Antibiotic Resistance Testing Research Articles

In Vitro Evaluation of Gastrointestinal Stability of Pediococcus pentosaceus Isolated from Fermented Maize and Pearl Millet for Possible Novel Chicken Probiotic Development

Research has identified certain bio-based products, such as probiotics, as alternatives to antibiotics for use in animal feed. They are capable of controlling, preventing or minimizing the colonization of the gastrointestinal tract by pathogenic bacteria. To isolate Pediococcus spp. and assess its technological properties for possible probiotic development, maize and pearl millet were used. The cereals were steeped and wet milled after 48 h of fermentation. The milled cereals were kneaded into dough for 24 h, after which a 10% slurry was prepared for tenfold serial dilution to enumerate the LAB by employing pour plate techniques using MRS Agar. Based on the cell morphology of the isolated bacteria, eight isolates (four from maize and four from millet) that were selected for identification using MALDI-TOF MS showed that five were Pediococcus pentosaceus (P. pentosaceus), one was Pediococcus acidilactici, and two did not match any organism. Subsequently, the six isolates were labeled as MZ1, MZ2, MZ3, MZ4 for the maize isolate and MLT5 and MLT7 for the millet isolate. The six Pediococcus spp. were assessed in vitro for acid and bile salt tolerance, gastric juice and intestinal fluid tolerance and antibiotic resistance and antimicrobial susceptibility tests were performed, and the survivability rate of the strains was calculated. With regard to the mean count, there was a reduction in log10 CFU/mL under the lower pH conditions and their duration of exposure with regard to time. Among the isolates, no differences were noted at the various periods of exposure (0 h, 1 h, 2 h and 3 h) at pH 4 (p > 0.05). However, significant differences were noted at pH 3, 2 and 1 among the isolates (p < 0.05). The percentage survival of MZ4 and MLT7 at pH 1 was higher compared to the other isolates at 0 h. Significant differences were observed among the isolated at pH 2, 3 and 4 across the various periods. The mean count of the isolates in gastric juice was similar at 0 and 1 h, but significant differences were noted at 2 and 3 h, where MLT7 was highest (p < 0.05). A similar trend was observed for percentage survival. The mean count and the percentage survival of isolates under different concentrations of bile salt were similar. Significant differences were noted among isolates in both mean count and percentage survival when exposed to intestinal fluid (p < 0.05). All of the isolates were highly tolerant to the antibiotics tested and possessed antibacterial properties against the selected pathogens. The LABs proved to be good probiotic materials, according to the results obtained. However, the Pediococcus strain MLT7 proved to be the LAB of choice; therefore, its molecular identity was verified using the 16S rRNA sequence and was labeled as Pediococcus pentosaceus GT001 after it was discovered to have 100% similarity with some strains of Pediococcus pentosaceus.

Genomic analysis of Clostridium perfringens type D isolates from goat farms

C. perfringens type D strains are the leading cause of enterotoxaemia in ruminants such as goats, sheep, and cattle. However, there has been no prior research on the genomic characteristics of C. perfringens type D strains from various regions in China. Here, we investigated the antibiotic resistance, genomic characteristics, and phylogenetic relationship of C. perfringens type D isolates recovered from goat farms in Shaanxi, Gansu, and Ningxia provinces. The antibiotic resistance test indicated that the isolates displayed high minimum inhibitory concentration (MIC) values to sulfafurazole, whereas the other antibiotics tested, such as penicillin, enrofloxacin, and florfenicol, worked well on them. Additionally, only tetracycline resistance genes [tetA(P) and tetB(P)] were identified from the isolates. A collective of 13 toxin genes, including etx and cpe were detected among the isolates. Sequence comparison revealed that the etx and cpe genes shared high sequence identities, and they could coexist on a pCW3-like plasmid, representing a potential risk to both animal breeding and public health. Phylogenetic analysis using core genome multi-locus sequence typing (cgMLST) and core genome single nucleotide polymorphisms (SNPs) revealed the close genetic relationship and potential regional/transregional transmission of the C. perfringens type D isolates in Shaanxi and Gansu provinces. Furthermore, pan-genomic analysis suggested the functional differences at the protein-coding gene level, although isolates from the same source shared a close genetic relationship. In conclusion, this study indicated the antibiotic resistance, virulence markers, potential transregional transmission, and genomic diversity of C. perfringens type D strains from various regions in China, which could provide references for the prevention of C. perfringens foodborne diseases and further research.

Serodiversity, antibiotic resistance, and virulence genes of Vibrio parahaemolyticus in oysters collected in coastal areas of northwestern Mexico between 2012 and 2020.

This study aimed to determine the prevalence of V. parahaemolyticus in oysters from the northwestern coast of Mexico and to identify the serotypes, virulence factors, and antibiotic resistance of the strains. Oyster samples were collected from 2012 to 2020 from the northwest coast of Mexico; biochemical and molecular methods were used to identify V. parahaemolyticus from oysters; antiserum reaction to determine V. parahaemolyticus serotypes, and PCR assays were performed to identify pathogenic (tdh and/or trh) or pandemic (toxRS/new, and/or orf8) strains and antibiotic resistance testing. A total of 441 oyster samples were collected and tested for V. parahaemolyticus. Forty-seven percent of oyster samples were positive for V. parahaemolyticus. Ten different O serogroups and 72 serovars were identified, predominantly serotype O1:KUT with 22.2% and OUT:KUT with 17.3%. Twenty new serotypes that had not been previously reported in our region were identified. We detected 4.3% of pathogenic clones but no pandemic strains. About 73.5% of strains were resistant to at least one antibiotic, mainly ampicillin and ciprofloxacin; 25% were multi-drug resistant. In conclusion, the pathogenic strains in oysters and antibiotic resistance are of public health concern, as the potential for outbreaks throughout northwestern Mexico is well established.

Neonatal Sepsis Due to Multidrug-resistant Bacteria at a Tertiary Teaching Hospital in Ethiopia.

The burden of multidrug-resistant bacterial infections in low-income countries is alarming. This study aimed to identify the bacterial etiologies and antibiotic resistance patterns among neonates in Jimma, Ethiopia. An observational longitudinal study was conducted among 238 presumptive neonatal sepsis cases tested with blood and/or cerebrospinal fluid culture. The bacterial etiologies were confirmed using matrix-assisted laser desorption ionization-time of flight mass spectrometry. The antibiotic resistance patterns were determined using the automated disc diffusion method (Bio-Rad) and the results were interpreted based on the European Committee on Antimicrobial Susceptibility Testing 2021 breakpoints. Extended-spectrum β-lactamases were detected using a double disc synergy test and confirmed by Mast discs (Mast Diagnostica GmbH). A total of 152 pathogens were identified. Of these, Staphylococcus aureus (18.4%) was the predominant isolate followed by Klebsiella pneumoniae (15.1%) and Escherichia coli (10.5%). All the isolates exhibited a high rate of resistance to first- and second-line antibiotics ranging from 73.3% for gentamicin to 93.3% for ampicillin. Furthermore, 74.4% of the Gram-negative isolates were extended-spectrum β-lactamase producers and 57.1% of S. aureus strains were methicillin resistant. The case fatality rate was 10.1% and 66.7% of the deaths were attributable to infections by multidrug-resistant pathogens. The study revealed a high rate of infections with multidrug-resistant pathogens. This poses a significant challenge to the current global and national target to reduce neonatal mortality rates. To address these challenges, it is important to employ robust infection prevention practices and continuous antibiotic resistance testing to allow targeted therapy.

Prevalence of Colistin Pan Resistance among Multidrug-Resistant and Extensively Drug-Resistant Escherichia Coli O157:H7

Antimicrobial resistance is an important problem threatening human health. With the appearance of colistin-resistant bacteria, the World Health Organization and Centers for Disease Control and Prevention are declaring a global emergency and an alarming disaster that goes back to the time before antibiotics. The usage of colistin rises as a result of the global growth of Enterobacteriaceae, which produces carbapenemase and certainly causes the emergence of resistance to investigate the prevalence of colistin resistance among multidrug-resistant and extensively drug-resistant E. coli. The cross-sectional study included 140 swab samples and 200 urine samples that were collected from patients attending Al Imam Al Hussein Medical City in Karbala. The identification of bacterial isolates and the pattern of antibiotic resistance were determined using the fully automated VITEK 2 compact system in addition to the manual antibiotic resistance testing confirmation. The isolates were highly resistant to Ticarcillin (94.4%), Trimethoprim/ Sulfamethoxazole (91.1%) and Piperacillin (87.3%). In contrast, colistin had the lowest (4.2%) out of the total multi-drug resistant (MDR) strains that formed (46.4%) and the extensively-drug resistant (XDR) strains (25.4). Antimicrobial resistance is one of the biggest health problems facing people today. In Iraq, the appearance of colistin resistance (2.8%) among extensively drug-resistant Escherichia coli O157:H7 may lead to failure of treatment, especially among burn and UTI patients. It is urgently recommended to lower the occurrence of antibiotic resistance through cautious antibiotic usage and stringent infection control protocols, which are priorities.

Assessment of antimicrobial resistance laboratory-based surveillance capacity of hospitals in Zambia: findings and implications for system strengthening

A well-established antimicrobial resistance (AMR) laboratory-based surveillance (LBS) is of utmost importance in a country like Zambia which bears a significant proportion of the world's communicable disease burden. This study assessed the capacity of laboratories in selected hospitals to conduct AMR surveillance in Zambia. This cross-sectional exploratory study was conducted among eight purposively selected hospitals in Zambia between August 2023 and December 2023. Data were collected using the self-scoring Laboratory Assessment of Antibiotic Resistance Testing Capacity (LAARC) tool. Of the assessed facilities, none had full capacity to conduct AMR surveillance with varying capacities ranging from moderate (63% (5/8)) to low (38% (3/8)). Some of the barriers of AMR-LBS were the lack of an electronic laboratory information system (63% (5/8)) and the lack of locally generated antibiograms (75% (6/8)). Quality control for antimicrobial susceptibility testing (AST), pathogen identification and media preparation had the lowest overall score among all of the facilities with a score of 14%, 20% and 44%, respectively. The highest overall scores were in specimen processing (79%), data management (78%), specimen collection, transport and management (71%), and safety (70%). Most facilities had standard operating procedures in place but lacked specimen-specific standard operating procedures. The absence of laboratories with full capacity to conduct AMR surveillance hinders efforts to combat AMR and further complicates the treatment outcomes of infectious diseases. Establishing and strengthening LBS systems are essential in quantifying the burden of AMR and supporting the development of local antibiograms and treatment guidelines.

Pseudomonas sp. AMGC1 takes on rice blast: Broad-spectrum antimicrobial activity underpins plant growth and disease tolerance.

A diverse group of gram-negative bacteria called Pseudomonas have been extensively researched for their ability to promote plant growth and suppress pathogens. The aim of the study was to identify the strain AMGC1 as a biocontrol agent against rice blast disease and a plant growth-promoting agent. The activity of AMGC1 against phytopathogens and its plant growth promotion activity were tested in vitro. Molecular identification by 16S rRNA gene sequencing, detection of antifungal antibiotic genes, biochemical characterization and antibiotic resistance testing were performed. Moreover, an in-planta biocontrol experiment with a blast susceptible rice cultivar was conducted to assess the effectiveness in managing the disease. Thin-layer chromatography was used to verify the presence of antifungal compounds. The results showed that AMGC1 had strong antimicrobial activity and multiple plant growth promotion traits. The strain was identified as Pseudomonas sp. and it contained genes for phenazine-1-carboxamide, hydrogen cyanide, and 2-hexyl, 5-propyl resorcinol antifungals. In the in-planta suppression experiment, applying AMGC1 strain two days before pathogen inoculation reduced the disease severity by 28% and disease incidence by 29% compared to control. Applying AMGC1 two days after pathogen inoculation resulted in lower reductions in disease severity (17.10%) and disease incidence (18.5%). Two putative bioactive compounds, phenazine-1-carboxamide and 2-hexyl, 5-propyl resorcinol, were isolated and purified from the AMGC1 growth medium. AMGC1 showed varied carbohydrate utilization patterns and both resistance and susceptibility to different antibiotics. The strain had multiple features that enhance plant growth and resistance against various phytopathogens, making it a potential biocontrol agent for sustainable agriculture.

Comparison of metronidazole versus clarithromycin in first-line vonoprazan-based triple therapy for Helicobacter pylori: A multicenter randomized trial in Japan.

To date, no randomized trials have compared the efficacy of 7-day vonoprazan, amoxicillin, and metronidazole triple therapy (VAM) versus 7-day vonoprazan, amoxicillin, and clarithromycin triple therapy (VAC) as a first-line treatment for Helicobacter pylori eradication. This study was performed to compare the efficacy of VAM and VAC as first-line treatments. This prospective multicenter randomized trial was performed in Japan and involved 124 H. pylori-positive patients without a history of eradication. Patients without antibiotic resistance testing of H. pylori were eligible. The patients were randomized to receive either VAC (vonoprazan 20 mg + amoxicillin 750 mg + clarithromycin 200 or 400 mg twice a day) or VAM (vonoprazan 20 mg + amoxicillin 750 mg + metronidazole 250 mg twice a day) for 7 days, with stratification by age and sex. Eradication success was evaluated using the 13C-urea breath test. We evaluated safety using patient questionnaires (UMIN000025773). The intention-to-treat and per-protocol eradication rates of VAM were 91.3% (95% confidence interval [CI], 82.0-96.7%) and 92.6% (95% CI, 83.7-97.6%), respectively, and those of VAC were 89.1% (95% CI, 77.8-95.9%) and 96.1% (95% CI, 86.5-99.5%), respectively. No significant difference was observed between VAM and VAC in either analysis (P = 0.76 and P = 0.70, respectively). Abdominal fullness was more frequent in patients who received VAM than VAC. These findings suggest that VAM as a first-line treatment in Japan can be categorized as grade B (intention-to-treat cure rate of 90-95%) and have potential as a first-line national insurance -approved regimen.

Genotypic Detection of Carbapenems Resistance Genes in Acinetobacter baumannii Isolated from Urinary Tract Infection Patients

Acinetobacter baumannii is a Gram-negative bacterium characterized by its short, round, rod-shaped morphology. It is an opportunistic pathogen that poses a significant threat, particularly to immunocompromised patients, often those with hospital stays lasting less than 90 days. Between June 2022 and July 2023, 214 urine samples were collected from individuals suspected of having urinary tract infections (UTIs). These samples were subjected to antibiotic resistance testing, focusing on detecting specific genes related to carbapenem resistance, namely blaNDM, blaKPC, and blaVIM.The study's results revealed a notable trend in antibiotic resistance among the bacterial isolates. Ceftazidime, cefotaxime, and ceftriaxone, commonly used antibiotics for UTIs, showed a high resistance rate among the tested isolates. This resistance highlights the challenges healthcare professionals face when treating UTIs caused by Acinetobacter baumannii. On the other hand, the isolates displayed a comparatively lower resistance rate to imipenem and meropenem, two necessary carbapenem antibiotics. This lower resistance to carbapenems is encouraging as these drugs are often considered the last line of defense against multidrug-resistant bacterial infections. The presence of carbapenem resistance genes, such as blaNDM, blaKPC, and blaVIM, in the Acinetobacter baumannii isolates is of particular concern. These genes confer resistance to carbapenem antibiotics, crucial for treating severe infections caused by multidrug-resistant bacteria. In conclusion, the study aims to study the growth of antibiotic resistance in Acinetobacter baumannii, especially in urinary tract infections in immunocompromised patients with more extended hospital stays. It also highlights the need for Surveys and periodic examinations to detect the spread of bacteria and their resistance. Keywords: Carbapenems, UTI, genes, blaNDM, blaKPC, and blaVIM.

Genotypic Detection of Carbapenems Resistance Genes in Acinetobacter baumannii Isolated from Urinary Tract Infection Patients

Acinetobacter baumannii is a Gram-negative bacterium characterized by its short, round, rod-shaped morphology. It is an opportunistic pathogen that poses a significant threat, particularly to immunocompromised patients, often those with hospital stays lasting less than 90 days. Between June 2022 and July 2023, 214 urine samples were collected from individuals suspected of having urinary tract infections (UTIs). These samples were subjected to antibiotic resistance testing, focusing on detecting specific genes related to carbapenem resistance, namely blaNDM, blaKPC, and blaVIM.The study's results revealed a notable trend in antibiotic resistance among the bacterial isolates. Ceftazidime, cefotaxime, and ceftriaxone, commonly used antibiotics for UTIs, showed a high resistance rate among the tested isolates. This resistance highlights the challenges healthcare professionals face when treating UTIs caused by Acinetobacter baumannii. On the other hand, the isolates displayed a comparatively lower resistance rate to imipenem and meropenem, two necessary carbapenem antibiotics. This lower resistance to carbapenems is encouraging as these drugs are often considered the last line of defense against multidrug-resistant bacterial infections. The presence of carbapenem resistance genes, such as blaNDM, blaKPC, and blaVIM, in the Acinetobacter baumannii isolates is of particular concern. These genes confer resistance to carbapenem antibiotics, crucial for treating severe infections caused by multidrug-resistant bacteria. In conclusion, the study aims to study the growth of antibiotic resistance in Acinetobacter baumannii, especially in urinary tract infections in immunocompromised patients with more extended hospital stays. It also highlights the need for Surveys and periodic examinations to detect the spread of bacteria and their resistance. Keywords: Carbapenems, UTI, genes, blaNDM, blaKPC, and blaVIM.

A comparative phenotypic and genomic analysis of methicillin-resistant Staphylococcus aureus ST45 isolates from cellulitis and from osteomyelitis in Taiwan.

Methicillin-resistant Staphylococcus aureus (MRSA) sequence type (ST) 45 is a globally disseminated MRSA lineage. Herein, we investigated whether MRSA ST45 isolates from cellulitis and from osteomyelitis display distinctive phenotypic and genomic characteristics. A total of 15 MRSA ST45 isolates from cellulitis (CL-MRSAs; n = 6) or osteomyelitis (OM-MRSAs; n = 9) were collected in a Taiwan hospital. These MRSA ST45 isolates were characterized for their antimicrobial susceptibility, biofilm-forming ability, cellular infectivity in vitro, and pathogenicity in vivo. Four CL-MRSA and six OM-MRSA ST45 isolates were selected for whole-genome sequencing (WGS). Antibiotic resistance tests showed that all OM-MRSA ST45 strains, but not CL-MRSA ST45 strains, were resistant to ciprofloxacin, levofloxacin, gentamicin and doxycycline. Compared to the CL-MRSA ST45 isolates, the OM-MRSA ST45 isolates had stronger biofilm-forming ability and cellular infectivity, and caused more severe disease in mice. WGS analysis revealed that these OM-MRSA ST45 isolates carry multiple common mutations or polymorphisms in genes associated with antibiotic resistance and virulence. Moreover, the transposable elements IS256 and IS257R2 were found only in the OM-MRSA ST45 isolates. The emergence and spread of the highly pathogenic and multidrug-resistant ST45 MRSAs identified from osteomyelitis may pose a serious threat on public health.

ESCHERICHIA COLI RESISTANCE CAUSES COLIBACILLOSIS TO ANTIBIOTICS IN PIG FARMS IN ALOK DISTRICT SIKKA REGENCY OF NTT

The phenomenon of antibiotic resistance is a very serious problem that needs attention and countermeasures, especially in the use of antibiotics on farms, especially in pigs. This study aimed to determine the resistance of Escherichia coli that causes colibacillosis to several types of antibiotics. The study sample was taken based on purposive sampling from pigs showing symptoms of colibacillosis. A total of ten faecal samples were taken from a total population of 257 heads from 32 pig farms. Antibiotic resistance tests were performed using the Kirby-Bauer disc diffusion method. Results showed that all samples examined were E. coli with haemolysis γ and resistant to ampicillin, bacitracin, erythromycin (90%) and streptomycin (10%). But all isolates were sensitive to chloramphenicol, sulfamethoxazole, doxycycline and kanamycin (90%) and streptomycin (70%). The isolated E. coli showed cross-resistance to antibiotics ampicillin, bacitracin, erythromycin and streptomycin. It was concluded that E. coli was resistant to a number of antibiotics and some were even multidrug resistant. The use of antibiotics ampicillin, bacitracin, erythromycin and streptomycin in pig farms in Alok district, Sikka regency should be stopped considering that there has been resistance to isolated E. coli.

Screening, biochemical characterization and antibiotics resistance/susceptibility of bacteria isolated from native soil and water samples.

The present study was conducted to isolate and characterize bacteria from water and soil sample taken from the Lahore Canal at different sites i.e. Mall Road, Mohlanwal and Khera site. Isolated bacterial strains were identified on the basis of morphological and biochemical tests. Identification was confirmed by culturing bacteria on selective media. Antibiotic resistance test was also performed to observe the resistance of bacteria against different antibiotics. Blood agar test was performed for identification of different pathogenic bacteria. The result revealed that water and soil samples of Lahore Canal Lahore from different sites were contaminated with Escherichia coli, Salmonella sp., Vibrio sp., Bacillus spp., Enterococcus sp. and Staphylococcus spp. Due to presence of these pathogens, this water is not suitable for any domestic and irrigation use. Study also revealed that water of the Lahore Canal is harmful for human health as it is contaminated with bacteria that can cause severe disease e.g., Escherichia coli can cause gastroenteritis, Bacillus spp. can cause nausea and vomiting, Enterococcus may infect urinary tract, Salmonella sp. is responsible for Bacteremia, Staphylococcus spp. can cause mild fever and Vibrio sp. can be the reason of cholera. Thus it is rendered unfit for any kind of human use even other than drinking like swimming, bathing, washing etc., until and unless some remedial measures are employed to eradicate pathogenic microorganisms by WASA and LWMS according to standards of WHO. Similarly, it is quite harmful, when and where ever it is used for irrigation without proper treatment.

Two-stage tuberculosis diagnostics: combining centrifugal microfluidics to detect TB infection and Inh and Rif resistance at the point of care with subsequent antibiotic resistance profiling by targeted NGS.

Globally, tuberculosis (TB) remains the deadliest bacterial infectious disease, and spreading antibiotic resistances is the biggest challenge for combatting the disease. Rapid and comprehensive diagnostics including drug susceptibility testing (DST) would assure early treatment, reduction of morbidity and the interruption of transmission chains. To date, rapid genetic resistance testing addresses only one to four drug groups while complete DST is done phenotypically and takes several weeks. To overcome these limitations, we developed a two-stage workflow for rapid TB diagnostics including DST from a single sputum sample that can be completed within three days. The first stage is qPCR detection of M. tuberculosis complex (MTBC) including antibiotic resistance testing against the first-line antibiotics, isoniazid (Inh) and rifampicin (Rif). The test is automated by centrifugal microfluidics and designed for point of care (PoC). Furthermore, enriched MTBC DNA is provided in a detachable sample tube to enable the second stage: if the PCR detects MTBC and resistance to either Inh or Rif, the MTBC DNA is shipped to specialized facilities and analyzed by targeted next generation sequencing (tNGS) to assess the complete resistance profile. Proof-of-concept testing of the PoC test revealed an analytical sensitivity of 44.2 CFU ml-1, a diagnostic sensitivity of 96%, and a diagnostic specificity of 100% for MTBC detection. Coupled tNGS successfully provided resistance profiles, demonstrated for samples from 17 patients. To the best of our knowledge, the presented combination of PoC qPCR with tNGS allows for the fastest comprehensive TB diagnostics comprising decentralized pathogen detection with subsequent resistance profiling in a facility specialized in tNGS.

Efficacy comparison of 7- and 14-day P-CAB based bismuth-containing quadruple regimen with PPI based bismuth-containing quadruple regimen for Helicobacter pylori infection: rationale and design of an open-label, multicenter, randomized controlled trial

BackgroundOwing to its strong acid inhibition, potassium-competitive acid blocker (P-CAB) based regimens for Helicobacter pylori (H. pylori) eradication are expected to offer clinical advantages over proton pump inhibitor (PPI) based regimens. This study aims to compare the efficacy and adverse effects of a 7-day and a 14-day P-CAB-based bismuth-containing quadruple regimen (PC-BMT) with those of a 14-day PPI-based bismuth-containing quadruple regimen (P-BMT) in patients with high clarithromycin resistance.MethodsThis randomized multicenter controlled clinical trial will be performed at five teaching hospitals in Korea. Patients with H. pylori infection who are naive to treatment will be randomized into one of three regimens: 7-day or 14-day PC-BMT (tegoprazan 50 mg BID, bismuth subcitrate 300 mg QID, metronidazole 500 mg TID, and tetracycline 500 mg QID) or 14-day P-BMT. The eradication rate, treatment-related adverse events, and drug compliance will be evaluated and compared among the three groups. Antibiotic resistance testing by culture will be conducted during the trial, and these data will be used to interpret the results. A total of 366 patients will be randomized to receive 7-day PC-BMT (n = 122), 14-day PC-BMT (n = 122), or 14-day P-BMT (n = 122). The H. pylori eradication rates in the PC-BMT and P-BMT groups will be compared using intention-to-treat and per-protocol analyses.DiscussionThis study will demonstrate that the 7-day or 14-day PC-BMT is well tolerated and achieve similar eradication rates to those of 14-day P-BMT. Additionally, the 7-day PC-BMT will show fewer treatment-related adverse effects and higher drug compliance, owing to its reduced treatment duration.Trial registrationKorean Clinical Research Information Service registry, KCT0007444. Registered on 28 June 2022, https://cris.nih.go.kr/cris/index/index.do.

Evaluation of mycobacteria infection prevalence and optimization of the identification process in North Sardinia, Italy.

Mycobacterial infection is a major threat to public health worldwide. Accurate identification of infected species and drug resistance detection are critical factors in treatment. We focused on shortening the turn-around time of identifying mycobacteria species and antibiotic resistance tests.

Potentially Pathogenic Bacteria in Nesting Olive Ridley Turtles in Northwestern Mexico.

Olive ridleys (Lepidochelys olivacea) are the most common sea turtle found in the Gulf of California. Unfortunately, the bacterial flora of nesting olive ridley turtles is still unknown. We conducted a study to identify, characterize, serotype, and determine the antibiotic resistance of potentially pathogenic bacteria isolated from olive ridley turtles nesting in northwestern Mexico. Bacteria were isolated and identified from the oral cavity and cloaca of 47 postnesting turtles. Escherichia coli and Vibrio parahaemolyticus were characterized, and antibiotic resistance testing was performed. One hundred bacteria belonging to 21 species were isolated, 53 from the oral cavity and 47 from the cloaca, the most prevalent being Pseudomonas aeruginosa, followed by Aeromonas hydrophila, Vibrio alginolyticus, Vibrio parahaemolyticus, Klebsiella pneumoniae, and E. coli, among others. Moreover, two to three different bacterial species were found co-colonizing both anatomical sites in some turtles. E. coli phylogroups B1, A, F, and unknown were identified as diarrheagenic E. coli (enteroaggregative and enteropathogenic E. coli). O1, O4, K8, K12, OUT, and KUT of V. parahaemolyticus serogroups were identified, also comprising pathogenic and nonpathogenic strains. Finally, 100% of the bacterial species tested were antibiotic resistant, and both MDR and XDR strains were found. In conclusion, olive ridley turtles are colonized by a diversity of bacterial species with a high rate of antibiotic resistance, some with pathogenic potential to turtles, representing a health risk factor for the species.

Comparison of culture and PCR-DGGE methods to evaluate the airways of cystic fibrosis patients and determination of their antibiotic resistance profile.

Respiratory infections are the most serious condition in cystic fibrosis (CF) patients; therefore, a thorough comprehension of the diversity and dominant microbial species in CF airways has a crucial role in treatment. Our objective was to determine the antibiotic resistance profile of CF airways microbiota and compare culture methods and PCR-DGGE to evaluate bacterial diversity. Pharyngeal swabs from 121 CF patients were collected. The samples were then cultured, identified and antibiotic resistance testing was performed. Thirty samples were subjected to further molecular surveys. DNA contents of these samples were extracted and amplified using nested-PCR technique and their bacterial diversity was assessed by DGGE. The DGGE patterns were visualized and certain bands were excised and purified. Next, the DNA was amplified by another round of PCR and sent out for sequencing. Staphylococcus aureus, Pseudomonas aeruginosa, and Klebsiella pneumoniae were the most prevalent species isolated using culture methods. S. aureus was the most common bacteria among 6 years and younger patients; while, P. aeruginosa had more prevalence among older ones. The PCR-DGGE results showed more diversity than culture methods, particularly in younger patients who exhibited more bacterial diversity than the older groups. Sequencing results unveiled the presence of certain bacterial species including Haemophilus parainfluenzae and Stenotrophomonas maltophilia which were completely missed in culture. Even though culture-dependent methods are cost-effective, PCR-DGGE appeared to be more efficient to determine bacterial diversity. PCR-DGGE detects less abundant species, though their viability could not be determined using this method.

Antibiotic Resistance Clinical Research in Iran: A Scoping Review

Context: In recent years, antimicrobial resistance (AMR) has become a global public health threat. Health system decision-makers need valid and reliable situation analysis to better plan for mitigating this threat. Objectives: This scoping review investigated the research gaps in AMR publications in Iran and provided an evidential base to support the identification of priority research to better address antibiotic resistance needs in Iran. Methods: A search of academic databases, including Scopus, Institute for Scientific Information (ISI), Web of Science, MEDLINE/PubMed, EMBASE, and Iranian Database of Medical Literature (IDML), was performed in February 2018. The identified studies evaluated the resistance or susceptibility of antibiotics against any bacteria in an Iranian population. Title, abstract, and full-text screening were conducted, and the included studies were accordingly analyzed with respect to the study protocol. Results: From 37,769 identified studies, 1,718 studies met all inclusion criteria. These studies evaluated the susceptibility of 131 antibiotics to 82 types of bacteria by conducting 3,509 antibiotic resistance tests. Ofloxacin, ciprofloxacin, and gentamicin had the highest number of studies, samples, and tested bacteria. Regarding the characteristics of the studies, 306 studies had an insufficient explicit definition of study characteristics, 231 studies published their results more than three years after conducting them, and 803 studies (46.7%) were published in local journals. Conclusions: Considering the importance of the AMR crisis, this scoping review debates the low quality of reporting in AMR-related publications in Iran despite extensive research.

Evaluation of 16S rRNA gene sequencing for species level microbiome analysis in Channa striata

Microbiota plays a crucial role in a host organism due to its phylogenetic diversity and wild distribution. Though microbiome study of various fresh water fishes was conducted, so far, no such studies focused on Channa striata. In this study we evaluated the microbiota of Channa Striata gut (stomach, intestine and rectum) using 16S rRNA amplicon sequencing.Live fishes were sampled and dissected to obtain the respective regions of the gut. These regions were incubated in a nutrient medium and the grown broth cultures were then subjected to serial dilution followed by spread plating. Isolated colonies obtained from the spread plates were subjected to colony PCR using 16S V3-V4 region primers. PCR amplicons were visualized and amplified products were sequenced both in forward and reverse directions. The resulting sequences were analyzed phylogenetically using index metrics such as Shannon and ChaoI. Concurrently, an antibiotic resistance test was carried out using the same procedure to identify antibiotic-resistant varieties in the microbiota. Fish were fed with antibiotic-mixed food for 14 days before dissection and colony isolation.Our analysis of 16S rRNA amplicon sequencing revealed a diverse array of flora in the gut microbiome of Channa striata. Bacteria belonging to Pseudomonas, Staphylococcus, Microbacterium, E. coli, Microcystis and three unknown species were identified in the gut of the organism. Those belonging to Microbacterium and Pseudomonas were considered to be predominant in the stomach of the fish. Phylogenetic tree construction revealed that Microcystis flos-aquae formed a separate clade along with three unknown species. Some of the microbiota persisted in the gut even after feeding with antibiotics, indicating that these species are resistant to the fed antibiotic.Results obtained indicate a strong influence of the host environment in the microbiota composition. Knowledge of the microbiota is the first step in exploring proper management strategies for this freshwater fish.