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The Two Weeks in the World research project has resulted in a dataset of 3087 clinically relevant bacterial genomes with pertaining metadata, collected from 59 diagnostic units in 35 countries around the world during 2020. A relational database is available with metadata and summary data from selected bioinformatic analysis, such as species prediction and identification of acquired resistance genes.
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Bactérias , Genoma Bacteriano , Bactérias/genética , Biologia Computacional , Bases de Dados Factuais , MetadadosRESUMO
Strict anaerobes have been reported to account for 0.5-13% of episodes of bacteremia in the adult population, with a growing awareness among clinicians regarding anaerobic bacteremia, especially in patients with specific predisposing factors. The aim of our present study was to assess the incidence and clinical characteristics of anaerobic bacteremia during a 5-year period (2016-2020) at a tertiary care teaching hospital, and to compare our findings with other studies in Hungary. Overall, n = 160 strict anaerobes were detected, out of which, 44.4% (n = 71; 0.1% of positive blood cultures, 0.1/1000 hospitalizations, 3.3/100,000 patient days) were clinically significant, while Cutibacterium spp. accounted for 55.6% (n = 89) of isolates. Among relevant pathogens, the Bacteroides/Parabacteroides spp. group (32.4%; n = 23), Clostridium spp. (22.5%; n = 16) and Gram-positive anaerobic cocci (15.5%; n = 11) were the most common. The mean age of patients was 67.1 ± 14.1 years, with a male majority (59.2%; n = 42). A total of 38.0% of patients were affected by a malignancy or immunosuppression, while an abscess was identified in 15.5% of cases. A total of 74.7% (n = 53) of patients received antibiotics prior to blood culture sampling; in instances where antimicrobials were reported, anaerobic coverage of the drugs was appropriate in 52.1% (n = 37) of cases. The 30-day crude mortality rate was 39.4% (n = 28); age ≥ 75 years was a significant predictor of 30-day mortality (OR: 5.0; CI: 1.8-14.4; p = 0.003), while malignancy and immunosuppression, lack of anti-anaerobic coverage or female sex did not show a significant relationship with the mortality of these patients. Early recognition of the role played by anaerobes in sepsis and timely initiation of adequate, effective antimicrobial treatment have proven efficient in reducing the mortality of patients affected by anaerobic bacteremia.
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Recent studies showed that the current endemic of carbapenem-resistant Enterobacterales (CRE) in the Emirate of Abu Dhabi is dominated by highly resistant Klebsiella pneumoniae clones ST14, ST231, and CC147, respectively. In the absence of continuous, molecular typing-based surveillance, it remained unknown whether they lately emerged and rapidly became dominant, or they had been present from the early years of the endemic. Therefore, antibiotic resistance, the presence of carbapenemase and 16S methylase genes, and the sequence types of CRE strains collected between 2009 and 2015 were compared with those collected between 2018 and 2019. It was found that members of these three clones, particularly those of the most prevalent ST14, started dominating already in the very early years of the CRE outbreak. Furthermore, while severely impacting the overall antibiotic resistance patterns, the effect of these clones was not exclusive: for example, increasing trends of colistin or decreasing rates of tigecycline resistance were also observed among nonclonal isolates. The gradually increasing prevalence of few major, currently dominating clones raises the possibility that timely, systematic, molecular typing-based surveillance could have provided tools to public health authorities for an early interference with the escalation of the local CRE epidemic.
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Antimicrobials in wastewater promote the emergence of antibiotic resistance, facilitated by selective pressure and transfer of resistant genes. Enteric bacteria belonging to Escherichia coli, Klebsiella pneumoniae, Klebsiella oxytoca, Enterobacter cloacae, and Citrobacter species (n = 126) from hospital effluents and proximate wastewater treatment plant were assayed for susceptibility to four antimicrobial classes. The ß-lactamase encoding genes harbored in plasmids were genotyped and the plasmids were sequenced. A multidrug resistance phenotype was found in 72% (n = 58) of E. coli isolates, 70% (n = 43) of Klebsiella species isolates, and 40% (n = 25) of Enterobacter and Citrobacter species. Moreover, 86% (n = 50) of E. coli, 77% (n = 33) of Klebsiella species, and 25% (n = 4) of Citrobacter species isolates phenotypically expressed extended spectrum ß-lactamase. Regarding ESBL genes, blaCTX-M-27 and blaTEM-1 were found in E. coli, while Klebsiella species harbored blaCTX-M-15, blaCTX-M-30, or blaSHV-12. Genes coding for aminoglycoside modifying enzymes, adenylyltransferases (aadA1, aadA5), phosphotransferases (aph(6)-1d, aph(3â³)-Ib), acetyltransferases (aac(3)-IIa), (aac(6)-Ib), sulfonamide/trimethoprim resistant dihydropteroate synthase (sul), dihydrofolate reductase (dfrA), and quinolone resistance protein (qnrB1) were also identified. Monitoring wastewater from human sources for acquired resistance in clinically important bacteria may provide a cheaper alternative in regions facing challenges that limit clinical surveillance.
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OBJECTIVES: To assess the current prevalence, distribution, and main clonal types of carbapenem-resistant Enterobacterales (CRE) in the United Arab Emirates. METHODS: A total of 504 CRE collected over a 9-month period in 15 hospitals were studied. Antibiotic susceptibility and the presence of common carbapenemase, 16S methylase, and mobile colistin resistance genes were assessed. Selected strains forming larger clusters by pulsed field gel electrophoresis were subjected to whole genome sequencing to identify their sequence types and core genome MLST. RESULTS: Strains expressing OXA and NDM type carbapenemases and 16S methylases were present in all major hospitals. Considerable interhospital differences were noticed, suggesting the role of specific clones. A total of three major Klebsiella pneumoniae clones (CC14, ST231, and CC147) were identified, accounting for 48.6% of all CRE. All clones were significantly more resistant than sporadic isolates. CC14 strains exhibited a significant association with Emirati patients. CONCLUSIONS: Nearly half of CRE infections in the country are due to a limited number of clones. The data indicate the possibility of interhospital transmission, combined in some hospitals with inadequate stewardship practices. The study also revealed an association of the largest, most resistant clone (CC14) with Emirati patients. The specific reasons for it should be clarified by further investigations.
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Gammaproteobacteria , Infecções por Klebsiella , Antibacterianos/farmacologia , Proteínas de Bactérias/genética , Carbapenêmicos/farmacologia , Células Clonais , Humanos , Infecções por Klebsiella/tratamento farmacológico , Infecções por Klebsiella/epidemiologia , Klebsiella pneumoniae , Testes de Sensibilidade Microbiana , Tipagem de Sequências Multilocus , Emirados Árabes Unidos/epidemiologia , beta-Lactamases/genéticaRESUMO
Data on the prevalence of MCR-producing Enterobacterales of animal origin are scarce from the Arabian Peninsula. We investigated the presence and variety of such strains from fecal specimens of poultry collected in four farms in the United Arab Emirates. Colonies from ten composite samples per farm grown on colistin-supplemented plates were PCR-screened for alleles of the mcr gene. Thirty-nine isolates selected based on species, colony morphology, and plasmid profile were subjected to whole genome sequencing. The panel of their resistance and virulence genes, MLST and cgMLST were established. Transferability and incompatibility types of the MCR-plasmids were determined. mcr-1.1 positive strains were identified in 36 of the 40 samples. Thirty-four multi-drug resistant Escherichia coli of 16 different sequence types, two Escherichia albertii, two Klebsiella pneumoniae and one Salmonella minnesota were identified. Beyond various aminoglycoside, tetracycline, and co-trimoxazole resistance genes, seven of them also carried ESBL genes and one blaCMY-2. Six IncHI2, 26 IncI2 and 4 IncX4 MCR-plasmids were mobilized, in case of the IncHI2 plasmids co-transferring ampicillin, chloramphenicol and tetracycline resistance. The diversity of mcr-1 positive strains suggest a complex local epidemiology calling for a coordinated surveillance including animals, retail meat and clinical cases.
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To understand the reasons of successful spread of carbapenem-resistant Klebsiella pneumoniae ST14 (CRKP-ST14) in countries of the Arabian Peninsula, the resistome, capsular locus, carbapenemase carrying plasmid types, and core genome of isolates from the region were compared to global isolates. Thirty-nine CRKP-ST14 strains isolated from 13 hospitals in the United Arab Emirates, Bahrain, and Saudi Arabia were selected for whole genome sequencing on Illumina MiSeq platform based on the variety of carbapenemase genes carried and plasmids bearing these genes. Their resistome, capsular locus, and core genome MLST were compared to 173 CRKP-ST14 genomes available in public databases. The selected 39 CRKP-ST14 produced either NDM-1, OXA-48, OXA-162, OXA-232, KPC-2, or co-produced NDM-1 and an OXA-48-like carbapenemase. cgMLST revealed three clusters: 16 isolates from five UAE cities (C1), 11 isolates from three UAE cities and Bahrain (C2), and 5 isolates from Saudi Arabia (C3), respectively, and seven singletons. Resistance gene profile, carbapenemase genes, and their plasmid types were variable in both C1 and C2 clusters. The majority of CRKP-ST14 had KL2, but members of the C2 cluster and two further singletons possessed KL64 capsular locus. Based on cgMLST comparison of regional and global isolates, CRKP-ST14 with KL64 from four continents formed a distinct cluster, suggesting a recent emergence and spread of this variant. Our findings confirmed clonal transmission coupled with likely horizontal gene transfer in carbapenem-resistant Klebsiella pneumoniae ST14. Dissemination of this genetically flexible, highly resistant clone warrants further monitoring.
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OBJECTIVES: Our aim was to assess the susceptibility of carbapenem-resistant Enterobacterales (CRE) from the Arabian Peninsula to a broad spectrum of antibiotics, including fosfomycin, ceftazidime-avibactam, and aztreonam-avibactam. METHODS: 1192 non-repeat CRE isolated in 2009-2017 from 33 hospitals in five countries of the Arabian Peninsula were tested. The minimum inhibitory concentration of 14 antibiotics was determined. Carbapenemase and 16S methylase genes were detected by PCR. Clonality was assessed by PFGE. RESULTS: The highest rate of susceptibility was detected to aztreonam-avibactam (95.5%) followed by colistin (79.8%), fosfomycin (71.8%) and tigecycline (59.9%). Isolates co-producing two carbapenemases (12.4%) were the least susceptible. Aminoglycoside susceptibility was affected by the frequent production of a 16S methylase. Susceptibility to ceftazidime-avibactam was impacted by the high rate of metallo-beta-lactamase producers (46.3%), while aztreonam-avibactam resistance occurred mostly in clonally unrelated, carbapenemase non-producing Escherichia coli. CONCLUSION: Of the currently available drugs: colistin, tigecycline, and ceftazidime-avibactam co-administered with aztreonam appear to be the most effective to treat CRE infections. However, the presence of non-clonal CRE isolates, in which avibactam does not lower the aztreonam MIC below the clinical breakpoint, is of notable concern. Based on the relatively high rate of fosfomycin susceptibility, it would be desirable to license parenteral fosfomycin in the region.
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Antibacterianos/farmacologia , Compostos Azabicíclicos/farmacologia , Aztreonam/farmacologia , Enterobacteriáceas Resistentes a Carbapenêmicos/efeitos dos fármacos , Ceftazidima/farmacologia , Proteínas de Bactérias , Enterobacteriáceas Resistentes a Carbapenêmicos/genética , Carbapenêmicos/farmacologia , Combinação de Medicamentos , Farmacorresistência Bacteriana/genética , Fosfomicina/farmacologia , Humanos , Testes de Sensibilidade Microbiana , Oriente Médio , Tigeciclina/farmacologia , beta-Lactamases/genéticaRESUMO
BACKGROUND: Environmental and clinical carbapenem-resistant Acinetobacter baumannii (CRAb) isolated in a hospital of the Eastern Region of Saudi Arabia were compared to assess the potential environmental contamination by this pathogen. METHODS: Frequent-hand-touch surfaces of intensive care (ICU), medical (MW), and surgical (SW) units were randomly sampled for a month-long period, and the CRAb identified were compared to clinical isolates of the same period by PFGE and blaOXA-51-like gene sequencing. Carbapenemase and ribosomal methylase genes, ISAba1 link to blaOXA51-like or to blaOXA-23, respectively were detected by PCR. RESULTS: CRAb was identified from 35.5% of surfaces. All environmental and clinical isolates were multi- or extremely drug resistant. PFGE of all clinical (n=21) and selected environmental (n=30) isolates identified a singleton and four clusters, all of which included both clinical and environmental isolates. In the two largest clusters isolates carried blaOXA-66, ISAba1-linked blaOXA-23, and were from the ICU, MW and the male SW. Isolates of the female SW carried blaOXA-69, ISAba1-linked blaOXA-23 and blaGES-11. A pair of clinical and environmental CRAb from the Male SW harboured blaNDM-1 in addition to ISAba1-linked blaOXA-94. CONCLUSION: A worrying level of environmental contamination, often by CRAb belonging to international clones, was revealed, highlighting the importance of environmental hygiene.
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Infecções por Acinetobacter/tratamento farmacológico , Acinetobacter baumannii/efeitos dos fármacos , Carbapenêmicos/farmacologia , Infecção Hospitalar/microbiologia , Infecções por Acinetobacter/epidemiologia , Infecções por Acinetobacter/microbiologia , Acinetobacter baumannii/genética , Acinetobacter baumannii/isolamento & purificação , Carbapenêmicos/uso terapêutico , Infecção Hospitalar/tratamento farmacológico , Infecção Hospitalar/epidemiologia , Feminino , Genes Bacterianos/genética , Humanos , Masculino , Filogenia , Arábia Saudita/epidemiologia , Resistência beta-Lactâmica/genéticaRESUMO
PURPOSE: Plasmids of the incompatibility group X type 3 (IncX3) were described carrying various carbapenemase genes in carbapenemase-producing Enterobacteriaceae (CPE) worldwide and in the United Arab Emirates (UAE), as well. To understand the driving force behind the emergence of such plasmids in the UAE, the relationship between IncX3 plasmids encountered locally and globally was investigated. METHODS: CPE strains isolated in the UAE during 2009-2014 were screened by X3 PCR-based replicon typing. The clonal relationship of CPE carrying IncX3 plasmids was determined by multi-locus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE). Complete sequence of selected IncX3 plasmids was determined. Phylogenetic relationship between the carbapenemase carrying IncX3 plasmids from the UAE and of those reported worldwide was established by comparing the plasmid backbones. RESULTS: 10.2% of the 295 CPE tested were identified to carry IncX3 plasmids: 13 Escherichia coli, 13 Klebsiella pneumoniae, two Enterobacter cloacae, one Citrobacter freundii and one Morganella morganii isolate, respectively. Most of them were non-clonal; with small clusters of triplets and pairs of E. coli and K. pneumoniae, and a cluster of five K. pneumoniae ST11 exhibiting >90% similar PFGE patterns, respectively. The 30 isolates harbored either bla NDM-1, bla NDM-4, bla NDM-5, bla NDM-7, bla OXA-181 or bla KPC-2 carbapenemase genes on IncX3 plasmids. Phylogenetic analysis of the backbone region of IncX3 plasmids carrying various beta-lactamase genes from the UAE (n=23) and that of North-America, Europe, Asia and Australia (n=35) revealed three clusters based on the carbapenemase genes carried: plasmids harboring bla OXA-181 and bla NDM-5 formed two distinct groups, whereas backbones of plasmids with bla NDM-1, bla NDM-4 and bla NDM-7 clustered together. Each cluster contained plasmids of diverse geographical origin. CONCLUSION: The findings suggest that different carbapenemase gene carrying IncX3 plasmids encountered in the UAE do not evolve locally, rather are subtypes of this epidemic plasmid emerging in this country due to international transfer.
RESUMO
Plasmid-encoded colistin resistance is emerging among extraintestinal pathogenic Escherichia coli strains, including those of the epidemic clone sequence type 131 (ST131)-H30. Mcr-1 transfers a phosphoethanolamine to the lipid A portion of lipopolysaccharide (LPS), conferring resistance to polymyxins. We investigated whether this modification changed the activity of the monoclonal antibody ASN-4, specific to the O25b side chain of ST131 LPS. We confirmed that, unlike colistin, ASN-4 retained its bactericidal and endotoxin-neutralizing activities and therefore offers a treatment option against extremely drug-resistant ST131 isolates.
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Antibacterianos/farmacologia , Anticorpos Monoclonais/farmacologia , Infecções por Escherichia coli/tratamento farmacológico , Proteínas de Escherichia coli/metabolismo , Escherichia coli Extraintestinal Patogênica/efeitos dos fármacos , Animais , Colistina/farmacologia , Farmacorresistência Bacteriana Múltipla/genética , Endotoxinas/metabolismo , Escherichia coli Extraintestinal Patogênica/genética , Feminino , Humanos , Lipopolissacarídeos/química , Camundongos , Camundongos Endogâmicos BALB CRESUMO
Few studies have addressed the molecular epidemiology of carbapenem-resistant Enterobacteriaceae (CRE) isolates in the Arabian Peninsula, and such investigations have been missing from Dubai, a major economical, tourism and medical centre of the region. The antibiotic susceptibility, the carbapenemase type produced, and the clonality of 89 CRE strains isolated in five major Dubai hospitals in June 2015 to June 2016 were determined. Thirty-three percent of the collection of 70 Klebsiella pneumoniae, 13 Escherichia coli and 6 other Enterobacteriaceae were extremely drug resistant, 27% were resistant to colistin, and 4.5% (4 K. pneumoniae isolates) were resistant to all antibiotics tested. The colistin resistance rate in K. pneumoniae was 31.4%. None of the isolates carried mobile colistin resistance genes. Seventy-seven isolates produced carbapenemase: 53.3% OXA-48-like, 24.7% NDM and 22.1% both OXA-48-like and NDM, respectively. Pulsed-field gel electrophoresis clustered 50% of K. pneumoniae into a 35-membered group, which showed significant association with double carbapenemase production, with extreme drug resistance, and with being isolated from Emirati patients. Members of the cluster belonged to sequence type ST14. The rate of colistin resistance in K. pneumoniae ST14 was 37.1% vs. 27.1% of K. pneumoniae isolates outside of the cluster. Two of the panresistant K. pneumoniae isolates also belonged to ST14, whereas the other two were ST15 and ST231, respectively. In conclusion, beyond the overall high colistin resistance rate in CRE, the emergence of a highly resistant clone of K. pneumoniae ST14 in all Dubai hospitals investigated is a serious problem requiring immediate attention.
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Proteínas de Bactérias/genética , Colistina/farmacologia , Farmacorresistência Bacteriana/genética , Enterobacteriaceae/efeitos dos fármacos , beta-Lactamases/genética , Proteínas de Bactérias/metabolismo , Farmacorresistência Bacteriana/efeitos dos fármacos , Enterobacteriaceae/genética , Enterobacteriaceae/isolamento & purificação , Infecções por Enterobacteriaceae/microbiologia , Humanos , Klebsiella pneumoniae/efeitos dos fármacos , Klebsiella pneumoniae/genética , Klebsiella pneumoniae/isolamento & purificação , Testes de Sensibilidade Microbiana , Emirados Árabes Unidos , beta-Lactamases/metabolismoRESUMO
The sequence type 131 (ST131)-H30 clone is responsible for a significant proportion of multidrug-resistant extraintestinal Escherichia coli infections. Recently, the C1-M27 clade of ST131-H30, associated with blaCTX-M-27, has emerged. The complete genome sequence of E. coli isolate 81009 belonging to this clone, previously used during the development of ST131-specific monoclonal antibodies, is reported here.
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Enterobacteriaceae co-producing NDM- and OXA-48-type carbapenemases were encountered in higher frequency in the United Arab Emirates (UAE) than in the neighboring countries in our earlier study. The aim of this investigation was to characterize the seven double carbapenemase producer Klebsiella pneumoniae found in the region to assess factors contributing to their emergence. Three K. pneumoniae ST14 isolated in the UAE harboring blaNDM-1 on IncHI1b and blaOXA-232 on IncColE plasmids were clonally related. Furthermore, two K. pneumoniae from the UAE, ABC106 and ABC137 belonged to ST307 and ST1318, respectively. ABC106 carried blaNDM-1 on IncHI1b, and blaOXA-162 on IncL/M plasmids, whereas ABC137 possessed blaNDM-1 on IncX3 and blaOXA-48 on IncL/M plasmids. The double carbapenemase-producing K. pneumoniae from Oman (OMABC109) and Saudi Arabia (SA54) belonged to ST11 and ST152, respectively. OMABC109 harbored blaNDM-1 on an IncHI1b plasmid highly similar to the NDM-plasmid of ABC106 and carried a chromosomally coded blaOXA-181 located on Tn2013. SA54 possessed a blaNDM-1 on an IncFIb/FII plasmid and a blaOXA-48 on an IncL/M plasmid. Based on these findings, clonal spread and horizontal transfer of carbapenemase genes located on transposons or self-transmissible plasmids contributed equally to the emergence of double carbapenemase-producing Enterobacteriaceae in the region.
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Antibacterianos/farmacologia , Proteínas de Bactérias/metabolismo , Klebsiella pneumoniae/efeitos dos fármacos , Klebsiella pneumoniae/enzimologia , beta-Lactamases/metabolismo , Proteínas de Bactérias/classificação , Proteínas de Bactérias/genética , Farmacorresistência Bacteriana Múltipla , Regulação Bacteriana da Expressão Gênica , Regulação Enzimológica da Expressão Gênica , Humanos , Infecções por Klebsiella/epidemiologia , Infecções por Klebsiella/microbiologia , Klebsiella pneumoniae/isolamento & purificação , Omã/epidemiologia , Arábia Saudita/epidemiologia , Emirados Árabes Unidos/epidemiologia , beta-Lactamases/classificação , beta-Lactamases/genéticaRESUMO
AIMS: To identify plasmid-mediated colistin resistance in clinical Enterobacteriaceae isolates in Oman, where this resistance mechanism has not been encountered yet. MATERIALS/METHODS: Twenty-two colistin-resistant Enterobacteriaceae clinical isolates collected between July 2014 and June 2016 in a tertiary care hospital in Muscat were screened by PCR for the mcr-1 and mcr-2 genes. The strain identified as mcr-1 positive was genotyped and its antibiotic susceptibility was established. The mcr-1 containing plasmid was mobilized into Escherichia coli K-12 and its sequence was determined. RESULTS: A single E. coli isolate (OM97) carrying mcr-1 gene was identified, while no strains carrying the mcr-2 gene was found. E. coli OM97 was isolated in June 2016 from blood culture of a male patient with multiple comorbidities. It belonged to ST10. Beyond colistin, it was resistant to amoxicillin-clavulanic acid, piperacillin-tazobactam, amikacin, ciprofloxacin, tetracycline, and cotrimoxazole. The mcr-1 gene was located on a conjugative IncI2-type plasmid of 63722 bp size, which did not harbor any further resistance genes. The genetic surrounding of the mcr-1 gene lacked the ISApl1 element. CONCLUSIONS: Although colistin resistance caused by the mcr-1 gene is not common in our collection of clinical isolates, the occurrence of the plasmid-mediated colistin resistance in an E. coli ST10 strain is of concern as this clonal group was already shown to spread ESBL genes and quinolone resistance worldwide. It is especially worrisome that as the mcr-1 gene occurred in a non-ESBL, carbapenem-susceptible E. coli strain, current susceptibility testing algorithms may not detect its presence.
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Antibacterianos/farmacologia , Bacteriemia/epidemiologia , Colistina/farmacologia , Infecções por Escherichia coli/epidemiologia , Proteínas de Escherichia coli/genética , Escherichia coli/genética , Proteínas de Membrana/genética , Amicacina/farmacologia , Combinação Amoxicilina e Clavulanato de Potássio/farmacologia , Bacteriemia/tratamento farmacológico , Bacteriemia/microbiologia , Ciprofloxacina/farmacologia , Farmacorresistência Bacteriana/genética , Escherichia coli/classificação , Escherichia coli/efeitos dos fármacos , Escherichia coli/isolamento & purificação , Infecções por Escherichia coli/tratamento farmacológico , Infecções por Escherichia coli/microbiologia , Proteínas de Escherichia coli/metabolismo , Expressão Gênica , Humanos , Proteínas de Membrana/metabolismo , Testes de Sensibilidade Microbiana , Omã/epidemiologia , Ácido Penicilânico/análogos & derivados , Ácido Penicilânico/farmacologia , Piperacilina/farmacologia , Combinação Piperacilina e Tazobactam , Plasmídeos/química , Plasmídeos/metabolismo , Isoformas de Proteínas/genética , Isoformas de Proteínas/metabolismo , Tetraciclina/farmacologia , Combinação Trimetoprima e Sulfametoxazol/farmacologiaRESUMO
Carbapenem-resistant Enterobacteriaceae encountered in countries of the Arabian Peninsula usually produce OXA-48-like and New Delhi metallo-beta-lactamases (NDM) carbapenemases. However, a temporary increase in VIM-4-producing, clonally unrelated Enterobacteriaceae strains was described earlier in a Kuwaiti hospital. We investigated the genetic support of blaVIM-4 in six Klebsiella pneumoniae strains, one Escherichia coli, and one Enterobacter cloacae strain and compared it to that of VIM-4-producing isolates from other countries of the region. Five K. pneumoniae strains and the E. coli strain from Kuwait carried an ~165 kb IncA/C-type plasmid indistinguishable by restriction fragment length polymorphism. The complete sequence of one of them (pKKp4-VIM) was established. pKKp4-VIM exhibited extensive similarities to episomes pKP-Gr642 carrying blaVIM-19 encountered in Greece and to the partially sequenced pCC416 harboring blaVIM-4 detected in Italy. In other countries of the region, the only similar plasmid was the one detected in the isolate from the UAE. In all Kuwaiti strains, irrespective of the species and their VIM plasmids, the blaVIM-4 gene was located within the same integron structure (In416), different from those of other countries of the region. Our data show that the spread of this IncA/C plasmid and particularly that of the In416 integron caused a considerable, albeit temporary, increase in the rate of mostly clonally unrelated VIM-producing Enterobacteriaceae strains of multiple species. Monitoring of such events is of high importance as the interference with the spread of mobile genetic elements may represent a formidable challenge to infection control.
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The emergence of pan-resistant Klebsiella pneumoniae strains is an increasing concern. In the present study, we describe a cluster of 9 pan-resistant K. pneumoniae sequence type 147 (ST147) isolates encountered in 4 patients over nearly 1 year in 3 hospitals of the United Arab Emirates (UAE). The isolates exhibited highly similar genotypes. All produced chromosomally encoded OXA-181, and the majority also produced the NDM-5 carbapenemase. As with the previously described single isolate from the UAE, MS6671, the mgrB was disrupted by a functional, ISEcp1-driven blaOXA-181 insertion causing resistance to carbapenems. The mutation was successfully complemented with an intact mgrB gene, indicating that it was responsible for colistin resistance. blaNDM-5 was located within a resistance island of an approximately 100-kb IncFII plasmid carrying ermB, mph(A), blaTEM-1B, rmtB, blaNDM-5, sul1, aadA2, and dfrA12 resistance genes. Sequencing this plasmid (pABC143-NDM) revealed that its backbone was nearly identical to that of plasmid pMS6671E from which several resistance genes, including blaNDM-5, had been deleted. More extensive similarities of the backbone and the resistance island were found between pABC143C-NDM and the blaNDM-5-carrying IncFII plasmids of two K. pneumoniae ST147 isolates from South Korea, one of which was colistin resistant, and both also produced OXA-181. Notably, one of these strains was isolated from a patient transferred from the UAE. Our data show that this pan-resistant clone has an alarming capacity to maintain itself over an extended period of time and is even likely to be transmitted internationally.
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Antibacterianos/farmacologia , Carbapenêmicos/farmacologia , Klebsiella pneumoniae/enzimologia , Klebsiella pneumoniae/genética , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Colistina/farmacologia , Genótipo , Humanos , Klebsiella pneumoniae/efeitos dos fármacos , Testes de Sensibilidade Microbiana , Plasmídeos/genética , República da Coreia , Emirados Árabes Unidos , beta-Lactamases/genética , beta-Lactamases/metabolismoRESUMO
AIM: The purpose of this study was to characterize the New Delhi metallo-beta lactamase (NDM)-7-producing Enterobacteriaceae isolated in the Arabian Peninsula. METHODS: Enterobacteriaceae identified to carry blaNDM-7 in a collection of 157 NDM-producing isolates from Kuwait, Oman, Saudi Arabia, and the United Arab Emirates (UAE) were investigated for their antibiotic and disinfectant susceptibility, and resistance gene content. The virulence profile, phylogenetic and sequence types of the isolates were also determined. The plasmids carrying the blaNDM-7 were transferred, and their complete nucleotide sequence was determined. RESULTS: Four NDM-7-producing Escherichia coli isolated in Kuwait, Oman, and the UAE, respectively, were identified. They were clonally unrelated, carried a few virulence determinants only, and belonged to clonal complexes CC10 and CC23, or ST448. They were all multi-drug resistant but remained susceptible to fosfomycin, tigecycline, and colistin. In all isolates, blaNDM-7 was located on IncX3 type plasmids of a variable size, not harboring any further resistance genes. The plasmids exhibited a high degree of similarity to each other and to pKpN01-NDM7 from Canada, with various size deletions and insertions. CONCLUSIONS: Our findings show that IncX3 type plasmids play an important role in the spread of the currently rare NDM-7 variant in the Arabian Peninsula. This association of blaNDM-7 with the IncX3-type plasmid is particularly worrisome, as this type of plasmid was proved to spread other carbapenemases in various species of Enterobacteriaceae worldwide at a high efficiency.
Assuntos
Farmacorresistência Bacteriana Múltipla/genética , Infecções por Escherichia coli/epidemiologia , Escherichia coli/genética , Plasmídeos/química , beta-Lactamases/genética , Antibacterianos/farmacologia , Carbapenêmicos/farmacologia , Células Clonais , Colistina/farmacologia , Escherichia coli/classificação , Escherichia coli/efeitos dos fármacos , Escherichia coli/isolamento & purificação , Infecções por Escherichia coli/tratamento farmacológico , Infecções por Escherichia coli/microbiologia , Infecções por Escherichia coli/transmissão , Fosfomicina/farmacologia , Expressão Gênica , Humanos , Kuweit/epidemiologia , Testes de Sensibilidade Microbiana , Minociclina/análogos & derivados , Minociclina/farmacologia , Tipagem de Sequências Multilocus , Omã/epidemiologia , Filogenia , Plasmídeos/metabolismo , Arábia Saudita/epidemiologia , Tigeciclina , Emirados Árabes Unidos/epidemiologia , beta-Lactamases/metabolismoRESUMO
OBJECTIVES: Searching for the presence of the mcr-1 gene in colistin resistant Enterobacteriaceae in countries of the Arabian Peninsula. METHODS: Seventy-five independent, colistin resistant Enterobacteriaceae strains isolated from clinical cases in Bahrain, Kuwait, Oman, Saudi Arabia and the United Arab Emirates were tested by PCR for the mcr-1 gene. mcr-1 positive strains were genotyped, and their antibiotic susceptibility was established. The mcr-1 containing plasmids were mobilized into Escherichia coli K-12 and their sequence was determined. RESULTS: Four E. coli isolates (two from Bahrain, one from Saudi Arabia and one from the United Arab Emirates) were identified carrying the mcr-1 gene on conjugative plasmids. They belonged to global multidrug resistant E. coli clones, i.e. ST648, ST224, ST68 and ST131, respectively. One strain carried the blaNDM-1 carbapenemase gene. Three strains carried mcr-1 on IncI2 type plasmids, one of them also harboring a blaCTX-M-64 gene. In the fourth strain mcr-1 was located on a 240kb IncHI2 plasmid co-harboring 13 other resistance genes. CONCLUSIONS: This is the first report on the presence of the plasmid-coded mcr-1 gene in a variety of multi-resistant clinical isolates from the Arabian Peninsula indicating that several commonly used antibiotics can potentially facilitate the spread of mcr-1 carrying strains, or directly, mcr-1 containing plasmids.
Assuntos
Antibacterianos/farmacologia , Colistina/farmacologia , Farmacorresistência Bacteriana , Infecções por Escherichia coli/microbiologia , Escherichia coli/efeitos dos fármacos , Plasmídeos/genética , Farmacorresistência Bacteriana/genética , Escherichia coli/genética , Escherichia coli/isolamento & purificação , Infecções por Escherichia coli/tratamento farmacológico , Humanos , Kuweit , Omã , Plasmídeos/metabolismo , Arábia Saudita , Emirados Árabes Unidos , beta-Lactamases/genética , beta-Lactamases/metabolismoRESUMO
To establish the role of local transmission versus possible pathogen import due to previous foreign exposure in infections caused by carbapenem non-susceptible Enterobacteriaceae in the Arabian Peninsula, 200 independent isolates collected in 16 hospitals of Saudi Arabia, Kuwait, Oman and the United Arab Emirates were studied. All strains were multidrug resistant; 42.5% of them also qualified as extremely drug resistant. The frequency of various carbapenemases varied according to the participating countries, but in the collection, as a whole, blaNDM-1 was the most frequently encountered carbapenemase gene (46.5%) followed by blaOXA-48-like gene (32.5%). A comparatively high rate (8.9%) of multi-clonal strains carrying both blaNDM and blaOXA-48-like genes in the United Arab Emirates, representing the most resistant subgroup, was encountered. No KPC-expressing isolates were detected. Three major clones of blaNDM-1 carrying Klebsiella pneumoniae of ST152 (n = 22, Saudi Arabia), ST14 (n = 7, United Arab Emirates) and ST147 types (n = 9, Oman) were identified, the latter two clones carrying similar, but not identical HI1b incompatibility type plasmids of >170 kb. While from 78.6% of the cases with documented foreign hospitalization blaNDM positive strains were isolated, these strains formed only 25.6% of all the isolates expressing this enzyme. In fact, 56.8% of the NDM, 75.7% of OXA-48-like and 90.9% of VIM positive strains were recovered from patients without documented foreign exposure, neither in the form of travel or prior hospitalization abroad, suggesting a high rate of autochthonous infections. This, considering the extensive links of these countries to the rest of the world, predicts that trends in the local epidemiology of carbapenem resistant strains may increasingly affect the spread of these pathogens on the global scale. These results call for improved surveillance of carbapenem resistant Enterobacteriaceae in the countries of the Arabian Peninsula.