been proposed as promising alternatives to face antimicrobial resistance-associated health problems. Isolates of the Staphylococcus genus are well-known bacteriocin producers, especially coagulase-negative species. METHODS: Twenty-eight bacteriocin-producing staphylococcal isolates were selected from a previous study for in-depth characterisation. The antimicrobial activities (AA) of the producing isolates were studied by the spot-on-lawn method and their crude cell-free supernatants (CFS) and butanol extracts (BT) were evaluated by agar diffusion assays against six indicator bacteria, including multidrug-resistant and zoonotic isolates (such as Listeria monocytogenes or methicillin-resistant Staphylococcus aureus [MRSA]). RESULTS: Six bacteriocin-producing isolates showed AA in their CFS, whereas all staphylococcal BT extracts inhibited at least one of the tested indicator bacteria. Micrococcin P1 (MP1) bacteriocin was detected by mass spectrometry in four producing isolates: Staphylococcus aureus-C5802, Staphylococcus hominis-C5835, Staphylococcus sciuri-X3041, and -X3011. Growth curves performed with CFS and BT extracts of the four MP1 producers revealed a strong AA profile against MRSA and Listeria monocytogenes, even when considerably diluted. Moreover, synergism between the BT extract of MP1-producing Staphylococcus sciuri-X3041 and several antibiotics against an MRSA indicator was observed: BT-clindamycin (> 80%) and BT-oxacillin (30%) combinations. For the BT-chloramphenicol combination, synergism and near synergism values were observed in 37% of the combinations. Competition studies revealed potent inhibitory effects of the MP1-producing isolates against the MRSA indicator. CONCLUSION: These results help to identify Staphylococcus isolates or their bacteriocins as interesting candidates for potential future applications.
Subject(s)
Bacteriocins , Methicillin-Resistant Staphylococcus aureus , Staphylococcal Infections , Humans , Staphylococcus , Bacteriocins/pharmacology , Anti-Bacterial Agents/pharmacology , Staphylococcal Infections/drug therapy , Staphylococcal Infections/microbiology , Microbial Sensitivity TestsABSTRACT
Bacteriocins are antimicrobial peptides produced by bacteria. This study aimed to in silico analyze the presence of bacteriocin gene clusters (BGCs) among the genomes of 22 commensal Staphylococcus isolates from different origins (environment/human/food/pet/wild animals) previously identified as bacteriocin producers. The resistome and plasmidome were studied in all isolates. Five types of BGC were detected in 18 genomes of the 22 bacteriocin-producing staphylococci included in this study: class I (Lanthipeptides), class II, circular bacteriocins, the non-ribosomal-peptide lugdunin and the thiopeptide micrococcin P1 (MP1). A high frequency of lanthipeptides was detected in this collection: BGC variants of BSA, bacCH91, and epilancin15X were identified in two Staphylococcus aureus and one Staphylococcus warneri isolates from food and wild animals. Moreover, two potentially new lanthipeptide-like BGCs with no identity to database entries were found in Staphylococcus epidermidis and Staphylococcus simulans from food and wild animal, respectively. Interestingly, four isolates (one S. aureus and one Staphylococcus hominis, environmental origin; two Staphylococcus sciuri, food) carried the MP1 BGC with differences to those previously described. On the other hand, seven of the 22 genomes (~32%) lacked known genes related with antibiotic or disinfectant-acquired resistance mechanisms. Moreover, the potential carriage of plasmids was evaluated, and several Rep-proteins were identified (~73% of strains). In conclusion, a wide variety of BGCs has been observed among the 22 genomes, and an interesting relationship between related Staphylococcus species and the type of bacteriocin has been revealed. Therefore, bacteriocin-producing Staphylococcus and especially coagulase-negative staphylococci (CoNS) can be considered good candidates as a source of novel bacteriocins.
ABSTRACT
BACKGROUND: This was a substudy of a Phase IV, randomized clinical trial (ClinicalTrials.gov identifier: NCT04295460) aiming to compare the activity of dolutegravir/lamivudine versus dolutegravir plus tenofovir alafenamide/emtricitabine (DTGâ+âTAF/FTC) in the male genital tract. METHODS: Participants were asymptomatic adults without sexually transmitted diseases, treatment-naive people living with HIV (PLWH), with CD4+ T cell counts >200 cells/mm3 and plasma HIV-1-RNA levels >5000 and <500â000 copies/mL, randomized (1:1) to DTGâ+âTAF/FTC or dolutegravir/lamivudine. Blood plasma (BP) and seminal plasma (SP) were collected at baseline and Weeks 4, 8, 12 and 24. HIV-1-RNA was measured in BP and SP using the Cobas 6800 system (Roche Diagnostics) with a lower detection limit of 20 copies/mL. The primary efficacy endpoint was the proportion of subjects with undetectable SP HIV-1-RNA at Week 12 by intention-to-treat analysis. RESULTS: Fifteen participants in the DTGâ+âTAF/FTC and 16 in the dolutegravir/lamivudine arms were analysed, with basal SP viral load of 4.81 (4.30-5.43) and 4.76 (4.09-5.23), Pâ=â0.469, respectively. At Week 12, only one participant in each treatment arm had a detectable SP HIV-1-RNA (DTGâ+âTAF/FTC, 141 copies/mL; dolutegravir/lamivudine, 61 copies/mL). Based on the estimated means, there was no significant difference in the decay of HIV-1-RNA in both BP and SP over time between the two arms of treatment (Fâ=â0.452, Pâ=â0.662, and Fâ=â1.147, Pâ=â0.185, respectively). CONCLUSIONS: After 12 weeks of treatment, there were no differences in the percentage of undetectable SP HIV-1-RNA in naive PLWH who started dolutegravir/lamivudine compared with DTGâ+âTAF/FTC.
Subject(s)
Anti-HIV Agents , HIV Infections , HIV-1 , Adult , Humans , Male , Lamivudine/therapeutic use , HIV-1/genetics , HIV Infections/drug therapy , Semen , Kinetics , Drug Therapy, Combination , Emtricitabine/therapeutic use , Heterocyclic Compounds, 3-Ring/therapeutic use , Pyridones/therapeutic use , Oxazines/therapeutic use , RNA, Viral , Anti-HIV Agents/therapeutic useABSTRACT
The antimicrobial resistance (AMR) genes of 268 non-duplicated coagulase-negative staphylococci (CoNS) previously obtained from nasotracheal cavities of nestling storks were characterized. They included S. sciuri isolates (n = 191), and non-sciuri-CoNS isolates (NSc-CoNS, n = 77). All S. sciuri carried the intrinsic salA gene (for clindamycin-resistance) and so, clindamycin was not considered for general analysis in this species. About 71.7%/41.6% of the S. sciuri/NSc-CoNS isolates were susceptible to all antibiotics tested; moreover, 14.1%/16.9% and 3.1%/20.8% of S. sciuri/NSc-CoNS showed single antibiotic resistance and multidrug resistance (MDR) phenotype, respectively. Of the ten mecA-positive CoNS isolates, six were associated with SCCmec types-III, -IV or -V elements. Remarkably was the detection of one MDR-S. lentus isolate carrying both mecA and mecC genes, as well as the SCCmec type-XI element. MDR-CoNS was relatively higher in nestlings of parent storks foraging in landfills (21.3%) than those in natural areas (9.7%) (χ2 = 3.421, df=1, p = 0.064). AMR phenotypes (and genes detected) include penicillin (blaZ, blaARL), erythromycin-clindamycin-constitutive (ermA, ermC, ermT), clindamycin (lnuA, salA, vgaA), erythromycin (msrA, mphC), tetracycline (tetK, tetL, tetM), tobramycin (ant4'), tobramycin-gentamicin (aac6'-aph2â³), sulfamethoxazole-trimethoprim (dfrA, dfrG, dfrK), chloramphenicol (fexA, fexB, catPC221), and mupirocin (mupA). Interestingly, one S. epidermidis isolate carried the ermT gene. About 29.9% of nestlings harboured more than one non-duplicated CoNS (with varied 2-5 AMR profiles). This study demonstrated that most of the CoNS isolates were susceptible to all the antibiotics tested (63.1%). However, AMR genes of public health importance were found, including the mecC-mediated methicillin resistance trait.
Subject(s)
Coagulase , Staphylococcal Infections , Animals , Coagulase/genetics , Spain , Microbial Sensitivity Tests/veterinary , Staphylococcus , Anti-Bacterial Agents/pharmacology , Clindamycin , Tobramycin , Erythromycin , Staphylococcal Infections/veterinaryABSTRACT
This study investigated the diversity and carriage rate of nasal Staphylococcus spp., and within-host variability of antimicrobial resistance (AMR), virulence determinants, immune evasion cluster (IEC) types and genetic lineages of S. aureus isolates. Also, the co-carriage rate of CoNS with S. aureus in the same nasal niche of healthy pigs and pig-farmers were studied in four pig-farms (A-D) in Aragon (Spain). Nasal samples of 40 pigs (10 pigs/farm) and 10 pig-farmers (2-3/farm) were collected for staphylococci recovery and isolates (up to 9 per sample) were identified by MALDI-TOF-MS. The virulence and AMR genes and spa-types of S. aureus isolates were investigated by PCR/sequencing. Of the 243 staphylococci identified (10 different species), 142 were S. aureus and 51 distinct isolates were selected for further characterization (that corresponded to one S. aureus/sample or more than one if they showed different AMR phenotypes). The highest carriage rate in pigs was S. aureus (65%) and S. chromogenes (22.5%), whereas in the pig-farmers, S. aureus (80%) and S. epidermidis (40%). Methicillin-resistant S. aureus (MRSA) were detected in 60% of pigs and 70% of pig-farmers. Only six S. aureus isolates were methicillin-susceptible (MSSA), all from farm-C. A multidrug resistance (MDR) phenotype was detected in all MRSA and in 83.3% of the MSSA isolates. All MRSA isolates were CC398 with spa-type t011 being the predominant (92.7%), while t034, t1451 (only in pig-farmers) and t4571 (in pigs) were also found. MSSA-CC9 isolates (t191, t1430) were detected in farm-C. All S. aureus isolates were negative for luk-S/F-PV, tst, and scn genes, except one MSSA-CC45-t065-IEC-type C isolate from a pig-farmer. About 34.6% and 75.0% of the pigs and pig-farmers S. aureus carriers, respectively, harboured within-host varied spa-types or resistomes. Moreover, 40% of pigs and pig-farmers with MRSA-CC398 had no CoNS nasal co-carriage, and 23.3% had ≥2 CoNS carriage. Conversely, only 16.7% of MSSA carriers had no CoNS co-carriage, whereas 50% had ≥2 CoNS carriages. The very high MRSA level and within-host resistome diversities highlight the need for multiple samplings to account for the dynamics of AMR crisis and control of inter-host transmission of S. aureus in pig-farms using "One Health" approach.
ABSTRACT
Novel and sustainable approaches are required to curb the increasing threat of antimicrobial resistance (AMR). Within the last decades, antimicrobial peptides, especially bacteriocins, have received increased attention and are being explored as suitable alternatives to antibiotics. Bacteriocins are ribosomally synthesized antimicrobial peptides produced by bacteria as a self-preservation method against competitors. Bacteriocins produced by Staphylococcus, also referred to as staphylococcins, have steadily shown great antimicrobial potential and are currently being considered promising candidates to mitigate the AMR menace. Moreover, several bacteriocin-producing Staphylococcus isolates of different species, especially coagulase-negative staphylococci (CoNS), have been described and are being targeted as a good alternative. This revision aims to help researchers in the search and characterization of staphylococcins, so we provide an up-to-date list of bacteriocin produced by Staphylococcus. Moreover, a universal nucleotide and amino acid-based phylogeny system of the well-characterized staphylococcins is proposed that could be of interest in the classification and search for these promising antimicrobials. Finally, we discuss the state of art of the staphylococcin applications and an overview of the emerging concerns.
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A collection of 259 staphylococci of 13 different species [212 coagulase-negative (CoNS) and 47 coagulase-positive (CoPS)] recovered from nasotracheal samples of 87 healthy nestling white storks was tested by the spot-on-lawn method for antimicrobial-activity (AA) against 14 indicator bacteria. Moreover, extracts of AP isolates were obtained [cell-free-supernatants (CFS) both crude and concentrated and butanol extracts] and tested against the 14 indicator bacteria. The microbiota modulation capacity of AP isolates was tested considering: (a) intra-sample AA, against all Gram-positive bacteria recovered in the same stork nasotracheal sample; (b) inter-sample AA against a selection of representative Gram-positive bacteria of the nasotracheal microbiota of all the storks (30 isolates of 29 different species and nine genera). In addition, enzymatic susceptibility test was carried out in selected AP isolates and bacteriocin encoding genes was studied by PCR/sequencing. In this respect, nine isolates (3.5%; seven CoNS and two CoPS) showed AA against at least one indicator bacteria and were considered antimicrobial-producing (AP) isolates. The AP isolates showed AA only for Gram-positive bacteria. Three of these AP isolates (S. hominis X3764, S. sciuri X4000, and S. chromogenes X4620) revealed AA on all extract conditions; other four AP isolates only showed activity in extracts after concentration; the remaining two AP isolates did not show AA in any of extract conditions. As for the microbiota modulation evaluation, three of the nine AP-isolates revealed intra-sample AA. It is to highlight the potent inter-sample AA of the X3764 isolate inhibiting 73% of the 29 representative Gram-positive species of the nasotracheal stork microbiota population. On the other hand, enzymatic analysis carried out in the two highest AP isolates (X3764 and X4000) verified the proteinaceous nature of the antimicrobial compound and PCR analysis revealed the presence of lantibiotic-like encoding genes in the nine AP isolates. In conclusion, these results show that nasotracheal staphylococci of healthy storks, and especially CoNS, produce antimicrobial substances that could be important in the modulations of their nasal microbiota.
ABSTRACT
Migratory storks could be vectors of transmission of bacteria of public health concern mediated by the colonization, persistence and excretion of such bacteria. This study aims to determine genera/species diversity, prevalence, and co-colonization indices of bacteria obtained from tracheal (T) and nasal (N) samples from storks in relation to exposure to point sources through foraging. One-hundred and thirty-six samples from 87 nestlings of colonies of parent white storks with different foraging habits (natural habitat and landfills) were obtained (84 T-samples and 52 N-samples) and processed. Morphologically distinct colonies (up to 12/sample) were randomly selected and identified by MALDI-TOF-MS. About 87.2% of the total 806 isolates recovered were identified: 398 from T-samples (56.6%) and 305 from N-samples (43.4%). Among identified isolates, 17 genera and 46 species of Gram-positive and Gram-negative bacteria were detected, Staphylococcus (58.0%) and Enterococcus (20.5%) being the most prevalent genera. S. sciuri was the most prevalent species from T (36.7%) and N (34.4%) cavities of total isolates, followed by E. faecalis (11.1% each from T and N), and S. aureus [T (6.5%), N (13.4%)]. Of N-samples, E. faecium was significantly associated with nestlings of parent storks foraging in landfills (p = 0.018). S. sciuri (p = 0.0034) and M. caseolyticus (p = 0.032) from T-samples were significantly higher among nestlings of parent storks foraging in natural habitats. More than 80% of bacterial species in the T and N cavities showed 1-10% co-colonization indices with one another, but few had ≥ 40% indices. S. sciuri and E. faecalis were the most frequent species identified in the stork nestlings. Moreover, they were highly colonized by other diverse and potentially pathogenic bacteria. Thus, storks could be sentinels of point sources and vehicles of bacterial transmission across the "One Health" ecosystems.
Subject(s)
Ecosystem , Staphylococcus aureus , Animals , Spain/epidemiology , Anti-Bacterial Agents , Gram-Negative Bacteria , Gram-Positive Bacteria , BirdsABSTRACT
Background: Data on SARS-CoV-2 mRNA vaccine immunogenicity in people living with human immunodeficiency virus (PLWH) and discordant immune response (DIR) are currently limited. Therefore, we compare the immunogenicity of these vaccines in DIR and immunological responders (IR). Methods: A prospective cohort that enrolled 89 participants. Finally, 22 IR and 24 DIR were analyzed before vaccination (T0), one (T1) and six months (T2) after receiving BNT162b2 or mRNA-1273 vaccine. Additionally, 10 IR and 16 DIR were evaluated after a third dose (T3). Anti-S-RBD IgG, neutralizing antibodies (nAb), neutralization activity, and specific memory B cells were quantified. Furthermore, specific CD4+ and CD8+ responses were determined by intracellular cytokine staining and polyfunctionality indexes (Pindex). Results: At T1, all participants developed anti-S-RBD. 100% IR developed nAb compared to 83.3% DIR. Spike-specific B cells were detected in all IR and 21/24 DIR. Memory CD4+ T cells responded in 5/9 IR and 7/9 DIR, mainly based on the expression of IFN-γ and TNF-α, with a higher Pindex in DIR. Memory CD8+ T cells responded in only four participants in each group. At T2, anti-S-RBD and nAb titers were higher in DIR than in IR. In both groups, there was an increase in specific B memory cells, higher in DIR. Six IR and five DIR maintained a specific memory CD4+ response. Memory CD8+ response was preserved in IR but was lost in DIR. In a multivariate linear regression analysis, receiving mRNA-1273 instead of BNT162b2 played a prominent role in the results. Conclusions: Our data suggest that PLWH with DIR can mount an immune response similar to those with higher CD4+, provided they receive the mRNA-1273 vaccine instead of others less immunogenic.
Subject(s)
COVID-19 , Vaccines , Humans , COVID-19 Vaccines , BNT162 Vaccine , 2019-nCoV Vaccine mRNA-1273 , SARS-CoV-2 , CD8-Positive T-Lymphocytes , Prospective Studies , COVID-19/prevention & control , Vaccination , mRNA Vaccines , Immunity, Cellular , Antibodies, NeutralizingABSTRACT
BACKGROUND: Older people achieve lower levels of antibody titers than younger populations after Covid-19 vaccination and show a marked waning humoral immunity over time, likely due to the senescence of the immune system. Nevertheless, age-related predictive factors of the waning humoral immune response to the vaccine have been scarcely explored. In a cohort of residents and healthcare workers from a nursing home that had received two doses of the BNT162b2 vaccine, we measured specific anti-S antibodies one (T1), four (T4), and eight (T8) months after receiving the second dose. Thymic-related functional markers, including thymic output, relative telomere length, and plasma thymosin-α1 levels, as well as immune cellular subsets, and biochemical and inflammatory biomarkers, were determined at T1, and tested for their associations with the magnitude of the vaccine response (T1) and the durability of such response both, at the short- (T1-T4) and the long-term (T1-T8). We aimed to identify age-related factors potentially associated with the magnitude and persistence of specific anti-S immunoglobulin G (IgG)-antibodies after COVID-19 vaccination in older people. RESULTS: Participants (100% men, n = 98), were subdivided into three groups: young (< 50 years-old), middle-age (50-65 years-old), and older (≥65 years-old). Older participants achieved lower antibody titers at T1 and experienced higher decreases in both the short- and long-term. In the entire cohort, while the magnitude of the initial response was mainly associated with the levels of homocysteine [ß (95% CI); - 0.155 (- 0.241 to - 0.068); p = 0.001], the durability of such response at both, the short-term and the long-term were predicted by the levels of thymosin-α1 [- 0.168 (- 0.305 to - 0.031); p = 0.017, and - 0.123 (- 0.212 to - 0.034); p = 0.008, respectively]. CONCLUSIONS: Higher plasma levels of thymosin-α1 were associated with a lower waning of anti-S IgG antibodies along the time. Our results suggest that plasma levels of thymosin-α1 could be used as a biomarker for predicting the durability of the responses after COVID-19 vaccination, possibly allowing to personalize the administration of vaccine boosters.
ABSTRACT
This study determined the carriage rates and antimicrobial resistance (AMR) genes of enterococci from nasotracheal samples of three healthy animal species and in-contact humans. Nasal samples were collected from 27 dog-owning households (34 dogs, 41 humans) and 4 pig-farms (40 pigs, 10 pig-farmers), and they were processed for enterococci recovery (MALDI-TOF-MS identification). Also, a collection of 144 enterococci previously recovered of tracheal/nasal samples from 87 white stork nestlings were characterized. The AMR phenotypes were determined in all enterococci and AMR genes were studied by PCR/sequencing. MultiLocus-Sequence-Typing was performed for selected isolates. About 72.5% and 60% of the pigs and pig-farmers, and 29.4% and 4.9%, of healthy dogs and owners were enterococci nasal carriers, respectively. In storks, 43.5% of tracheal and 69.2% of nasal samples had enterococci carriages. Enterococci carrying multidrug-resistance phenotype was identified in 72.5%/40.0%/50.0%/23.5%/1.1% of pigs/pig-farmers/dogs/dogs' owners/storks, respectively. Of special relevance was the detection of linezolid-resistant enterococci (LRE) in (a) 33.3% of pigs (E. faecalis-carrying optrA and/or cfrD of ST59, ST330 or ST474 lineages; E. casseliflavus-carrying optrA and cfrD); (b) 10% of pig farmers (E. faecalis-ST330-carrying optrA); (c) 2.9% of dogs (E. faecalis-ST585-carrying optrA); and (d) 1.7% of storks (E. faecium-ST1736-carrying poxtA). The fexA gene was found in all optrA-positive E. faecalis and E. casseliflavus isolates, while fexB was detected in the poxtA-positive E. faecium isolate. The enterococci diversity and AMR rates from the four hosts reflect differences in antimicrobial selection pressure. The detection of LRE carrying acquired and transferable genes in all the hosts emphasizes the need to monitor LRE using a One-Health approach.