Importance of antimicrobial susceptibility testing for the management of eradication in Helicobacter pylori infection

The management of Helicobacter pylori(H. pylori) infection treatment differs from the common treatment protocol for other infectious diseases. Because culture-or molecular-guided approaches face several practical issues, such as the invasive procedures required to obtain gastric biopsy specimens and the lack of availability of routine laboratory testing in some places, H. pylori treatment includes the administration of two or three empirically selected antibiotics combined with a proton pump inhibitor rather than evidence-based eradication treatment. The efficacy of empirical therapy is decreasing, mostly due to increasing multiple resistance. Multiresistance to levofloxacin, clarithromycin, and metronidazole, which are commonly used in empirical treatments, appears to have increased in many countries. Mutations play a primary role in the antimicrobial resistance of H. pylori, but many different mechanisms can be involved in the development of antibiotic resistance. Determining and understanding these possible mechanisms might allow the development of new methods for the detection of H. pylori and the determination of antimicrobial resistance. A treatment based on the detection of antimicrobial resistance is usually more effective than empirical treatment. Nevertheless, such an approach before treatment is still not recommended in the Maastricht guidelines due to the difficulty associated with the routine application of available cultureor molecular-based susceptibility tests, which are usually administered in cases of treatment failure. The management of first and rescue treatments requires further research due to the steadily increase in antimicrobial resistance.

Expert Consensus on Polymyxin Antimicrobial Susceptibility Testing and Clinical Interpretation

The polymyxins are important antimicrobial agents against antibiotic-resistant gram-negative bacilli.In 2020,the Clinical and Laboratory Standards Institute modified the clinical breakpoints for polymyxin susceptibility test by eliminating the"susceptible"interpretive category,only reporting intermediate(≤2 mg/L)and resistant(≥4 mg/L).However,the European Committee on Antimicrobial Susceptibility Testing recommended the use of clinical breakpoints of W2 mg/L as susceptible and>2 mg/L as resistant.The first-line laboratorians and clinicians in China have been perplexed by the inconsistence of international polymyxin clinical breakpoints and discouraged by the difficulty of conducting polymyxin susceptibility testing.Therefore,it is urgently needed to make it clear for the laboratorians in China to know how to accurately carry out polymyxin susceptibility testing and standardize the interpretation of susceptibility testing results.To this end,the experts from relevant fields were convened to formulate this consensus statement on the testing and clinical interpretation of polymyxin susceptibility.Relevant recommendations are proposed accordingly for laboratorians and clinicians to streamline their daily work.

Rapid antimicrobial susceptibility testing for mixed bacterial infection in urine by AI-stimulated Raman scattering metabolic imaging

Urinary tract infection with mixed microorganisms may lead to false-positive resistance detection.Current antimicrobial susceptibility testing(AST)performed in clinical laboratories is based on bacterial culture and takes a long time for mixed bacterial infections.Here,we propose a machine learning-based single-cell metabolism inactivation concentration(ML-MIC)model to achieve rapid AST for mixed bacterial infections.Using E.coli and S.aureus as a demonstration of mixed bacteria,we performed feature extraction and multi-feature analysis on stimulated Raman scattering(SRS)images of bacteria with the ML-MIC model to determine the subtypes and AST of the mixed bacteria.Furthermore,we assessed the AST of mixed bacteria in urine and obtained single-cell metabolism inactivation concentration in only 3 h.Collectively,we demonstrated that SRS imaging of bacterial metabolism can be extended to mixed bacterial infection cases for rapid AST.

Intraprocedural gastric juice analysis as compared to rapid urease test for real-time detection of Helicobacter pylori

BACKGROUND Endofaster is an innovative technology that can be combined with upper gastrointestinal endoscopy(UGE)to perform gastric juice analysis and real-time detection of Helicobacter pylori(H.pylori).AIM To assess the diagnostic performance of this technology and its impact on the management of H.pylori in the real-life clinical setting.METHODS Patients undergoing routine UGE were prospectively recruited.Biopsies were taken to assess gastric histology according to the updated Sydney system and for rapid urease test(RUT).Gastric juice sampling and analysis was performed using the Endofaster,and the diagnosis of H.pylori was based on real-time ammonium measurements.Histological detection of H.pylori served as the diagnostic gold standard for comparing Endofaster-based H.pylori diagnosis with RUT-based H.pylori detection.RESULTS A total of 198 patients were prospectively enrolled in an H.pylori diagnostic study by Endofasterbased gastric juice analysis(EGJA)during the UGE.Biopsies for RUT and histological assessment were performed on 161 patients(82 men and 79 women,mean age 54.8±19.2 years).H.pylori infection was detected by histology in 47(29.2%)patients.Overall,the sensitivity,specificity,accuracy,positive predictive value,and negative predictive value(NPV)for H.pylori diagnosis by EGJA were 91.5%,93.0%,92.6%,84.3%,and 96.4%,respectively.In patients on treatment with proton pump inhibitors,diagnostic sensitivity was reduced by 27.3%,while specificity and NPV were unaffected.EGJA and RUT were comparable in diagnostic performance and highly concordant in H.pylori detection(κ-value=0.85).CONCLUSION Endofaster allows for rapid and highly accurate detection of H.pylori during gastroscopy.This may guide taking additional biopsies for antibiotic susceptibility testing during the same procedure and then selecting an individually tailored eradication regimen.

Causative Microorganisms Isolated from Patients with Intra-Abdominal Infections and Their Drug Resistance Profiles:An 11-Year(2011–2021)Single-Center Retrospective Study

Objective To investigate the distribution and antimicrobial susceptibility of causative microorganisms recovered from patients with intra-abdominal infections(IAIs).Methods A total of 2,926 bacterial and fungal strains were identified in samples collected from 1,679 patients with IAIs at the Peking Union Medical College Hospital between 2011 and 2021.Pathogenic bacteria and fungi were identified using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.Antimicrobial susceptibility testing(AST)was performed using the VITEK 2 compact system and the Kirby–Bauer method.AST results were interpreted based on the M100-Ed31 clinical breakpoints of the Clinical and Laboratory Standards Institute.Results Of the 2,926 strains identified,49.2%,40.8%,and 9.5%were gram-negative bacteria,gram-positive bacteria,and fungi,respectively.Escherichia coli was the most prevalent pathogen in intensive care unit(ICU)and non-ICU patients;however,a significant decrease was observed in the isolation of E.coli between 2011 and 2021.Specifically,significant decreases were observed between 2011 and 2021 in the levels of extended-spectrumβ-lactamase(ESBL)-producing E.coli(from 76.9%to 14.3%)and Klebsiella pneumoniae(from 45.8%to 4.8%).Polymicrobial infections,particularly those involving co-infection with gram-positive and gram-negative bacteria,were commonly observed in IAI patients.Moreover,Candida albicans was more commonly isolated from hospital-associated IAI samples,while Staphylococcus epidermidis had a higher ratio in community-associated IAIs.Additionally,AST results revealed that most antimicrobial agents performed better in non-ESBL-producers than in ESBL-producers,while the overall resistance rates(56.9%–76.8%)of Acinetobacter baumanmii were higher against all antimicrobial agents than those of other common gram-negative bacteria.Indeed,Enterococcus faecium,Enterococcus faecalis,S.epidermidis,and S.aureus were consistently found to be susceptible to vancomycin,teicoplanin,and linezolid.Similarly,C.albicans exhibited high susceptibility to all the tested antifungal drugs.Conclusion The distribution and antimicrobial susceptibility of the causative microorganisms from patients with IAls were altered between 2011 and 2021.This finding is valuable for the implementation of evidence-based antimicrobial therapy and provides guidance for the control of hospital infections.

Combined antrum and corpus biopsy protocol improves Helicobacter pylori culture success

BACKGROUND Helicobacter pylori(H.pylori)causes chronic gastritis,peptic ulcer disease,gastric adenocarcinoma and mucosa-associated lymphoid tissue lymphoma.Eradication rates have fallen,mainly due to antimicrobial resistance.Consensus guidelines recommend that first-line treatment is based on the local prevalence of antimicrobial resistance and that rescue therapies are guided by antimicrobial susceptibility testing(AST).However,H.pylori culture is challenging and culture-based AST is not routinely performed in the majority of hospitals.Optimisation of H.pylori culture from clinical specimens will enable more widespread AST to determine the most appropriate antimicrobials for H.pylori eradication.AIM To determine whether dual antrum and corpus biopsy sampling is superior to single antrum biopsy sampling for H.pylori culture.METHODS The study received ethical approval from the joint research ethics committee of Tallaght University Hospital and St.James’s Hospital.Patients referred for upper gastrointestinal endoscopy were invited to participate.Biopsies were collected in tubes containing Dent’s transport medium and patient demographics were recorded.Biopsies were used to inoculate Colombia blood agar plates.Plates were incubated under microaerobic conditions and evaluated for the presence of H.pylori.Statistical analyses were performed using Graphpad PRISM.Continuous variables were compared using the two-tailed independent t-test.Categorical variables were compared using the two-tailed Fisher exact test.In all cases,a P value less than 0.05 was considered significant.RESULTS In all,samples from 219 H.pylori-infected patients were analysed in the study.The mean age of recruited patients was 48±14.9 years and 50.7%(n=111)were male.The most common endoscopic finding was gastritis(58.9%;n=129).Gastric ulcer was diagnosed in 4.6%(n=10)of patients,while duodenal ulcer was diagnosed in 2.7%(n=6).Single antrum biopsies were collected from 73 patients,whereas combined antrum and corpus biopsies were collected from 146 patients.There was no significant difference in age,sex or endoscopic findings between the two groups.H.pylori was successfully cultured in a significantly higher number of cases when combined antrum and corpus biopsies were used compared to a single antrum biopsy[64.4%(n=94/146)vs 49.3%(36/73);P=0.04)].CONCLUSION Combined corpus and antrum biopsy sampling improves H.pylori culture success compared to single antrum biopsy sampling.

Evidence-Based Use of Antibiotics in Veal Calves with Diarrhea

Diarrhea is the leading cause of mortality in beef and dairy calves during the first week of life and results in substantial financial loss [1]. Diarrhea is a multifactorial disease and can be infectious or non-infectious. However, in the majority of calves, infectious organisms, especially Cryptosporidium parvum, rotavirus, coronavirus, and E. coli, are the primary cause [2]. The aim of this study was to generate a decision tree, based on prevalence, diagnostic testing and treatment and to estimate associated costs or risk. For each of the four main pathogens, two principal approaches are outlined and compared. The first approach relies on a detailed diagnostic workup and allows for specific etiological treatment. The second approach relies on the trial-and-error method, which involves the use of a first-choice antibiotic, followed by a second- and third-choice antibiotic if the previous ones failed to resolve the disease. In Switzerland, the prevalence of diarrheic calves infected with E. coli is approximately 1% suggesting that the use of antimicrobials for the treatment of scouring calves, in the absence of a diagnostic workup, is not always justified. However, for all four major pathogens, the trial-and-error method affords cheaper treatment compared with treatment based on an etiological diagnosis. This creates a quandary in view of the current worldwide efforts to reduce the use of antibiotics in animal agriculture.

Rapid, automated, and reliable antimicrobial susceptibility test from positive blood culture by CAST‐R

Antimicrobial susceptibility tests(ASTs)are pivotal in combating multidrug resistant pathogens,yet they can be time‐consuming,labor‐intensive,and unstable.Using the AST of tigecycline for sepsis as the main model,here we establish an automated system of Clinical Antimicrobials Susceptibility Test Ramanometry(CAST‐R),based on D2O‐probed Raman microspectroscopy.Featuring a liquid robot for sample pretreatment and a machine learning‐based control scheme for data acquisition and quality control,the 3‐h,automated CAST‐R process accelerates AST by>10‐fold,processes 96 paralleled antibiotic‐exposure reactions,and produces high‐quality Raman spectra.The Expedited Minimal Inhibitory Concentration via Metabolic Activity is proposed as a quantitative and broadly applicable parameter for metabolism‐based AST,which shows 99%essential agreement and 93%categorical agreement with the broth microdilution method(BMD)when tested on 100 Acinetobacter baumannii isolates.Further tests on 26 clinically positive blood samples for eight antimicrobials,including tigecycline,meropenem,ceftazidime,ampicillin/sulbactam,oxacillin,clindamycin,vancomycin,and levofloxacin reveal 93%categorical agreement with BMD‐based results.The automation,speed,reliability,and general applicability of CAST‐R suggest its potential utility for guiding the clinical administration of antimicrobials.

Isolation of Pathogenic Gram-Negative Bacteria from Urinary Tract Infected Patients

This study investigated the susceptibility pattern of different bacteria isolated from urinary tract infection to different antibiotics. 83 uropathogen bacteria were isolated from 300 urine samples taken from patients attended to Tikrit Teaching Hospital from March, 2011 through February, 2012. The patients were males and females aged between 4 days to 95 years. Bacteria obtained from urine samples were cultured and tested for antimicrobial susceptibility to 16 kinds of antibiotics. Urine samples were cultured on different media and incubated, thereafter bacteria were isolated and purified by streaking four times on the same media;isolates were identified depending on morphological, microscopic, and biochemical characteristics. The isolated strains of bacteria were tested for their susceptibility to some antibiotics using disk diffusion method. The antagonistic activity was evaluated by observing a clear zone of inhibition growth. The results showed that the bacterial species of Eschericia coli, Proteus mirabilis, Klebsiella pneumonia, Citrobacter diversus, Citrobacter freundii, Enterobacter aerogenes, Yersinia pestis, Pseudomonas aeruginosa, Klebsiella oxytoca and Hafnia alvei were identified in 44 (53%), 18 (21.7%), 4 (4.8%), 4 (4.8%), 3 (3.6%), 3 (3.6%), 3 (3.6%), 2 (2.4%), 1 (1.2%) and 1 (1.2%), respectively, of the isolates. The results of antimicrobial susceptibility test showed that 83 (100%) isolates were resistant to Ampicillin, Rifampicin and Erythromycin. 75 (90.3%) isolates were resistant to Cefotaxime, 67 (80.7%) isolates were resistant to Tobramyci. 66 (79.5%), 65 (78.3%), 56 (67.4%) and 48 (57.8%) isolates showed susceptibility to Nalidixic acid, Tetracycline, Nitrofurantoin, Chloramphenicol, respectively. 45 (54.2%) isolates were resistant to Azithromycin, Norfloxacin and Ciprofloxacin. Meropenem, Gentamicin, Amikacin, and Imipenem show significant effect on 35 (42.1%), 32 (38.5%), 27 (32.5%) and 1 (1.2%) isolates, respectively. In conclusion, significant bacteria count isolated from urine samples is pathogenic. The most effective antibiotic in inhibiting the bacterial growth was Imipenem while Ampicillin, Rifampicin and Erythromycin showed no effect on all 83 isolates (100%).

Susceptibility-guided bismuth quadruple therapies for resistant Helicobacter pylori infections

Increasing Helicobacter pylori resistance to antibiotics has ledthat molecular testing is appropriate as a sub to adoption of seven different bismuth quadruple therapies(BQT)in China without differentiation of first-line or second-line regimens.The objective of this study was to evaluate the efficacy of susceptibility-guided BQT for patients who had experienced previous treatment failures.A total of 133 patients was included and H.pylori was successfully cultured from 101 patients(75.9%)for subsequent antimicrobial susceptibility testing(AST).Based on the AST results,88 patients completed one of five AST-guided 14-day BQT regimens:esomeprazole and bismuth colloidal pectin,along with either,amoxicillin and clarithromycin(EBAC),amoxicillin and levofloxacin(EBAL),amoxicillin and furazolidone(EBAF),amoxicillin and tetracycline(EBAT),or tetracycline and furazolidone(EBTF).H.pylori eradication rateswere 100%for EBAC(5/5),EBAL(13/13),EBAF(14/14),and EBTF(43/43),but 76.9%for EBAT(10/13).The three patients that failed the EBAT regimenwere all cured after subsequent treatment with the EBTF regimen.Our study demonstrates the excellent efficacy of the AST-guided BQT for referred H.pylori patients,and that the current EBAT regimen,used in clinics,needs to be optimized.In addition,57 of the isolates were subjected to whole-genome sequencing.Analysis of the sequences revealed that point mutations in 23S rRNA correlated well with the phenotypic clarithromycin resistance with a concordance of 91.2%,while the concordance between phenotypic levofloxacin resistance and gyrA point mutations was 82.3%.This suggests that molecular testing is appropriate as a substitute for AST as a more rapid and cost-effective method for determining clarithromycin and levofloxacin resistance in Chinese patients.

Investigation on phytochemical,antimicrobial activity and essential oil constituents of Nardostachys jatamansi DC.in different regions of Nepal

Objective:To study chemical constituents of essential oil of the roots of Nardostachys jatamansi found in different regions of Nepal and also to investigate phytochemical as well as antimicrobial activity of the sample with high yield of essential oil.Methods:The essential oils of roots of plant from five different regions were extracted by hydro-distillation and analyzed by gas chromatography-mass spectroscopy for their chemical constituents.The root samples were also subjected to hydro-alcoholic extraction and then fractionated with hexane,chloroform,n-butanol and water so as to perform phytochemical screening and antimicrobial activity.Results:The essential oil yield of sample from Jumla was found to be the highest followed by a sample from Nepalgunj,Surkhet and Kathmandu whereas that of sample from Dharan was found to be the lowest.Gas chromatography-mass spectrometer analysis of essential oil of five samples showed that“2-beta pinene”appeared dominated in three samples,namely,6VJ Nepalgunj,9VJA Jumla and 10VJ Surkhet.Similarly“alkohol aus neoclovenoxid”in 8VJ Dharan and“methoxy phenyloxime”in 13VJA Kathmandu was found to be present in the highest amount.Phytochemical screening of different fractions of sample 9VJA Jumla showed the presence of alkaloids,terpenoids,glycosides,proteins and amino acids,and carbohydrates etc.Antimicrobial susceptibility test of same fractions showed the n-butanol fraction potent against all pathogens and most affected one was Escherichia coli.Conclusions:Our study suggests that the essential oil of Nardostachys jatamansi found in Nepal contains more than 80 compounds with their quality and quantity differing from place to place.

Helicobacter pylori infection is an infectious disease and the empiric therapy paradigm should be changed

Helicobacter pylori infection is an infectious disease.Given the alarmingly high antibiotic resistance in H.pylori,gastroenterologists should change the empiric H.pylori treatment paradigm to an antimicrobial susceptibility testing-guided precision treatment.Antimicrobial stewardship programs for H.pylori should be implemented locally,regionally,and nationally to monitor the antibiotic resistance pattern.

Azithromycin Exerts Bactericidal Activity and Enhances Innate Immune Mediated Killing of MDR Achromobacter xylosoxidans

Azithromycin(AZM),the most commonly prescribed antibiotic in the United States,is thought to have no activity against multidrugresistant Gram-negative pathogens such as Achromobacter xylosoxidans(AX)per standard minimum inhibitory concentration testing in cation-adjusted Mueller Hinton Broth.Here we provide the first report of AZM bactericidal activity against carbapenemresistant isolates of AX,with a multifold decrease in minimum inhibitory concentration across 12 clinical isolates when examined under physiologic testing conditions that better recapitulate the in vivo human environment.This pharmaceutical activity,evident in eukaryotic tissue culture media,is associated with enhanced AZM intracellular penetration and synergistic killing with human whole blood,serum,and neutrophils.Additionally,AZM monotherapy inhibited preformed AX biofilm growth in a dose-dependent manner together with a reduction in viable bacteria.In an illustrative case,AZM in combination with piperacillin-tazobactam exerted clear therapeutic effects in a patient with carbapenem-resistant AX mediastinitis,sternal osteomyelitis,and aortic graft infection.Our study reinforces how current antimicrobial testing practices fail to recapitulate the host environment or host-pathogen interactions and may misleadingly declare complete resistance to useful agents,adversely affecting patient outcomes.We conclude that AZM merits further exploration in the treatment of drug-resistant AX infections.Novel approaches to antimicrobial susceptibility testing that better recapitulate the host environment should be considered,especially as infections caused by multidrug-resistant Gram-negative bacterial pathogens are expanding globally with high morbidity and mortality.

Determination of the prevalence of extended spectrum β-lactamase in clinical samples collected from Dehradun City Hospital

Objective:To detect extended spectrumβ-lactamase(ESBL)and determine its prevalence in various clinical samples collected from Dehradun City Hospital.Methods:The samples were first cultured in MacConkey’s agar plates by streak plate method,then identified by Gram staining and biochemical tests.The isolated bacterial strains were then tested for antibiotic susceptibility by Kirby-Bauer method.The ESBL detection is then carried out by double disc diffusion method.Results:Off the 56 samples cultured,21 strains were identified which were six Escherichia coli(E.coli),six Klebsiella,four Proteus,four Pseudomonas aeruginosa(P.aeruginosa)and only one Acinetobacter.Eight out of 21(38.1%)strains including three of E.coli,three of Klebsiella and two of P.aeruginosa,were found to be resistance to all five antibiotics(piperacillin,amikacin,ampicillin,gentamicin,and ciprofloxacin).Initial screening using four antibiotics(cefotaxime,ceftazidime,aztreonam and ceftriaxone)and the final confirmatory test using ceftazidime/clavulanic acid and ceftazidime alone showed that 19.05%of all strains isolated were ESBL producers.Individually,16.67%E.coli,16.67%Klebsiella pneumoniae,25%P.aeruginosa and 100%Acinetobacter were found to be ESBL producers.Conclusions:Antibiotic resistance by ESBL has become a major risk factor worldwide,therefore routine checkup and accordingly prescription are suggested.