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1.
Food Microbiol ; 85: 103295, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31500701

RESUMO

Fermented red pepper (FRP) sauce has been eaten in worldwide for many years. The salt content and resident microbial community influences the quality of the FRP sauce and may confer health (e.g., probiotics) or harm (e.g., antibiotic resistance genes) to the consumers in some circumstances; however, the salt-mediated alteration of microbial community and antibiotic resistance genes are little known. In this study, a combination of whole genome sequencing and amplicon analysis was used to investigate the changes in microbial community and antimicrobial resistance genes in response to different salt content during red pepper fermentation. While the family Enterobacteriaceae dominated in high-salt (15-25%) samples, Lactobacillaceae quickly became the dominant population in place of Enterobacteriaceae after 24 days in 10% salt samples. Compared to 0.05 antibiotic resistance genes (ARGs) per cell number on average in 10% salt sample, 16.6 ARGs were present in high-salt samples, wherein the bacterial hosts were major assigned to Enterobacteriaceae including genera Enterobacter, Citrobacter, Escherichia, Salmonella and Klebsiella. Multidrug resistance genes were the predominant ARG type. Functional profiling showed that histidine kinase functions were of much higher abundance in high-salt samples and included several osmotic stress-related two-component systems that simultaneously encoded ARGs. These results give first metagenomic insights into the salt-mediated changes in microbial community composition and a broad view of associated antibiotic resistance genes in the process of food fermentation.


Assuntos
Capsicum/química , Farmacorresistência Bacteriana/genética , Enterobacteriaceae/genética , Lactobacillaceae/genética , Metagenoma , Microbiota , Cloreto de Sódio/química , Enterobacteriaceae/crescimento & desenvolvimento , Fermentação , Genes Bacterianos , Lactobacillaceae/crescimento & desenvolvimento , Metagenômica , Pressão Osmótica
2.
Sci Total Environ ; 700: 134446, 2020 Jan 15.
Artigo em Inglês | MEDLINE | ID: mdl-31648121

RESUMO

Bacteriophage may play an important role in antimicrobial resistance genes (ARGs) transmission. However, the contribution of bacteriophage to the spread of ARGs in environment, especially in poultry farm environment, is rarely known. In this study, the prevalence of ARGs in bacteriophage DNA was investigated in chicken feces from 30 different poultry farms in China. Then the abundance of the aac(6')-Ib-cr, blaCTX-M, ermB, floR, mcr-1, sul1, tetM and intI1 genes was determined by qPCR in bacteriophage and compared with certain representative plasmid DNA samples. The results showed that 12 ARGs (aac(6')-Ib-cr, aph(3')-IIIa, blaCTX-M, ermB, ermF, floR, mcr-1, qnrS, sul1, sul2, vanA, tetM genes) and class 1 integron gene intI1 were detected in bacteriophage DNA fraction. The sul1, tetM and aac(6')-Ib-cr genes were most prevalent with high detection rates of 77%, 61% and 55%, respectively. To our best knowledge, this study firstly reported the presence of the mcr-1 gene in bacteriophage DNA derived from farms environments. We found that the gene copy (GC) numbers of the aac(6')-Ib-cr, ermB and sul1 genes were as high as 5.47, 5.22 and 5.54 log10 GC/g, respectively. Both the prevalence and abundance of ARGs in broiler fecal wastes were also generally higher than in laying hens. In addition, although the GC numbers of the aac(6')-Ib-cr, floR and tetM genes in plasmid DNA was higher than that in phage DNA fraction by 4.68, 3.59 and 3.9 orders of magnitude, respectively, the absolute abundances of the blaCTX-M and mcr-1 genes in phage DNA were close to or even higher than that in plasmid DNA at farm SIL2, SIL4 and SIB1. As potential vessels for ARGs, bacteriophage could not be ignored due to their unique extracellular persistence in environments. Overall, this is the first comprehensive survey about bacteriophage carried ARGs from farms in different regions in China.


Assuntos
Farmacorresistência Bacteriana/genética , Fezes/virologia , Genes Bacterianos , Animais , Bacteriófagos/genética , Galinhas , China , Fazendas , Integrons , Plasmídeos
3.
APMIS ; 128(1): 41-47, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31692136

RESUMO

Campylobacteriosis is one of the most frequently reported zoonoses worldwide. The well-documented increase in the ciprofloxacin resistance has increased the importance of rapid detection of the resistance. The incidence of ciprofloxacin resistance was investigated using real-time PCR. Identification of one hundred and fifty-eight strains was performed by PCR. Minimum inhibitory concentration (MIC) of ciprofloxacin was determined by Epsilometer test. Following the confirmation of the efficiencies of singleplex real-time PCR methods using two different probes, a cytosine to thymine point mutation at codon 86 was detected by allelic discrimination. Of the 158 strains, 114 (72.2%) were determined to be resistant to ciprofloxacin. The MIC50 and the MIC90 of ciprofloxacin were found to be 8 and ≥32 mg/L, respectively. By real-time PCR, the presence of the mutation was confirmed in all, but one, resistant strains and the absence of the mutation was demonstrated in all, but one, susceptible strains. The rate of resistance is high among C. jejuni strains and ciprofloxacin should not be used in the treatment of such infections in Turkey. A cytosine to thymine mutation is the most frequently detected mechanism for the resistance. Real-time PCR can be used for the quick screening of the resistance.


Assuntos
Antibacterianos/farmacologia , Campylobacter jejuni/efeitos dos fármacos , Campylobacter jejuni/genética , Ciprofloxacino/farmacologia , Farmacorresistência Bacteriana/genética , Mutação Puntual , Alelos , Infecções por Campylobacter/epidemiologia , Infecções por Campylobacter/microbiologia , Testes de Sensibilidade a Antimicrobianos por Disco-Difusão , Eletroforese em Gel de Campo Pulsado , Humanos , Concentração Inibidora 50 , Testes de Sensibilidade Microbiana , Fenótipo , Prevalência , Turquia
4.
Yi Chuan ; 41(12): 1138-1147, 2019 Dec 20.
Artigo em Chinês | MEDLINE | ID: mdl-31857285

RESUMO

Pathogenic Escherichia coli (E. coli) is the most common pathogen causing urinary tract infection in animals. We investigated the antibiotic resistance and virulence genes of pathogenic E. coli CCHTP derived from urine with occult blood of the giant panda by whole genome sequencing. The flanking sequencing of resistance and virulence genes in genomic islands were also analyzed. Our results demonstrate that E. coli CCHTP contains different families of antibiotic resistance genes, most of which are efflux pump related genes, including multiple drug resistance efflux pump genes mdfA, emrE, and mdtN. A total of 166 virulence factors and 563 virulence genes were identified, and the most virulence factors and related genes are involved in host cell attachment and invasion processes. Furthermore, sequence analysis of 19 genomic islands revealed that antibiotic and virulence genes are associated with mobile genetic elements (transposon and insertion sequence) in GIs011 and GIs017. These structures can mediate horizontal transfer of antibiotic and virulence genes. Our work described the distribution of antibiotic resistance genes and virulence genes in E. coli CCHTP, which may provide an important guidance for treatment and rational drug use of E. coli CCHTP infection in the giant panda.


Assuntos
Farmacorresistência Bacteriana , Proteínas de Escherichia coli , Escherichia coli , Urina , Ursidae , Animais , Farmacorresistência Bacteriana/genética , Escherichia coli/genética , Proteínas de Escherichia coli/genética , Genoma Bacteriano , Urina/microbiologia , Ursidae/microbiologia , Virulência/genética , Fatores de Virulência/genética , Sequenciamento Completo do Genoma
5.
Int J Food Microbiol ; 311: 108356, 2019 Dec 02.
Artigo em Inglês | MEDLINE | ID: mdl-31670141

RESUMO

Different samples of three products including Bikalga and Soumbala from Burkina Faso (West Africa) and Ntoba Mbodi from Congo-Brazzaville (Central Africa) were evaluated. The bacteria (400) were phenotyped and genotypically characterized by Rep-PCR, PFGE, 16S rRNA and rpoB gene sequencing and spa typing. Their PFGE profiles were compared with those of 12,000 isolates in the Center for Disease Control (CDC, USA) database. They were screened for the production of enterotoxins, susceptibility to 19 antimicrobials, presence of 12 staphylococcal toxin and 38 AMR genes and the ability to transfer erythromycin and tetracycline resistance genes to Enterococcus faecalis JH2-2. Fifteen coagulase negative (CoNS) and positive (CoPS) species characterized by 25 Rep-PCR/PFGE clusters were identified: Staphylococcus arlettae, S. aureus, S. cohnii, S. epidermidis, S. gallinarum, S. haemolyticus, S. hominis, S. pasteuri, S. condimenti, S. piscifermentans, S. saprophyticus, S. sciuri, S. simulans, S. warneri and Macrococcus caseolyticus. Five species were specific to Soumbala, four to Bikalga and four to Ntoba Mbodi. Two clusters of S. gallinarum and three of S. sciuri were particular to Burkina Faso. The S. aureus isolates exhibited a spa type t355 and their PFGE profiles did not match any in the CDC database. Bacteria from the same cluster displayed similar AMR and toxin phenotypes and genotypes, whereas clusters peculiar to a product or a location generated distinct profiles. The toxin genes screened were not detected and the bacteria did not produce the staphylococcal enterotoxins A, B, C and D. AMR genes including blazA, cat501, dfr(A), dfr(G), mecA, mecA1, msr(A) and tet(K) were identified in CoNS and CoPS. Conjugation experiments produced JH2-2 isolates that acquired resistance to erythromycin and tetracycline, but no gene transfer was revealed by PCR. The investigation of the heterogeneity of Staphylococcus species from alkaline fermented foods, their relationship with clinical and environmental isolates and their safety in relation to antimicrobial resistance (AMR) and toxin production is anticipated to contribute to determining the importance of staphylococci in alkaline fermented foods, especially in relation to the safety of the consumers.


Assuntos
Enterotoxinas/genética , Staphylococcus , Antibacterianos/farmacologia , Burkina Faso , Coagulase/genética , Congo , RNA Polimerases Dirigidas por DNA/genética , Farmacorresistência Bacteriana/genética , Eritromicina/farmacologia , Genótipo , Testes de Sensibilidade Microbiana , Fenótipo , Reação em Cadeia da Polimerase , RNA Ribossômico 16S/genética , Staphylococcus/classificação , Staphylococcus/efeitos dos fármacos , Staphylococcus/genética , Staphylococcus/isolamento & purificação , Tetraciclina/farmacologia
6.
BMC Infect Dis ; 19(1): 928, 2019 Nov 04.
Artigo em Inglês | MEDLINE | ID: mdl-31684890

RESUMO

BACKGROUND: Endemic presence of Klebsiella pneumoniae resistant to carbapenem in Italy has been due principally to the clonal expansion of CC258 isolates; however, recent studies suggest an ongoing epidemiological change in this geographical area. METHODS: 50 K. pneumoniae strains, 25 carbapenem-resistant (CR-Kp) and 25 susceptible (CS-Kp), collected from march 2014 to march 2016 at the Laboratory of Bacteriology of the Paolo Giaccone Polyclinic University hospital of Palermo, Italy, were characterized for antibiotic susceptibility and fully sequenced by next generation sequencing (NGS) for the in silico analysis of resistome, virulome, multi-locus sequence typing (MLST) and core single nucleotide polymorphism (SNP) genotypes RESULTS: MLST in silico analysis of CR-Kp showed that 52% of isolates belonged to CC258, followed by ST395 (12%), ST307 (12%), ST392 (8%), ST348 (8%), ST405 (4%) and ST101 (4%). In the CS-Kp group, the most represented isolate was ST405 (20%), followed by ST392 and ST15 (12%), ST395, ST307 and ST1727 (8%). The in silico ß-lactamase analysis of the CR-Kp group showed that the most detected gene was blaSHV (100%), followed by blaTEM (92%), blaKPC (88%), blaOXA (88%) and blaCTX-M (32%). The virulome analysis detected mrk operon in all studied isolates, and wzi-2 was found in three CR-Kp isolates (12%). Furthermore, the distribution of virulence genes encoding for the yersiniabactin system, its receptor fyuA and the aerobactin system did not show significant distribution differences between CR-Kp and CS-Kp, whereas the Klebsiella ferrous iron uptake system (kfuA, kfuB and kfuC genes), the two-component system kvgAS and the microcin E495 were significantly (p < 0.05) prevalent in the CS-Kp group compared to the CR-Kp group. Core SNP genotyping, correlating with the MLST data, allowed greater strain tracking and discrimination than MLST analysis. CONCLUSIONS: Our data support the idea that an epidemiological change is ongoing in the Palermo area (Sicily, Italy). In addition, our analysis revealed the co-existence of antibiotic resistance and virulence factors in CR-Kp isolates; this characteristic should be considered for future genomic surveillance studies.


Assuntos
Farmacorresistência Bacteriana/genética , Klebsiella pneumoniae/efeitos dos fármacos , Klebsiella pneumoniae/genética , Fatores de Virulência/genética , Adulto , Idoso , Idoso de 80 Anos ou mais , Antibacterianos/farmacologia , Proteínas de Bactérias/genética , Técnicas de Tipagem Bacteriana , Carbapenêmicos/farmacologia , Farmacorresistência Bacteriana/efeitos dos fármacos , Genótipo , Humanos , Infecções por Klebsiella/microbiologia , Klebsiella pneumoniae/classificação , Klebsiella pneumoniae/isolamento & purificação , Pessoa de Meia-Idade , Tipagem de Sequências Multilocus , Filogenia , Polimorfismo de Nucleotídeo Único , Sicília , beta-Lactamases/genética
7.
Zhonghua Wei Zhong Bing Ji Jiu Yi Xue ; 31(10): 1212-1218, 2019 Oct.
Artigo em Chinês | MEDLINE | ID: mdl-31771717

RESUMO

OBJECTIVE: To evaluate the in vitro activity of ceftazidime-avibactam (CAZ-AVI) alone or in combination with colistin (COL) against clinically isolated extensively drug-resistant Pseudomonas aeruginosa (XDR-PA). METHODS: Minimum inhibitory concentration (MIC) of 16 clinical XDR-PA isolates was determined by broth dilution method and chessboard design when CAZ-AVI and COL were used alone or in combination, then the combined inhibitory concentration index (FICI) was calculated. Class A [Klebsiella pneumoniae carbapenemase ß-lactamase (blaKPC), Guiana extended-spectrum ß-lactamase (blaGES)], Class B [imipenemase ß-lactamase (blaIMP), Verona-Integronmetallo ß-lactamase (blaVIM), New Delhi metallo ß-lactamase (blaNDM), German imipenemase ß-lactamase (blaGIM), Sao Paulo metallo-ß-lactamase (blaSPM)], Class C [AmpC ß-lactamase (blaAmpC)], Class D [oxacillinase ß-lactamase (blaOXA)] ß-lactamase-related resistance genes were detected by polymerase chain reaction. Drug-resistant mutation frequencies of each strain were determined on a drug-containing plate. The time kill curves of three XDR-PA were plotted by colony counting method. A biofilm model was established in vitro, and the synergistic effect of CAZ-AVI and COL on biofilm inhibition was detected by methythiazolyl tetrazolium assay (MTT). RESULTS: The MICs of 16 XDR-PA for CAZ-AVI ranged from 1 mg/L to 128 mg/L, and three of the isolates showed resistance (MIC > 8 mg/L). The FICI range of CAZ-AVI combined with COL was 0.312-1.000. Four isolates were synergistic, while the other 12 isolates were additive. Three isolates resistant to CAZ-AVI contained Class B resistance genes such as blaIMP and blaVIM, while 13 susceptible isolates carried resistance genes belonging to Class A, C or D. The logarithm values of mutation frequencies of drug resistance in CAZ-AVI group, COL group and combination group were -4.81±0.88, -7.06±0.69 and -9.70 (-9.78, -9.53), respectively. There were significant differences among the three groups (H = 33.601, P < 0.001), and between every two groups (adjusted P < 0.05). In time kill curves, the phytoplankton load of three XDR-PA decreased more than 6 log CFU/L when these two drugs were used together, and number of PA1819 planktonic bacteria decreased more than 5.1 log CFU/L compared with monotherapy group. Viable quantity in biofilm (A490) of normal saline group, CAZ-AVI group, COL group and CAZ-AVI-COL group were 0.665±0.068, 0.540±0.072, 0.494±0.642 and 0.317±0.080, respectively. There was significant difference between the other two groups (all P < 0.001), except for that between CAZ-AVI group and COL group (P = 0.109). CONCLUSIONS: CAZ-AVI combined with COL can effectively improve the bactericidal effect of each drug alone on XDR-PA. The regimen can also reduce the production of drug-resistant bacteria and inhibit the formation of biofilm. Therefore, it is a potential treatment for XDR-PA infection.


Assuntos
Antibacterianos/uso terapêutico , Compostos Azabicíclicos/uso terapêutico , Ceftazidima/uso terapêutico , Colistina/uso terapêutico , Farmacorresistência Bacteriana/genética , Infecções por Pseudomonas/tratamento farmacológico , Pseudomonas aeruginosa , Combinação de Medicamentos , Testes de Sensibilidade Microbiana , beta-Lactamases
8.
Sci Total Environ ; 695: 133781, 2019 Dec 10.
Artigo em Inglês | MEDLINE | ID: mdl-31756854

RESUMO

Livestock manure is a major reservoir of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs). This study investigated the distribution characteristics of ARB, ARGs in fresh and composted manures of traditional breading industry in rural areas in China. Samples collected were naturally piled without professional composting, and will be applied to farmland. The real-time quantitative polymerase chain reaction (qPCR) results showed the presence of ten target ARGs and two mobile genetic elements (MGEs) in the tested manure samples. The relative abundance of tetracycline and sulfonamide resistance genes (TRGs and SRGs) was generally higher than that of macrolide resistance genes (MRGs), followed by quinolone resistance genes (QRGs). There were significant positive correlations between the abundance of sul1, sul2, tetW and MGEs (intl1, intl2). In addition, the distribution of target ARGs was associated with the residual concentrations of doxycycline (DOX), sulfamethazine (SM2), enrofloxacin (ENR) and tylosin (TYL). Overall, a total of 24 bacterial genera were identified. The resistance rates of ARB were 17.79%-83.70% for SM2, followed 0.40%-63.77% for TYL, 0.36%-43.90% for DOX and 0.00%-13.36% for ENR, which showed a significant dose-effect. This study also demonstrated that the abundance of clinically relevant ARB and ARGs in chicken, swine and cow fresh manures significantly greater than that in composted manures, and chicken and swine manures had higher proportion of ARB and higher abundance of ARGs than that in cow manures.


Assuntos
Farmacorresistência Bacteriana/genética , Monitoramento Ambiental , Genes Bacterianos , Animais , Compostagem , Fazendas , Gado , Esterco/microbiologia
9.
Sichuan Da Xue Xue Bao Yi Xue Ban ; 50(5): 629-634, 2019 Sep.
Artigo em Chinês | MEDLINE | ID: mdl-31762229

RESUMO

OBJECTIVE: To establish a way for screening Mycobacterium mutants through adding the screening markers into pJV53. METHODS: The sucrose counter selection gene SacB and mutant hygromycin-resistant gene hygS were inserted into pJV53; The recovery of the hygromycin-resistance indicated the successful homologous recombination in Mycobacterium smegmatis (Ms), which could serve as mutant screening marker; The sucrose counter selection could be used to screen the plasmid-free mutants. RESULTS: The recombinant plasmid pJV53-SacB-hygS were successfully constructed. The rifampin-resistant rpoB D516Y and rpoB H526Q mutants and MSMEG_4487 G188A mutant were efficiently screened out. All mutants had shed the plasmid successfully. CONCLUSION: pJV53-SacB-hygS can efficiently contribute to construct and screen the mutants and to get the mutants shedding the plasmid self, which has high value of extensive application; the D516Y and H526Q mutations in gene rpoB of Mycobacterium tuberculosis contribute to its rifampin-resistance.


Assuntos
Farmacorresistência Bacteriana/genética , Recombinação Homóloga , Mycobacterium smegmatis/genética , Mycobacterium tuberculosis/genética , Proteínas de Bactérias/genética , RNA Polimerases Dirigidas por DNA/genética , Testes de Sensibilidade Microbiana , Mutação , Mycobacterium tuberculosis/efeitos dos fármacos , Plasmídeos/genética , Rifampina/farmacologia
10.
Mem Inst Oswaldo Cruz ; 114: e190232, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31778426

RESUMO

BACKGROUND: Acinetobacter baumannii is a leading cause of nosocomial infections. This species is characterised by the presence of pandemic lineages (International Clones) that present a broad antimicrobial resistance profile. OBJECTIVE: To perform the molecular epidemiology of carbapenem-resistant A. baumannii from a clinical setting in the Amazon Basin, and to characterise their antimicrobial resistance determinants. METHODS: The genetic relationship of carbapenem-resistant A. baumannii were assessed by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). Class A, B and D ß-lactamase genes were screened by polymerase chain reaction (PCR) and sequencing. The antimicrobial susceptibility profile was obtained by Disc-diffusion method and minimum inhibitory concentration (MIC) determination. FINDINGS: All carbapenem-resistant A. baumannii strains belonged to three international clones, IC-1, IC-5 and IC-6, the latter recently reported by the first time in Brazil. The major determinant of carbapenem resistance in IC-1 and IC-5 strains was bla OXA-23, associated with ISAba1 and ISAba3, respectively, while IC-6 harboured the bla OXA-72. CONCLUSIONS: The A. baumannii epidemiology in Brazilian Amazon Region was unknown. It was demonstrated that A. baumannii XDR international clones were responsible for nosocomial infections in Boa Vista during 2016-2018, revealing that the epidemiological scenario of A. baumannii infections in Amazon Region resembles those from the cosmopolitan regions worldwide.


Assuntos
Infecções por Acinetobacter/virologia , Acinetobacter baumannii/genética , Antibacterianos/farmacologia , Farmacorresistência Bacteriana/genética , beta-Lactamases/genética , Acinetobacter baumannii/classificação , Acinetobacter baumannii/efeitos dos fármacos , Brasil , Testes de Sensibilidade a Antimicrobianos por Disco-Difusão , Eletroforese em Gel de Campo Pulsado , Genótipo , Humanos , Tipagem de Sequências Multilocus , Fenótipo
11.
Sci Total Environ ; 688: 1335-1347, 2019 Oct 20.
Artigo em Inglês | MEDLINE | ID: mdl-31726563

RESUMO

The environmental reservoirs of sulfonamide (SA) resistome are still poorly understood. We investigated the potential sources and reservoir of SA resistance (SR) in Larut River and Sangga Besar River by measuring the SA residues, sulfamethoxazole resistant (SMXr) in bacteria and their resistance genes (SRGs). The SA residues measured ranged from lower than quantification limits (LOQ) to 33.13 ng L-1 with sulfadiazine (SDZ), sulfadimethoxine (SDM) and SMX as most detected. Hospital wastewater effluent was detected with the highest SA residues concentration followed by the slaughterhouse and zoo wastewater effluents. The wastewater effluents also harbored the highest abundance of SMXr-bacteria (107 CFU mL-1) and SRGs (10-1/16S copies mL-1). Pearson correlation showed only positive correlation between the PO4 and SMXr-bacteria. In conclusion, wastewater effluents from the zoo, hospital and slaughterhouse could serve as important sources of SA residues that could lead to the consequent emergence of SMXr-bacteria and SRGs in the river.


Assuntos
Farmacorresistência Bacteriana/genética , Monitoramento Ambiental , Rios/microbiologia , Sulfonamidas/análise , Poluentes Químicos da Água/análise , Genes Bacterianos , Rios/química
12.
BMC Genomics ; 20(1): 768, 2019 Oct 23.
Artigo em Inglês | MEDLINE | ID: mdl-31646960

RESUMO

BACKGROUND: The Hafnia genus is an opportunistic pathogen that has been implicated in both nosocomial and community-acquired infections. Although Hafnia is fairly often isolated from clinical material, its taxonomy has remained an unsolved riddle, and the involvement and importance of Hafnia in human disease is also uncertain. Here, we used comparative genomic analysis to define the taxonomy of Hafnia, identify species-specific genes that may be the result of ecological and pathogenic specialization, and reveal virulence-related genetic profiles that may contribute to pathogenesis. RESULTS: One complete genome sequence and 19 draft genome sequences for Hafnia strains were generated and combined with 27 publicly available genomes. We provided high-resolution typing methods by constructing phylogeny and population structure based on single-copy core genes in combination with whole genome average nucleotide identity to identify two distant Hafnia species (alvei and paralvei) and one mislabeled strain. The open pan-genome and the presence of numerous mobile genetic elements reveal that Hafnia has undergone massive gene rearrangements. Presence of species-specific core genomes associated with metabolism and transport suggests the putative niche differentiation between alvei and paralvei. We also identified possession of diverse virulence-related profiles in both Hafnia species., including the macromolecular secretion system, virulence, and antimicrobial resistance. In the macromolecular system, T1SS, Flagellum 1, Tad pilus and T6SS-1 were conserved in Hafnia, whereas T4SS, T5SS, and other T6SSs exhibited the evolution of diversity. The virulence factors in Hafnia are related to adherence, toxin, iron uptake, stress adaptation, and efflux pump. The identified resistance genes are associated with aminoglycoside, beta-lactam, bacitracin, cationic antimicrobial peptide, fluoroquinolone, and rifampin. These virulence-related profiles identified at the genomic level provide insights into Hafnia pathogenesis and the differentiation between alvei and paralvei. CONCLUSIONS: Our research using core genome phylogeny and comparative genomics analysis of a larger collection of strains provides a comprehensive view of the taxonomy and species-specific traits between Hafnia species. Deciphering the genome of Hafnia strains possessing a reservoir of macromolecular secretion systems, virulence factors, and resistance genes related to pathogenicity may provide insights into addressing its numerous infections and devising strategies to combat the pathogen.


Assuntos
Genoma Bacteriano , Hafnia/classificação , Hafnia/patogenicidade , Virulência , Sistemas de Secreção Bacterianos/genética , Hibridização Genômica Comparativa , Farmacorresistência Bacteriana/genética , Genótipo , Filogenia , Especificidade da Espécie , Fatores de Virulência/genética
13.
BMC Infect Dis ; 19(1): 852, 2019 Oct 15.
Artigo em Inglês | MEDLINE | ID: mdl-31615537

RESUMO

BACKGROUND: The dual challenge of low diagnostic sensitivity of microscopy test and technical challenge of performing a TB culture test poses a problem for case detection and initiation of Tuberculosis (TB) second-line treatment. There is thus need for a rapid, reliable and easily accessible assay. This comparative analysis was performed to assess diagnostic performance characteristics of GeneXpert MTB/RIF and Line Probe Assay (LPA). METHODS: Three hundred twenty nine sputum samples of patients across the 47 counties in Kenya suspected to have drug resistant TB were picked and subjected to GeneXpert, LPA and Culture MGIT at the National TB Reference Laboratory. Sensitivity, specificity and predictive values were then determined to assess the performance characteristics of the various assays. RESULTS: Against culture MGIT as the gold standard for TB diagnosis, GeneXpert had a sensitivity, specificity, positive predictive value, and negative predictive value of 78.5, 64.9, 59.4 and 82.2% respectively while LPA had 98.4, 66.0, 65.4 and 98.4%. For diagnosis of rifampicin mono-resistance GeneXpert had a moderate agreement (Kappa 0.59, P < 0.01) (sensitivity 62.50%, specificity 96.50%) while LPA that had almost perfect agreement (Kappa = 0.89, p < 0.01) with a (sensitivity 90.0% and specificity 99.1%). CONCLUSION: LPA has a better performance characteristic to GeneXpert and an alternative to culture with regards to detection of RIF's mono-resistance.


Assuntos
Farmacorresistência Bacteriana/genética , Mycobacterium tuberculosis/genética , Rifampina/uso terapêutico , Tuberculose/diagnóstico , Proteínas de Bactérias/genética , Feminino , Humanos , Quênia , Masculino , Reação em Cadeia da Polimerase Multiplex/métodos , Mycobacterium tuberculosis/isolamento & purificação , Hibridização de Ácido Nucleico/métodos , Oxirredutases/genética , Kit de Reagentes para Diagnóstico , Sensibilidade e Especificidade , Escarro/microbiologia , Tuberculose/tratamento farmacológico
14.
Environ Pollut ; 255(Pt 2): 113327, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31600703

RESUMO

Fish-associated antibiotic resistance genes (ARGs) have attracted increasing attention due to their potential risks to human beings via the food chain. However, data are scarce regarding the antibiotic resistance in fish themselves. Herein, the antibiotic resistance genes (ARGs) were assessed in the gut of four major Chinese freshwater carp (i.e., silver carp, grass carp, bighead carp, and crucian carp) from food retail markets. Results show that the abundances of target ARGs (e.g., tetA, tetO, tetQ, tetW, sulI, sulII, and blaTEM-1) and class 1 integrase (intI1) were in the range 9.4 × 10-6 - 1.6 × 10-1 and 6.7 × 10-5 - 5.2 × 10-2 gene copies per 16S rRNA gene, respectively. The sulI, sulII, and tetQ strongly correlated with silver and mercury resistance genes (e.g., silE and merR). The microbial taxa of fish gut could be partly separated among retail markets based on the PCA analysis. About 15.0% of the OTUs in fish gut were shared and 74.5% of the shared OTUs were identified as Acidobacteria, Bacteroidetes, Chloroflexi, Cyanobacteria, Firmicutes, and Proteobacteria. These phyla may constitute the core microbiota in the guts of the four Chinese freshwater carp. The possible ARG hosts were revealed based on the network analysis, and the presence of pathogen-associated resistant genera in fish gut highlights the need to fully understand their potential human health risks.


Assuntos
Carpas/microbiologia , Farmacorresistência Bacteriana/genética , Microbioma Gastrointestinal/efeitos dos fármacos , Alimentos Marinhos/microbiologia , Acidobacteria/efeitos dos fármacos , Acidobacteria/genética , Acidobacteria/isolamento & purificação , Animais , Antibacterianos/farmacologia , Bacteroidetes/efeitos dos fármacos , Bacteroidetes/genética , Bacteroidetes/isolamento & purificação , Chloroflexi/efeitos dos fármacos , Chloroflexi/genética , Chloroflexi/isolamento & purificação , Cianobactérias/efeitos dos fármacos , Cianobactérias/genética , Cianobactérias/isolamento & purificação , Firmicutes/efeitos dos fármacos , Firmicutes/genética , Firmicutes/isolamento & purificação , Água Doce/microbiologia , Microbioma Gastrointestinal/genética , Genes Bacterianos/genética , Metais Pesados/toxicidade , Proteobactérias/efeitos dos fármacos , Proteobactérias/genética , Proteobactérias/isolamento & purificação , RNA Ribossômico 16S/genética
15.
BMC Infect Dis ; 19(1): 873, 2019 Oct 22.
Artigo em Inglês | MEDLINE | ID: mdl-31640587

RESUMO

BACKGROUND: There have been no reports regarding the molecular characteristics, virulence features, and antibiotic resistance profiles of Staphylococcus aureus (S. aureus) from Hainan, the southernmost province of China. METHODS: Two hundred twenty-seven S. aureus isolates, consisting of 76 methicillin-resistant S. aureus (MRSA) and 151 methicillin-susceptible S. aureus (MSSA), were collected in 2013-2014 and 2018-2019 in Hainan, and investigated for their molecular characteristics, virulence genes, antibiotic resistance profiles and main antibiotic resistance genes. RESULTS: Forty sequence types (STs) including three new STs (ST5489, ST5492 and ST5493), and 79 Staphylococcal protein A (spa) types were identified based on multilocus sequence typing (MLST) and spa typing, respectively. ST398 (14.1%, 32/227) was found to be the most prevalent, and the prevalence of ST398-MSSA increased significantly from 2013 to 2014 (5.5%, 5/91) to 2018-2019 (18.4%, 25/136). Seventy-six MRSA isolates were subject to staphylococcus chromosomal cassette mec (SCCmec) typing. SCCmec-IVa was the predominant SCCmec type, and specifically, ST45-SCCmec IVa, an infrequent type in mainland China, was predominant in S. aureus from Hainan. The antibiotic resistance profiles and antibiotic resistance genes of S. aureus show distinctive features in Hainan. The resistant rates of the MRSA isolates to a variety of antibiotics were significantly higher than those of the MSSA isolates. The predominant erythromycin and tetracycline resistance genes were ermC (90.1%, 100/111) and tetK (91.8%, 78/85), respectively. Eleven virulence genes, including the Panton-Valentine leukocidin (pvl) and eta, were determined, and the frequency of eta and pvl were found to be 57.3 and 47.6%. Such high prevalence has never been seen in mainland China before. CONCLUSION: S. aureus isolates in Hainan have unique molecular characteristics, virulence gene and antibiotic resistance profiles, and main antibiotic resistance genes which may be associated with the special geographical location of Hainan and local trends in antibiotic use.


Assuntos
Farmacorresistência Bacteriana/genética , Infecções Estafilocócicas/microbiologia , Staphylococcus aureus/genética , Staphylococcus aureus/patogenicidade , Fatores de Virulência/genética , Antibacterianos/farmacologia , Proteínas de Bactérias/genética , Toxinas Bacterianas/genética , China , Farmacorresistência Bacteriana/efeitos dos fármacos , Exotoxinas/genética , Humanos , Leucocidinas/genética , Staphylococcus aureus Resistente à Meticilina/efeitos dos fármacos , Staphylococcus aureus Resistente à Meticilina/genética , Staphylococcus aureus Resistente à Meticilina/isolamento & purificação , Staphylococcus aureus Resistente à Meticilina/patogenicidade , Testes de Sensibilidade Microbiana , Tipagem de Sequências Multilocus , Infecções Estafilocócicas/tratamento farmacológico , Staphylococcus aureus/efeitos dos fármacos , Staphylococcus aureus/isolamento & purificação , Virulência/genética
16.
BMC Infect Dis ; 19(1): 871, 2019 Oct 22.
Artigo em Inglês | MEDLINE | ID: mdl-31640591

RESUMO

BACKGROUND: On 7th June, 2018, a primary school in Beijing, China notified Shunyi CDC of an outbreak of acute respiratory disease characterized by fever and cough among students and resulting in nine hospitalization cases during the preceding 2 weeks. We started an investigation to identify the etiologic agent, find additional cases, develop and implement control measures. METHODS: We defined probable cases as students, teachers and other staffs in the school developed fever (T ≥ 37.5 °C) with cough or sore throat; or a diagnosis of pneumonia during May 1-June 31, 2018. Confirmed cases were probable cases with Mycoplasma pneumoniae detected in oropharyngeal (OP) swabs by quantitative real-time polymerase chain reaction (qPCR). We searched case by reviewing school absenteeism records and interviewing students, teachers and staff in this school. Oropharyngeal swabs were collected from symptomatic students. Two qPCR) assay, a duplex qPCR assay, and sequencing were performed to determine the pathogen, genotype and macrolide resistance at the gene level, respectively. RESULTS: From May 1st to June 31st, 2018, we identified 55 cases (36 probable and 19 confirmed), of whom 25 (45%) were hospitalized for complications. All cases were students, none of the teachers and other staffs in the school were with similar symptoms. The attack rate (AR) was 3.9% (55/1398) for all students. The cases were mainly male (58%), with an age range of 7-8 years (median: 7 years). 72% (18/25) of inpatients had radiograph findings consistent with pneumonia, and some cases were hospitalized for up to 4 weeks. Pathogen detection results indicated that Mycoplasma pneumonia (M. pneumoniae) P1 type 1 was the causative agent in this outbreak, and the strain harbored one point mutation of A to G at position 2063. CONCLUSIONS: The infections by macrolide-resistant M. pneumoniae are not always mild and pneumonia was common and M. pneumoniae could causes serious complications which require long-term hospitalization. In the future infectious disease prevention and control practice, M. pneumoniae should be paid more attention. It is necessary to establish and improve the pathogen and drug resistance surveillance system in order to prevent and control such mutated strains of M. pneumoniae from causing future outbreaks or epidemics in China.


Assuntos
Antibacterianos/uso terapêutico , Farmacorresistência Bacteriana/genética , Macrolídeos/uso terapêutico , Mycoplasma pneumoniae/efeitos dos fármacos , Pneumonia por Mycoplasma/tratamento farmacológico , Pneumonia por Mycoplasma/epidemiologia , Pequim/epidemiologia , Criança , Tosse/epidemiologia , Surtos de Doenças , Farmacorresistência Bacteriana/efeitos dos fármacos , Feminino , Febre/epidemiologia , Febre/microbiologia , Genótipo , Humanos , Masculino , Mycoplasma pneumoniae/genética , Mycoplasma pneumoniae/patogenicidade , Faringite/epidemiologia , Pneumonia por Mycoplasma/complicações , Mutação Puntual , Reação em Cadeia da Polimerase em Tempo Real , Instituições Acadêmicas , Estudantes
17.
BMC Infect Dis ; 19(1): 900, 2019 Oct 28.
Artigo em Inglês | MEDLINE | ID: mdl-31660862

RESUMO

BACKGROUND: Carbapenem resistance among Acinetobacter species has become a life-threatening problem. As a last resort in the treatment of gram-negative bacteria infection, resistance to colistin is also a serious problem. The aim of study was to analyze the mechanism of resistance and perform genotyping of carbapenem-resistant Acinetobacter from clinical infection and fecal survey samples in Southern China. METHODS: One hundred seventy and 74 carbapenem-resistant Acinetobacter were isolated from clinical infection samples and fecal survey samples, respectively. We detected the related genes, including carbapenemase genes (blaKPC, blaIMP, blaSPM, blaVIM, blaNDM, blaOXA-23-like, blaOXA-24/40-like, blaOXA-51-like, and blaOXA-58-like), colistin resistance-related genes (mcr-1, mcr-2, mcr-3, mcr-4, and mcr-5), a porin gene (carO), efflux pump genes (adeA, adeB, adeC, adeI, adeJ, and adeK), mobile genetic element genes (intI1, intI2, intI3, tnpU, tnp513, IS26, ISAba1, and ISAba125), and the integron variable region. Genotyping was analyzed by enterobacterial repetitive intergenic consensus (ERIC)-PCR and dendrogram cluster analysis. RESULTS: Among the 244 carbapenem-resistant Acinetobacter, the common carbapenemase-positive genes included the following: blaOXA-51-like, 183 (75.00%); blaOXA-23-like, 174 (71.30%); blaNDM-1, 57 (23.40%); and blaOXA-58-like, 30 (12.30%). The coexistence of mcr-1 and blaNDM-1 in five strains of A. junii was found for the first time. Eleven distinct carO gene variants were detected in 164 (67.20%) strains, and ten novel variants, which shared 92-99% identity with sequences in the Genbank database, were first reported. Efflux system genes were present in approximately 70% of the isolates; adeABC and adeIJK were observed in 76.23 and 72.13%, respectively. Class 1 integrons were detected in 180 (73.80%) strains and revealed that four gene cassette arrays contained 11 distinct genes. The genotyping by ERIC-PCR demonstrated a high genetic diversity of non-baumannii Acinetobacter, and greater than 90% similarity to A. baumannii. CONCLUSIONS: The blaNDM-1 gene was identified in up to 77% of the carbapenem-resistant Acinetobacter isolated from fecal survey samples, indicating that the gut might be a reservoir of resistant opportunistic bacteria. Intestinal bacteria can be transmitted through the fecal-hand, which is a clinical threat, thus, the monitoring of carbapenem-resistant bacteria from inpatients' feces should be improved, especially for patients who have been using antibiotics for a long time.


Assuntos
Infecções por Acinetobacter/tratamento farmacológico , Acinetobacter baumannii/genética , Antibacterianos/efeitos adversos , Antibacterianos/uso terapêutico , Carbapenêmicos/efeitos adversos , Carbapenêmicos/uso terapêutico , Farmacorresistência Bacteriana/genética , Acinetobacter baumannii/isolamento & purificação , Proteínas de Bactérias/genética , China , Colistina/efeitos adversos , Colistina/uso terapêutico , Doenças Transmissíveis/tratamento farmacológico , Fezes/microbiologia , Variação Genética , Genótipo , Humanos , Integrons/genética , Testes de Sensibilidade Microbiana , Reação em Cadeia da Polimerase/métodos , Análise de Sequência de DNA , beta-Lactamases/genética
18.
BMC Infect Dis ; 19(1): 898, 2019 Oct 28.
Artigo em Inglês | MEDLINE | ID: mdl-31660876

RESUMO

BACKGROUND: Salmonella infection poses significant public health threat globally, especially in resource-limited countries. Emergence and spread of antibiotic resistant strains to fluoroquinolones have led to treatment failures and increased mortality in Salmonella infection. However, there is dearth of information regarding mechanisms of resistance to fluoroquinolones in Ghana. This study therefore sought to identify chromosomal mutations and plasmid-mediated resistance as possible mechanisms of fluoroquinolone resistance from clinical isolates in Ghana. METHODS: This was a retrospective study of archived isolates biobanked at Kumasi Centre for Collaborative Research in Tropical Medicine, Ghana. Isolates were obtained from blood, stool and oropharynx samples at two hospitals, between May, 2016 and January, 2018. Salmonella identification was done using standard microbiological protocols and antibiotic susceptibility testing performed by Kirby-Bauer disc diffusion method. Isolates with intermediate susceptibility and/or resistance to nalidixic acid and/or ciprofloxacin were selected and examined for chromosomal mutations by Sanger sequencing and plasmid-mediated resistance by PCR. RESULTS: Of 133 biobanked isolates cultured, 68 (51.1%) and 16 (12%) were identified as Salmonella Typhi and non-typhoidal Salmonella (NTS), respectively. Sequence analysis of gyrA gene revealed the presence of 5 different nonsynonymous mutations, with the most frequent mutation (Ile203Ser) occurring in 12 out of 13 isolates tested. Gyrase B (gyrB) gene had 1 nonsynonymous mutation in 3 out of 13 isolates, substituting phenylalanine with leucine at codon 601 (Phe601Leu). No mutation was observed in parC and parE genes. Two NTS isolates were found to harbour qnrS plasmid-mediated resistant gene of molecular size 550 bp with high ciprofloxacin MIC of 0.5 µg/ml. CONCLUSION: This study reports for the first time in Ghana plasmid-mediated fluoroquinolone resistant gene qnrS in Salmonella clinical isolates. Nonsynonymous mutations of gyrA and gyrB genes likely to confer Salmonella reduced susceptibility to ciprofloxacin were also reported.


Assuntos
Antibacterianos/efeitos adversos , Antibacterianos/uso terapêutico , Farmacorresistência Bacteriana/genética , Fluoroquinolonas/efeitos adversos , Fluoroquinolonas/uso terapêutico , Genes Bacterianos/genética , Plasmídeos/metabolismo , Infecções por Salmonella/tratamento farmacológico , Salmonella enterica/genética , Adolescente , Pré-Escolar , Ciprofloxacino/efeitos adversos , Ciprofloxacino/uso terapêutico , DNA Girase/genética , DNA Topoisomerase IV/genética , Testes de Sensibilidade a Antimicrobianos por Disco-Difusão , Feminino , Gana , Humanos , Masculino , Mutação , Estudos Retrospectivos , Salmonella enterica/isolamento & purificação , Adulto Jovem
19.
Water Sci Technol ; 80(3): 551-562, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31596266

RESUMO

Exposure to antibiotics, biocides, chemical preservatives, and heavy metals in different settings such as wastewater treatment plants (WWTPs) may apply selective pressure resulting in the enrichment of multiple resistant, co- and cross-resistant strains of bacteria. The purpose of this study was to identify and characterize potentially pathogenic triclosan (TCS) - and/or, chloroxylenol (PCMX) tolerant bacteria from sewage and river water in the North-West, Potchefstroom, South Africa. Several potential pathogens were identified, with Aeromonas isolates being most abundant. Clonal relationships between Aeromonas isolates found at various sampling points were elucidated using ERIC-PCR. Selected isolates were characterized for their minimum inhibitory concentrations against the biocides, as well as antibiotic resistance profiles, followed by an evaluation of synergistic and antagonistic interactions between various antimicrobials. Isolates were also screened for the presence of extracellular enzymes associated with virulence. High-performance liquid chromatography revealed the presence of both biocides in the wastewater, but fingerprinting methods did not reveal whether the WWTP is the source from which these organisms enter the environment. Isolates exhibited various levels of resistance to antimicrobials as well as several occurrences of synergy and antagonisms between the biocides and select antibiotics. Several isolates had a very high potential for virulence but further study is required to identify the specific virulence and resistance genes associated with the isolates in question.


Assuntos
Desinfetantes , Eliminação de Resíduos Líquidos , Águas Residuárias/microbiologia , Antibacterianos , Farmacorresistência Bacteriana/genética , Testes de Sensibilidade Microbiana , Rios , Esgotos , África do Sul
20.
Int J Food Microbiol ; 308: 108305, 2019 Nov 02.
Artigo em Inglês | MEDLINE | ID: mdl-31476731

RESUMO

In recent years, the number of human salmonellosis cases in Western Australia (WA) has increased more dramatically than in any other Australian state. In 2017, the number of cases in WA was more than double the five-year average, and eggs had emerged as the key culprit for several Salmonella foodborne disease outbreaks. To better understand such an epidemiologically intriguing situation, our research goal was to investigate the prevalence, serovar diversity, multilocus sequence types, and antimicrobial resistance of non-typhoidal Salmonella contamination in retail eggs produced and sold in WA. A total of 200 visually clean and intact retail egg samples (each containing a dozen eggs) were purchased for one year (2017-2018) from supermarkets in metropolitan Perth, the capital of WA. For each sample, the contents and shells of the 12 eggs were separately pooled and cultured according to standard methods. Overall, Salmonella was detected in 11.5% (23/200) of the tested egg samples. Salmonella was isolated from 4.5% (9/200) and 3% (6/200) of eggshells and egg contents, respectively. In 4% (8/200) of the samples, Salmonella was recovered from both eggshell and egg contents. Isolates from positive retail egg samples were serotyped as either S. Typhimurium (52.2% [12/23]) or S. Infantis (39.1% [9/23]). Both serotypes were concurrently recovered from two different retail egg samples. We retained a set of both S. Typhimurium (n = 29) and S. Infantis (n = 12) isolates from all Salmonella-positive retail packs (n = 23) for further characterization. Only two (S. Typhimurium) isolates showed resistance to ampicillin, of which one carried ß-lactamase resistance gene blaTEM-1b. The remaining isolates (39/41) were susceptible to all 14 antimicrobials included in the minimum inhibitory concentrations (MICs) testing panel. Multilocus sequence typing and serotyping were perfectly mirrored, as all S. Typhimurium isolates were characterized as sequence type (ST)-19, and all S. Infantis isolates were ST-32. This study points to the noteworthy Salmonella prevalence rate in retail egg samples in WA. Our results illustrate minimal public health risks arising from antimicrobial resistance Salmonella from Australian eggs.


Assuntos
Antibacterianos/farmacologia , Farmacorresistência Bacteriana/genética , Casca de Ovo/microbiologia , Ovos/microbiologia , Microbiologia de Alimentos/métodos , Salmonella/isolamento & purificação , Animais , Austrália , Genômica , Humanos , Testes de Sensibilidade Microbiana , Tipagem de Sequências Multilocus , Salmonella/classificação , Salmonella/genética , Intoxicação Alimentar por Salmonella/epidemiologia , Infecções por Salmonella/epidemiologia , Sorogrupo , Sorotipagem , Austrália Ocidental/epidemiologia
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