Antimicrobial susceptibility testing for Helicobacter pylori in times of increasing antibiotic resistance

The gram-negative bacterium Helicobacter pylori(H.pylori)causes chronic gastritis,gastric and duodenal ulcers,gastric cancer and mucosa-associated lymphoid tissue lymphoma.Treatment is recommended in all symptomatic patients.The current treatment options for H.pylori infection are outlined in this review in light of the recent challenges in eradication success,largely due to the rapid emergence of antibiotic resistant strains of H.pylori.Antibiotic resistance is a constantly evolving process and numerous studies have shown that the prevalence of H.pylori antibiotic resistance varies significantly from country to country,and even between regions within the same country.In addition,recent data has shown that previous antibiotic use is associated with harbouring antibiotic resistant H.pylori.Local surveillance of antibiotic resistance is warranted to guide clinicians in their choice of therapy.Antimicrobial resistance is assessed by H.pylori culture and antimicrobial susceptibility testing.Recently developed molecular tests offer an attractive alternative to culture and allow for the rapid molecular genetic identification of H.pylori and resistance-associated mutations directly from biopsy samples or bacterial culture material.Accumulating evidence indicates that surveillance of antimicrobial resistance by susceptibility testing is feasible and necessary to inform clinicians in their choice of therapy for management of H.pylori infection.

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.

Antimicrobial susceptibility testing before first-line treatment for Helicobacter pylori infection in patients with dual or triple antibiotic resistance

To evaluate the efficacy of antimicrobial susceptibility-guided therapy before first-line treatment for infection in patients with dual or triple antibiotic resistance.METHODSA total of 1034 patients infected by Helicobacter pylori (H. pylori) during 2013-2014 were tested for antimicrobial susceptibility. 157 of 1034 (15%) patients showed resistance to two (127/1034; 12%) and to three (30/1034; 3%) antibiotics. Sixty-eight patients with dual H. pylori-resistance (clarithromycin, metronidazole or levofloxacin) were treated for 10 d with triple therapies: OAL (omeprazole 20 mg b.i.d., amoxicillin 1 g b.i.d., and levofloxacin 500 mg b.i.d.) 43 cases, OAM (omeprazole 20 mg b.i.d., amoxicillin 1 g b.i.d., and metronidazole 500 mg b.i.d.) 12 cases and OAC (omeprazole 20 mg b.id., amoxicillin 1 g b.i.d., and clarithromycin 500 mg b.i.d.) 13 cases based on the antimicrobial susceptibility testing. Twelve patients showed triple H. pylori-resistance (clarithromycin, metronidazole and levofloxacin) and received for 10 d triple therapy with OAR (omeprazole 20 mg b.id., amoxicillin 1 g b.i.d., and rifabutin 150 mg b.i.d.). Eradication was confirmed by 13C-urea breath test. Adverse effects and compliance were assessed by a questionnaire.RESULTSIntention-to-treat eradication rates were: OAL (97.6%), OAM (91.6%), OAC (92.3%) and OAR (58.3%). Cure rate was significantly higher in naïve patients treated with OAR-10 compared to patients who had two or three previous treatment failures (83% vs 33%). Adverse events rates for OAL, OAM, OAC and OAR were 22%, 25%, 23% and 17%, respectively, all of them mild-moderate.CONCLUSIONAntimicrobial susceptibility-guided triple therapies during 10 d for first-line treatment leads to an eradication rate superior to 90% in patients with dual antibiotic H. pylori resistance.

External Bacterial Flora and Antimicrobial Susceptibility Patterns of Staphylococcus spp. and Pseudomonas spp. Isolated from Two Household Cockroaches, Blattella germanica and Blatta orientalis

A study was performed to estimate the prevalence of the external bacterial flora of two domestic cockroaches （Blattella germanica and Blatta orientalis） collected from households in Tebessa （northeast AIgeria）.Three major bacterial groups were cultured （total aerobic, enterobacteria, and staphylococci） from 14 specimens of cockroaches, and antibiotic susceptibility was tested for both Staphylococcus and Pseudomonas isolates. Culturing showed that the total bacterial load of cockroaches from different households were comparable （P〈0.001） and enterobacteria were the predominant colonizers of the insect surface, with a bacterial load of （2.1×10^5 CFU/insect）, whereas the staphylococci group was the minority. Twenty-eight bacterial species were isolated, and susceptibility patterns showed that most of the staphylococci isolates were highly susceptible to chloramphenicol, gentamycin, pristinamycin, ofloxacin, clindamycin, and vancomycin; however, Pseudomonas strains exhibited resistance to amoxicillin/clavulanic acid, imipenem, and the second-generation antibiotic cephalosporin cefuroxime.

Genetic Characteristics and Antimicrobial Susceptibility of Arcobacter butzleri Isolates from Raw Chicken Meat and Patients with Diarrhea in China

Arcobacter is an emerging foodborne pathogen worldwide.In this study,the prevalence,antimicrobial susceptibility and genetic characteristics of Arcobacter from different sources were investigated.Eighteen A.butzleri isolates were obtained from 60 raw chicken meat samples(16/60,27%)and 150 patients with diarrhea(2/150,1.3%).The resistance ratios to nalidixic acid,ciprofloxacin,clindamycin,chloramphenicol,and florfenicol were 83.33%(15/18),38.89%(7/18),38.89%(7/18),33.33%(6/18)and 33.33%(6/18),respectively.We performed whole genome sequencing of the 18 isolates,and we predicted antibiotic resistance genes and virulence factors by using assembled genomes through blastx analysis.Two resistance genes,blaOXA-464 and tet(H),and the C254T mutation in gyrA,were identified in the genomes of some resistant isolates.Furthermore,virulence genes,such as flgG,flhA,flhB,fliI,fliP,motA,cadF,cjl349,ciaB,mviN,pldA and tlyA,were found in all strains,whereas hecA,hecB and iroE were found in only some strains.Phylogenetic tree analysis of A.butzleri isolates on the basis of the core-genome single nucleotide polymorphisms showed that two isolates from patients with diarrhea clustered together,separately from the isolates from raw chicken and the chicken strains.This study is the first comprehensive analysis of Arcobacter isolated in Beijing.

Prevalence and antimicrobial susceptibility patterns of bacteria in ICU patients with lower respiratory tract infection: A cross-sectional study

Objective: To investigate the prevalence of isolated organisms in patients with lower respiratory tract infections and the antibiotic susceptibilities at a tertiary care center. Methods: In this observational and cross-sectional analysis, 114 patients admitted in the intensive care unit were enrolled. The endotracheal aspirates and bronchoalveolar lavage were collected. The bacteria were isolated and identified, and finally, antimicrobial sensitive pattern of the isolated bacteria was examined. Results: The prevalence of infection was 72.72% in male patients and 27.28% in females. The predominant bacteria were Klebsiella pneumoniae (37.50%) followed by Acinetobacter spp. (36.36%), Pseudomonas aeruginosa (7.95%),Escherichia coli (6.81%), Proteus mirabilis (2.27%), atypical Escherichia coli (1.13%), Enterococcus spp. (1.13%),Elizabethkingia meningoseptica (1.13%),Staphylococcus aureus (1.13%),Proteus vulgaris (1.13%), Citrobacter freundii (1.13%), and Citrobacter koseri (1.13%). High resistance to cephalosporins (82.18%) was demonstrated in all Gram-negative bacteria. Bacteria showed susceptibility to colistin (88.75%) followed by tigecycline (83.11%), gentamycin (36.18%), and amikacin (49.23%). Conclusions: As the most frequent respiratory organisms, Klebsiella pneumoniae and Acinetobacter spp. have increased resistance to cephalosporins and susceptibility to colistin followed by tigecycline.

Streptococcus agalactiae:Identification methods,antimicrobial susceptibility, and resistance genes in pregnant women

BACKGROUND Group B Streptococcus(GBS)is a normal component of the gastrointestinal and genital microbiota in humans and can lead to important infections in newborns.AIM To compare GBS isolation and identification methods as well as to assess the antibiotic susceptibility and to identify resistance genes in GBS strains from pregnant women attended in healthcare services from the city of Vitória da Conquista,in Bahia State,Brazil.METHODS From January 2017 to February 2018,vaginorectal swabs were obtained from 186 participants and the samples were seeded onto chromogenic agar for GBS before and after inoculation in selective broth.Confirmatory identification using 3 CAMP and latex tests was performed in samples with GBS-suggestive colonies.Then,disk diffusion antibiograms were performed in GBS-positive samples,and the detection of the resistance genes ermB,ermTR,mefA,and linB in the clindamycin and/or erythromycin-resistant samples was carried out.RESULTS Thirty-two samples(17.2%)were GBS-positive.The culture in chromogenic agar after sample incubation in selective broth was the most sensitive method(96.9%)for GBS detection.All isolates were susceptible to penicillin,ampicillin,cefotaxime,and vancomycin.Clindamycin resistance was observed in 6 samples(18.8%),while 8 samples(25%)were erythromycin-resistant.All erythromycin and/or clindamycin-resistant GBS strains had negative D-tests.Two strains(25%)presented an M phenotype and 6 isolates(75%)presented a cMLSB phenotype.The ermB gene was identified in 4 samples(44.4%),the mefA gene was also found in 4 samples(44.4%),the ermTR gene was identified in 1 isolate(11.1%),and the linB gene was not found in any isolate.CONCLUSION This study evidenced that the screening for SGB can be performed by means of various methods,including chromogenic media,and that the chemoprophylaxis for pregnant women who cannot use penicillin must be susceptibility-guided.

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.

Antimicrobial Susceptibility Patterns of Staphylococcus aureus Strains Isolated at the Namibia Institute of Pathology from 2012 to 2014

Staphylococcus aureus (S. aureus) is known to acquire resistance to new drugs and continues to defy at-tempts to control it. Infections caused by antibiotic resistant strains of S. aureus have reached epidemic proportions globally and the increasing rates of antimicrobial resistance are resulting in fewer treatment options. Methicillin resistant S. aureus (MRSA) has also emerged as a serious therapeutic problem worldwide. However, data on the antimicrobial susceptibility patterns of this bacterium over a period of time in Namibia are not available. A descriptive retrospective study was therefore conducted to investigate the antimicrobial susceptibility patterns of 600 Staphylococcus aureus strains isolated at the Namibia Institute of Pathology (NIP) from January 2012 to December 2014. The results showed that a high proportion of isolates were resistant to penicillin (92.4%) and cotrimoxazole (44.9%), while the antibiotics to which the isolates were least resistant included vancomycin (0%), fusidic acid (0.3%) and ciprofloxacin (4.4%). Methicillin resistance was observed in 13.5% of the staphylococcal isolates. Apart from clindamycin (P value = 0.039) and cotrimoxazole (P value = 0.030), the susceptibility patterns of the antibiotics did not differ significantly over the three years. Moreover, wound swabs and sputum were the clinical samples from which S. aureus was most commonly isolated at NIP. The results from this study suggest that continuous local surveillance on the resistance patterns of S. aureus should be performed on regular basis in Namibia, in order to have adequate information for the empirical treatment of S. aureus infections.

Genomic characterization and antimicrobial susceptibility of bovine intrauterine Escherichia coli and its relationship with postpartum uterine infections

To investigate the roles of Escherichia coli in the pathogenesis of postpartum uterine diseases in dairy cows, a total of 145 E. coli isolates were recovered from 18 healthy cows （61 isolates） and 25 cows with clinical endometritis （84 isolates） at 25-35 days after parturition. Genomic characteristics including phylogenetic grouping, genetic diversity and virulence genes of E. coli isolates were screened to profile the characteristics related to uterine infections. The susceptibility of the bacteria against 23 antibiotics was also evaluated to support prevention and treatment of clinical cases. Genetic diversity of E. coli identified by random amplification of polymorphic DNA （RAPD） revealed 103 clonal types, including 3 common types to unaffected cows and endometritis cows, 39 types specific to healthy cows and 61 types in endometritis subjects. In addition, the isolates from endometritis uteri showed more genetic variability compared with that of healthy cows. Ac- cording to the findings of phylogenetic grouping, the E. coil isolates were assigned to group A （35.9%）, B1 （59.3%） and D （4.8%）. The expression of 10 of 20 virulence gens were detected positively, and only fimH gene was revealed significantly （P〈0.05） associated with endometritis. From antimicrobial susceptibility test, E. coli was found highly resistant to tetracy- cline, ampicillin, carbenicillin and amoxicillin, but sensitive to amikacin, netilmicin, tobramycin, cefepime and ceftazidime. In conclusion, E. cofiwere extensively observed in both healthy and endometritis cows, and presented a large clonal types, however, fimH was the only gene observed associated with clinical endometritis. Our results suggest that the drugs like amikacin, netilmicin, tobramycin and cefepime could be considered for preventing and treating clinical endometritis in the practical management of dairy cow.

Antimicrobial Susceptibility of Streptococcus sp. to Quinupristin-dalfopristin in China

This study aimed to determine the in vitro activity of quinupristin-alfopristin against Streptococcus sp. isolated in China. This agent is not yet available for clinical use, but it has been tested against a high proportion of resistant Staphylococcus oureus strains. A total of 156 streptococcal isolates, which were recovered from various geographic areas and diseases, were tested using the Etest （AB Biodisk, Solna, Sweden）. Quinupristin-alfopristin showed excellent activity against all of the tested streptococci isolates. These results provide useful data for the clinical use of quinupristin-alfopristin in China.

Enumeration,Genetic Characterization and Antimicrobial Susceptibility of Lactobacillus and Streptococcus Isolates from Retail Yoghurt in Beijing,China

Lactic acid bacteria （LAB） are widely used in food industries. Correct identification and safety evaluation of these bacteria at the species even strain level should take considerations into account. In this study, the LAB were recovered from yoghurt and characterized phenotypically and genetically. Fifty-two isolates of LAB from 31 yoghurt samples were cultured and grouped into 6 species including Luctobucillus bulguricus （24 isolates）, Streptococcus thermophilus （15 isolates）, L. ucidophilus （7 isolates）, L. porucusei/cusei （3 isolates）, L. delbrueckii （2 isolates）, and L. fermentum （1 isolate）, based on their Gram-staining, colony morphology and biochemical properties.

Urinary Tract Infection among Adults Seeking Medicare at Kiambu Level 5 Hospital, Kenya: Prevalence, Diversity, Antimicrobial Susceptibility Profiles and Possible Risk Factors

Urinary tract infections are among the most prevalent extra-intestinal infections, with high prevalence globally. This cross-sectional study established prevalence of bacterial aetiology causing urinary tract infection (UTI) and their antimicrobial susceptibility profiles. A questionnaire was used to capture socio-demographic data and possible UTI risk factors among the 206 consented adults seeking medicare at Kiambu Level 5 Hospital. The collected midstream urine samples were subjected to dipstick analysis, microscopy and culture for UTI diagnosis. Results: The overall prevalence rate of UTIs was 27.6%, with women’s prevalence rate being significantly higher at 80.7% compared to men 19.2%. Pregnant women had UTI prevalence at 34% which was higher than other sets of participants. Women who did not frequently change their underpants daily had a higher UTI cases at 34.8%. Escherichia coli, Staphylococcus aureus and Klebsiella pneumoniae were the most prevalent bacterial pathogens at 38.5%, 21% and 19.3%, respectively. Antimicrobial sensitivity analysis revealed high resistances towards Sulfamethoxazole and Ampicillin at range between 50% - 85%, suggesting that these drugs are no longer effective for UTI empirical treatment. The resistance patterns towards Cefotaxime, Cefepime and Ciprofloxacin were below 40%. However, more resistance patterns at a range between 14% - 40% revealed towards Amoxicillin-clavulanic and Nitrofurantoin imply that these are drugs remain potent but there is the need to revise the current UTI management guidelines. In addition, to elude treatment failure, innovation of prophylactic measures is key to halt UTI contraction and offer support to pharmaceutical industries that have fewer new antibiotics in the pipeline.

Bacteriological Profile, Antimicrobial Susceptibility Patterns and Predictors of Bacteremia in Neonates with Clinical Sepsis at KCMC Hospital, Northern Tanzania

Background: Despite a significant decline in neonatal deaths in the last 20 years (5 million in 1990 to 2.4 million in 2019), the risk of death is still high, especially in developing countries. In Tanzania, neonatal sepsis is the third leading cause of neonatal death, accounting for 25% of all deaths. The rising global threat of antimicrobial resistance and the rising burden of neonatal death due to neonatal sepsis have been of great concern and have delayed progress toward reaching SDG goal 3.2 by 2030. This study aims to determine the bacteriological profile, antibiotic susceptibility patterns, and predictors of bacteremia among neonates with clinical sepsis at KCMC Hospital in Northern Tanzania. Methodology: This study had a cross-sectional design conducted at KCMC Hospital, Northern Tanzania. The study population was neonates admitted to the neonatal unit at KCMC Hospital. Data were collected using questionnaires and blood cultures from neonates. Frequencies and proportions were used to summarize categorical variables, while continuous variables were summarized using mean and standard deviation. The frequencies and proportions of bacteria isolated and the antimicrobial susceptibility results were analyzed and compared using Pearson’s chi-square test and Fisher’s exact test where applicable. Modified Poisson regression model was used to determine factors associated with positive blood culture. Results: Out of 411 neonates with a clinical diagnosis of neonatal sepsis, 175 (42.9%) had positive blood cultures. Gram-positive bacteria were most frequently isolated at 52.3%, and gram-negative bacteria were 47.7%. Coagulase-negative Staphylococcus (30.7%) and Staphylococcus aureus (19.9%) were the predominant gram-positive isolates. Gram-negative isolates were Klebsiella spp 47 (26.7%), E. coli 10 (5.7%), and Citrobacter spp 10 (5.1%). The gram-positive isolates were sensitive to vancomycin, piperacillin/tazobactam, and ceftazidime, whereas the gram-negative were sensitive to amikacin, meropenem, and vancomycin. The study did not find statistically significant associations between clinical factors and positive blood cultures in bacteremia. Conclusion: Gram-positive bacteria are the dominant pathogens in early-onset and late-onset neonatal sepsis. High levels of resistance to ampicillin and ceftriaxone and moderate resistance to gentamycin were observed in both gram-positive and gram-negative bacteria. Gram-positive organisms exhibit better susceptibility rates to vancomycin and ciprofloxacin, while gram-negative micro-organisms are more sensitive to amikacin and meropenem. An effective initial treatment approach for neonatal sepsis would involve a combination of drugs.

Clinical characteristics,molecular epidemiology and antimicrobial susceptibility of pertussis among children in southern China

Background Increasing numbers of pertussis cases have been reported in recent years.The reported cases from Shenzhen Children's Hospital were close to one tenth of all cases in China.The epidemiology of antigenic genotype and antibiotic resistance of circulating strains in children have been unknown in Shenzhen,southern China.The aim of this study was to describe the clinical features and explore the genotypes and antimicrobial susceptibility of circulating Bordetella pertussis among children in Shenzhen.Methods Data of hospitalized children with pertussis in Shenzhen Children's Hospital from August 2015 to April 2017 were collected.The genetic variability of isolates was investigated and Etest was performed for phenotypic susceptibility to erythromycin,azithromycin,clarithromycin,clindamycin,and trimethoprim/sulfamethoxazole.Results 469 children with pertussis confirmed by real-time quantitative polymerase chain reaction were hospitalized and strains were isolated from 105 patients.White blood cell count≥20×10^9/L and lymphocyte proportion≥60%were observed in 39.29%of infants younger than 3 months.The two predominant profiles of virulence-associated allelic genes were ptxA1/ptxC1/ptxPl/prnl(48.6%)and ptxA1/ptxC2/ptxP3/prn2(44.8%).Among the isolates,48.6%(51/105)were found resistant to macrolides.Conclusions These findings indicate that leukocytosis is not a sensitive indicator of pertussis.Isolates with the gene profile ptxP3/prn2 were highly circulating in Shenzhen and less resistant to macrolides,different from patterns observed in other parts of China.

Molecular characteristics and antimicrobial susceptibility of Staphylococcus aureus among children with respiratory tract infections in southwest China

Background The molecular characteristics and antimicrobial susceptibility of Staphylococcus aureus (S.aureus) in general pediatric wards and county-level hospitals were rarely reported in China.Methods Staphylococcus aureus was isolated from children hospitalized with respiratory tract infection (RTI) in Zhongjiang and Youyang counties in 2015.All isolates were typed by multilocus sequence,staphylococcal protein A,accessory gene regulator (agr),and staphylococcal cassette chromosome mec [SCCmec,for methicillin-resistant S.aureus (MRSA) only].Polymerase chain reaction was used to screen 21 super-antigen (SAg) genes and panton-valentine leukocidin (pvl).Antimicrobial susceptibility testing was performed by E test.Results A total of 2136 children were enrolled.Overall,125 (5.9%) children carried S.aureus,among which MRSA accounted for 42.4%.ST59-SCCmec type Ⅳ-t437-agr group Ⅰ (58.5%) was the most prevalent genotype in MRSA,and ST188-t189-agr group Ⅰ (22.2%) was the top genotype in methicillin-sensitive S.aureus (MSSA).The pvl carriage rate in MRSA and MSSA was 15.1% and 9.7%,respectively (P =0.4112).About 96.8% of S.aureus isolates were positive for at least one SAg gene.The most common SAg gene profile in the dominant ST59 clone was seb-sek-seq (42.8%).All S.aureus isolates were resistant to penicillin and erythromycin (minimum inhibitory concentration 90 was > 32 and 256 mg/L to penicillin and erythromycin,respectively),but usually susceptible to other tested non-β-lactam antimicrobials.Conclusions Staphylococcus aureus and MRSA were detected with a high frequency in children with RTI in county-level hospitals of China.ST59-SCCmec type Ⅳ-t437-agr group Ⅰ was the dominant MRSA clone.The S.aureus isolates exhibited high resistance to penicillin and erythromycin.

Epidemiologically characteristics of human brucellosis and antimicrobial susceptibility pattern of Brucella melitensis in Hinggan League of the Inner Mongolia Autonomous Region,China

Background:Hinggan League is located in the Northeast of the Inner Mongolia Autonomous Region,the historically endemic area of animal and human brucellosis.In this study,the epidemiological characteristics of human brucellosis were analyzed,and the genotypic profile and antimicrobial susceptibilities of Brucella melitensis strains isolated from humans in Hinggan League were investigated.Methods:The epidemic characteristics were described using case number,constituent ratio,and rate.The 418 human blood samples were collected and tested by bacteriology,and suspect colonies were isolated and identified by conventional biotyping assays,the VITEK 2.0 microbial identification system,and AMOS(Brucella abortus,B.melitensis,B.ovis,and B.suis)-PCR.Subsequently,all strains were genotyped using multiple-locus variable-number tandem repeat analysis(MLVA)assays,and the antimicrobial susceptibility pattern of Brucella strains against the 10 most commonly used antibiotics was determined by microdilution method.Results:A total of 22848 cases of human brucellosis were reported from 2004 to 2019,with an annual average incidence of 87.2/100000.The incidence rates in developed areas of animal husbandry(Horqin Youyi Qianqi[161.2/100000]and Horqin Youyi Zhongqi[112.1/100000])were significantly higher than those in forest areas(Arxan[19.2/100000])(χ2=32.561,P<0.001).In addition,peak morbidity occurred during May–August,accounting for 72.6%(16582/22848)of cases.The highest number of cases occurred in the 40+age group,accounting for 44.4%(10137/22484)of cases,and morbidity in males was significantly higher than that in females in all age groups(χ2=299.97,P<0.001),the most common occupation was farmers.A total of 54 B.melitensis strains were divided into 37 genotypes(GT1–37)with 80–100%genetic similarity.All 25 strains were sensitive to seven tested antibiotics,phenotypic resistance to cotrimoxazole and azithromycin was observed in 5(20%)and 25(100%)of the isolates,respectively.Conclusions:Human brucellosis exhibited a significant increasing trend and B.melitensis is the main pathogen responsible for human brucellosis in this region.Improved surveillance of infected animals(sheep)and limiting their transfer and trade are optional strategies for decreasing the incidence of this disease.

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.

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.

Antimicrobial susceptibility testing in veterinary medicine:performance,interpretation of results,best practices and pitfalls

The performance of antimicrobial susceptibility testing(AST)of bacteria and the interpretation of AST results for bacteria isolated from animals are complex tasks which must be performed using standard published methodology and overseen by experts in clinical microbiology and in consultation with clinical pharmacologists.Otherwise,AST has significant potential for errors and mistakes.In this review,we provide guidance on how to correctly perform AST of bacteria isolated from animals and interpret the AST results.Particular emphasis is placed on the various approved or published methodologies for the different bacteria as well as the application of interpretive criteria,including clinical breakpoints and epidemiological cut-off values(ECVs/ECOFFs).Application of approved interpretive criteria and definitions of susceptible,susceptible dose-dependent,nonsusceptible,intermediate,and resistant for clinical breakpoints as well as wild-type and non-wildtype for ECVs,are explained and the difficulties resulting from the lack of approved clinical breakpoints for other bacteria,indications,and animal species is discussed.The requirement of quality controls in any AST approach is also emphasized.In addition,important parameters,often used in monitoring and surveillance studies,such as MIC50,MIC90,and testing range,are explained and criteria for the classification of bacteria as multidrug-resistant,extensively drug-resistant or pandrug-resistant are provided.Common mistakes are presented and the means to avoid them are described.To provide the most accurate AST,one must strictly adhere to approved standards or validated methodologies,like those of the Clinical and Laboratory Standards Institute or other internationally accepted AST documents and the detailed information provided therein.