RESUMO
Because the diagnosis of co/superinfection in COVID-19 patients is challenging, empirical antibiotic therapy is frequently initiated until microbiological analysis results. We evaluated the performance and the impact of the BioFire® FilmArray® Pneumonia plus Panel on 112 respiratory samples from 67 COVID-19 ICU patients suspected of co/superinfections. Globally, the sensitivity and specificity of the test were 89.3% and 99.1%, respectively. Positive tests led to antibiotic initiation or adaptation in 15% of episodes and de-escalation in 4%. When negative, 28% of episodes remained antibiotic-free (14% no initiation, 14% withdrawal). Rapid multiplex PCRs can help to improve antibiotic stewardship by administering appropriate antibiotics earlier and avoiding unnecessary prescriptions.
Assuntos
Antibacterianos/uso terapêutico , Bactérias/isolamento & purificação , Infecções Bacterianas/tratamento farmacológico , COVID-19/complicações , Reação em Cadeia da Polimerase Multiplex/métodos , Idoso , Gestão de Antimicrobianos , Bactérias/classificação , Bactérias/efeitos dos fármacos , Bactérias/genética , Infecções Bacterianas/diagnóstico , Infecções Bacterianas/microbiologia , COVID-19/virologia , Feminino , Hospitalização , Humanos , Unidades de Terapia Intensiva/estatística & dados numéricos , Masculino , Pessoa de Meia-Idade , Estudos Retrospectivos , SARS-CoV-2/genética , SARS-CoV-2/fisiologiaRESUMO
BACKGROUND: Colistin is an antibiotic of last resort in the management of highly drug-resistant Enterobacterales infections. Travel to some destinations presents a high risk of acquiring multidrug-resistant Enterobacterales, but little data are available on the risk of acquiring colistin-resistant strains. Here, we use the VOYAG-R sample collection (2012-2013) in order to evaluate the rate of acquisition of colistin-resistant Enterobacterales, excluding species with intrinsic resistance (CRE), following travel to tropical regions. METHODS: A total of 574 frozen stool samples of travellers returning from tropical regions were screened for colistin-resistant strains using ChromID Colistin R agar (bioMerieux®) after pre-enrichment culture with 1 mg/L of colistin. Genomes were obtained by Illumina sequencing and genetic determinants of colistin resistance (mutational events and mcr genes) were searched. RESULTS: A total of 22 travellers (3.8%) acquired colistin-resistant Enterobacterales carrying an mcr gene. Acquisition rates varied between visited regions: 9.2% (18/195) for Asia (southeast Asia: 17/18), 2.2% (4/184) for Latin America (Peru: 4/4) and 0% from Africa (0/195). Acquired strains were predominantly Escherichia coli (92%) and carried mostly the mcr-1 variant (83%). Escherichia coli strains belonged mainly to commensal phylogroups A and B1, and were genetically highly diverse (5 non-clonal sequence type (ST)10 and 17 ST singletons). Only four non mcr colistin-resistant strains (two E. coli and two Enterobacter cloacae complex) were identified. Among all the strains, two also carried extended-spectrum beta-lactamase genes. CONCLUSIONS: Travel to tropical regions, and particularly to Southeast Asia, is a risk factor for the acquisition of mcr-carrying Enterobacterales. This study highlights the community dissemination of mcr in humans as early as 2012, 4 years prior to its first published description.
Assuntos
Colistina , Proteínas de Escherichia coli , Humanos , Escherichia coli , Proteínas de Escherichia coli/genética , Farmacorresistência Bacteriana , Antibacterianos/farmacologia , Testes de Sensibilidade Microbiana , beta-LactamasesRESUMO
Multidrug-resistant Enterobacterales, including carbapenemase producers, are currently spreading in health care facilities and the community. The Bichat Claude Bernard hospital in Paris faced a prolonged NDM-producing Enterobacterales (NDM-CPE) outbreak. Whole-genome sequencing (WGS) was performed on all isolated NDM-CPE to evaluate its benefits for outbreak surveillance and comprehension. All NDM-CPE isolates collected during the outbreak period (August 2016 to January 2018) were sequenced using the Illumina NextSeq platform. Gene content and core genomes were compared. Genomics results underwent epidemiological analysis which classified NDM-CPE cases as imported (positive sample during the 48 h after admission), hospital acquired, or uncertain. Over the epidemic period, 61 patients were colonized or infected with 81 distinct NDM-CPE isolates. Klebsiella pneumoniae was the most common species (n = 52, 64%), followed by Escherichia coli (13.5%) and other species (22.5%). In all, 43/52 (83%) K. pneumoniae isolates were clonal (≤18 single nucleotide polymorphisms [SNPs] except for three isolates) and belonged to ST307. The IncFIIK [K2:A-/B-] plasmid carrying blaNDM-1 present in all ST307 K. pneumoniae isolates was also detected in 18 other NDM-CPE isolates. Additionally, eight clonal ST144 Klebsiella oxytoca (≤18 SNPs) isolates lacking the epidemic plasmid were observed. The WGS analyses confirmed the acquired and imported cases except for two patients and resolved uncertain cases, which all turned out to be hospital acquisitions. WGS coupled with epidemiological analysis unraveled three epidemic phenomena: mainly the spread of a clonal ST307 K. pneumoniae strain and its conjugative plasmid carrying blaNDM-1 but also the unexpected clonal spread of an ST144 K. oxytoca strain. IMPORTANCE Carbapenemase-producing Enterobacterales (CPE) can spread and cause outbreaks in health care facilities, resulting in increased lengths of stay and morbidity. Control of outbreaks requires epidemiological surveillance, usually based on microbiological screening and patient follow-up. These data are sometimes insufficient to identify the routes of dissemination. There is therefore a need for more accurate tools such as whole-genome sequencing (WGS), which allows comparison of isolates but also plasmids carrying resistance with a high definition. In this work, we retrospectively sequenced the genomes of all NDM-producing Enterobacterales isolated during a prolonged NDM outbreak in our hospital. We demonstrated the value of combining WGS with epidemiological data that unveiled the multiple mechanisms of dissemination involved in the outbreak and confirmed transmission cases. This work reinforces the potential of WGS in outbreak surveillance and suggests that it could improve outbreak control if used in real time by confirming transmission cases more rapidly.
Assuntos
Surtos de Doenças , Klebsiella pneumoniae , Escherichia coli/genética , Hospitais , Humanos , Klebsiella pneumoniae/genética , Estudos Retrospectivos , beta-LactamasesRESUMO
Among 197 COVID-19 patients hospitalized in ICU, 88 (44.7%) experienced at least one bacterial infection, with pneumonia (39.1%) and bloodstream infections (15,7%) being the most frequent. Unusual findings include frequent suspicion of bacterial translocations originating from the digestive tract as well as bacterial persistence in the lungs despite adequate therapy.
Assuntos
Infecções Bacterianas/complicações , COVID-19/complicações , Pneumonia Bacteriana/complicações , Idoso , Infecções Bacterianas/epidemiologia , COVID-19/epidemiologia , Feminino , França/epidemiologia , Hospitalização , Humanos , Unidades de Terapia Intensiva , Pulmão/microbiologia , Pulmão/virologia , Masculino , Pessoa de Meia-Idade , Pneumonia Bacteriana/epidemiologiaRESUMO
Travel to tropical regions is associated with high risk of acquiring extended-spectrum beta-lactamase-producing Enterobacterales (ESBL-E) that are typically cleared in less than 3 months following return. The conditions leading to persistent carriage that exceeds 3 months in some travellers require investigation. Whole-genome sequencing (Illumina MiSeq) was performed on the 82 ESBL-E isolates detected upon return and 1, 2, 3, 6 and 12 months later from the stools of 11 long-term (>3 months) ESBL-E carriers following travel abroad. One to five different ESBL Escherichia coli strains were detected per traveller upon return, and this diminished to one after 3 months. Long-term carriage was due to the presence of the same ESBL E. coli strain, for more than 3 months, in 9 out of 11 travellers, belonging to epidemic sequence type complexes (STc 10, 14, 38, 69, 131 and 648). The mean carriage duration of strains belonging to phylogroups B2/D/F, associated with extra-intestinal virulence, was higher than that for commensal-associated A/B1/E phylogroups (3.5 vs 0.5 months, P=0.021). Genes encoding iron capture systems (fyuA, irp), toxins (senB, sat), adhesins (flu, daaF, afa/nfaE, pap, ecpA) and colicin (cjrA) were more often present in persistent strains than in transient ones. Single-nucleotide polymorphism (SNP) analysis in persistent strains showed a maximum divergence of eight SNPs over 12 months without signs of adaptation. Genomic plasticity was observed during the follow-up with the loss or gain of mobile genetic elements such as plasmids, integrons and/or transposons that may contain resistance genes at different points in the follow-up. Long-term colonization of ESBL-E following travel is primarily due to the acquisition of E. coli strains belonging to epidemic clones and harbouring 'virulence genes', allowing good adaptation to the intestinal microbiota.
Assuntos
Portador Sadio/epidemiologia , Farmacorresistência Bacteriana Múltipla/genética , Escherichia coli/efeitos dos fármacos , Escherichia coli/genética , Viagem , beta-Lactamases/genética , Escherichia coli/classificação , Escherichia coli/patogenicidade , Microbioma Gastrointestinal/genética , Genoma Bacteriano/genética , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Sequências Repetitivas Dispersas/genética , Polimorfismo de Nucleotídeo Único/genética , Sequenciamento Completo do GenomaRESUMO
We report a case of an infective endocarditis caused by a Thalassospira sp. in a 53-year-old man with pre-existing valvular lesions and living in French Polynesia as a fisherman. The strain was identified with DNA-sequecing methods while it was not by mass spectrometry.
RESUMO
Travel abroad is associated with a high risk of acquiring multidrug-resistant Enterobacterales (MDR-E) [i.e., extended-spectrum beta-lactamase-producing Enterobacterales (ESBL-E) and plasmid-mediated-AmpC beta-lactamase-producing Enterobacterales (pAmpC-E)]. Here, we evaluated the utility of pre-enrichment and performance of screening for MDR-E using 2 different media (ChromID-ESBL and biplate-ESBL) from 574 traveler stool samples. ESBL-E and MDR-E were detected in 49% (281/574) and 51% (296/574) of travelers, respectively. Pre-enrichment improved the detection of ESBL-E and MDR-E by 11.7% and 12.5%, respectively, without decreasing specificity (88.4% versus 87.4% for ESBL-E screening and 92.4% versus 89.9% for MDR-E screening). Sensitivity of the biplate-ESBL agar was higher than for ChromID-ESBL for ESBL-E detection (92.9% versus 86.1%), but specificity was lower (64.2% versus 87.4%). Whereas pAmpC-E were all detected by biplate-ESBL, 96% (47/49) and 82% (40/49) were detected by ChromID-ESBL, respectively, with and without pre-enrichment. Pre-enrichment increases the performance of MDR-E screening, especially in individuals with low MDR-E digestive abundance.
Assuntos
Técnicas Bacteriológicas/métodos , Portador Sadio/diagnóstico , Farmacorresistência Bacteriana Múltipla , Infecções por Enterobacteriaceae/diagnóstico , Enterobacteriaceae/isolamento & purificação , Antibacterianos/farmacologia , Meios de Cultura , Enterobacteriaceae/efeitos dos fármacos , Fezes/microbiologia , Seguimentos , Humanos , Testes de Sensibilidade Microbiana , Sensibilidade e Especificidade , Manejo de Espécimes , ViagemRESUMO
To comparatively evaluate the performance of the rapid antimicrobial susceptibility testing (AST) system QMAC-dRAST V2.0 and of standard disk diffusion in agar, AST was performed directly from 100 positive blood culture bottles with Gram-negative bacilli. AST results provided by QMAC-dRAST showed 92.9% agreement with disk diffusion method results. Discrepancies observed between results obtained with QMAC-dRAST and disk diffusion method conducted to 10 very major errors (0.8%, S with QMAC-dRAST vs R with disk diffusion method), 40 major errors (3.2%, R vs S, respectively), 15 minor errors (1.2%, S vs I or I vs R, respectively) and 23 very minors errors (1.8%, I vs S or R vs I, respectively). For very major and major errors, in only 36% of the cases did the repeat QMAC-dRAST confirm the initial result, whereas a repeat AST using disk diffusion method confirmed the initial result in 92% of cases. AST results obtained using microdilution in liquid medium confirmed those obtained with QMAC-dRAST and disk diffusion method in 4% and 89%, respectively. Repeatability and reproducibility tests performed on QMAC-dRAST using reference strains showed 94% to 100% of R/S/I categorical agreement.
Assuntos
Antibacterianos , Hemocultura/métodos , Testes de Sensibilidade a Antimicrobianos por Disco-Difusão/métodos , Bactérias Gram-Negativas/isolamento & purificação , Bacteriemia/diagnóstico , Bacteriemia/microbiologia , Meios de Cultura , Bactérias Gram-Negativas/classificação , Humanos , Estudos Prospectivos , Reprodutibilidade dos Testes , Fatores de TempoRESUMO
Background: The R-GNOSIS (Resistance in Gram-Negative Organisms: Studying Intervention Strategies) WP3 study was the first multicenter randomized clinical trial systematically investigating fecal microbiota transplantation (FMT) for intestinal decolonization of extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-E) or carbapenemase-producing Enterobacteriaceae (CPE). Here, we characterized the temporal dynamics of fecal microbiota changes in a sub-cohort of the R-GNOSIS WP3 participants before and after antibiotics/FMT using whole metagenome shotgun sequencing. Methods: We sequenced fecal DNA obtained from 16 ESBL-E/CPE carriers having received oral colistin/neomycin followed by FMT and their corresponding seven donors. Ten treatment-naïve controls from the same trial were included. Fecal samples were collected at baseline (V0), after antibiotics but before FMT (V2) and three times after FMT (V3, V4 and V5). Results: Antibiotic treatment transiently decreased species richness and diversity and increased the abundance of antibiotic resistance determinants (ARDs). Bifidobacterium species, together with butyrate- and propionate-producing species from Lachnospiraceae and Ruminococcaceae families were significantly enriched in post-FMT microbiota of treated carriers. After FMT, the proportion of Enterobacteriaceae was lower compared to baseline but without statistical significance. Conclusions: Combined antibiotic and FMT treatment resulted in enrichment of species that are likely to limit the gut colonization by ESBL-E/CPE.
Assuntos
Elementos de DNA Transponíveis , Enterobacter cloacae/genética , Escherichia coli/genética , beta-Lactamases/genética , Idoso , DNA Bacteriano/química , DNA Bacteriano/genética , Enterobacter cloacae/enzimologia , Enterobacter cloacae/isolamento & purificação , Infecções por Enterobacteriaceae/microbiologia , Escherichia coli/enzimologia , Escherichia coli/isolamento & purificação , Humanos , Dados de Sequência Molecular , Análise de Sequência de DNARESUMO
Travelers are at high risk of acquiring multi-drug resistant Enterobacteriaceae (MRE) while traveling abroad. Acquisition of extended spectrum beta-lactamase producing Enterobacteriaceae (ESBL-E) while traveling has been extensively described, but not that of plasmid-mediated cephalosporinase producing Enterobacteriaceae (pAmpC-E). Here, we characterized the pAmpC-E acquired in 574 French travelers to tropical areas enrolled in the VOYAG-R study. Among the 526 MRE isolated at return, 57 (10.8%) from 49 travelers were pAmpC-E. The acquisition rate of pAmpC-E was 8.5% (49/574) ranging from 12.8% (25/195) in Asia, 7.6% (14/184) in Latin America to 5.1% (10/195) in Africa. The highest acquisition rates were observed in Peru (21.9%), India (21.4%) and Vietnam (20%). The carriage of pAmpC-E decreased quickly after return with 92.5% of colonized travelers being negative at one month. Most enzymes were CMY types (96.5%, n = 55, only met in Escherichia coli), including 40 CMY-2 (70.2%), 12 CMY-42 (21.1%), 1 CMY-6 and two new CMY-2 variants. The remaining were two DHA observed in Klebsiella pneumoniae. CMY-2 producing strains were acquired worldwide whereas CMY-42, except for one, were all acquired in Asia. BlaCMY-2 genes were associated with different plasmid types, including IncI1 (45. 2%), IncF (10%), IncF-IncI (7.5%), IncA/C (5%) and IncR (2.5%) whereas blaCMY-42 were all associated with IncI1 plasmids. Even though the pAmpC-E acquisition rate was much lower than that of ESBL-E, it was significant, especially in Asia, showing that pAmpC-E, especially CMY-type producing E. coli have spread in the community settings of tropical regions.
Assuntos
Cefalosporinase/biossíntese , Enterobacteriaceae/isolamento & purificação , Enterobacteriaceae/metabolismo , Plasmídeos/genética , Viagem , Clima Tropical , Adolescente , Adulto , Resistência Microbiana a Medicamentos , Resistência a Múltiplos Medicamentos , Enterobacteriaceae/efeitos dos fármacos , Enterobacteriaceae/genética , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Adulto JovemRESUMO
The worldwide dissemination of extended-spectrum beta-lactamase producing Enterobacteriaceae, (ESBL-E) and their subset producing carbapenemases (CPE), is alarming. Limited data on the prevalence of such strains in infections from patients from Sub-Saharan Africa are currently available. We determined, here, the prevalence of ESBL-E/CPE in bacteriemic patients in two teaching hospitals from Bamako (Mali), which are at the top of the health care pyramid in the country. During one year, all Enterobacteriaceae isolated from bloodstream infections (E-BSI), were collected from patients hospitalized at the Point G University Teaching Hospital and the pediatric units of Gabriel Touré University Teaching Hospital. Antibiotic susceptibility testing, enzyme characterization and strain relatedness were determined. A total of 77 patients had an E-BSI and as many as 48 (62.3%) were infected with an ESBL-E. ESBL-E BSI were associated with a previous hospitalization (OR 3.97 95% IC [1.32; 13.21]) and were more frequent in hospital-acquired episodes (OR 3.66 95% IC [1.07; 13.38]). Among the 82 isolated Enterobacteriaceae, 58.5% were ESBL-E (20/31 Escherichia coli, 20/26 Klebsiella pneumoniae and 8/15 Enterobacter cloacae). The remaining (5 Salmonella Enteritidis, 3 Morganella morganii 1 Proteus mirabilis and 1 Leclercia adecarboxylata) were ESBL negative. CTX-M-1 group enzymes were highly prevalent (89.6%) among ESBLs; the remaining ones being SHV. One E. coli produced an OXA-181 carbapenemase, which is the first CPE described in Mali. The analysis of ESBL-E relatedness suggested a high rate of cross transmission between patients. In conclusion, even if CPE are still rare for the moment, the high rate of ESBL-BSI and frequent cross transmission probably impose a high medical and economic burden to Malian hospitals.
Assuntos
Bacteriemia/microbiologia , Enterobacteriaceae/enzimologia , beta-Lactamases/metabolismo , Adolescente , Adulto , Idoso , Idoso de 80 Anos ou mais , Antibacterianos/farmacologia , Farmacorresistência Bacteriana , Enterobacter cloacae/efeitos dos fármacos , Enterobacter cloacae/fisiologia , Enterobacteriaceae/efeitos dos fármacos , Enterobacteriaceae/isolamento & purificação , Enterobacteriaceae/fisiologia , Escherichia coli/efeitos dos fármacos , Escherichia coli/fisiologia , Feminino , Hospitais de Ensino/estatística & dados numéricos , Humanos , Klebsiella pneumoniae/efeitos dos fármacos , Klebsiella pneumoniae/fisiologia , Masculino , Mali , Pessoa de Meia-Idade , Morganella morganii/efeitos dos fármacos , Morganella morganii/fisiologia , Prevalência , Estudos Prospectivos , Adulto JovemRESUMO
Three enterobacterial isolates (two Klebsiella pneumoniae and one Escherichia coli) were recovered from three patients transferred from India to France in 2011. All three isolates were resistant or of intermediate susceptibility to all ß-lactams and of decreased susceptibility to carbapenems. These three isolates expressed a novel carbapenem-hydrolysing ß-lactamase, OXA-232, differing from OXA-181 and OXA-48 by one and five amino acid substitutions, respectively. Compared with OXA-181, OXA-232 had a lower ability to hydrolyse carbapenems but conversely possessed higher hydrolytic activities against penicillins. The bla(OXA-232) gene was located on a 6.1-kb ColE-type non-conjugative plasmid.