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1.
Nat Commun ; 12(1): 4188, 2021 07 07.
Artigo em Inglês | MEDLINE | ID: mdl-34234121

RESUMO

Klebsiella pneumoniae is a leading cause of antimicrobial-resistant (AMR) healthcare-associated infections, neonatal sepsis and community-acquired liver abscess, and is associated with chronic intestinal diseases. Its diversity and complex population structure pose challenges for analysis and interpretation of K. pneumoniae genome data. Here we introduce Kleborate, a tool for analysing genomes of K. pneumoniae and its associated species complex, which consolidates interrogation of key features of proven clinical importance. Kleborate provides a framework to support genomic surveillance and epidemiology in research, clinical and public health settings. To demonstrate its utility we apply Kleborate to analyse publicly available Klebsiella genomes, including clinical isolates from a pan-European study of carbapenemase-producing Klebsiella, highlighting global trends in AMR and virulence as examples of what could be achieved by applying this genomic framework within more systematic genomic surveillance efforts. We also demonstrate the application of Kleborate to detect and type K. pneumoniae from gut metagenomes.


Assuntos
Proteínas de Bactérias/genética , Infecção Hospitalar/microbiologia , Infecções por Klebsiella/microbiologia , Klebsiella pneumoniae/genética , Tipagem Molecular/métodos , Antibacterianos/farmacologia , Antibacterianos/uso terapêutico , Infecção Hospitalar/diagnóstico , Infecção Hospitalar/tratamento farmacológico , Infecção Hospitalar/epidemiologia , Conjuntos de Dados como Assunto , Farmacorresistência Bacteriana Múltipla/genética , Monitoramento Epidemiológico , Microbioma Gastrointestinal/genética , Genoma Bacteriano , Humanos , Lactente , Recém-Nascido , Infecções por Klebsiella/diagnóstico , Infecções por Klebsiella/tratamento farmacológico , Infecções por Klebsiella/epidemiologia , Klebsiella pneumoniae/isolamento & purificação , Klebsiella pneumoniae/patogenicidade , Metagenoma/genética , Epidemiologia Molecular/métodos , Mutação , Filogenia , Software , Virulência/genética , Fatores de Virulência/genética , Sequenciamento Completo do Genoma , beta-Lactamases/genética
2.
BMC Infect Dis ; 21(1): 683, 2021 Jul 14.
Artigo em Inglês | MEDLINE | ID: mdl-34261450

RESUMO

BACKGROUND: Third-generation cephalosporin-resistant Gram-negatives (3GCR-GN) and vancomycin-resistant enterococci (VRE) are common causes of multi-drug resistant healthcare-associated infections, for which gut colonisation is considered a prerequisite. However, there remains a key knowledge gap about colonisation and infection dynamics in high-risk settings such as the intensive care unit (ICU), thus hampering infection prevention efforts. METHODS: We performed a three-month prospective genomic survey of infecting and gut-colonising 3GCR-GN and VRE among patients admitted to an Australian ICU. Bacteria were isolated from rectal swabs (n = 287 and n = 103 patients ≤2 and > 2 days from admission, respectively) and diagnostic clinical specimens between Dec 2013 and March 2014. Isolates were subjected to Illumina whole-genome sequencing (n = 127 3GCR-GN, n = 41 VRE). Multi-locus sequence types (STs) and antimicrobial resistance determinants were identified from de novo assemblies. Twenty-three isolates were selected for sequencing on the Oxford Nanopore MinION device to generate completed reference genomes (one for each ST isolated from ≥2 patients). Single nucleotide variants (SNVs) were identified by read mapping and variant calling against these references. RESULTS: Among 287 patients screened on admission, 17.4 and 8.4% were colonised by 3GCR-GN and VRE, respectively. Escherichia coli was the most common species (n = 36 episodes, 58.1%) and the most common cause of 3GCR-GN infection. Only two VRE infections were identified. The rate of infection among patients colonised with E. coli was low, but higher than those who were not colonised on admission (n = 2/33, 6% vs n = 4/254, 2%, respectively, p = 0.3). While few patients were colonised with 3GCR- Klebsiella pneumoniae or Pseudomonas aeruginosa on admission (n = 4), all such patients developed infections with the colonising strain. Genomic analyses revealed 10 putative nosocomial transmission clusters (≤20 SNVs for 3GCR-GN, ≤3 SNVs for VRE): four VRE, six 3GCR-GN, with epidemiologically linked clusters accounting for 21 and 6% of episodes, respectively (OR 4.3, p = 0.02). CONCLUSIONS: 3GCR-E. coli and VRE were the most common gut colonisers. E. coli was the most common cause of 3GCR-GN infection, but other 3GCR-GN species showed greater risk for infection in colonised patients. Larger studies are warranted to elucidate the relative risks of different colonisers and guide the use of screening in ICU infection control.


Assuntos
Infecção Hospitalar , Farmacorresistência Bacteriana Múltipla/genética , Escherichia coli , Trato Gastrointestinal/microbiologia , Controle de Infecções , Unidades de Terapia Intensiva , Enterococos Resistentes à Vancomicina , Antibacterianos/farmacologia , Austrália/epidemiologia , Resistência às Cefalosporinas/genética , Infecção Hospitalar/epidemiologia , Infecção Hospitalar/microbiologia , Infecção Hospitalar/prevenção & controle , Escherichia coli/genética , Escherichia coli/isolamento & purificação , Escherichia coli/patogenicidade , Humanos , Controle de Infecções/métodos , Controle de Infecções/normas , Unidades de Terapia Intensiva/normas , Unidades de Terapia Intensiva/estatística & dados numéricos , Estudos Prospectivos , Enterococos Resistentes à Vancomicina/genética , Enterococos Resistentes à Vancomicina/isolamento & purificação
3.
BMC Infect Dis ; 21(1): 526, 2021 Jun 05.
Artigo em Inglês | MEDLINE | ID: mdl-34090384

RESUMO

BACKGROUND: Klebsiella spp. are important pathogens associated with bacteremia among admitted children and is among the leading cause of death in children < 5 years in postmortem studies, supporting a larger role than previously considered in childhood mortality. Herein, we compared the antimicrobial susceptibility, mechanisms of resistance, and the virulence profile of Klebsiella spp. from admitted and postmortem children. METHODS: Antimicrobial susceptibility and virulence factors of Klebsiella spp. recovered from blood samples collected upon admission to the hospital (n = 88) and postmortem blood (n = 23) from children < 5 years were assessed by disk diffusion and multiplex PCR. RESULTS: Klebsiella isolates from postmortem blood were likely to be ceftriaxone resistant (69.6%, 16/23 vs. 48.9%, 43/88, p = 0.045) or extended-spectrum ß-lactamase (ESBL) producers (60.9%, 14/23 vs. 25%, 22/88, p = 0.001) compared to those from admitted children. blaCTX-M-15 was the most frequent ESBL gene: 65.3%, 9/14 in postmortem isolates and 22.7% (5/22) from admitted children. We found higher frequency of genes associated with hypermucoviscosity phenotype and invasin in postmortem isolates than those from admitted children: rmpA (30.4%; 7/23 vs. 9.1%, 8/88, p = 0.011), wzi-K1 (34.7%; 8/23 vs. 8%; 7/88, p = 0.002) and traT (60.8%; 14/23 vs. 10.2%; 9/88, p < 0.0001), respectively. Additionally, serine protease auto-transporters of Enterobacteriaceae were detected from 1.8% (pic) to 12.6% (pet) among all isolates. Klebsiella case fatality rate was 30.7% (23/75). CONCLUSION: Multidrug resistant Klebsiella spp. harboring genes associated with hypermucoviscosity phenotype has emerged in Mozambique causing invasive fatal disease in children; highlighting the urgent need for prompt diagnosis, appropriate treatment and effective preventive measures for infection control.


Assuntos
Antibacterianos/farmacologia , Farmacorresistência Bacteriana Múltipla/genética , Infecções por Enterobacteriaceae/mortalidade , Klebsiella/efeitos dos fármacos , Klebsiella/genética , Fatores de Virulência/genética , Autopsia , Bacteriemia/epidemiologia , Bacteriemia/microbiologia , Pré-Escolar , Infecções por Enterobacteriaceae/microbiologia , Feminino , Humanos , Lactente , Recém-Nascido , Klebsiella/isolamento & purificação , Masculino , Testes de Sensibilidade Microbiana , Moçambique/epidemiologia , beta-Lactamases/genética
4.
BMC Infect Dis ; 21(1): 611, 2021 Jun 26.
Artigo em Inglês | MEDLINE | ID: mdl-34174823

RESUMO

BACKGROUND: Carbapenem-resistant Enterobacter cloacae complex (CREC) is a new emerging threat to global public health. The objective of the study was to investigate the clinical characteristics and molecular epidemiology of CREC infections in the medical center of northeast China. METHODS: Twenty-nine patients were infected/colonized with CREC during a ten-year period (2010-2019) by WHONET analysis. Antibiotic susceptibilities were tested with VITEK 2 and micro broth dilution method (for polymyxin B and tigecycline). Carbapenemase encoding genes, ß-lactamase genes, and seven housekeeping genes for MLST were amplified and sequenced for 18 cryopreserved CREC isolates. Maximum likelihood phylogenetic tree was built with the concentrated sequences to show the relatedness between the 18 isolates. RESULTS: There was a rapid increase in CREC detection rate during the ten-year period, reaching 8.11% in 2018 and 6.48% in 2019. The resistance rate of CREC isolates to imipenem and meropenem were 100.0 and 77.8%, however, they showed high sensitivity to tigecycline, polymyxin B and amikacin. The 30-day crude mortality of CREC infection was 17.4%, indicating that it may be a low-virulence bacterium. Furthermore, molecular epidemiology revealed that ST93 was the predominant sequence type followed by ST171 and ST145, with NDM-1 and NDM-5 as the main carbapenemase-encoding genes. Moreover, E. hormaechei subsp. steigerwaltii and E. hormaechei subsp. oharae were the main species, which showed different resistance patterns. CONCLUSION: Rising detection rate of CREC was observed in a tertiary hospital, which showed heterogeneity in drug resistance patterns, resistance genes, and MLST types. Effective infection prevention and control measures should be taken to reduce the spread of CREC.


Assuntos
Enterobacteriáceas Resistentes a Carbapenêmicos , Carbapenêmicos/uso terapêutico , Farmacorresistência Bacteriana Múltipla , Enterobacter cloacae , Infecções por Enterobacteriaceae/epidemiologia , Adolescente , Adulto , Idoso , Idoso de 80 Anos ou mais , Antibacterianos/uso terapêutico , Enterobacteriáceas Resistentes a Carbapenêmicos/efeitos dos fármacos , Enterobacteriáceas Resistentes a Carbapenêmicos/genética , Enterobacteriáceas Resistentes a Carbapenêmicos/isolamento & purificação , China/epidemiologia , Farmacorresistência Bacteriana Múltipla/genética , Enterobacter cloacae/efeitos dos fármacos , Enterobacter cloacae/genética , Enterobacter cloacae/isolamento & purificação , Infecções por Enterobacteriaceae/microbiologia , Feminino , História do Século XXI , Humanos , Recém-Nascido , Masculino , Testes de Sensibilidade Microbiana , Pessoa de Meia-Idade , Epidemiologia Molecular , Tipagem de Sequências Multilocus , Filogenia , Centros de Atenção Terciária/estatística & dados numéricos , Adulto Jovem , beta-Lactamases/genética
5.
Rev Peru Med Exp Salud Publica ; 38(1): 130-135, 2021.
Artigo em Espanhol, Inglês | MEDLINE | ID: mdl-34190905

RESUMO

The present report is the original description of bla TEM-176. The mechanisms of resistance to antimicrobial agents were determined in an enterotoxigenic Escherichia coli, determining the susceptibility to 22 antimicrobials classified in 15 different groups by agar diffusion and establishing the phylogenetic group, mechanisms of resistance and presence of Class 1 and 2 integrons. Integrons and ß-lactam resistance genes were sequenced. The isolate, belonging to phylogenetic group A, showed the presence of resistance or diminished susceptibility to a ampicillin, amoxicillin plus clavulanic acid, nalidíxic acid, ciprofloxacin, streptomycin, kanamycin, tetracycline, trimethoprim, sulfisoxazole, cotrimoxazole, azithromycin and nitrofurantoin, carrying bla TEM, aadA1/2, aphA1, sul3, tet(A) and a Class 2 integron containing a dfrA1 gene. Quinolone resistance was related to the substitution Ser83Ala. The TEM sequencing showed the presence of the new substitution Ala222Val, which led to the description of the new ß-lactamase bla TEM-176.


Assuntos
Escherichia coli , beta-Lactamases , Antibacterianos/farmacologia , Farmacorresistência Bacteriana , Farmacorresistência Bacteriana Múltipla/genética , Escherichia coli/genética , Escherichia coli/metabolismo , Integrons/genética , Testes de Sensibilidade Microbiana , Filogenia , beta-Lactamases/genética
6.
Int J Food Microbiol ; 351: 109268, 2021 Aug 02.
Artigo em Inglês | MEDLINE | ID: mdl-34098467

RESUMO

The increase in multidrug-resistant Salmonella enterica and its spread from food to humans are considered a serious public health concern worldwide. Little is currently known about the prevalence of extended-spectrum ß-lactamase (ESBL)-producing S. enterica in fish in Africa. Therefore, this study aimed to investigate the existence of ESBL-producing S. enterica in retail fish in Egypt. In total, 200 fish samples were collected randomly from various retail fish markets in Egypt. S. enterica were detected in 19 (9.5%; 95% CI: 5.8-14.4) of the fish samples analyzed. Of the 19 non-repetitive S. enterica isolates, 18 were serologically categorized into eight S. enterica serovars and a non-typable serovar. All 19 S. enterica isolates (100%) showed multidrug-resistant phenotypes to at least three classes of antimicrobials, and 11 (57.9%) exhibited an ESBL-resistant phenotype and harbored at least one ESBL-encoding gene. The ESBL-producing S. enterica serovars were as follows: Kentucky (3 isolates; 15.8%), Enteritidis (2 isolates; 10.5%), Typhimurium (2 isolates; 10.5%), and 1 isolate (5.3%) each of Infantis, Virchow, Paratyphi B, and Senftenberg. The identified ß-lactamase-encoding genes included ESBL-encoding genes blaCTX-M-3, blaCTX-M-14, blaCTX-M-15, blaSHV-1, blaSHV-2 and blaSHV-12; the AmpC ß-lactamase-encoding gene blaCMY-2; and the narrow-spectrum ß-lactamase-encoding genes blaTEM-1 and blaOXA-1. All S. enterica isolates were negative for carbapenemase-encoding genes. Molecular analysis of plasmid transferability and replicon typing revealed that most plasmids (with ß-lactamase-encoding genes) were transferrable, and the most common incompatibility groups were IncI1, IncA/C, IncHI1, and IncN. To the best of our knowledge, this is the first report for molecular characterization of ESBL-producing S. enterica in fish in Egypt. The occurrence of ESBL-producing S. enterica in retail fish constitutes a potential public health threat with the possibility of transmission of these strains with resistance genes to humans. Such transmission would exacerbate the resistance to an important class of antibiotics commonly used in hospitals to treat typhoid and non-typhoidal Salmonella infections.


Assuntos
Peixes/microbiologia , Salmonelose Animal/microbiologia , Salmonella enterica/metabolismo , beta-Lactamases/metabolismo , Animais , Antibacterianos/farmacologia , Farmacorresistência Bacteriana Múltipla/efeitos dos fármacos , Farmacorresistência Bacteriana Múltipla/genética , Egito/epidemiologia , Humanos , Plasmídeos/genética , Prevalência , Saúde Pública , Salmonelose Animal/epidemiologia , Salmonella enterica/efeitos dos fármacos , Salmonella enterica/genética , Salmonella enterica/isolamento & purificação , beta-Lactamases/genética
7.
Nat Commun ; 12(1): 2879, 2021 05 17.
Artigo em Inglês | MEDLINE | ID: mdl-34001879

RESUMO

As whole-genome sequencing capacity becomes increasingly decentralized, there is a growing opportunity for collaboration and the sharing of surveillance data within and between countries to inform typhoid control policies. This vision requires free, community-driven tools that facilitate access to genomic data for public health on a global scale. Here we present the Pathogenwatch scheme for Salmonella enterica serovar Typhi (S. Typhi), a web application enabling the rapid identification of genomic markers of antimicrobial resistance (AMR) and contextualization with public genomic data. We show that the clustering of S. Typhi genomes in Pathogenwatch is comparable to established bioinformatics methods, and that genomic predictions of AMR are highly concordant with phenotypic susceptibility data. We demonstrate the public health utility of Pathogenwatch with examples selected from >4,300 public genomes available in the application. Pathogenwatch provides an intuitive entry point to monitor of the emergence and spread of S. Typhi high risk clones.


Assuntos
Antibacterianos/farmacologia , Farmacorresistência Bacteriana Múltipla/genética , Salmonella typhi/efeitos dos fármacos , Febre Tifoide/prevenção & controle , Proteínas de Bactérias/genética , Genoma Bacteriano/genética , Genômica/métodos , Genótipo , Geografia , Humanos , Malaui , Proteínas de Membrana Transportadoras/genética , Testes de Sensibilidade Microbiana/métodos , Mutação , Salmonella typhi/genética , Salmonella typhi/fisiologia , Tanzânia , Febre Tifoide/microbiologia
8.
Nat Commun ; 12(1): 2684, 2021 05 11.
Artigo em Inglês | MEDLINE | ID: mdl-33976138

RESUMO

Shigella sonnei is the most common agent of shigellosis in high-income countries, and causes a significant disease burden in low- and middle-income countries. Antimicrobial resistance is increasingly common in all settings. Whole genome sequencing (WGS) is increasingly utilised for S. sonnei outbreak investigation and surveillance, but comparison of data between studies and labs is challenging. Here, we present a genomic framework and genotyping scheme for S. sonnei to efficiently identify genotype and resistance determinants from WGS data. The scheme is implemented in the software package Mykrobe and tested on thousands of genomes. Applying this approach to analyse >4,000 S. sonnei isolates sequenced in public health labs in three countries identified several common genotypes associated with increased rates of ciprofloxacin resistance and azithromycin resistance, confirming intercontinental spread of highly-resistant S. sonnei clones and demonstrating the genomic framework can facilitate monitoring the spread of resistant clones, including those that have recently emerged, at local and global scales.


Assuntos
Disenteria Bacilar/diagnóstico , Genoma Bacteriano/genética , Genômica/métodos , Shigella sonnei/genética , Antibacterianos/farmacologia , Austrália , Azitromicina/farmacologia , Ciprofloxacina/farmacologia , Farmacorresistência Bacteriana Múltipla/genética , Disenteria Bacilar/microbiologia , Inglaterra , Genética Populacional , Genótipo , Geografia , Saúde Global , Humanos , Testes de Sensibilidade Microbiana/métodos , Filogenia , Polimorfismo de Nucleotídeo Único , Shigella sonnei/classificação , Shigella sonnei/fisiologia , Estados Unidos , Sequenciamento Completo do Genoma
9.
Nat Commun ; 12(1): 2653, 2021 05 11.
Artigo em Inglês | MEDLINE | ID: mdl-33976161

RESUMO

Plasmid persistence in bacterial populations is strongly influenced by the fitness effects associated with plasmid carriage. However, plasmid fitness effects in wild-type bacterial hosts remain largely unexplored. In this study, we determined the fitness effects of the major antibiotic resistance plasmid pOXA-48_K8 in wild-type, ecologically compatible enterobacterial isolates from the human gut microbiota. Our results show that although pOXA-48_K8 produced an overall reduction in bacterial fitness, it produced small effects in most bacterial hosts, and even beneficial effects in several isolates. Moreover, genomic results showed a link between pOXA-48_K8 fitness effects and bacterial phylogeny, helping to explain plasmid epidemiology. Incorporating our fitness results into a simple population dynamics model revealed a new set of conditions for plasmid stability in bacterial communities, with plasmid persistence increasing with bacterial diversity and becoming less dependent on conjugation. These results help to explain the high prevalence of plasmids in the greatly diverse natural microbial communities.


Assuntos
Bactérias/genética , Transferência Genética Horizontal , Genes Bacterianos/genética , Variação Genética , Genoma Bacteriano/genética , Plasmídeos/genética , Algoritmos , Antibacterianos/farmacologia , Bactérias/classificação , Farmacorresistência Bacteriana Múltipla/genética , Enterobacteriaceae/classificação , Enterobacteriaceae/genética , Microbioma Gastrointestinal/genética , Humanos , Microbiota/genética , Filogenia , Especificidade da Espécie
10.
Curr Microbiol ; 78(6): 2414-2419, 2021 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-33961094

RESUMO

The presence of multidrug-resistant Escherichia coli of fecal origin in seafood is a serious concern. Seafood containing MDR E. coli can serve as a medium for the transfer of resistant bacteria to consumers. The aim of the present study is to isolate and identify multidrug-resistant E. coli and associated resistant genes from selected seafood (catfish, crabs and tilapia fish) purchased from wholesalers and retailers at sea landing areas in Lagos state, Nigeria. A total of two hundred and thirty-eight (238) samples consisting of catfish (52), tilapia fish (78) and crab (108) were collected and investigated for the presence of E. coli from the period of June 2018-April 2019. Colonies that showed metallic sheen were considered presumptive E. coli isolates, and positive isolates were chosen for further confirmed by biochemical methods using IMViC tests, Oxidase test, triple sugar iron agar test and sugar fermentation test. Antimicrobial susceptibility of the isolates to eight classes of antibiotics was determined by disc diffusion methods while amplification of suspected antibiotic resistance genes were done by the polymerase chain reaction (PCR) using specific primers. A total of 105 (44.1%) E. coli were isolated from selected samples by standard microbiological procedures. The grand total of 59 (56.2%) isolates showed multiple antibiotic-resistant patterns. The overall result showed high-level resistance to tetracycline 101/105 (96.1%) and trimethoprim 90/105 (85.7%), cefotaxime 67/105 (42.9%) while the highest susceptibility of 101/105 (96.2%) was recorded for amikacin followed by gentamicin 84/105 (80%), meropenem 75/105 (71.4%), ceftazidime (69.5). The presence of tetA and blaTEM was prevalent among the isolates. Our results indicate that seafood may be a reservoir of ß-lactam and tetracycline-resistance determinants.


Assuntos
Peixes-Gato , Escherichia coli , Animais , Antibacterianos/farmacologia , Farmacorresistência Bacteriana Múltipla/genética , Escherichia coli/genética , Incidência , Testes de Sensibilidade Microbiana , Nigéria , Alimentos Marinhos
11.
Microb Pathog ; 155: 104922, 2021 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-33932545

RESUMO

Acinetobacter baumannii is an important pathogen in clinical. The factors of biofilm formation, antibiotic resistance and motility contribute great to A. baumannii in persisting in stressed environment, and further leads to nosocomial infections. 70 A. baumannii clinical isolates were investigated for their clinical characteristics of infection. Among the tested strains, 54 (77.1%) isolates were obtained from ICUs, with the frequency of multidrug-resistance (MDR) at 55.7%, and that of extensively drug-resistance (XDR) at 31.4%. 97.1% of the clinical isolates could form biofilms, in which 4.3% possessed weak biofilm formation ability, while 41.4% and 51.4% were moderate and strong biofilm producers, respectively. A strong correlation between antibiotic resistance and biofilm formation ability was found that all the resistant strains could form biofilms, with the majority in moderate and strong levels, but 2.9% sensitive isolates had no such ability. However, the sensitive strains that could produce biofilms showed stronger biofilm formation capacity in the early stage before 24 h compared to the resistant isolates, though they became weaker afterwards. 24 biofilm-related genes and two blaOXA genes were found in both biofilm-forming and non-biofilm-forming strains, but with higher prevalence in the strains that could produce biofilms. No correlation was detected between twitching motility with antibiotic susceptibility or biofilm formation. These results raised a viewpoint that examining timepoint is a key factor for determining the biofilm formation ability, and further highlighted the importance of the appropriate surveillance and control measures in preventing the emergence and transmission of MDR and XDR A. baumannii.


Assuntos
Infecções por Acinetobacter , Acinetobacter baumannii , Acinetobacter baumannii/genética , Antibacterianos/farmacologia , Biofilmes , Farmacorresistência Bacteriana Múltipla/genética , Humanos
12.
Microb Pathog ; 157: 104989, 2021 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-34044048

RESUMO

This study assessed the correlation between biofilm formation in Pseudomonas aeruginosa strains with both the level of antibiotic resistance, and the number of virulence- and biofilm-related genes encoded. A total of sixty-six, non-replicate and prospectively collected P. aeruginosa strains were identified and tested. Potential ampD mutations that may impose resistance to extended-spectrum ß-lactam (ESBL) agents were further explored. Of the sixty-six tested isolates, 40 demonstrated the multidrug resistance (MDR) phenotype, while twenty-six were non-MDR strains. An inverse correlation was observed between antibiotic resistance and the potential capacity to form biofilms. In addition, no correlation was observed between novel ampD mutations and the tendency for MDR isolates to acquire a ß-lactam-resistant phenotype. The present study emphasizes the need for enhanced infection preventive measures in various hospital units, since both MDR and non-MDR P. aeruginosa isolates exhibited a high level of biofilm-forming capacity and the presence of virulence-associated genes.


Assuntos
Infecções por Pseudomonas , Pseudomonas aeruginosa , Antibacterianos/farmacologia , Biofilmes , Farmacorresistência Bacteriana , Farmacorresistência Bacteriana Múltipla/genética , Humanos , Testes de Sensibilidade Microbiana , Pseudomonas aeruginosa/genética
13.
Antimicrob Agents Chemother ; 65(7): e0028921, 2021 06 17.
Artigo em Inglês | MEDLINE | ID: mdl-33941520

RESUMO

Two novel blaDIM-1- or blaIMP-1-containing genomic islands (GIs) were discovered by whole-genome sequence analyses in four extensively drug-resistant (XDR) Pseudomonas aeruginosa isolates from inpatients at a tertiary hospital in Ghana. The strains were of sequence type 234 (ST234) and formed a phylogenetic clade together with ST111, which is recognized as a global high-risk clone. Their carbapenem resistance was encoded by two Tn402-type integrons, In1592 (blaDIM-1) and In1595 (blaIMP-1), both carrying complete tni mobilization modules. In1595 was bound by conserved 25-bp inverted repeats (IRs) flanked by 5-bp direct repeats (DRs) associated with target site duplication. The integrons were embedded in two GIs that contained cognate integrases and were distinguished by a lower GC content than the chromosomal average. PAGI-97A (52.659 bp; In1592), which encoded a P4-type site-specific integrase of the tyrosine recombinase family in its 3' border, was integrated into tRNA-Pro(ggg) and bracketed by a 49-bp perfect DR created by 3'-end target duplication. GIs with the same structural features, but diverse genetic content, were identified in 41/226 completed P. aeruginosa genomes. PAGI-97B (22,636 bp; In1595), which encoded an XerC/D superfamily integrase in its 5' border, was inserted into the small RNA (sRNA) PrrF1/PrrF2 locus. Specific insertions into this highly conserved locus involved in iron-dependent regulation, all leaving PrrF1 intact, were identified in an additional six phylogenetically unrelated P. aeruginosa genomes. Our molecular analyses unveiled a hospital-associated clonal dissemination of carbapenem-resistant ST234 P. aeruginosa in which the XDR phenotype resulted from novel insertions of two GIs into specific chromosomal sites.


Assuntos
Preparações Farmacêuticas , Infecções por Pseudomonas , Antibacterianos/farmacologia , Carbapenêmicos/farmacologia , Farmacorresistência Bacteriana Múltipla/genética , Gana , Humanos , Integrons/genética , Testes de Sensibilidade Microbiana , Filogenia , Infecções por Pseudomonas/tratamento farmacológico , Pseudomonas aeruginosa/genética , beta-Lactamases/genética
14.
Nat Commun ; 12(1): 2716, 2021 05 11.
Artigo em Inglês | MEDLINE | ID: mdl-33976135

RESUMO

Polyclonal infections occur when at least two unrelated strains of the same pathogen are detected in an individual. This has been linked to worse clinical outcomes in tuberculosis, as undetected strains with different antibiotic resistance profiles can lead to treatment failure. Here, we examine the amount of polyclonal infections in sputum and surgical resections from patients with tuberculosis in the country of Georgia. For this purpose, we sequence and analyse the genomes of Mycobacterium tuberculosis isolated from the samples, acquired through an observational clinical study (NCT02715271). Access to the lung enhanced the detection of multiple strains (40% of surgery cases) as opposed to just using a sputum sample (0-5% in the general population). We show that polyclonal infections often involve genetically distant strains and can be associated with reversion of the patient's drug susceptibility profile over time. In addition, we find different patterns of genetic diversity within lesions and across patients, including mutational signatures known to be associated with oxidative damage; this suggests that reactive oxygen species may be acting as a selective pressure in the granuloma environment. Our results support the idea that the magnitude of polyclonal infections in high-burden tuberculosis settings is underestimated when only testing sputum samples.


Assuntos
Farmacorresistência Bacteriana Múltipla/genética , Genoma Bacteriano , Granuloma/patologia , Mycobacterium tuberculosis/genética , Tuberculose Resistente a Múltiplos Medicamentos/patologia , Tuberculose Pulmonar/patologia , Antituberculosos/uso terapêutico , Biópsia , Células Clonais , Estudos de Coortes , Variação Genética , República da Geórgia , Granuloma/tratamento farmacológico , Granuloma/microbiologia , Granuloma/cirurgia , Humanos , Pulmão/microbiologia , Pulmão/patologia , Pulmão/cirurgia , Mycobacterium tuberculosis/classificação , Mycobacterium tuberculosis/efeitos dos fármacos , Mycobacterium tuberculosis/patogenicidade , Espécies Reativas de Oxigênio/metabolismo , Escarro/microbiologia , Tuberculose Resistente a Múltiplos Medicamentos/tratamento farmacológico , Tuberculose Resistente a Múltiplos Medicamentos/microbiologia , Tuberculose Resistente a Múltiplos Medicamentos/cirurgia , Tuberculose Pulmonar/tratamento farmacológico , Tuberculose Pulmonar/microbiologia , Tuberculose Pulmonar/cirurgia
15.
J Med Microbiol ; 70(4)2021 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-33830906

RESUMO

Introduction. Nitrofurantoin is one of the preferred antibiotics in the treatment of uropathogenic multidrug-resistant (MDR) infections. However, resistance to nitrofurantoin in extensively drug-resistant (XDR) bacteria has severely limited the treatment options.Gap statement. Information related to co-resistance or collateral sensitivity (CS) with reference to nitrofurantoin resistant bacteria is limited.Aim. To study the potential of nitrofurantoin resistance as an indicator of the XDR phenotype in Enterobacteriaceae.Methods. One hundred (45 nitrofurantoin-resistant, 21 intermediately resistant and 34 nitrofurantoin-susceptible) Enterobacteriaceae were analysed in this study. Antibiotic susceptibility testing (AST) against nitrofurantoin and 17 other antimicrobial agents across eight different classes was performed by using the Vitek 2.0 system. The isolates were screened for the prevalence of acquired antimicrobial resistance (AMR) and efflux pump genes by PCR.Results. In total, 51 % of nitrofurantoin-resistant and 28 % of intermediately nitrofurantoin resistant isolates exhibited XDR characteristics, while only 3 % of nitrofurantoin-sensitive isolates were XDR (P=0.0001). Significant co-resistance was observed between nitrofurantoin and other tested antibiotics (ß-lactam, cephalosporin, carbapenem, aminoglycoside and tetracycline). Further, the prevalence of AMR and efflux pump genes was higher in the nitrofurantoin-resistant strains compared to the susceptible isolates. A strong association was observed between nitrofurantoin resistance and the presence of bla PER-1, bla NDM-1, bla OXA-48, ant(2) and oqxA-oqxB genes. Tigecycline (84 %) and colistin (95 %) were the only antibiotics to which the majority of the isolates were susceptible.Conclusion. Nitrofurantoin resistance could be an indicator of the XDR phenotype among Enterobacteriaceae, harbouring multiple AMR and efflux pump genes. Tigecycline and colistin are the only antibiotics that could be used in the treatment of such XDR infections. A deeper understanding of the co-resistance mechanisms in XDR pathogens and prescription of AST-based appropriate combination therapy may help mitigate this problem.


Assuntos
Antibacterianos/farmacologia , Farmacorresistência Bacteriana Múltipla/efeitos dos fármacos , Enterobacteriaceae/efeitos dos fármacos , Nitrofurantoína/farmacologia , Proteínas de Bactérias/genética , Farmacorresistência Bacteriana Múltipla/genética , Enterobacteriaceae/genética , Enterobacteriaceae/isolamento & purificação , Enterobacteriaceae/fisiologia , Infecções por Enterobacteriaceae/microbiologia , Humanos , Testes de Sensibilidade Microbiana
16.
J Med Microbiol ; 70(4)2021 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-33826489

RESUMO

As the representative multidrug-resistant pathogen, Stenotrophomonas maltophilia has multiple intrinsic and acquired resistances, including carbapenem resistance. In companion animals, the antimicrobial susceptibility and sequence types (STs) of S. maltophilia are not well understood due to its limited isolation rate. We investigated the antimicrobial susceptibilities and multilocus sequence types (MLSTs) of 38 S. maltophilia strains isolated from dogs and cats in Japan. Prevalence of resistance was detected for imipenem (100 %), aztreonam (94.7 %), piperacillin (65.8 %), trimethoprim-sulfamethoxazole (65.8 %), and ceftazidime (60.5 %). Rates of resistances to chloramphenicol, minocycline, and levofloxacin were low (2.6-5.3 %). MLST analysis revealed that all 38 strains were assigned to 34 STs, including 11 previously reported STs and 23 newly identified STs. Phylogenetic analysis of MLSTs enabled categorization of 13 isolates (34.2 %) into genogroup 6, which is a major genogroup of human isolates. Multinational surveillance would be needed to clarify the significance of antimicrobial-resistant S. maltophilia isolates from companion animals.


Assuntos
Doenças do Gato/microbiologia , Doenças do Cão/microbiologia , Farmacorresistência Bacteriana Múltipla/genética , Infecções por Bactérias Gram-Negativas/veterinária , Stenotrophomonas maltophilia/efeitos dos fármacos , Animais , Antibacterianos/uso terapêutico , Doenças do Gato/tratamento farmacológico , Gatos , Doenças do Cão/tratamento farmacológico , Cães , Genótipo , Infecções por Bactérias Gram-Negativas/microbiologia , Japão , Tipagem de Sequências Multilocus , Stenotrophomonas maltophilia/classificação
17.
Rev Chilena Infectol ; 38(1): 69-80, 2021 Feb.
Artigo em Espanhol | MEDLINE | ID: mdl-33844795

RESUMO

Pseudomonas aeruginosa is one of the major pathogens causing healthcare-associated infections (HAI). Its capacity of adaptation, dissemination, intrinsic resistance to antimicrobials and of acquiring new mechanisms through mobile genetic elements, make the treatment of infections by this microorganism a challenge for the clinician. Intrinsically, P. aeruginosa, presents a reduced permeability in the external membrane, due to the expression of efflux pumps, and an inducible AmpC-type cephalosporinase. In addition, P. aeruginosa is able to acquire new resistance determinants by horizontal transfer in the form of cassettes located in integrons, and in turn located in transposons or plasmids. Within the enzymatic resistance that P. aeruginosa presents, betalactamases, including extended spectrum (ESBL) and carbapenemases. But also aminoglycoside modifying enzymes, stand out, causing this microorganism to present multi-resistance phenotypes (MDR), extreme resistance (XDR) and pan-resistance (PDR) to the called antipseudomonal antibiotics, including the new cephalosporins with betalactamase inhibitors.


Assuntos
Infecções por Pseudomonas , Pseudomonas aeruginosa , Antibacterianos/farmacologia , Farmacorresistência Bacteriana Múltipla/genética , Humanos , Laboratórios , Testes de Sensibilidade Microbiana , Plasmídeos , Infecções por Pseudomonas/tratamento farmacológico , Pseudomonas aeruginosa/genética , beta-Lactamases/genética
18.
BMC Infect Dis ; 21(1): 394, 2021 Apr 29.
Artigo em Inglês | MEDLINE | ID: mdl-33926375

RESUMO

BACKGROUND: Whole-genome sequencing has shown that the Mycobacterium tuberculosis infection process can be more heterogeneous than previously thought. Compartmentalized infections, exogenous reinfections, and microevolution are manifestations of this clonal complexity. The analysis of the mechanisms causing the microevolution -the genetic variability of M. tuberculosis at short time scales- of a parental strain into clonal variants with a patient is a relevant issue that has not been yet completely addressed. To our knowledge, a whole genome sequence microevolution analysis in a single patient with inadequate adherence to treatment has not been previously reported. CASE PRESENTATION: In this work, we applied whole genome sequencing analysis for a more in-depth analysis of the microevolution of a parental Mycobacterium tuberculosis strain into clonal variants within a patient with poor treatment compliance in Argentina. We analyzed the whole-genome sequence of 8 consecutive Mycobacterium tuberculosis isolates obtained from a patient within 57-months of intermittent therapy. Nineteen mutations (9 short-term, 10 fixed variants) emerged, most of them associated with drug resistance. The first isolate was already resistant to isoniazid, rifampicin, and streptomycin, thereafter the strain developed resistance to fluoroquinolones and pyrazinamide. Surprisingly, isolates remained susceptible to the pro-drug ethionamide after acquiring a frameshift mutation in ethA, a gene required for its activation. We also found a novel variant, (T-54G), in the 5' untranslated region of whiB7 (T-54G), a region allegedly related to kanamycin resistance. Notably, discrepancies between canonical and phage-based susceptibility testing to kanamycin were previously found for the isolate harboring this mutation. In our patient, microevolution was mainly driven by drug selective pressure. Rare short-term mutations fixed together with resistance-conferring mutations during therapy. CONCLUSIONS: This report highlights the relevance of whole-genome sequencing analysis in the clinic for characterization of pre-XDR and MDR resistance profile, particularly in patients with incomplete and/or intermittent treatment.


Assuntos
Farmacorresistência Bacteriana Múltipla/genética , Mycobacterium tuberculosis/efeitos dos fármacos , Mycobacterium tuberculosis/genética , Tuberculose Resistente a Múltiplos Medicamentos/tratamento farmacológico , Tuberculose Resistente a Múltiplos Medicamentos/microbiologia , Adulto , Antituberculosos/farmacologia , Antituberculosos/uso terapêutico , Argentina , Farmacorresistência Bacteriana Múltipla/efeitos dos fármacos , Feminino , Humanos , Isoniazida/uso terapêutico , Adesão à Medicação , Testes de Sensibilidade Microbiana , Mutação , Mycobacterium tuberculosis/isolamento & purificação , Filogenia , Pirazinamida/uso terapêutico , Rifampina/uso terapêutico , Estreptomicina/farmacologia , Tuberculose Pulmonar/tratamento farmacológico , Tuberculose Pulmonar/microbiologia , Sequenciamento Completo do Genoma
19.
Int J Mol Sci ; 22(8)2021 Apr 10.
Artigo em Inglês | MEDLINE | ID: mdl-33920239

RESUMO

Post-weaning diarrhea due to enterotoxigenic Escherichia coli (ETEC) is a common disease of piglets and causes great economic loss for the swine industry. Over the past few decades, decreasing effectiveness of conventional antibiotics has caused serious problems because of the growing emergence of multidrug-resistant (MDR) pathogens. Various studies have indicated that antimicrobial peptides (AMPs) have potential to serve as an alternative to antibiotics owing to rapid killing action and highly selective toxicity. Our previous studies have shown that AMP GW-Q4 and its derivatives possess effective antibacterial activities against the Gram-negative bacteria. Hence, in the current study, we evaluated the antibacterial efficacy of GW-Q4 and its derivatives against MDR ETEC and their minimal inhibition concentration (MIC) values were determined to be around 2~32 µg/mL. Among them, AMP Q4-15a-1 with the second lowest MIC (4 µg/mL) and the highest minimal hemolysis concentration (MHC, 256 µg/mL), thus showing the greatest selectivity (MHC/MIC = 64) was selected for further investigations. Moreover, Q4-15a-1 showed dose-dependent bactericidal activity against MDR ETEC in time-kill curve assays. According to the cellular localization and membrane integrity analyses using confocal microscopy, Q4-15a-1 can rapidly interact with the bacterial surface, disrupt the membrane and enter cytosol in less than 30 min. Minimum biofilm eradication concentration (MBEC) of Q4-15a-1 is 4× MIC (16 µg/mL), indicating that Q4-15a-1 is effective against MDR ETEC biofilm. Besides, we established an MDR ETEC infection model with intestinal porcine epithelial cell-1 (IPEC-1). In this infection model, 32 µg/mL Q4-15a-1 can completely inhibit ETEC adhesion onto IPEC-1. Overall, these results suggested that Q4-15a-1 may be a promising antibacterial candidate for treatment of weaned piglets infected by MDR ETEC.


Assuntos
Farmacorresistência Bacteriana Múltipla/efeitos dos fármacos , Escherichia coli Enterotoxigênica/efeitos dos fármacos , Infecções por Escherichia coli/tratamento farmacológico , Proteínas Citotóxicas Formadoras de Poros/farmacologia , Doenças dos Suínos/tratamento farmacológico , Animais , Antibacterianos/efeitos adversos , Antibacterianos/farmacologia , Aderência Bacteriana/efeitos dos fármacos , Biofilmes/efeitos dos fármacos , Farmacorresistência Bacteriana Múltipla/genética , Escherichia coli Enterotoxigênica/patogenicidade , Infecções por Escherichia coli/microbiologia , Infecções por Escherichia coli/veterinária , Testes de Sensibilidade Microbiana , Suínos/microbiologia , Doenças dos Suínos/microbiologia , Doenças dos Suínos/patologia
20.
BMC Infect Dis ; 21(1): 330, 2021 Apr 08.
Artigo em Inglês | MEDLINE | ID: mdl-33832459

RESUMO

OBJECTIVES: To explore the drug susceptibility of levofloxacin (LFX), moxifloxacin (MFX), bedaquiline (BDQ), linezolid (LZD), clofazimine (CFZ) and delamanid (DLM) against multidrug resistant tuberculosis (MDR-TB) isolates from drug resistance survey of southwest China, and to illustrate the genetic characteristics of MDR-TB isolates with acquired drug resistance. METHODS: A total of 339 strains were collected from smear-positive TB patients in the drug resistance survey of southwest China between January 2014 and December 2016. The MICs for the above mentioned drugs were determined for MDR-TB by conventional drug susceptibility testing. Genes related to drug resistance were amplified with their corresponding pairs of primers. RESULTS: MDR was observed in 88 (26.0%; 88/339) isolates. LFX had the highest resistance rate (50.0%; 44/88), followed by MFX (38.6%; 34/88). The resistance rate to LZD, CFZ, and DLM was 4.5% (4/88), 3.4% (3/88), and 4.5% (4/88), respectively, and the lowest resistance rate was observed in BDQ (2.3%; 2/88). Of the 45 isolates resistant to LFX and MFX, the most prevalent resistance mutation was found in gyrA with the substitution of codon 94 (34/45, 75.6%). Two strains with CFZ - BDQ cross resistance had a mutation in the Rv0678 gene. Of the four LZD resistant isolates, two carried mutations in rplC gene. For the four isolates resistant to DLM, one isolate had mutations in codon 318 of fbiC gene, and two isolates were with mutations in codon 81 of ddn gene. CONCLUSION: This study provided evidence of the usefulness of new anti-TB drugs in the treatment of MDR-TB in China.


Assuntos
Antituberculosos/farmacologia , Farmacorresistência Bacteriana Múltipla/genética , Mycobacterium tuberculosis/efeitos dos fármacos , Mycobacterium tuberculosis/genética , Tuberculose Resistente a Múltiplos Medicamentos/microbiologia , China , Farmacorresistência Bacteriana Múltipla/efeitos dos fármacos , Humanos , Testes de Sensibilidade Microbiana , Mutação , Mycobacterium tuberculosis/isolamento & purificação
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