RESUMEN
Carbapenemase-producing Enterobacter spp. Serratia marcescens, Citrobacter freundii, Providencia spp., and Morganella morganii (CP-ESCPM) are increasingly identified as causative agents of nosocomial infections but are still not under systematic genomic surveillance. In this study, using a combination of whole-genome sequencing and conjugation experiments, we sought to elucidate the genomic characteristics and transferability of resistance genes in clinical CP-ESCPM isolates from Bulgaria. Among the 36 sequenced isolates, NDM-1 (12/36), VIM-4 (11/36), VIM-86 (8/36), and OXA-48 (7/36) carbapenemases were identified; two isolates carried both NDM-1 and VIM-86. The majority of carbapenemase genes were found on self-conjugative plasmids. IncL plasmids were responsible for the spread of OXA-48 among E. hormaechei, C. freundii, and S. marcescens. IncM2 plasmids were generally associated with the spread of NDM-1 in C. freundii and S. marcescens, and also of VIM-4 in C. freundii. IncC plasmids were involved in the spread of the recently described VIM-86 in P. stuartii isolates. IncC plasmids carrying blaNDM-1 and blaVIM-86 were observed too. blaNDM-1 was also detected on IncX3 in S. marcescens and on IncT plasmid in M. morganii. The significant resistance transfer rates we observed highlight the role of the ESCPM group as a reservoir of resistance determinants and stress the need for strengthening infection control measures.
RESUMEN
The aim of this study was to report the characterization of the first mcr-positive Enterobacterales isolated from Czech hospitals. In 2019, one Citrobacter freundii and four Enterobacter isolates were recovered from Czech hospitals. The production of carbapenemases was examined by a matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) imipenem hydrolysis assay. Additionally, bacteria were screened for the presence of carbapenemase-encoding genes and plasmid-mediated colistin resistance genes by PCR. To define the genetic units carrying mcr genes, the genomic DNAs of mcr-carrying clinical isolates were sequenced on the PacBio Sequel I platform. Results showed that all isolates carried blaVIM- and mcr-like genes. Analysis of whole-genome sequencing (WGS) data revealed that all isolates carried mcr-9-like alleles. Furthermore, the three sequence type 106 (ST106) Enterobacter hormaechei isolates harbored the blaVIM-1 gene, while the ST764 E. hormaechei and ST95 C. freundii included blaVIM-4 Analysis of plasmid sequences showed that, in all isolates, mcr-9 was carried on IncHI2 plasmids. Additionally, at least one multidrug resistance (MDR) region was identified in each mcr-9-carrying IncHI2 plasmid. The blaVIM-4 gene was found in the MDR regions of p48880_MCR_VIM and p51929_MCR_VIM. In the three remaining isolates, blaVIM-1 was localized on plasmids (â¼55 kb) exhibiting repA-like sequences 99% identical to the respective gene of pKPC-CAV1193. In conclusion, to the best of our knowledge, these 5 isolates were the first mcr-9-positive bacteria of clinical origin identified in the Czech Republic. Additionally, the carriage of the blaVIM-1 on pKPC-CAV1193-like plasmids is described for the first time. Thus, our findings underline the ongoing evolution of mobile elements implicated in the dissemination of clinically important resistance determinants.IMPORTANCE Infections caused by carbapenemase-producing bacteria have led to the revival of polymyxins as the "last-resort" antibiotic. Since 2016, several reports describing the presence of plasmid-mediated colistin resistance genes, mcr, in different host species and geographic areas were published. Here, we report the first detection of Enterobacterales carrying mcr-9-like alleles isolated from Czech hospitals in 2019. Furthermore, the three ST106 Enterobacter hormaechei isolates harbored blaVIM-1, while the ST764 E. hormaechei and ST95 Citrobacter freundii isolates included blaVIM-4 Analysis of WGS data showed that, in all isolates, mcr-9 was carried on IncHI2 plasmids. blaVIM-4 was found in the MDR regions of IncHI2 plasmids, while blaVIM-1 was localized on pKPC-CAV1193-like plasmids, described here for the first time. These findings underline the ongoing evolution of mobile elements implicated in dissemination of clinically important resistance determinants. Thus, WGS characterization of MDR bacteria is crucial to unravel the mechanisms involved in dissemination of resistance mechanisms.
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Enterobacter/genética , beta-Lactamasas/genética , Antibacterianos/farmacología , Antibacterianos/uso terapéutico , Proteínas Bacterianas/genética , República Checa , Enterobacter/aislamiento & purificación , Hospitales , Humanos , Plásmidos/genéticaRESUMEN
Carbapenem-resistant Enterobacterales have become a major public-health issue worldwide. Here we report an outbreak caused by a clonal multidrug-resistant Proteus mirabilis strain producing VIM-4 metallo-ß-lactamase (MBL) and TEM-2 ß-lactamase in a Greek tertiary-care hospital. From July 2015 to February 2016, 27 imipenem-resistant P. mirabilis isolates were recovered from 14 patients hospitalised in two intensive care units (ICUs) and the internal medicine department in AHEPA University Hospital, Thessaloniki. The isolates were either susceptible or resistant to meropenem and were resistant to all remaining ß-lactams except aztreonam. Phenotypic and molecular analysis revealed that all of the isolates harboured a blaVIM-4 MBL gene. Resistome analysis of a representative isolate showed the presence of an IncQ1 plasmid harbouring the blaVIM-4 carbapenemase and blaTEM-2 ß-lactamase genes among resistance genes coding for resistance to ß-lactams, aminoglycosides, trimethoprim, sulfonamides and lincosamides. Genotyping by pulsed-field electrophoresis (PFGE) revealed that the isolates were epidemiologically related. After recovery of the index carbapenemase-producing P. mirabilis clinical isolate, infection control measures were intensified in the affected departments. Rectal sampling for carbapenem-resistant bacteria was initiated on a weekly basis among patients admitted to the general ICU. The outbreak was finally interrupted 6 months later in February 2016. This is the first documentation of the blaVIM-4 MBL gene in P. mirabilis as well as the first hospital outbreak caused by a MBL-producing P. mirabilis strain.
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Antibacterianos/farmacología , Proteínas Bacterianas/genética , Infecciones por Proteus/microbiología , Proteus mirabilis/genética , beta-Lactamasas/genética , Adulto , Anciano , Anciano de 80 o más Años , Aztreonam/farmacología , ADN Bacteriano , Brotes de Enfermedades , Farmacorresistencia Bacteriana Múltiple/genética , Femenino , Técnicas de Genotipaje , Grecia/epidemiología , Humanos , Imipenem/farmacología , Masculino , Meropenem/farmacología , Pruebas de Sensibilidad Microbiana , Persona de Mediana Edad , Infecciones por Proteus/epidemiología , Proteus mirabilis/clasificación , Proteus mirabilis/aislamiento & purificación , Centros de Atención Terciaria , Secuenciación Completa del Genoma , Adulto Joven , Resistencia betalactámica , beta-Lactamas/farmacologíaRESUMEN
Abstract: This study describes the first full genomic sequence of an mcr-9 and blaVIM-4-carrying multidrug-resistant Enterobacter hormaechei clinical isolate from Egypt. The strain was isolated in April 2015 from the sputum of a patient in Cairo, Egypt. The mcr-9 and blaVIM-4 genes were identified by PCR screening and DNA sequencing; the isolate was subjected to antimicrobial susceptibility testing, conjugation experiments, and whole genomic sequencing. mcr-9 and blaVIM-4 were carried by an IncHI2 plasmid, pAMS-38a (281,121 bp in size); the plasmid also carried genes conferring resistance against sulfonamides (sul1), quinolones (qnrA1), trimethoprim (dfrA1), ß-lactams (blaTEM-1B), aminoglycosides (aac (6')-II, aadA23, aadA2b, and ant(2'')-Ia). The strain was susceptible to colistin (MIC, <0.25 µg/mL); this could be due to the absence of the qseC/qseB regulatory system located downstream of mcr-9 in Enterobacterales, which is involved in the induction of colistin-resistance. The genetic context of mcr-9 and blaVIM-4 was identified as IS1-mcr-9-IS903-pcoS-∆pcoE-rcnA and intI1-blaVIM-4-aac (6')-II-dfrA1-∆aadA23-smr-ISPa21-qacE∆1, respectively. This is the first report of an mcr-9 and blaVIM-4 /IncHI2-carrying multidrug-resistant E. hormaechei clinical isolate from Africa and the Middle East. Plasmids of the IncHI2 group and the two insertion sequences (IS1, and IS903) might be the main vehicles for dissemination of mcr-9. Further screening for mcr-9 is essential for identifying its incidence and to prevent its dissemination.
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An Enterobacter hormaechei isolate harboring blaVIM-4 and mcr-9 was recovered from a pediatric patient in a U.S. hospital. The blaVIM-4 and mcr-9 genes are carried on the same IncH12 plasmid, pME-1a. The isolate tested susceptible to colistin, without observed induction of colistin resistance. The mcr-9 gene is located between two insertion elements, IS903 and IS1, but lacks the downstream regulatory genes (qseC and qseB) found in other isolates that harbor mcr-9IMPORTANCE We describe the complete genome assembly and sequence of a clinical Enterobacter isolate harboring both blaVIM-4 and mcr-9 recovered from a pediatric patient in the United States with a history of travel to Egypt. Moreover, to the best of our knowledge, this is the first report of an Enterobacter isolate harboring both blaVIM-4 and mcr-9 from the United States. The blaVIM-4 and mcr-9 genes are carried on the same IncH12 plasmid, pME-1a. The isolate tested susceptible to colistin, without observed induction of colistin resistance. The mcr-9 gene is located between two insertion elements, IS903 and IS1, but lacks the downstream regulatory genes (qseC and qseB) found in other isolates that harbor mcr-9.
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Enterobacter/genética , Enterobacter/aislamiento & purificación , Genoma Bacteriano , beta-Lactamasas/genética , Preescolar , Egipto , Enterobacter/enzimología , Infecciones por Enterobacteriaceae/diagnóstico , Infecciones por Enterobacteriaceae/microbiología , Humanos , Masculino , Plásmidos/genética , Análisis de Secuencia de ADN , Enfermedad Relacionada con los Viajes , Estados UnidosRESUMEN
INTRODUCTION: Pseudomonas aeruginosa is one of the most common nosocomial pathogens, known with a wide resistance to antimicrobials. Carbapenemases producing Pseudomonas aeruginosa is a growing global public health concern as this pathogen is easily transmissible among patients. Metallo-Beta-lactamases is the most important class of these carbapenemases with their broad-spectrum resistance profile. This study was conducted to investigate the prevalence of MBL-producing P. aeruginosa collected in an Algerian hospital. METHODOLOGY: All Metallo-ß-lactamase (MBL)-producing P. aeruginosa isolates recovered from patients during a 2 years period (2015-2016) were studied using a combination of phenotypic and molecular typing methods (susceptibility testing, molecular characterization of carbapenemase-encoding genes, multi-locus sequence typing and pulsed-field gel electrophoresis). RESULTS: A total of twenty-six MBL producing P. aeruginosa of 188 isolates were investigated. The burns unit ranked in the first position of the majority of identified cases with 73.07%. About 73.07% of total MBL isolates were mainly isolated from pus samples. The studied isolates were subjected to the molecular typing, in which 4 different Dra1-PFGE patterns and 3 sequences type were assigned (ST244, ST381, and ST1076), and all isolates were revealed positive for VIM-4. CONCLUSIONS: We report the third description of blaVIM-4 in Algeria indicating the emergence and spread of carbapenemase-encoding genes among P. aeruginosa in the hospital environment.
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Infección Hospitalaria/epidemiología , Infección Hospitalaria/microbiología , Infecciones por Pseudomonas/epidemiología , Infecciones por Pseudomonas/microbiología , Pseudomonas aeruginosa/enzimología , beta-Lactamasas/análisis , Adolescente , Adulto , Anciano , Anciano de 80 o más Años , Argelia/epidemiología , Niño , Preescolar , Electroforesis en Gel de Campo Pulsado , Femenino , Hospitales , Humanos , Lactante , Recién Nacido , Masculino , Pruebas de Sensibilidad Microbiana , Persona de Mediana Edad , Tipificación de Secuencias Multilocus , Prevalencia , Pseudomonas aeruginosa/clasificación , Pseudomonas aeruginosa/genética , Pseudomonas aeruginosa/aislamiento & purificación , Adulto Joven , beta-Lactamasas/genéticaRESUMEN
We investigated unusual carbapenemase-producing Enterobacter cloacae complex isolates (n = 8) in the novel sequence type (ST) 873, which caused nosocomial infections in 2 hospitals in France. Whole-genome sequence typing showed the 1-year persistence of the epidemic strain, which harbored a blaVIM-4 ST1-IncHI2 plasmid, in 1 health institution and 2 closely related strains harboring blaCTX-M-15 in the other. These isolates formed a new subgroup in the E. hormaechei metacluster, according to their hsp60 sequences and phylogenomic analysis. The average nucleotide identities, specific biochemical properties, and pangenomic and functional investigations of isolates suggested isolates of a novel species that had acquired genes associated with adhesion and mobility. The emergence of this novel Enterobacter phylogenetic lineage within hospitals should be closely monitored because of its ability to persist and spread.
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Antibacterianos/farmacología , Infección Hospitalaria , Brotes de Enfermedades , Enterobacter cloacae/enzimología , Infecciones por Enterobacteriaceae/microbiología , beta-Lactamasas/metabolismo , Anciano , Anciano de 80 o más Años , Farmacorresistencia Bacteriana Múltiple , Enterobacter cloacae/efectos de los fármacos , Enterobacter cloacae/genética , Femenino , Regulación Bacteriana de la Expresión Génica , Regulación Enzimológica de la Expresión Génica , Humanos , Masculino , Persona de Mediana Edad , beta-Lactamasas/genéticaRESUMEN
PURPOSE: The aim of the study was to investigate the prevalence and molecular support of carbapenem resistance in gram-negative bacilli clinical isolates collected between March 2013 and March 2015 in three cities (Annaba, Skikda, and Guelma) in northeastern Algeria. RESULTS: One hundred eighty-six isolates were identified as Enterobacteriaceae (161), Pseudomonas aeruginosa (18), and Acinetobacter baumannii (7). Thirty-six of 186 (19.3%) were resistant to carbapenems. Among them, 11 harbored carbapenemase genes, including blaOXA-48 (2 Klebsiella pneumoniae), blaVIM-4 (2 P. aeruginosa), blaNDM-1 (2 A. baumannii), and blaOXA-23 (5 A. baumannii). In addition, other ß-lactamases were detected: blaCTX-M-(15/66/139), blaSHV-(28/85/1/133), and blaTEM-1. All imipenem-resistant P. aeruginosa displayed OprD mutations. Multilocus sequence typing demonstrated the presence of ST 404 and ST 219 in K. pneumoniae, ST 2 and ST 85 in A. baumannii, and ST (244, 1076, 241, 227, and 233) in P. aeruginosa. CONCLUSION: In this study, we report the first detection of P. aeruginosa ST 1076 harboring the blaVIM-4 gene in African countries in two cities (Annaba and Skikda) in northeastern Algeria. Additionally, we report the first detection of blaOXA-48 in K. pneumoniae ST 404 and ST 219 in Algerian cities (Annaba and Skikda).
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Klebsiella pneumoniae/genética , Klebsiella pneumoniae/aislamiento & purificación , Pseudomonas aeruginosa/genética , Pseudomonas aeruginosa/aislamiento & purificación , beta-Lactamasas/genética , Infecciones por Acinetobacter/tratamiento farmacológico , Infecciones por Acinetobacter/microbiología , Acinetobacter baumannii/efectos de los fármacos , Acinetobacter baumannii/genética , Argelia , Antibacterianos/farmacología , Proteínas Bacterianas/genética , Carbapenémicos/farmacología , Farmacorresistencia Bacteriana Múltiple/genética , Humanos , Imipenem/farmacología , Klebsiella pneumoniae/efectos de los fármacos , Pruebas de Sensibilidad Microbiana/métodos , Tipificación de Secuencias Multilocus/métodos , Pseudomonas aeruginosa/efectos de los fármacosRESUMEN
Since November 2009 carbapenemase-producing Klebsiella pneumoniae isolates have been detected in increasing numbers at the Clinical Centre University of Pécs. Molecular typing was performed for 102 clinical isolates originating from different time periods and various departments of the Clinical Centre. Pulsed-field gel electrophoresis revealed the predominance of a single clone (101/102), identified as sequence type ST15. PCR and sequencing showed the presence of blaCTX-M-15 and blaVIM-4 genes. The blaVIM-4 was located on a class 1 integron designated In238b. To our knowledge, this is the first description of a blaVIM-4 gene in the predominant CTX-M-15 extended spectrum ß-lactamase-producing Hungarian Epidemic Clone/ST15.