Lactam Resistance Research Articles

Genomic characteristics of antimicrobial resistance and virulence factors of carbapenem-resistant Stutzerimonas nitrititolerans isolated from the clinical specimen

BackgroundStutzerimonas nitrititolerans (S. nitrititolerans) is a rare human pathogenic bacterium and has been inadequately explored at the genomic level. Here, we report the first case of carbapenem-resistant S. nitrititolerans isolated from the peritoneal dialysis fluid of a patient with chronic renal failure. This study analyzed the genomic features, antimicrobial resistance, and virulence factors of the isolated strain through whole genome sequencing (WGS).MethodsThe bacterial isolate from the peritoneal dialysis fluid was named PDI170223, and preliminary identification was conducted through Matrix-assisted laser desorption ionization/time of flight mass spectrometry (MALDI-TOF MS). WGS of the strain PDI170223 was performed using the Illumina platform, and a phylogenetic tree was constructed based on the 16S rRNA gene sequences. Antimicrobial susceptibility test (AST) was conducted using the TDR-200B2 automatic bacteria identification/drug sensitivity tester.ResultsS. nitrititolerans may emerge as a human pathogen due to its numerous virulence genes, including those encoding toxins, and those involved in flagellum and biofilm formation. The AST results revealed that the strain is multidrug- and carbapenem-resistant. The antimicrobial resistance genes of S. nitrititolerans are complex and diverse, including efflux pump genes and β⁃lactam resistance genes.ConclusionThe analysis of virulence factors and antimicrobial resistance of S. nitrititolerans provides clinical insight into the pathogenicity and potential risks of this bacterium. It is crucial to explore the mechanisms through which S. nitrititolerans causes diseases and maintains its antimicrobial resistance, thereby contributing to development of effective treatment and prevention strategies.

A sophisticated virulence repertoire and colistin resistance of Citrobacter freundii ST150 from a patient with sepsis admitted to ICU in a tertiary care hospital in Uganda, East Africa: Insight from genomic and molecular docking analyses

Sepsis and multidrug resistance comprise a complex of factors attributable to mortality among intensive care unit (ICU) patients globally. Pathogens implicated in sepsis are diverse, and their virulence and drug resistance remain elusive. From a tertiary care hospital ICU in Uganda, we isolated a Citrobacter freundii strain RSM030 from a patient with sepsis and phenotypically tested it against a panel of 16 antibiotics including imipenem levofloxacin, cotrimoxazole and colistin, among others. We sequenced the organism's genome and integrated multilocus sequencing (MLST), PathogenFinder with Virulence Factor analyzer (VFanalyzer) to establish its pathogenic relevance. Thereafter, we combined antiSMASH and PRISM genome mining with molecular docking to predict biosynthetic gene clusters (BGCs), pathways, toxin structures and their potential targets in-silico. Finally, we coupled ResFinder with comprehensive antibiotic resistance database (CARD) to scrutinize the genomic antimicrobial resistance profile of the isolate. From PathogenFinder and MLST, this organism was confirmed to be a human pathogen (p = 0.843), sequence type (ST)150, whose virulence is determined by chromosomal type III secretion system (T3SS) (the injectosome) and plasmid-encoded type IV secretion system (T4SS), the enterobactin biosynthetic gene cluster and biofilm formation through the pgaABCD operon. Pathway and molecular docking analyses revealed that the shikimate pathway can generate a toxin targeting multiple host proteins including spectrin, detector of cytokinesis protein 2 (Dock2) and plasmalemma vesicle-associated protein (PLVAP), potentially distorting the host cell integrity. From phenotypic antibiotic testing, we found indeterminate results for amoxicillin/clavulanate and levofloxacin, with resistance to cotrimoxazole and colistin. Detailed genome analysis revealed chromosomal beta lactam resistance genes, i.e. blaCMY-79, blaCMY-116 and blaTEM-1B, along with multiple mutations of the lipopolysaccharide modifying operon genes PmrA/PmrB, pmrD, mgrA/mgrB and PhoP/PhoQ, conferring colistin resistance. From these findings, we infer that Citrobacter freundii strain RSM030 is implicated in sepsis and resistance to standard antibiotics, including colistin, the last resort.

Molecular characterization of antibiotic-resistant bacteria associated with maggots obtained from chicken droppings

BackgroundThe use of maggots, developed from chicken droppings as alternative fish meal might serve as a reservoir and vehicle for the widespread of single and multiple antibiotic resistant bacteria (MARB). This study aimed at investigating antibiotic resistant bacteria from chicken droppings and maggots developed from them, and the associated resistance genes and mobile genetic elements in their genomes. Freshly collected poultry droppings obtained from three commercial poultry farms, in Akure, Nigeria and maggots developed from their composting were plated on Luria–Bertani (LB) agar plates that had been incorporated with antibiotics. The emerged MARB were presumptively identified by conventional cultural microbiological methods and then authenticated using 16S rRNA gene sequence analysis. The antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in the genome of MARB were detected by standard molecular tools.ResultsPotential bacterial pathogens isolated include Escherichia coli, Bacillus cereus, Salmonella enterica, Providencia stuartii, P. rettgeri, Pseudomonas aeruginosa, Staphylococcus aureus, Alcaligenes faecalis, Paelnalcaligenes hominis and Micrococcus luteus. Seventeen ARGs were widely distributed among the 19 ARB/MARB. Tetracycline resistance gene was widely distributed among the ARB/MARB with prevalence of 62%, while macrolides and beta lactam resistance gene had 17% and 13%, respectively. At least six MARB isolates showed the presence of two or more class 1 integron, while five isolates was detected to carry two or more class 2 integron among the 19 MARB.ConclusionsThe results highlight a much higher risk of ARGs spreading through maggots derived from chicken droppings to humans and environmental microbiota.

EMERGENCE OF MULTIDRUG RESISTANT BACTERIA AMONG PATIENTS WITH RESPIRATORY TRACT INFECTIONS

In this study, 25 Pseudomonas aeruginosa isolates were diagnosed in 160 clinical samples collected from patients attending the Tuberculosis Institute/ Medical city and Al-Muhmodia Public Hospital, in addition to a number of private laboratories in Baghdad during the period from September 2020 to February 2021. The bacterial isolates from clinical samples were biochemically diagnosed by API® 20E system then further identified by VITEK 2 system. P. aeruginosa represented the most prevalent bacteria in lower respiratory tract specimens. These isolates showed moderate to high susceptibility towards 11 antimicrobial agents tested in this study except that of ceftazidime and ceftriaxone. Extra-chromosomal resistance of the top three of the most resistant P. aeruginosa isolates were subjected for molecular investigation. Bacterial transformation of E. coli S1 cells with plasmid DNA extracted from the selected P. aeruginosa isolates exhibited increased resistance to ceftazidime and penicillin G. The data clearly suggest that the plasmid DNA content is implicated in enhancement of P. aeruginosa resistance through horizontal transfer of extra- chromosomal beta lactam resistance associated genes.

In host evolution of beta lactam resistance during active treatment for Pseudomonas aeruginosa bacteremia.

Multidrug-resistant (MDR) Pseudomonas aeruginosa has been declared a serious threat by the United States Centers for Disease Control and Prevention. Here, we used whole genome sequencing (WGS) to investigate recurrent P. aeruginosa bloodstream infections in a severely immunocompromised patient. The infections demonstrated unusual, progressive increases in resistance to beta lactam antibiotics in the setting of active treatment with appropriate, guideline-directed agents. WGS followed by comparative genomic analysis of isolates collected over 44 days demonstrated in host evolution of a single P. aeruginosa isolate characterized by stepwise acquisition of two de-novo genetic resistance mechanisms over the course of treatment. We found a novel deletion affecting the ampC repressor ampD and neighboring gene ampE, which associated with initial cefepime treatment failure. This was followed by acquisition of a porin nonsense mutation, OprD, associated with resistance to carbapenems. This study highlights the potential for in-host evolution of P. aeruginosa during bloodstream infections in severely immunocompromised patients despite appropriate antimicrobial therapy. In addition, it demonstrates the utility of WGS for understanding unusual resistance patterns in the clinical context.

Drug resistance and susceptibility testing of Gram negative bacterial isolates from healthy cattle with different β - Lactam resistance Phenotypes from Shandong province China.

The objective of this study was to evaluate the effectiveness of common antibiotics against different microorganisms in apparently healthy cattle in Shandong province and its suburb. A total of 220 nasal swab samples were collected and cultured for bacteriological evaluation. All the bacteria isolates after preliminary identification were subjected to antibiogram studies following disc diffusion method. It was found in the study that E. coli is the most commonly associated isolate (21%), followed by Klebsiella spp. (18%), Pseudomonas aeruginosa (13%), Salmonella spp. (15%), Shigella spp (12%), and Proteus spp (11%). While the antibiogram studies reveled that highest number of bacterial isolates showed resistance to Ampicillin (95%), followed by Augmentin (91%), Cefuroxime (85%) and Tetracycline (95%) of (Escherichia coli and Klebsiella spp). In the case of pseudomonas spp. and Salmonella the highest resistance was showed by Ampicillin (90%) followed by Amoxicillin + Clavulanic Acid (80%), Cefixime (90%), and Erythromycin (80%). In Shigella spp and Salmonella spp highest resistance was showed by Amoxicillin, Ceftazidime, Augmentin (60%), and Amoxicillin + Clavulanic Acid (50%). It is concluded that in vitro antibiogram studies of bacterial isolates revealed higher resistance for Ampicillin, Augmentin, Cefuroxime, Cefixime, Tetracycline, Erythromycin, and Amoxicillin + Clavulanic Acid. The high multiple Antibiotics resistance indexes (MARI) observed in all the isolates in this study ranging from 0.6 to 0.9. MARI value of >0.2 is suggests multiple antibiotic resistant bacteria and indicate presence of highly resistant bacteria.

Occurrence Of CTX-M I gene in Beta lactam resistance Neisseria gonorrhoeae isolated Form women with endocervical infection

Occurrence Of CTX-M I gene in Beta lactam resistance Neisseria gonorrhoeae isolated Form women with endocervical infection

137. Comparison of genotypic resistance pattern between Enterococcus faecium and Enterococcus faecalis to better understand the occurrence of mutations.

Abstract Background Enterococcus is one of the major causes of nosocomial infections many with vancomycin resistance. About 50,000 infections are reported per year due to vancomycin-resistant Enterococci. Understanding the genotypic mutations can help recognize the potential burden for antibiotic resistance that exists in a population. In this study, using whole genome sequencing (WGS) we aim to analyze the prevalence of genetic resistance markers for commonly used antibiotics for Enterococcal treatment. Methods Whole genome sequencing was performed using the NextSeq (Illumina Inc., CA) on 60 isolates of E. faecium and 29 isolates of E. faecalis. The isolates were obtained from two different Detroit area hospitals from 2017-2019. The data from WGS was analyzed using EPISEQ CSTM (BIOMÉRIEUX, Marcy l ‘Etoile, France) bioinformatic database to obtain specific resistance genes which would correspond to commonly used antibiotics for treatment of Enterococcal infections. Results Among the 89 Enterococcus faecium and Enterococcus faecalis investigated, we identified a total of 33 unique resistance genes across 18 classes of antibiotics (Table 1). We detected genetic mutations efmA, pbp5, tet(L), liar, liaS unique to E. faecium and only emeA unique to E. faecalis. E. faecium and E. faecalis share 14 similar resistance genes. E. faecium and E. faecalis had 12 and 7 unique resistance genes, respectively but are of same drug classes. The most common antibiotic classes include aminoglycosides, tetracyclines, quinolones, beta-lactams, glycopeptides, macrolides, and pyrimidine analogs. Table 1:Enterococcus faecium and E. faecalis genetic mutations and drug class resistance Conclusion Enterococcus faecium had a greater number of resistance genes with glycopeptide, aminoglycoside, and beta lactam resistance when compared to Enterococcus faecalis. Whereas Enterococcus faecalis had more resistance genes associated with macrolides, tetracyclines, pyrimidine analogs, and Bactrim. In general, both appear to have many genes that encode for resistance to major classes of antibiotics which are used for treatment of Enterococcal infections. Further comparison with phenotypic susceptibility testing data would help better understand the practical implications of our resistance gene testing. Disclosures Piyali Chatterjee, PhD, AHRQ Grant # 1R03HS027667-01: Grant/Research Support|AHRQ Grant # 1R03HS027667-01: Central Texas Veterans Health Care System Keith S. Kaye, MD, MPH, Allecra: Advisor/Consultant|GlaxoSmithKline plc.: Receiving symposia honoraria|GlaxoSmithKline plc.: GlaxoSmithKline plc.-sponsored study 212502|Merck: Advisor/Consultant|qpex: Advisor/Consultant|Shionogi: Grant/Research Support|Spero: Advisor/Consultant Chetan Jinadatha, MD, MPH, AHRQ R01 Grant-5R01HS025598: Grant/Research Support|EOS Surfaces: Copper Coupons and materials for testing.

Studying the resistance of methicillin –resistant staphylococcus aureus against Different groups of antibiotics.

Back ground: MRSA developed resistance to β-lactam antibiotics through the acquisition ofthe mecA gene that encodes penicillin-binding protein 2a (PBP2a), which has a significantlyreduced affinity for β-lactam antibiotics, thereby conferring β- lactam resistance . The detectionof mecA by the (PCR) is considered a gold-standard technique for methicillin resistancedetection .Objective:This study was aimed to isolation and identification of S.aureus by traditional andmolecular methods and determine their susceptibility to different groups of antibiotics.Materials and Methods: Two hundred and ten samples were collected from different sourcesof patients in different age groups and for the period from the beginning of January 2015 untilthe end of June 2015, from different Hospitals in Baghdad (Ibn Albalady, Al Yarmouk,Baghdad teaching hospital and AlKindy).Results: Depending on the molecular methods (137) out of (210) isolates were methicillin–resistant Staphylococcus aureus MRSA. Antibiotic sensitivity test was conducted using 20types of antibiotics include:- Amikacin, Amoxicillin, Ampicillin, Azithromycin, Cefoxitin,Ciprofloxacin, Clarerythromycin, Clindamycin, Chloramphenicol, Erythromycin, Gentamycin,Methicillin, Norfloxacin, Oxacillin, Penicillin, Rifampin, Teicoplanin, Tetracycline,Tobramycin and Vancomycin.Conclusion: The results showed that the highest resistance was among beta-lactam group,where the ratio was 100% resistance to Ampicillin and Penicillin, and ratio of 91% to 86.66%and 86.66% resistance to Methicillin, Oxacillin and Amoxicillin respectively.The lowest resistance was among a group of antagonists Aminoglycosides resistance and ratioswas 37.77%, 31.11% and 35.55% to Amikacin, Tobramycin and Gentamycin, respectively,while the rest have different kinds of antibiotics effects.

Analysis of morphological change mechanism of linear Arthrospira platensis based on transcriptome results

Arthrospira platensis is a kind of filament cyanobacteria, which is mainly helical with a few linear. The shape of the filaments, such as the length and the pitch, may change with the changes in the environment. Natural Arthrospira platensis FACHB793 is linear, although it has become helical due to a mutation introduced in the process of cultivation. To study the molecular mechanism responsible for the morphological changes of the filaments, two samples were isolated from a natural mutant of Arthrospira platensis FACHB793, which were helical shaped (named A793_H) and linear shaped (named A793_L). Transcriptome sequencing, GO and KEGG enrichment analysis showed that the expression of genes related to or involved in peptidoglycan biosynthesis, beta lactam resistance, photosynthetic antenna protein expression, bacterial secretion, and ABC transporter activity changed between the two samples. The expression of murE and murG in the peptidoglycan biosynthesis pathway and that of oppD in beta lactam resistance were all down-regulated in the helical filaments, which may be related to the longer cell wall and higher peptidoglycan synthesis in linear filaments than helical filaments. In helical filaments, the up-regulation of tatC gene expression in bacterial secretion may be related to the secretion of peptidoglycan degrading enzymes, which may help to change the shape from linear to helical. Moreover, apcA and cpcA in photosynthetic antenna protein expression and nrt and nirA in nitrogen metabolism were all down regulated in the helical filaments, which may be due to the deformed shape of A. platensis FACHB793, resulting in decreased photosynthetic activity in helical filaments. This research provides a foundation for elucidating the possible morphogenetic mechanism of Arthrospira platensis.

MP37-06 ANTIMICROBIAL RESISTANCE AND MICROBIAL PATTERNS WITHIN THE CHRONIC PROSTATITIS UROBIOME COMPARED TO ASYMPTOMATIC HEALTHY CONTROLS

You have accessJournal of UrologyCME1 May 2022MP37-06 ANTIMICROBIAL RESISTANCE AND MICROBIAL PATTERNS WITHIN THE CHRONIC PROSTATITIS UROBIOME COMPARED TO ASYMPTOMATIC HEALTHY CONTROLS J. Curtis Nickel, Niccole Diaz, Craig D. Tipton, E. David Crawford, Rick Martin, and Caleb D. Phillips J. Curtis NickelJ. Curtis Nickel More articles by this author , Niccole DiazNiccole Diaz More articles by this author , Craig D. TiptonCraig D. Tipton More articles by this author , E. David CrawfordE. David Crawford More articles by this author , Rick MartinRick Martin More articles by this author , and Caleb D. PhillipsCaleb D. Phillips More articles by this author View All Author Informationhttps://doi.org/10.1097/JU.0000000000002591.06AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail Abstract INTRODUCTION AND OBJECTIVE: We present a comparative analysis of the urobiome and its antimicrobial resistance patterns from urine specimens submitted by patients with a clinical diagnosis of chronic prostatitis (CP) and asymptomatic healthy control males. METHODS: The urobiome of 763 subjects with a confirmed physician diagnosis of CP (from data base of 2,397 with CP ICD-10 code) were compared to 92 healthy males with no urological pain or infection. Microbiome and antibiotic resistance gene data were analyzed by NGS and qPCR respectively (MicroGenDx). Differences in each group’s urinary microbiome were investigated from perspectives of compositional differences and antibiotic resistance patterns. RESULTS: In respect to alpha diversity, CP cohort had similar number of species (richness; p=0.1: Fig 1a) but higher Shannon Diversity (richness and evenness of species abundances; F=5, p=0.03, R2=0.6%: Fig 1b) compared to healthy controls. Escherichia coli and Streptococcus agalactiae had significantly higher incidence rate in CP (p = 0. 04) and controls (p = 0.002) respectively. Diagnosis of CP vs controls explained a significant proportion of overall compositional dissimilarity (F=5.51. p=0.001, R2=0.64%). Five species E. coli, C. acnes, K. pneumoniae, C. glucuronolyticum and P. harei had higher average abundance in CP (Fig 1c); present in 50% of CP but only 16% of controls. While frequency of beta lactam (TEM) resistance was higher in CP (p=0.059), no significant differences in resistance patterns were identified for beta latam SHV (p=0.62) aminoglycosides (antia or alph3; p=0.4-0.81), macrolides (emB; p=0.84), methicillin (mecA: p=0.31), quinolones (qnr; p=0.15), tetracycline (tetB or tetM; p=0.37-1.0) or vancomycin (vanA; p=1.0). CONCLUSIONS: CP is associated with significantly different species incidence rates and relative abundances (notably E. coli, K. pneumoniae, C. acnes and C. glucuronolyticum), and with small but statistically significant components of variation in both alpha and beta diversity, but no clinically significant difference in antibiotic resistance patterns compared to healthy controls. The clinical relevance of detecting potential uropathogens with their associated resistance data in CP management needs to be addressed. Source of Funding: MicroGenDx © 2022 by American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 207Issue Supplement 5May 2022Page: e610 Advertisement Copyright & Permissions© 2022 by American Urological Association Education and Research, Inc.MetricsAuthor Information J. Curtis Nickel More articles by this author Niccole Diaz More articles by this author Craig D. Tipton More articles by this author E. David Crawford More articles by this author Rick Martin More articles by this author Caleb D. Phillips More articles by this author Expand All Advertisement PDF DownloadLoading ...

Prevalence of b-lactamase produced in Klebsiella pneumoniae and Enterobacter cloacae isolated from gingivitis in Al-Najaf Province, Iraq

Abstract. Motaweq ZY. 2022. Prevalence of ?-lactamase produced in Klebsiella pneumoniae and Enterobacter cloacae isolated from gingivitis in Al-Najaf Province, Iraq. Nusantara Bioscience 14: 78-83. This study provides phenotypic and genotypic ?-lactamase formation data on 26 isolates of Klebsiella pneumoniae and Enterobacter cloacae isolated from patients suffering from gingivitis checked at Al-Kafeel clinic and private clinic in Al-Najaf Province-Iraq during the period from September 2020 to February 2021. In this study, some of them were detected by traditional phenotypic methods, while others were detected by phenotypic and then genotypically by using monoplex-PCR technique. The results revealed that out of 14 ?-lactam resistance K. pneumoniae isolates, 8 isolates (57.1%) gave positive results with the direct capillary tubes method, while 12 ?-lactam resistance E. cloacae gave 6 (50%) positive results. This result indicated that the enzymatic resistance was prevalent among isolates. Furthermore, the results showed that most isolates were ESBL producers according to initial and confirmatory methods. Molecular amplification of the ?-lactamase enzyme blaSHV gene was detected in 8 (57.1%) and 5 (41.6%) for K. pneumoniae and E. cloacae, respectively. While all 100% of K. pneumoniae and E. cloacae isolates gave negative results for blaGES gene. This study aimed to investigate the ?-lactamase formation and detection of blaSHV and blaGES genes in K. pneumoniae and E. cloacae isolated from gingivitis diseases.

Mass Spectrometry-Based Detection of Beta Lactam Hydrolysis Enables Rapid Detection of Beta Lactamase Mediated Antibiotic Resistance.

Antibiotic resistance by beta lactamase expression is a serious and growing threat. We aimed to determine whether beta-lactamase activity is detectable in urine specimens to enable faster identification of resistance. Urine specimens from patients with extended spectrum beta lactamase (ESBL)-expressing urinary infections were incubated with beta lactam antibiotics. Beta lactam hydrolysis was determined by mass spectrometry methods. Ceftriaxone hydrolysis was observed in 45 of 45 ESBL-containing specimens from patients not treated with a beta lactamase inhibitor before specimen collection. Ceftriaxone hydrolysis was not observed in 108 of 108 non-ESBL-containing specimens. Spiking studies show that beta lactam hydrolysis can be observed within 30 minutes. Beta lactam hydrolysis is evidenced by mass spectrometry preceded by either liquid chromatography or matrix-assisted laser desorption ionization specimen processing methods. Clinically significant beta lactamase activity is detectable directly from urine specimens. The described methods would enable the detection of beta lactam resistance 24 to 48 hours sooner than culture based methods.

Conjugative Plasmids Disseminating CTX-M-15 among Human, Animals and the Environment in Mwanza Tanzania: A Need to Intensify One Health Approach.

Background: Globally, blaCTX-M-15 beta-lactamases are the most popular extended spectrum beta-lactamase alleles that are widely distributed due its mobilisation by mobile genetic elements in several compartments. We aimed to determine the conjugation frequencies and replicon types associated with plasmids carrying blaCTX-M-15 gene from Extended Spectrum Beta-lactamase producing isolates in order to understand the dissemination of resistance genes in different compartments. Material and methods: A total of 51 archived isolates carrying blaCTX-M-15 beta-lactamases were used as donors in this study. Antibiotic susceptibility tests were performed as previously described for both donors and transconjugants. Conjugation experiment was performed by a modified protocol of the plate mating experiment, and plasmid replicon types were screened among donor and transconjugant isolates by multiplex Polymerase Chain Reaction in a set of three primer panels. Results: The conjugation efficiency of plasmids carrying blaCTX-M-15 was 88.2% (45/51) with conjugation frequencies in the order of 10−1 to 10−9 and a 100% transfer efficiency observed among E. coli of animal origin. Majority of donors (n = 21) and transconjugants (n = 14) plasmids were typed as either Inc FIA or Inc FIB. Resistance to non-beta-lactam antibiotics was transferrable in 34/45 (75.6%) of events. Ciprofloxacin, tetracycline and sulphamethoxazole-trimethoprim resistance was co-transferred in 29/34 (85.3%) such events. Gentamicin resistance was transferred in 17/34 (50%) of events. Conclusions: Majority of plasmids carrying blaCTX-M-15 were conjugatively transferred by IncF plasmids along with non-beta lactam resistance. There is a need for more research on plasmids to understand how plasmids especially multi replicon plasmids interact and the effect of such interaction on conjugation. One Health approach is to be intensified to address antimicrobial resistance which is a public health threat.

WGS-Based Prediction and Analysis of Antimicrobial Resistance in Campylobacter jejuni Isolates From Israel.

Rapid developments in the field of whole genome sequencing (WGS) make in silico antimicrobial resistance (AMR) a target within reach. Campylobacter jejuni is a leading cause of foodborne infections in Israel with increasing rates of resistance. We applied WGS analysis to study the prevalence and genetic basis of AMR in 263 C. jejuni human and veterinary representative isolates retrieved from a national collection during 2003–2012. We evaluated the prediction of phenotypic AMR from genomic data. Genomes were screened by the NCBI AMRFinderPlus and the BioNumerics tools for acquired AMR genes and point mutations. The results were compared to phenotypic resistance determined by broth microdilution. The most prevalent resistant determinants were the multi-drug efflux transporter gene cmeABC (100%), the tetracycline resistance tet(O) gene (82.1%), the quinolone resistance gyrA T861 point mutation (75.7%), and the aadE streptomycin resistance gene. A variety of 12 known β lactam resistance genes (blaOXA variants) were detected in 241 (92%) isolates, the most prevalent being blaOXA−193, blaOXA−461, and blaOXA−580 (56, 16, and 7%, respectively). Other aminoglycoside resistance genes and the macrolide resistance point mutation were rare (<1%). The overall correlation rate between WGS-based genotypic prediction and phenotypic resistance was 98.8%, sensitivity, specificity, positive, and negative predictive values being 98.0, 99.3, 99.1, and 98.5%, respectively. wgMLST-based phylogeny indicated a high level of clonality and clustering among the studied isolates. Closely related isolates that were part of a genetic cluster (single linkage distance ≤ 15 alleles) based on wgMLST phylogeny mostly shared a homogenous AMR determinant profile. This was observed in 18 of 20 (90.0%) clusters within clonal complex-21, suggesting clonal expansion of resistant isolates. Strong association to lineage was noted for the aadE gene and the various blaOXA genes. High resistance rates to tetracycline and quinolones and a low resistance rate to macrolides were detected among the Israeli C. jejuni isolates. While a high genotypic-phenotypic correlation was found, some resistance phenotypes could not be predicted by the presence of AMR determinants, and particularly not the level of resistance. WGS-based prediction of antimicrobial resistance in C. jejuni requires further optimization in order to integrate this approach in the routine workflow of public health laboratories for foodborne surveillance.

P0285A COMPARISON OF URINE MICROSCOPY AND CULTURE IN HIV-INFECTED AND NON HIV-INFECTED INDIVIDUALS IN THE ANTI-RETROVIRAL ERA

Abstract Background and Aims Urinary tract infection is among the most common causes of sepsis presenting in hospitals. The aim was to collect data to enable empirical treatment of urinary tract infections in HIV negative and positive nephrology patients while waiting for urine culture results in order to reduce hospital stay. Our aim is also to assess incidence and antimicrobial susceptibility of urinary tract infections in HIV negative and positive patients. Method A retrospective chart review of nephrology patients admitted from January to December 2014 in Nephrology ward and the first consecutive 200 outpatients seen in Nephrology clinic in 2014 at Inkosi Albert Luthuli Central Hospital was conducted. Information was gathered with the use of a data collection sheet and urinary tract infection was based on urine culture results. All data was analysed using Statistical Package for Social Sciences version 23. Percentages of basic characteristics were calculated between groups. Logistic regression analysis was used to identify factors associated with positive urine culture. Results There were 654 patients in the study, 514 (79%) were HIV negative and 139 (21%) were HIV positive. The incidence of UTI in nephrology patients was 9%, 10.1% in inpatients and 6.5% in outpatients. 22% were HIV positive (p value 0.883, 95% CI 0.550-2.003). 19% had Diabetes mellitus, 15% had Systemic Lupus Erythematosus and 5% were post renal transplant patients. Escherichia coli and Klebsiella pneumonia were the common causes of urinary tract infection at 40.7% and 15.3% respectively with 22% cases on extended beta lactam resistance. Conclusion There was no statistically significant difference on the incidence and anti-microbial isolates between HIV infected and HIV negative nephrology patients with urinary tract infection. Hence, empirical treatment for UTI should remain the same in the 2 groups. Escherichia coli and Klebsiella pneumoniae were the most commonly cultured organisms in both groups. There is microbial resistance to commonly used antibiotics. Constant assessment of anti-microbial sensitivity of urinary tract infections is of paramount importance.

Linking perturbations to temporal changes in diversity, stability, and compositions of neonatal calf gut microbiota: prediction of diarrhea.

Perturbations in early life gut microbiota can have long-term impacts on host health. In this study, we investigated antimicrobial-induced temporal changes in diversity, stability, and compositions of gut microbiota in neonatal veal calves, with the objective of identifying microbial markers that predict diarrhea. A total of 220 samples from 63 calves in first 8 weeks of life were used in this study. The results suggest that increase in diversity and stability of gut microbiota over time was a feature of “healthy” (non-diarrheic) calves during early life. Therapeutic antimicrobials delayed the temporal development of diversity and taxa–function robustness (a measure of microbial stability). In addition, predicted genes associated with beta lactam and cationic antimicrobial peptide resistance were more abundant in gut microbiota of calves treated with therapeutic antimicrobials. Random forest machine learning algorithm revealed that Trueperella, Streptococcus, Dorea, uncultured Lachnospiraceae, Ruminococcus 2, and Erysipelatoclostridium may be key microbial markers that can differentiate “healthy” and “unhealthy” (diarrheic) gut microbiota, as they predicted early life diarrhea with an accuracy of 84.3%. Our findings suggest that diarrhea in veal calves may be predicted by the shift in early life gut microbiota, which may provide an opportunity for early intervention (e.g., prebiotics or probiotics) to improve calf health with reduced usage of antimicrobials.

Antibiotic resistance: Current global issue and future challenges

Understanding antibiotic resistance and control measure is a challenge because it causes dissemination of multidrug resistance bacteria, and it causes high morbidity and mortality. Bacteria expressing extended spectrum beta lactamases (ESBL) have been recently reported globally at an alarming level and these issues exist in Middle East and Iraq. Bacteria bearing beta lactam resistance genes shows multi-drug resistance and it cause delay in treatment. The huge number of studies has been carried out to indicate the causes of drug resistances and the outcome of this problem in clinical fields. Therefore, this study is about to reviewing different causes and aspects of drug resistances such as: causes of drug resistance, antibiotic resistance mechanisms, antibiotic resistance reversibility, and different types of beta lactamase resistance genes, Resistance Genes (ESBL) in Middle East, and Resistance Genes (ESBL) in Iraq. The review highlighted all research showing the existence of different types of ESBL in humans, animals and environments in different places of Middle East and Iraq. Bacteria bearing β-lactamases resistance genes have been spread in all parts of Middle East which is public health threating; therefore, it’s important to limit Antibiotic use by people. Further research is required in the studied area to understand the reason of antibiotic resistance and an attempt to find new antibiotic is very necessary to save future humans life.

Characterization of Staphylococcus aureus isolated from tilapia and utensils used in the commerciali- zation of tilapia in the street markets of a semi-arid Brazilian municipality.

The production and commercialization of tilapia (Oreochromis niloticus) is fundamentally important to the semi-arid region of northeastern Brazil. In this region, one of the main forms of commercialization occurs in street markets (fairs). A high incidence of methicillin-resistant Staphylococcus aureus (MRSA) strains was previously detected in different food-related environments in Brazil. However, limited data is available about the presence of MRSA in street markets commercializing tilapias. In this study, we identified Staphylococcus aureus from tilapia and utensils used in the commercialization of tilapia in the street markets of a semi-arid Brazilian municipality and characterized the virulence potential of the isolates by analyzing their &beta;-lactam resistance, intercellular adhesion and enterotoxin genes. The study used samples from the 5 main markets in the city. Phenotypic tests to determine antimicrobial resistance, exopolysaccharide (EPS) production, the potential for biofilm formation and cell surface hydrophobicity were conducted on S. aureus isolates. The presence of antimicrobial resistance genes (mecA and blaZ), potential biofilm production genes (icaA and icaD) and enterotoxin (se) genes was investigated. Coagulase-positive staphylococci (CoPS) were detected in samples from all markets in discordance with the legal limits in force. Twelve isolates were confirmed to be S. aureus. Ten isolates demonstrated multidrug resistance (MDR). All isolates were able to produce EPS and form biofilms. Eight isolates exhibited strong hydrophobicity and six a high potential for biofilm formation. Twelve isolates were positive for mecA, blaZ, icaD and sed. Tilapia marketed in unsuitable conditions may be a vehicle for staphylococcal food poisoning and for the dissemination of MRSA to consumers. Additionally, the ability of the isolates to produce biofilms is an alert to the presence and persistence of these virulent microorganisms on utensils used for the commercial distribution of tilapia.

Microarray-based detection of resistance and virulence factors in commensal Escherichia coli from livestock and farmers in Egypt

The objective of our study was to provide a molecular analysis using DNA-microarray based assays of commensal E. coli populations from apparently healthy livestock and their attendants to assess the virulence potential as well as multidrug resistance (MDR) genotypes.We randomly collected 132 fecal samples from seemingly healthy smallholder´s food producing animals [buffalo (n = 32) and cattle (n = 50)] as well as from contacting farmers (n = 50). Bacterial isolation and identification were performed using standard protocols, while E. coli isolates were characterized using a DNA microarray system targeting 60 different virulence and 47 antibiotic resistance genes of clinical importance and allowing assignment to most common H and O types.From the fecal samples examined, 47 E. coli isolates were obtained. The array predicted serotypes for 14 out of the 47 E. coli isolates. Six E. coli isolates were identified as STEC since Shiga toxin genes were detected. In summary, 36 different virulence genes were identified; of which, hemL, lpfA and iss were most prevalent. Thirty-four E. coli isolates were found to carry at least one antimicrobial resistance gene. Of these, 20 did exhibit genes allowing strain classification as MDR. More than half of the isolates contained antimicrobial resistance genes associated with beta lactam resistance 27/47 (57.5 %). The 13 remaining isolates did not contain any resistance gene tested with the array.Our study demonstrated the presence of antimicrobial resistance genes and virulence genotypes among commensal E. coli of human and animal sources.