Secondary Antibiotic Resistance Research Articles

Functional Genomics of a Collection of Gammaproteobacteria Isolated from Antarctica.

Antarctica, one of the most extreme environments on Earth, hosts diverse microbial communities. These microbes have evolved and adapted to survive in these hostile conditions, but knowledge on the molecular mechanisms underlying this process remains limited. The Italian Collection of Antarctic Bacteria (Collezione Italiana Batteri Antartici (CIBAN)), managed by the University of Messina, represents a valuable repository of cold-adapted bacterial strains isolated from various Antarctic environments. In this study, we sequenced and analyzed the genomes of 58 marine Gammaproteobacteria strains from the CIBAN collection, which were isolated during Italian expeditions from 1990 to 2005. By employing genome-scale metrics, we taxonomically characterized these strains and assigned them to four distinct genera: Pseudomonas, Pseudoalteromonas, Shewanella, and Psychrobacter. Genome annotation revealed a previously untapped functional potential, including secondary metabolite biosynthetic gene clusters and antibiotic resistance genes. Phylogenomic analyses provided evolutionary insights, while assessment of cold-shock protein presence shed light on adaptation mechanisms. Our study emphasizes the significance of CIBAN as a resource for understanding Antarctic microbial life and its biotechnological potential. The genomic data unveil new horizons for insight into bacterial existence in Antarctica.

Helicobacter pylori Secondary Antibiotic Resistance after One or More Eradication Failure: A Genotypic Stool Analysis Study.

Helicobacter pylori (H. pylori) antibiotic resistance is the leading cause for unsuccessful eradication therapy. After one or more failures, the chance of encountering secondary antibiotic resistance increases. The aim of this study was to characterize genotypic secondary resistance in a cohort of southern Italian H. pylori patients with at least one previous failure. Such patients collected stool samples using a dedicated kit (THD fecal testTM), and bacterial DNA was extracted and amplified using RT-PCR. Resistance to clarithromycin, amoxicillin, metronidazole, levofloxacin, and tetracycline was assessed using a high-resolution melting curve. We enrolled 50 patients. A total of 72% of patients failed one previous antibiotic course, 16% failed two, 10% failed three, and 2% failed four. The rate of secondary antibiotic resistance was 16% for clarithromycin, 18% for metronidazole, 14% for amoxicillin, 14% for levofloxacin, and 2% for tetracycline. Among the eight clarithromycin-resistant patients, five (62.5%) previously received a clarithromycin-based regimen. The same rate was 33.3% (3/9) for metronidazole. The only tetracycline-resistant patient had received Pylera. In conclusion, our data seem to show that, even though secondary resistance is not very high, resistance to clarithromycin could be very likely related to previous exposure to this antibiotic.

The Effects of SARS-CoV-2 Pandemic on the Distribution of Secondary Bacterial Pneumonia Agents and Antibiotic Resistance Profile in Intensive Care Units

Since the World Health Organization declared COVID-19 (Coronavirus Disease 2019) a pandemic on March 11, 2020, SARS-CoV-2 has caused high rates of morbidity and mortality worldwide. The addition of secondary bacterial infections such as pneumonia to the clinical course led to more mortality of the disease. This situation has led to an increase in the use of antibiotics for both prophylactic and therapeutic purposes and has caused concerns about the increase in antibiotic resistance rates and multi-drug resistant strains. 679 COVID-19 patients (Group 1) with a diagnosis confirmed by polymerase chain reaction (PCR) and 366 patients who were followed up in the anesthesia intensive care unit (ICU) during the pandemic but had negative SARS-CoV-2 PCR test results (Group 2) were included in this study; all of them were treated in the ICU of our hospital between April 2020 - May 2022. In order to observe the possible effects of SARS-CoV-2 infection on the distribution of the causative agent and changes in antibiotic resistance patterns, the data of 363 patients (Group 3) who were treated in the anesthesia ICU between April 2017 and May 2019 (pre-pandemic period) were analyzed. Bacterial agents isolated from tracheal aspirate samples and antibiotic resistance rates of 1408 patients in the groups were determined. Pathogenic microorganism growth was detected in the tracheal aspirate samples of 430 (63.3%) of the patients followed in the COVID-19 ICUs. In the patients followed in COVID-19 ICUs, as secondary bacterial pneumonia agents, in order of frequency; Acinetobacter baumannii (39.6%), Klebsiella pneumoniae (35.5%) and Pseudomonas aeruginosa (3.5%) were isolated. A. baumannii and K. pneumoniae isolation rates were significantly higher in COVID-19 patients (Group 1) compared to non-COVID-19 ICU patients (Group 2) and were similarly higher in all patients in the pandemic period (Group 1 + Group 2) compared to the pre-epidemic period (p<0.001). Other remarkable findings were the presence of high antibiotic resistance rates in A. baumannii and K. pneumoniae strains isolated during the pandemic period, compared to the pre-pandemic period, and the observation of multi-drug resistance in the vast majority of isolates. In order to prevent the increased risk of mortality associated with concomitant secondary bacterial infections in patients followed in ICUs due to COVID-19; It is important to evaluate patients quickly in terms of bacterial infections, to take timely and appropriate antibiotic treatment and to take necessary isolation measures.

COVID-19 Pnömonili Hastaların Solunum Yolu Örneklerinde Sekonder Bakteriyel Ajanlar ve Antibiyotik Direnç Profilleri

Objective: To assess secondary bacterial pneumonia agents and antibiotic resistance rates in patients with COVID-19 pneumonia and to compare findings with the pre-pandemic period. Materials and Methods: Bacteria grown in endotracheal aspirate fluid and bronchoalveolar fluid samples of patients diagnosed with COVID-19 between January 2020 and December 2020, and antibiotic resistance rates were retrospectively compared with samples of the year before the pandemic. Isolates were identified at the species level with an automated system (VITEK 2, bioMérieux, France), and antimicrobial susceptibility was determined according to EUCAST criteria. Results: A total of 900 culture results were examined in 2019. Acinetobacter baumannii was detected in 36%, Klebsiella pneumoniae in 23%, Pseudomonas aeruginosa in 14%, and Staphylococcus aureus in 8%. In 2020, 660 culture results were examined, and the same bacteria were detected in 43%, 23%, 16%, and 5%, respectively. K. pneumoniae's resistance to third-generation cephalosporins, and A. baumannii's resistance to gentamycin and tobramycin, were found to have increased significantly during the pandemic period. Conclusions: The growth of multidrug-resistant Gram-negative bacteria was frequently detected in respiratory secretions obtained during the COVID-19 pandemic. Regional bacterial agents and antibiotic resistance profiles should be clarified, and empirical therapy should be selected accordingly in COVID-19.

Regulation of Multidrug Efflux Pumps by TetR Family Transcriptional Repressor Negatively Affects Secondary Metabolism in Streptomyces coelicolor A3(2).

Streptomyces spp. are well-known producers of bioactive secondary metabolites (SMs) that serve as pharmaceutical agents. In addition to their ability to produce SMs, Streptomyces spp. have evolved diverse membrane transport systems to protect cells against antibiotics produced by itself or other microorganisms. We previously screened mutants of Streptomyces coelicolor that show a phenotype of reduced undecylprodigiosin (RED) production in a combined-culture with Tsukamurella pulmonis. Here, we identified a point mutation, which reduced RED production, by performing genome resequencing and genetic complementation. We found that inactivation of the sco1718 gene encoding the TetR family transcriptional regulator (TFR) produced a deficient phenotype for several SMs in Streptomyces coelicolor A3(2). In the genome of S. coelicolor A3(2), two other sets of TFR and two-component ATP-binding cassette (ABC) transporter genes (sco4358-4360 and sco5384-5382) were found which had similar effects on the phenotype for both secondary metabolism and antibiotic resistance. An electrophoretic mobility shift assay and quantitative reverse transcription-PCR experiments demonstrated that TFRs repressed the expression of each adjacent two-component ABC transporter genes by binding to the operator sequence. Notably, the Δsco1718 mutant showed increased resistance to several antibiotics of other actinomycete origin. Our results imply the switching of cell metabolism to direct offense (antibiotic production) or defense (efflux pump activation) using costly and limited quantities of cell energy sources (e.g., ATP) in the soil ecosystem. IMPORTANCE The bacterial metabolic potential to synthesize diverse secondary metabolites in the environment has been revealed by recent (meta)genomics of both unculturable and culturable bacteria. These studies imply that bacteria are continuously exposed to harmful chemical compounds in the environment. Streptomyces spp. contain antibiotic efflux pumps and SM biosynthetic gene clusters. However, the mechanism by which soil bacteria, including Streptomyces, survive against toxic compounds in the environment remains unclear. Here, we identified three sets of TFR-ABC transporter genes in Streptomyces coelicolor A3(2). We found that each TFR controlled the expression of respective ABC transporter, and the expression of all ABC transporters negatively impacted SM production and increased antibiotic resistance. Notably, bioinformatic analysis indicated that these TFR-ABC transporter gene sets are highly conserved and widely distributed in the genome of Streptomyces species, indicating the importance of systematic regulation that directs antibiotic production and xenobiotic excretion.

Safety Evaluation of Bacillus subtilis IDCC1101, Newly Isolated from Cheonggukjang, for Industrial Applications.

The present study aimed to evaluate the safety of Bacillus subtilis (BS) IDCC1101, newly isolated from Cheonggukjang in Korea. Genome sequencing of BS IDCC1101 was performed to investigate the presence of secondary metabolites, virulence, antibiotic resistance, and mobile elements. Its phenotypic safety analyses included antibiotic susceptibility, enzyme activity, carbohydrate utilization, production of biogenic amines (BAs) and D-/L-lactate, hemolytic activity, and toxicities in HaCaT cells and rats. The genome of BS IDCC1101 consisted of 4,118,950 bp with 3077 functional genes. Among them, antimicrobial and antifungal secondary metabolites were found, such as fengycin, bacillibactin, and bacilysin. Antibiotic resistance and virulence genes did not exhibit transferability since they did not overlap with mobile elements in the genome. BS IDCC1101 was susceptible to almost all antibiotics suggested for assessment of BS's antibiotic susceptibility by EFSA guidelines, except for streptomycin. BS IDCC1101 showed the utilization of a wide range of 27 carbohydrates, as well as enzyme activities such as alkaline phosphatase, esterase, esterase lipase, naphthol-AS-BI-phosphohydrolase, α-galactosidase, β-galactosidase, α-glucosidase, and β-glucosidase activities. Additionally, BS IDCC1101 did not exhibit the production of D-/L-lactate and hemolytic activities. Its toxicity in HaCaT cells and rats was also not detected. Thus, these genotypic and phenotypic findings indicate that BS IDCC1101 can be safely used for industrial applications.

270. Secondary bacterial infection in hospitalized COVID-19 patients. Experience in Colombia, South America

Abstract Background Secondary infections are common among severe COVID-19 patients, increasing complications and mortality risk. These infections are not well characterized in Latin America and the Caribbean. Methods A cross-sectional observational study of adult patients with COVID-19 admitted to the hospital Fundación Valle del Lili in Cali-Colombia from March 2020 to March 2021. Demographic data, clinical characteristics, laboratory parameters, and clinical outcomes were collected. We describe secondary infection, antibiotic therapy, and antibiotic resistance profiles. Secondary infection was defined if the diagnosis occurred ≥48 hours after hospital admission for COVID-19. Results A total of 2138 patients with COVID-19 were analyzed; 350 (16.3%) presented secondary infection. 60% were male; the median age was 65 years [IQR: 55-72]. Glucocorticoid therapy was indicated in 335 patients (96.3%). 281 received high doses and 54 low doses. Bacterial infections were the most common, affecting 81.3 % of patients, followed by fungal (14.4%) and viral (4.3%) infections. Most bacterial isolates were orotracheal secretion, blood, urine, and bronchoalveolar lavage fluid culture. The three most frequently identified bacteria were Klebsiella pneumoniae, Staphylococcus aureus, and Pseudomonas aeruginosa. Most of the initial isolates were not antibiotic-resistant (75-89.7%). Empiric antibiotic therapy was indicated in 346 patients (98.9%), 268 received carbapenems (76.6%), 267 Vancomycin (76.3%), and 233 cefepime (66.6%). Of the 350 patients, 327 (93.4%) required management in the intensive care unit, and overall mortality was 35.4% (124/350). Conclusion Our results showed a lower frequency of secondary infection than previous reports; However, a high frequency of broad-spectrum antibiotics usage was found despite a high prevalence of non-resistant bacteria. Further studies are needed to establish the best approach for antibiotics therapy. Disclosures All Authors: No reported disclosures.

Multidrug-Resistant Helicobacter pylori Strains: A Five-Year Surveillance Study and Its Genome Characteristics.

Background: The emergence of multidrug-resistant Helicobacter pylori has undermined eradication strategies to prevent the development of gastric cancer. This study was conducted to estimate the prevalence of secondary antibiotic resistance of H. pylori in urban multicultural areas in Malaysia. Methods: From January 2017 to December 2021, gastric biopsies from 218 patients with a history of H. pylori eradication failure were sent to our laboratory for antibiotic susceptibility testing. A minimal inhibitory concentration was determined for six antibiotics, namely metronidazole, clarithromycin, levofloxacin, amoxicillin, tetracycline, and rifampicin using the E-test method. Two multidrug-resistant H. pylori strains identified in this study were subjected to whole genome sequencing. Results: Eradication failure was observed to be significantly higher in the Malaysian Chinese patients than in the Malaysian Indian and Malay patients. H. pylori were successfully isolated from 51 patients (23.4%). Overall, the antibiotic resistance rates of H. pylori to metronidazole, clarithromycin, levofloxacin, and amoxicillin were 82.4% (42/51), 72.5% (37/51), 52.9% (27/51), and 3.9% (2/51), respectively. Resistance to tetracycline and rifampicin were not observed during the study period. Resistance to more than one antibiotic was observed in 82.4% (42/51) of the isolates, of which 42.2% (19/42) were resistant to three antibiotic classes. Resistance to both clarithromycin and metronidazole were most frequently observed in isolates with dual resistance (56.5%; 13/23). Codon substitutions in penicillin-binding protein 1A (V346L, V374L, G595_V596InsG, Y604H, and N608S) were detected in amoxicillin-resistance H. pylori strains. Herein, we report amoxicillin resistance in H. pylori isolated from Malaysian patients, and its resistance mechanism, for the first time. Conclusion: Our results show the increase trend in secondary multidrug resistance in H. pylori isolates, which warrants continuous surveillance.

Aetiology and antibiotic susceptibility pattern of bacterial pathogens in respiratory specimens of COVID-19 patients on respiratory support: A tertiary care hospital study.

Objective: To describe aetiology and antibiotic susceptibility pattern of bacterial pathogens in respiratory specimens of covid-19 patients on respiratory support in tertiary care hospital of Lahore. Study Design: Descriptive study. Setting: Microbiology Department, CMH, Lahore. Period: May 2021 to October 2021. Material & Methods: A total 107 isolates from 145 patients who were COVID-19 positive and on respiratory support were included in the study. Bacterial isolates were isolated from clinical samples according to standard protocol of culturing and incubation. Antibiotic sensitivity, carbapenamase detection was done according to CLSI 2021. Molecular identification of carbapenem resistant genes blaIMP and blaVIM was determined by PCR. Results: A total of 107 bacterial isolates were isolated from clinical specimens. A. baumannii was the most common isolated organism. Colistin and aminoglycosides were found to be the most effective antibiotics. Among carbapenem resistant isolates 89.5% were MHT positive and among these 59 (86.8%) were MBL positive. Among MBL positive isolates, 5.61% and 29.91% were positive for blaIMP and blaVIM respectively. Conclusion: Patients admitted for COVID-19 treatment are at higher risk of acquisition of secondary bacterial infections and antibiotic resistance among such pathogens is at alarming.

Efficacy and safety of high-dose esomeprazole-amoxicillin dual therapy for Helicobacter pylori rescue treatment: a multicenter, prospective, randomized, controlled trial.

Background:High-dose dual therapy (HDDT) with proton pump inhibitors (PPIs) and amoxicillin has attracted widespread attention due to its favorable efficacy in eradicating Helicobacter pylori (H. pylori). This study aimed to compare the efficacy and safety of high-dose PPI–amoxicillin dual therapy and bismuth-containing quadruple therapy for H. pylori rescue treatment.Methods:This was a prospective, randomized, multicenter, non-inferiority trial. Patients recruited from eight centers who had failed previous treatment were randomly (1:1) allocated to two eradication groups: HDDT (esomeprazole 40 mg and amoxicillin 1000 mg three times daily; the HDDT group) and bismuth-containing quadruple therapy (esomeprazole 40 mg, bismuth potassium citrate 220 mg, and furazolidone 100 mg twice daily, combined with tetracycline 500 mg three times daily; the tetracycline, furazolidone, esomeprazole, and bismuth [TFEB] group) for 14 days. The primary endpoint was the H. pylori eradication rate. The secondary endpoints were adverse effects, symptom improvement rates, and patient compliance.Results:A total of 658 patients who met the criteria were enrolled in this study. The HDDT group achieved eradication rates of 75.4% (248/329), 81.0% (248/306), and 81.3% (248/305) asdetermined by the intention-to-treat (ITT), modified intention-to-treat (MITT), and per-protocol (PP) analyses, respectively. The eradication rates were similar to those in the TFEB group: 78.1% (257/329), 84.2% (257/305), and 85.1% (257/302). The lower 95% confidence interval boundary (−9.19% in the ITT analysis, − 9.21% in the MITT analysis, and −9.73% in the PP analysis) was greater than the predefined non-inferiority margin of −10%, establishing a non-inferiority of the HDDT group vs. the TFEB group. The incidence of adverse events in the HDDT group was significantly lower than that in the TFEB group (11.1% vs. 26.8%, P < 0.001). Symptom improvement rates and patients’ compliance were similar between the two groups.Conclusions:Fourteen-day HDDT is non-inferior to bismuth-containing quadruple therapy, with fewer adverse effects and good treatment compliance, suggesting HDDT as an alternative for H. pylori rescue treatment in the local region.Trial registration:Clinicaltrials.gov, NCT04678492.

Genomic Insights into Omega-3 Polyunsaturated Fatty Acid Producing Shewanella sp. N2AIL from Fish Gut.

Simple SummaryThe microbial production of health-beneficial omega-3 fatty acids has gained research attention due to the limitations of availability, sustainability, and contaminants associated with the conventional fish source. Among the marine bacteria, the Shewanella genus is well known for eicosapentaenoic acid (EPA) production along with bioremediation of organic and inorganic pollutants and bioelectricity generation. We report the genome sequence of an EPA-producing bacterium, Shewanella sp. N2AIL, isolated from the gut of a freshwater fish, Tilapia. Analysis of genomic data revealed a variety of antibiotic and stress-responsive genes, metal-reducing genes, and secondary metabolite genes. Overall, the study has provided an understanding of the biosynthetic gene cluster of omega-3 polyunsaturated fatty acids in addition to adaptation strategies of Shewanella sp. N2AIL and could be utilized in developing a strain for the commercial production of EPA.The genus Shewanella is widely distributed in niches ranging from an aquatic environment to spoiled fish and is loaded with various ecologically and commercially important metabolites. Bacterial species under this genus find application in bioelectricity generation and bioremediation due to their capability to use pollutants as the terminal electron acceptor and could produce health-beneficial omega-3 fatty acids, particularly eicosapentaenoic acid (EPA). Here, the genome sequence of an EPA-producing bacterium, Shewanella sp. N2AIL, isolated from the gastrointestinal tract of Tilapia fish, is reported. The genome size of the strain was 4.8 Mb with a GC content of 46.3% containing 4385 protein-coding genes. Taxonogenomic analysis assigned this strain to the genus Shewanella on the basis of average nucleotide identity (ANI) and in silico DNA-DNA hybridization (DDH), phylogenetically most closely related with S. baltica NCTC 10735T. The comparative genome analysis with the type strain of S. baltica revealed 693 unique genes in the strain N2AIL, highlighting the variation at the strain level. The genes associated with stress adaptation, secondary metabolite production, antibiotic resistance, and metal reduction were identified in the genome suggesting the potential of the bacterium to be explored as an industrially important strain. PUFA synthase gene cluster of size ~20.5 kb comprising all the essential domains for EPA biosynthesis arranged in five ORFs was also identified in the strain N2AIL. The study provides genomic insights into the diverse genes of Shewanella sp. N2AIL, which is particularly involved in adaptation strategies and prospecting secondary metabolite potential, specifically the biosynthesis of omega-3 polyunsaturated fatty acids.

Genetically engineered rpsL merodiploidy impacts secondary metabolism and antibiotic resistance in Streptomyces.

Certain point mutations within gene for ribosomal protein S12, rpsL, are known to dramatically change physiological traits of bacteria, most prominently antibiotic resistance and production of various metabolites. The rpsL mutants are usually searched among spontaneous mutants resistant to aminoglycoside antibiotics, such as streptomycin or paromomycin. The shortcomings of traditional selection are as follows: random rpsL mutants may carry undesired genome alterations; many rpsL mutations cannot be isolated because they are either not associated with increased antibiotic resistance or non-viable in the absence of intact rpsLWT gene. Introduction of mutant rpsL alleles in the rpsLWT background can be used to circumvent these obstacles. Here we take the latter approach and report the generation and properties of a set of stable rpsL merodiploids for Streptomyces albus J1074. We identified several rpsL alleles that enhance endogenous and heterologous antibiotic production by this strain and show that rpsLWTrpsLK88E merodiploid displays increased streptomycin resistance. We further tested several promising rpsL alleles in two more strains, Streptomyces cyanogenus S136 and Streptomyces ghanaensis ATCC14672. In S136, plasmid-borne rpsLK88E+P91S and rpsLK88R led to elevated landomycin production; no changes were detected for ATCC14672 merodiploids. Our data outline the prospects for and limitations to rpsL merodiploids as a tool for rapid enhancement of secondary metabolism in Streptomyces.

Antibiotic resistance of Helicobacter pylori in Australia and New Zealand: A systematic review and meta-analysis.

While the global prevalence of antibiotic-resistant Helicobacter pylori (H.pylori) is increasing, there is much regional variation, and local data are required to guide eradication therapy. We performed a systematic review and meta-analysis to determine rates of H.pylori antibiotic resistance in Australia and New Zealand. Random effects meta-analysis of data from 15 published studies and three published abstracts reporting prevalence of primary or secondary H.pylori antibiotic resistance in Australasia. PubMed, EMBASE, MEDLINE, PROSPERO, and the Cochrane Library were searched until August, 2020. Fifteen published studies and three published abstracts were identified; one study was excluded due to high risk of bias. Seventeen studies conducted between 1996 and 2013 were included in the final analysis, 12 reporting primary and five reporting secondary antibiotic resistance. Prevalence of primary resistance was clarithromycin 7.4% (95% confidence interval [CI], 5.3-9.7%), metronidazole 50.0% (95%CI, 23.9-56.1%), fluoroquinolones 3.7% (95%CI, 0.004-14.8%), and both amoxicillin and tetracycline <0.5%. Subgroup analysis (last 20years) showed doubling of clarithromycin resistance to 16.1% (95%CI 11.2-21.7%) with other resistance stable. Prevalence of secondary resistance was high for all antibiotics, particularly clarithromycin 78.7% (95%CI, 64.1-90.1%) and metronidazole 68.3% (95%CI, 59.9-76.1%). The outcomes reveal an increase in primary H.pylori clarithromycin resistance since the year 2000, while metronidazole resistance has remained stable and primary resistance to amoxicillin, tetracycline, and fluoroquinolones is low. Rates of secondary resistance to metronidazole and clarithromycin are high. The results highlight the need for contemporary local data on antibiotic resistance in Australia and New Zealand.

Secondary Antibiotic Resistance, Correlation between Genotypic and Phenotypic Methods and Treatment in Helicobacter pylori Infected Patients: A Retrospective Study.

The aim of this study was to evaluate the secondary resistance in Helicobacter pylori (Hp) infected patients who had failed a first-line therapy, and to compare the genotypic tests performed directly on gastric samples with phenotypic tests performed on culture media. The eradication rate of patients treated with bismuth quadruple therapy (BQT) is also evaluated. A total of 80 positive specimens were retrospectively examined. Antibiotic susceptibility testing of Hp strains was performed by E-test, whereas a molecular commercially available method was used for detecting the mutations involved in clarithromycin and levofloxacin resistance. High resistance levels to metronidazole and clarithromycin (61.6% and 35%, respectively) and worrying resistance levels to levofloxacin (15%) were found phenotypically. Multiple resistance to two or three antibiotics was observed as well. The polymorphism A2143G on clarithromycin 23S rRNA gene was found in 34/80 (42.5%) isolates including 10 mixed infections (29%), whereas 28/80 (35%) strains were resistant phenotypically. Levofloxacin resistance corresponded to 30% by PCR and 15% by E-test (statistically significant, p < 0.05). The knowledge of clarithromycin and levofloxacin resistance is crucial to establish an appropriate therapy in different geographical areas. The genetic methods were superior to phenotypic techniques in the absence of live bacteria or for identifying mixed infections that may lead to a resistance underestimation. The BQT eradication rate was effective (90%).

High prevalence and risk factors of multiple antibiotic resistance in patients who fail first-line Helicobacter pylori therapy in southern China: a municipality-wide, multicentre, prospective cohort study.

We aimed to study the prevalence of secondary antibiotic resistance of Helicobacter pylori in southern China and its risk factors, particularly geographical and socio-economic factors. This was a municipality-wide, multicentre, prospective cohort study involving five major hospitals. Patients aged ≥18 years who failed first-line bismuth-based quadruple anti-H. pylori therapy between September 2016 and February 2018 were recruited. Participants underwent upper gastrointestinal endoscopy with biopsy from the antrum and body for H. pylori culture and antimicrobial susceptibility testing for six antibiotics (clarithromycin, levofloxacin, metronidazole, amoxicillin, tetracycline and furazolidone). Patients with failure of H. pylori culture were excluded. Participants completed a questionnaire profiling 22 potential risk factors of H. pylori infection and antibiotic resistance, including medical, social, household and birthplace factors. A total of 1113 patients failed first-line therapy, with successful H. pylori culture in 791 (71.1%) [male = 433 (54.7%); median age = 43 years]. Secondary resistance rates of dual antibiotics (clarithromycin + metronidazole and levofloxacin + metronidazole) and triple antibiotics (clarithromycin + levofloxacin + metronidazole) were 34.0%, 38.7% and 17.8%, respectively. Risk factors for clarithromycin + metronidazole resistance were history of ≥2 courses of H. pylori therapies [adjusted OR (aOR) = 1.71; 95% CI = 1.17-2.54], ≥3 household members (aOR = 2.00; 95% CI = 1.07-3.90) and family history of gastric cancer (aOR = 1.85; 95% CI = 1.18-2.85). Risk factors for levofloxacin + metronidazole resistance were age ≥40 years (aOR = 1.94; 95% CI = 1.37-2.75), lower gross domestic product per capita (aOR = 0.29; 95% CI = 0.10-0.80) and higher number of doctors/10 000 population (aOR = 1.59; 95% CI = 1.07-2.39). A higher human development index was of borderline significance (aOR = 2.79; 95% CI = 0.97-8.70). The rates of secondary resistance of H. pylori to multiple antibiotics were high in southern China. Certain population-level risk factors were associated with levofloxacin + metronidazole resistance.

Trend of changes in antibiotic resistance in Helicobacter pylori from 2013 to 2019: a multicentre report from Taiwan.

Background:Antibiotic resistance plays a crucial role in the treatment failure of Helicobacter pylori (H. pylori) infection. This study aimed to determine the trend of changes in the primary, secondary and tertiary antibiotic resistance of H. pylori in Taiwan over the last 7 years.Methods:We retrospectively analysed H. pylori-infected isolates from patients with primary resistance (n = 1369), secondary resistance (n = 196) and tertiary resistance (n = 184) from January 2013 to December 2019. The H. pylori strains were tested for susceptibility to amoxicillin, clarithromycin, levofloxacin, metronidazole and tetracycline using the Epsilometer test method.Results:A progressively higher primary resistance rate was observed for clarithromycin (11.8–20.4%, p = 0.039 in χ2 test for linear trend), levofloxacin (17.3–38.8%, p < 0.001) and metronidazole (25.6–42.3%, p < 0.001) among naïve patients who received first-line eradication therapy. The dual primary resistance to clarithromycin and metronidazole also progressively increased in a linear trend (2.4–10.4%, p = 0.009). For secondary resistance, an increase was observed for levofloxacin (30.5–64.7%, p = 0.006) and metronidazole (40.5–77.4%, p < 0.001). For tertiary resistance, the observed increase was even more significant for levofloxacin (65.9–100.0%, p = 0.106) and metronidazole (44.4–88.2%, p < 0.001). The resistance to amoxicillin and tetracycline remained very low in Taiwan regardless of primary, secondary and tertiary resistance.Conclusion:Primary, secondary and tertiary antibiotic resistance to clarithromycin, levofloxacin and metronidazole for H. pylori has been increasing in Taiwan since 2013. Treatment should be targeted for eradication success rates of more than 90%. Third-line treatment should be based on antibiotic susceptibility.

Goals and Challenges in Bacterial Phosphoproteomics.

Reversible protein phosphorylation at serine, threonine and tyrosine is a well-known dynamic post-translational modification with stunning regulatory and signalling functions in eukaryotes. Shotgun phosphoproteomic analyses revealed that this post-translational modification is dramatically lower in bacteria than in eukaryotes. However, Ser/Thr/Tyr phosphorylation is present in all analysed bacteria (24 eubacteria and 1 archaea). It affects central processes, such as primary and secondary metabolism development, sporulation, pathogenicity, virulence or antibiotic resistance. Twenty-nine phosphoprotein orthologues were systematically identified in bacteria: ribosomal proteins, enzymes from glycolysis and gluconeogenesis, elongation factors, cell division proteins, RNA polymerases, ATP synthases and enzymes from the citrate cycle. While Ser/Thr/Tyr phosphorylation exists in bacteria, there is a consensus that histidine phosphorylation is the most abundant protein phosphorylation in prokaryotes. Unfortunately, histidine shotgun phosphorproteomics is not possible due to the reduced phosphohistidine half-life under the acidic pH conditions used in standard LC-MS/MS analysis. However, considering the fast and continuous advances in LC-MS/MS-based phosphoproteomic methodologies, it is expected that further innovations will allow for the study of His phosphoproteomes and a better coverage of bacterial phosphoproteomes. The characterisation of the biological role of bacterial Ser/Thr/Tyr and His phosphorylations might revolutionise our understanding of prokaryotic physiology.

Primary and secondary antibiotic resistance of Helicobacter pylori in Korea from 2003 to 2018.

Antimicrobial resistance of Helicobacter pylori (Hpylori) affects the efficacy of eradication therapy. The aim of this study was to estimate the prevalence of primary and secondary resistance of Hpylori isolates to antibiotics in Korea. The present study was performed from 2003 to 2018. Primary resistance was evaluated in 591 patients without any history of eradication and secondary resistance in 149 patients from whom Helicobacter pylori was cultured after failure of eradication. A minimal inhibitory concentration test was performed for amoxicillin, clarithromycin, metronidazole, tetracycline, levofloxacin, and rifabutin using the agar dilution method. An increase in the primary resistance rate was found in clarithromycin (P<.001), metronidazole (P<.001), and both levofloxacin (P<.001) during the study period. The primary resistance rates of amoxicillin and tetracycline were low and stable during the study period. The secondary resistance rate significantly increased in metronidazole and levofloxacin (P=.022 and .039, respectively). The primary and secondary resistance rates of clarithromycin, metronidazole, and levofloxacin for Helicobacter pylori in Korea were high and increased over time. However, the primary and secondary resistance rates of amoxicillin and tetracycline were low and stable over time. These results will help in selecting effective eradication regimens of Hpylori in Korea in the future.

Secondary bacterial infections and antibiotic resistance among tungiasis patients in Western, Kenya.

Tungiasis or jigger infestation is a parasitic disease caused by the female sand flea Tunga penetrans. Secondary infection of the lesions caused by this flea is common in endemic communities. This study sought to shed light on the bacterial pathogens causing secondary infections in tungiasis lesions and their susceptibility profiles to commonly prescribed antibiotics. Participants were recruited with the help of Community Health Workers. Swabs were taken from lesions which showed signs of secondary infection. Identification of suspected bacteria colonies was done by colony morphology, Gram staining, and biochemical tests. The Kirby Bauer disc diffusion test was used to determine the drug susceptibility profiles. Out of 37 participants, from whom swabs were collected, specimen were positive in 29 and 8 had no growth. From these, 10 different strains of bacteria were isolated. Two were Gram positive bacteria and they were, Staphylococcus epidermidis (38.3%) and Staphylococcus aureus (21.3%). Eight were Gram negative namely Enterobacter cloacae (8.5%), Proteus species (8.5%), Klebsiellla species (6.4%), Aeromonas sobria (4.3%), Citrobacter species (4.3%), Proteus mirabillis(4.3%), Enterobacter amnigenus (2.1%) and Klebsiella pneumoniae (2.1%). The methicillin resistant S. aureus (MRSA) isolated were also resistant to clindamycin, kanamycin, erythromycin, nalidixic acid, trimethorprim sulfamethoxazole and tetracycline. All the Gram negative and Gram positive bacteria isolates were sensitive to gentamicin and norfloxacin drugs. Results from this study confirms the presence of resistant bacteria in tungiasis lesions hence highlighting the significance of secondary infection of the lesions in endemic communties. This therefore suggests that antimicrobial susceptibility testing may be considered to guide in identification of appropriate antibiotics and treatment therapy among tungiasis patients.

Secondary antibiotic resistance of Helicobacter pylori isolates in Israeli children and adults.

Failure of standard therapy for Helicobacter pylori infections results primarily from increasing antibiotic resistance. Patients in Israel are referred for H. pylori culture after failure of at least two therapeutic regimens. To estimate the prevalence of secondary antimicrobial resistance of H. pylori in Israel. We retrospectively collected results of H. pylori cultures performed by gastric biopsies at Rambam Health Care Campus, Haifa, Israel, between the years 2012-2015. Antimicrobial susceptibility to five drugs was tested by gradient-diffusion. 107 patients, 46 adults and 61 children, were referred for performance of H. pylori cultures. Cultures were positive in 64 samples (63.7%). In adults, 23 (50%) patients had positive H. pylori cultures; 8.69% showed resistance to amoxicillin (AM), 39.1% to clarithromycin (CH), 61.9% to metronidazole (MZ), 8.69% to tetracycline (TC), and 21.7% to levofloxacin (LEV). In children, 41 (67%) patients had positive H. pylori cultures; 5.1% showed resistance to AM, 42.5% to CH, 46.66% to MZ, 2.5% to TC and 0% to LEV. In children, 94.9% of H. pylori strains were susceptible to both AM and LEV. In adults, 82.6% of the strains were susceptible to both AM and TC. 28.6% of adults and 24.1% children were resistant to both MZ and CH. The sensitivity of H. pylori culture was low. Resistance of H. pylori to MZ and CH was very high after failure of two therapeutic regimens in both adults and children. No LEV resistance was detected in children. AM resistance was higher in adults than in children.