Phylogenetic analysis and antimicrobial susceptibility profile of uropathogens.
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ABSTRACT:
SUBMITTER: Ullah H
PROVIDER: S-EPMC8797202 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BackgroundUrinary tract infection (UTI) is the commonest bacterial infections during pregnancy, leading to significant maternal and prenatal morbidity and mortality.MethodThis hospital-based cross-sectional study during November 2017 to January 2018 was aimed to determine hospital-based antibacterial susceptibility patterns of bacterial uropathogens among 200 pregnant women in Eastern Ethiopia. ~ 10-20 ml clean-catch midstream urine samples were collected by the study participants. The well-mixed urine samples standardized to 1 µl have inoculated onto Cystine Lactose Electrolyte-Deficient and MacConkey agar. The inoculum was cultured at 37 °C under aerobic conditions for 18-48 h and examined macroscopically to evaluate the colony appearance and size of colonies. The isolate on the plates with pure growth and colonies ≥ 105 CFU/ml were further subjected to biochemical identification and susceptibility testing according to the standard procedures explained in the Clinical and Laboratory Standards Institute guideline. SPSS version 25 was used for data analysis. Descriptive statistics such as frequency, percentage, and cross-tabulation were used to present the findings in the form of graphs and tables.ResultsThe response rate for this study was 98.04%. Thirty-one bacteria were isolated among the 200 urine samples processed, which gave the overall UTI prevalence of 15.5%. The majority (90.3%) of the isolates were Gram-negative. Escherichia coli (45.2%) was the most frequent isolated uropathogen which followed by Proteus spp. (22.6%), Klebsiella pneumoniae (16.1%), Staphylococcus aureus (9.7%), and Pseudomonas aeruginosa (6.5%). Among the isolates, 96.4% of them were susceptible to amikacin and followed by nitrofurantoin (90.3%), and gentamicin (83.9%). However, high rates of resistance to ampicillin (58.1%), amoxicillin-clavulanate (51.6%), and cotrimoxazole (51.6%) were observed. Overall, 16(51.6%) of the bacterial isolates had developed multiple drug resistance to the selected antimicrobials.ConclusionIn general, the overall prevalence of UTI was high, 15.5%. Most of isolated bacterial uropathogens were Gram-negative bacteria, and Escherichia coli was the most frequent isolate. The majority of the isolates were susceptible to amikacin, nitrofurantoin, and gentamicin. However, a high rate of resistance was observed to ampicillin, amoxicillin-clavulanate, and cotrimoxazole. More than half of the isolated bacteria had multiple drug-resistant features. Therefore, periodic and continuous urine culture for screening and diagnosis is mandatory to reduce the consequence of UTI and multidrug resistance bacteria in pregnancy.
| S-EPMC8348837 | biostudies-literature
Project description:Achieving fast antimicrobial susceptibility results is a primary goal in the fight against antimicrobial resistance. Standard antibiotic susceptibility testing (AST) takes, however, at least a day from patient sample to susceptibility profile. Here, we developed and clinically validated a rapid phenotypic AST based on a miniaturized nanotiter plate, the nanowell slide, that holds 672 wells in a 500 nl format for bacterial cultivation. The multitude of nanowells allows multiplexing with a panel of six antibiotics relevant for urinary tract infections. Inclusion of seven concentrations per antibiotic plus technical replicates enabled us to determine a precise minimum inhibitory concentration for 70 clinical uropathogenic Escherichia coli isolates. By combining optical recordings of bacterial growth with an algorithm for optical signal analysis, we calculated Tlag, the point of transition from lag to exponential phase, in each nanoculture. Algorithm-assisted analysis determined antibiotic susceptibility as early as 3 h 40 min. In comparison to standard disk diffusion assays, the nanowell AST showed a total categorical agreement of 97.9% with 2.6% major errors and 0% very major errors for all isolate-antibiotic combination tested. Taking advantage of the optical compatibility of the nanowell slide, we performed microscopy to illustrate its potential in defining susceptibility profiles based on bacterial morphotyping. The excellent clinical performance of the nanowell AST, combined with a short detection time, morphotyping, and the very low consumption of reagents clearly show the advantage of this phenotypic AST as a diagnostic tool in a clinical setting.
| S-EPMC6048231 | biostudies-literature
Project description:Mycoplasma hyopneumoniae is the etiologic agent of porcine enzootic pneumonia, responsible for major production losses worldwide. The bacteria have a limited metabolism and need to obtain molecules from the growth environment, which causes multiple difficulties for in vitro culture. These limitations have a negative influence on the ability to carry out research for the development of the rational use of antimicrobials and vaccines. The objective of this investigation was to evaluate the genetic profile and in vitro susceptibility of field isolates of M. hyopneumoniae to different antimicrobials. All 16 isolates obtained from the samples presented 100% of identity in the partial sequence of 16S rRNA gene when compared to M. hyopneumoniae. A dendrogram was created using the PCR results of the genes related to pathogenicity, and the isolates were distributed into four clusters, suggesting genetic variability among four different isolates circulating on the same farm. The minimum inhibitory concentration of the isolates was higher for the antimicrobials tylosin (< 0.001-16 mg/L) and spiramycin (< 0.001-16 mg/L) than for enrofloxacin (< 0.001-0.125 mg/L) and tiamulin (< 0.001-0.125 mg/L). Our results demonstrate the genetic variability among M. hyopneumoniae isolates from pigs of the same farm, with differences in their susceptibility to antimicrobial agents.
| S-EPMC7058719 | biostudies-literature
Project description:BackgroundAntimicrobial resistance (AMR) in urinary tract infections (UTI) is a global public health problem. However, estimates of the prevalence of AMR, required for empirical treatment guidelines, are lacking for many regions.ObjectivesTo perform a systematic review and summarize the available information about AMR prevalence among urinary Escherichia coli and Klebsiella pneumoniae, the two priority uropathogens, in the Asia-Pacific region (APAC).MethodsPubMed, EBSCO and Web of Science databases were searched for articles (2008-20), following PRISMA guidelines. The prevalence of resistance was calculated and reported as point estimate with 95% CI for antimicrobial drugs recommended in WHO treatment guidelines. Data were stratified by country and surveillance approach (laboratory- or population-based surveillance). The quality of included articles was assessed using a modified Newcastle-Ottawa Quality Assessment Scale.ResultsOut of 2400 identified articles, 24 studies, reporting on 11 (26.8%) of the 41 APAC countries, met the inclusion criteria. Prevalence of resistance against trimethoprim/sulfamethoxazole, ciprofloxacin, and ceftriaxone ranged between 33% and 90%, with highest prevalence reported from Bangladesh, India, Sri Lanka and Indonesia. Resistance against nitrofurantoin ranged between 2.7% and 31.4%. Two studies reported data on fosfomycin resistance (1.8% and 1.7%). Quality of reporting was moderate.ConclusionsWe show very high prevalence estimates of AMR against antibiotics commonly used for the empirical treatment of UTI, in the limited number of countries in the APAC for which data are available. Novel feasible and affordable approaches that facilitate population-based AMR surveillance are needed to increase knowledge on AMR prevalence across the region.
| S-EPMC8210283 | biostudies-literature
Project description:Mycobacterium abscessus is a highly antibiotic-resistant opportunistic pathogen causing clinically challenging infections in patients with preexisting lung diseases or under immunosuppression. Hence, reliable antibiotic susceptibility data are required for effective treatment. Aims of this study were to investigate (i) the congruence of genotypic and phenotypic antimicrobial susceptibility testing, (ii) the relationship between resistance profile and clinical course, and (iii) the phylogenetic relations of M. abscessus in a German patient cohort. A total of 39 isolates from 29 patients infected or colonized with M. abscessus underwent genotypic and phenotypic drug susceptibility testing. Clinical data were correlated with susceptibility data. Phylogenetic analysis was performed by means of whole-genome sequencing (WGS) and single-nucleotide polymorphism (SNP) analysis. Macrolide resistance was mainly mediated by functional Erm(41) methyltransferases (T28 sequevars) in M. abscessus subsp. abscessus (n = 25) and M. abscessus subsp. bolletii (n = 2). It was significantly associated with impaired culture conversion (P = 0.02). According to the core SNP phylogeny, we identified three clusters of closely related isolates with SNP distances below 25. Representatives of all circulating global clones (Absc. 1, Absc. 2, and Mass. 1) were identified in our cohort. However, we could not determine evidence for in-hospital interhuman transmission from clinical data. In our patient cohort, we identified three M. abscessus clusters with closely related isolates and representatives of the previously described international clusters but no human-to-human in-hospital transmission. Macrolide and aminoglycoside susceptibility data are critical for therapeutic decision-making in M. abscessus infections.
| S-EPMC7685876 | biostudies-literature
Project description:Campylobacter jejuni is a zoonotic pathogen and the most common bacterial cause of human gastroenteritis worldwide. With the increase of antibiotic resistance to fluoroquinolones and macrolides, the drugs of choice for treatment, C. jejuni was recently classified as a serious antimicrobial resistant threat. Here, we characterized 94 C. jejuni isolates collected from patients at four Michigan hospitals in 2011 and 2012 to determine the frequency of resistance and association with phylogenetic lineages. The prevalence of resistance to fluoroquinolones (19.1%) and macrolides (2.1%) in this subset of C. jejuni isolates from Michigan was similar to national reports. High frequencies of fluoroquinolone-resistant C. jejuni isolates, however, were recovered from patients with a history of foreign travel. A high proportion of these resistant isolates were classified as multilocus sequence type (ST)-464, a fluoroquinolone-resistant lineage that recently emerged in Europe. A significantly higher prevalence of tetracycline-resistant C. jejuni was also found in Michigan and resistant isolates were more likely to represent ST-982, which has been previously recovered from ruminants and the environment in the U.S. Notably, patients with tetracycline-resistant C. jejuni infections were more likely to have contact with cattle. These outcomes prompt the need to monitor the dissemination and diversification of imported fluoroquinolone-resistant C. jejuni strains and to investigate the molecular epidemiology of C. jejuni recovered from cattle and farm environments to guide mitigation strategies.
| S-EPMC4845714 | biostudies-literature
Project description:Members of the Bacillus cereus group are considered to be foodborne pathogens commonly associated with diarrheal and emetic gastrointestinal syndromes. Biofilm formation is a major virulence determinant of various pathogenic bacteria, including the B. cereus strains, since it can protect the bacteria against antimicrobial agents and the host immune response. Moreover, a biofilm allows the exchange of genetic material, such as antimicrobial resistance genes, among the different bacterial strains inside the matrix. The aim of the current study was to genotypically and phenotypically characterize Bacillus sp. B87, a strain that was isolated from food and which exhibited strong biofilm-forming capacity. Based on the analysis of the phylogenetic relationship, the isolate was phylogenetically mapped close to Bacillus pacificus. Antimicrobial susceptibility testing revealed that the isolate was resistant to tetracycline and β-lactam antimicrobial agents, which corresponded with the genotypic characterization using the whole-genome analysis. The genome of Bacillus sp. B87 carried the three-component non-hemolytic enterotoxin (NHE), which is a type of enterotoxin that causes diarrheal symptoms. In addition, the genome also contained several genes that participate in biofilm formation, including the pelDEADAFG operon. These findings expand our understanding of antimicrobial resistance and virulence in Bacillus species based on the link between genotypic and phenotypic characterization.
| S-EPMC8876208 | biostudies-literature
Project description:Antibiotic resistance along with biofilm formation increases the difficulty for antibiotic therapy in urinary tract infections. Bioactive molecules derived from plants, such as those present in essential oils, can be used to treat bacterial infections. Oregano is one of the spices to have antimicrobial activity. Therefore, three Mexican oregano essential oils (two Lippia berlandieri Schauer and one Poliomintha longiflora) were tested for antimicrobial capacity against multidrug-resistant, biofilm-forming bacterial isolates. Clinical isolates from urinary tract infections were tested for antibiotic resistance. Multidrug-resistant isolates were evaluated for biofilm formation, and Mexican oregano antimicrobial effect was determined by the minimal inhibitory (CMI) and minimal bactericidal concentrations (CMB). The selected isolates were identified by molecular phylogenetic analysis. Sixty-one isolates were included in the study; twenty were characterized as multidrug-resistant and from those, six were strong biofilm formers. Three isolates were identified as Escherichia coli, two as Pseudomonas aeruginosa and one as Enterococcus faecalis based on the phylogenetic analysis of 16 S rRNA gene sequences. The antimicrobial effect was bactericidal; E. faecalis was the most susceptible (<200 mg/L CMI/CMB), and P. aeruginosa was the most resistant (>2,000 mg/L CMI/CMB). There was a range of 500-1000 mg/L (CMI/CMB) for the E. coli isolates. Mexican oregano essential oils demonstrated antimicrobial efficacy against multidrug-resistant clinical isolates.
| S-EPMC6963208 | biostudies-literature
Project description:BackgroundTo support effective antibiotic selection in empirical treatments, infection control interventions, and antimicrobial resistance containment strategies, many medical institutions collect antimicrobial susceptibility test data conducted at their facilities to prepare cumulative antibiograms.AimTo evaluate how the setpoints of duplicate isolate removal period and data collection period affect the calculated susceptibility rates in antibiograms.MethodsThe Sakai City Medical Center is a regional core hospital for tertiary emergency medical care with 480 beds for general clinical care. In this study, all the Pseudomonas aeruginosa, Escherichia coli, and Klebsiella pneumoniae isolates collected at the Sakai City Medical Center Clinical Laboratory between July 2013 and December 2018 were subjected to antimicrobial susceptibility tests and the resulting data was analyzed.FindingsThe longer the duplicate isolate removal period, the fewer the isolates are available for every bacterial species. Differences in the length of the duplicate isolate removal period affected P. aeruginosa susceptibility rates to β-lactam antibiotics by up to 10.8%. The setpoint of the data collection period affected the antimicrobial susceptibility rates by up to 7.3%. We found that a significant change in susceptibility could be missed depending on the setting of the data collection period, in preparing antibiogram of β-lactam antibiotics for P. aeruginosa.ConclusionsWhen referring to antibiograms, medical professionals involved in infectious disease treatment should be aware that the parameter values, such as the duplicate isolate removal period and the data collection period, affect P. aeruginosa susceptibility rates especially to β-lactam antibiotics. And antibiogram should be updated within the shortest time period that is practically possible, taking into account restrictions such as numbers of specimen.
| S-EPMC7310835 | biostudies-literature
Project description:Swine dysentery (SD) is an economically important diarrheal disease in pigs caused by different strongly hemolytic Brachyspira (B.) species, such as B. hyodysenteriae, B. suanatina and B. hampsonii. Possible associations of epidemiologic data, such as multilocus sequence types (STs) to virulence gene profiles and antimicrobial susceptibility are rather scarce, particularly for B. hyodysenteriae isolates from Germany. In this study, B. hyodysenteriae (n = 116) isolated from diarrheic pigs between 1990 and 2016 in Germany were investigated for their STs, susceptibility to the major drugs used for treatment of SD (tiamulin and valnemulin) and genes that were previously linked with virulence and encode for hemolysins (tlyA, tlyB, tlyC, hlyA, BHWA1_RS02885, BHWA1_RS09085, BHWA1_RS04705, and BHWA1_RS02195), outer membrane proteins (OMPs) (bhlp16, bhlp17.6, bhlp29.7, bhmp39f, and bhmp39h) as well as iron acquisition factors (ftnA and bitC). Multilocus sequence typing (MLST) revealed that 79.4% of the isolates belonged to only three STs, namely ST52 (41.4%), ST8 (12.1%), and ST112 (25.9%) which have been observed in other European countries before. Another 24 isolates belonged to twelve new STs (ST113-118, ST120-123, ST131, and ST193). The temporal distribution of STs revealed the presence of new STs as well as the regular presence of ST52 over three decades (1990s-2000s). The proportion of strains that showed resistance to both tiamulin und valnemulin (39.1%) varied considerably among the most frequent STs ranging from 0% (0/14 isolates resistant) in ST8 isolates to 46.7% (14/30), 52.1% (25/48), and 85.7% (6/7) in isolates belonging to ST112, ST52, and ST114, respectively. All hemolysin genes as well as the iron-related gene ftnA and the OMP gene bhlp29.7 were regularly present in the isolates, while the OMP genes bhlp17.6 and bhmp39h could not be detected. Sequence analysis of hemolysin genes of selected isolates revealed co-evolution of tlyB, BHWA1_RS02885, BHWA1_RS09085, and BHWA1_RS02195 with the core genome and suggested independent evolution of tlyA, tlyC, and hlyA. Our data indicate that in Germany, swine dysentery might be caused by a limited number of B. hyodysenteriae clonal groups. Major STs (ST8, ST52, and ST112) are shared with other countries in Europe suggesting a possible role of the European intra-Community trade of pigs in the dissemination of certain clones. The identification of several novel STs, some of which are single or double locus variants of ST52, may on the other hand hint towards an ongoing diversification of the pathogen in the studied area. The linkage of pleuromutilin susceptibility and sequence type of an isolate might reflect a clonal expansion of the underlying resistance mechanism, namely mutations in the ribosomal RNA genes. A linkage between single virulence-associated genes (VAGs) or even VAG patterns and the phylogenetic background of the isolates could not be established, since almost all VAGs were regularly present in the isolates.
| S-EPMC5764319 | biostudies-literature