Spread Of Antimicrobial Resistance Strains Research Articles

Fisetin inhibits Salmonella Typhimurium type III secretion system regulator HilD and reduces pathology in vivo.

Salmonella spp. remains a major worldwide health concern that causes significant morbidity and mortality in both humans and animals. The spread of antimicrobial resistant strains has declined the efficacy of conventional chemotherapy. Thus, novel anti-infection drugs or strategies are needed. Anti-virulence strategy represents one of the promising means for the treatment of bacterial infections. In this study, we found that the natural compound fisetin could inhibit Salmonella invasion of host cells by targeting SPI-1 regulation. Fisetin treatment impaired the interaction of the regulatory protein HilD with the promoters of its target genes, thereby suppressing the expression of T3SS-1 effectors as well as structural proteins. Moreover, fisetin treatment could reduce pathology in the Salmonella murine infection model. Collectively, our results suggest that fisetin may serve as a promising lead compound for the development of anti-Salmonella drugs.

Prevalence and Antimicrobial Susceptibility Profile of Salmonella and Shigella among Diarrheic Patients Attending Selected Health Facilities in Addis Ababa, Ethiopia.

Diarrhea is one of the important public health problems in developing countries. Salmonella and Shigella species are the major bacterial causal agents of diarrhea. The increasing burden of antimicrobial resistance is posing difficulty in the treatment of these pathogens. This study aimed to assess the occurrence of Salmonella and Shigella in the feces of diarrheic patients receiving health services in Addis Ababa, Ethiopia, and to determine their antimicrobial susceptibility profile. A cross-sectional study involving 13 health centers was conducted where 428 diarrheic patients were recruited. Standard microbiology techniques were used to isolate Salmonella and Shigella from stool samples. In addition, Salmonella isolates were confirmed by polymerase chain reaction (PCR). The Kirby-Bauer disc diffusion method was employed to assess susceptibility to 11 antimicrobials for each of the Salmonella and Shigella isolates. The prevalence of Salmonella and Shigella spp. among diarrheic patients was 8.4%; n = 36 and 5.6%; n = 24, respectively. Thirty (83.3%) of Salmonella isolates were susceptible to all antimicrobials tested, whereas 4 (10.8%) of isolates were resistant to 2 or more antimicrobials and 2 (5.6%) were multidrug resistant. Resistance to ampicillin was recorded in only one (2.7%) of Salmonella isolates; however, resistance to ampicillin was recorded in 12 (50%) of the Shigella isolates. Half of the Shigella isolates (n = 12) were resistant to 2 or more antimicrobials while 5 (20.8%) of them were resistant to 3 or more antimicrobials. The overall rate of resistance to antimicrobials was more common in Shigella compared to Salmonella isolates. In conclusion, Salmonella and Shigella were isolated from the feces of diarrheic patients, with a higher rate of antimicrobial resistance in Shigella isolates, which could make the treatment of shigellosis challenging. Therefore, increasing hygienic practices during food preparation to reduce the burden of Salmonella and Shigella infection and prudent use of antimicrobials are recommended to limit the spread of antimicrobial resistant strains.

Phylogenetic lineages and antimicrobial resistance determinants of clinical Klebsiella oxytoca spanning local to global scales.

Klebsiella oxytoca is an opportunistic pathogen causing serious nosocomial infections. Knowledge about the population structure and diversity of healthcare-associated K. oxytoca from a genomic standpoint remains limited. Here, we characterized the phylogenetic relationships and genomic characteristics of 20 K. oxytoca sensu stricto isolates recovered from bloodstream infections at the Dartmouth-Hitchcock Medical Center, New Hampshire, USA from 2017 to 2021. Results revealed a diverse population consisting of 15 sequence types (STs) that together harbored 10 variants of the intrinsic beta-lactamase gene bla OXY-2, conferring resistance to penicillins. Similar sets of antimicrobial resistance (AMR) determinants reside in multiple distinct lineages, with no one lineage dominating the local population. To place the New Hampshire K. oxytoca in a broader context, we compared them to 304 publicly available genomes of clinical isolates from 18 countries. This global clinical K. oxytoca sensu stricto population is represented by over 65 STs that together harbored resistance genes against 14 antimicrobial classes, including eight bla OXY-2 variants. Three dominant STs in the global population (ST2, ST176, ST199) circulate across multiple countries and were also present in the New Hampshire population. The global K. oxytoca population is genetically diverse, but there is evidence for broad dissemination of a few lineages carrying distinct set of AMR determinants. Our findings reveal the clinical diversity of K. oxytoca sensu stricto and its importance in surveillance efforts aimed at monitoring the evolution of this drug-resistant nosocomial pathogen. IMPORTANCE The opportunistic pathogen Klebsiella oxytoca has been increasingly implicated in patient morbidity and mortality worldwide, including several outbreaks in healthcare settings. The emergence and spread of antimicrobial resistant strains exacerbate the disease burden caused by this species. Our study showed that clinical K. oxytoca sensu stricto is phylogenetically diverse, harboring various antimicrobial resistance determinants and bla OXY-2 variants. Understanding the genomic and population structure of K. oxytoca is important for international initiatives and local epidemiological efforts for surveillance and control of drug-resistant K. oxytoca.

Multidrug-Resistant Klebsiella, Pseudomonas and Acinetobacter Species at a Referral Hospital, Gondar, Ethiopia: a Retrospective Study.

Multidrug-resistant Gram-negative bacteria particularly Klebsiella, Pseudomonas and Acinetobacter species are recognized as a major health concern worldwide. As a result, the World Health Organization listed these bacteria in the critical priority pathogens group. This study aimed to assess the prevalence of carbapenem and multidrug-resistant Klebsiella, Pseudomonas, and Acinetobacter species at the University of Gondar Comprehensive Specialized Hospital. A five-year hospital based retrospective study was conducted from July to September 2021. Socio-demographic and laboratory data were collected from medical records in microbiology laboratory. The quality of the extracted data was assured through cross checking. The data were entered through Epi-data version 4.4.3.1, exported and analyzed using SPSS version 20. The variables were analyzed and presented through tables and graphics. In this study, the frequencies of male participants and neonates under the age of one week were 585 (62.8%) and 210 (22.6%), respectively. Approximately half (436; 46.8%) of the bacterial isolates were recovered from blood specimen. A total of 931 isolates were recorded, where 576 (61.9%) of these isolates were multidrug-resistant. More than two-third of Klebsiella ozaenae (87; 68.5%) and Klebsiella pneumoniae (398; 63.3%) were multidrug-resistant. Of the total bacterial isolates, 24 (13.1%) and 82 (22.9%) were resistant to imipenem and meropenem, respectively. The proportion of multidrug and carbapenem resistance in Klebsiella, Pseudomonas and Acinetobacter species were high. Therefore, urgent intervention including prevention of the spread of antimicrobial resistant strains and infection prevention practices is required. Treatment should also be guided with antimicrobial susceptibility testing.

Isolation, characterization, and antimicrobial susceptibility pattern of Escherichia coli O157:H7 from foods of bovine origin in Mekelle, Tigray, Ethiopia.

Escherichia coli O157:H7 is an emerging and major zoonotic foodborne pathogen. It has an increasing concern about the spread of antimicrobial-resistant strains. This study aimed to isolate and characterize Shiga toxin-producing E. coli O157:H7 from raw milk, yogurt, and meat of bovine origin and determine their antimicrobial susceptibility pattern. A cross-sectional study was conducted from December 2014 to June 2015, and a total of 284 milk and meat samples were collected from different sources in Mekelle. The collected samples were analyzed for the presence of E. coli and Shiga toxin-producing E. coli O157:H7 and the determination of their antimicrobial susceptibility pattern following the standard bacteriological and molecular techniques and procedures and antimicrobial sensitivity test. Out of the total 284 samples, 70 (24.6%) were bacteriologically positive for E. coli and 14.3% were found to be Shiga toxin-producing E. coli O157:H7. Of note, 100% of E. coli isolates carried the pal gene and 41.7% eaeA gene (EHEC). Of these EHEC isolates, 40% and 60% were positive for stx1 and stx2, respectively. E. coli isolates showed the highest level of susceptibility to gentamycin (91.7%) but the highest level of resistance to amoxicillin (95.8%). Of the tested isolates, 18 (75%) of E. coli showed multidrug-resistant. This study revealed the occurrence of Shiga toxin-producing E. coli O157:H7 in foods of bovine origin in the study area. In conclusion, a nationwide phenotypic and molecular characterization, in-depth typing, and drug-resistant gene identification of E. coli O157:H7 should be undertaken.

Assessment of Bacteriological and Antibiogram of Uropathogens among Students in the Faculty of Health Sciences, Imo State University, Owerri

The Assessment of bacteriological and antibiogram of uropathogens among students in the faculty of Health Sciences, Imo State University, Owerri with the aim to determine the prevalence of the isolates and to test which antibiotic has the greatest antagonistic activity against the different isolates in the study area. Fifty (50) students made up of both sexes were examined using their midstream urine samples as specimen. The study took note of the students’ age, sex and department. The urine samples were cultured on Nutrient agar, Mannitol salt agar, and MacConkey agar using pour plate method and were incubated at 37oC for 24 hours. After which the total bacterial counts were carried out and based on the count, it was categorized as being significant, suspected and non-significant. The colonies were then sub cultured for further identification. The pure isolates produced were stained using Gram stain, examined microscopically and further tested using relevant biochemical tests. It was found that a total of 35 bacteria were isolated which includes E.coli 14(40%) being the most predominant organism, followed by Staphylococus aureus 13(37.1%), Proteus mirabilis 7(20%) and Pseudomonas aeruginosa 1(2.9). Out of the fifty (50) urine samples investigated, 24 samples were significant for UTI (105 CFU/ml), 2 samples were suspected for UTI (102 – 104 CFU/ml), while 24 were not significant for UTI (below 102CFU/ml). Based on departmental studies, the subjects from the Department of Nutrition and Diatetics and Optometry had the highest significance of UTI, (60%) respectively. The results of susceptibility tests showed that Imipenem was the most effective antibiotic in inhibiting the bacterial growth (98.8% of antibiotic activity). The present study therefore, revealed that the urine samples collected from students in Faculty of Health sciences, Imo State University, Owerri had significant UTI and most of the isolates (98.8%) were sensitivity to Imipenem. UTI testing should be conducted periodically, and those who are infected should be treated with antibiotics like Imipenem to avoid complications. New antimicrobials and therapeutic agents with great efficacy, no side effects, ease of availability, and low cost should also be created. In order to reduce the risk of antimicrobial resistance, antibiotic medication should be started following a laboratory culture and sensitivity report. This would not only aid in the prudent use of antibiotics, but it would also help to limit the spread of antimicrobial resistant strains in the research region and the general community.

Magnitude and Antimicrobial Susceptibility Profile of Salmonella Recovered from Export Abattoirs Located in East Shewa, Ethiopia.

BackgroundSalmonella is one of the most common foodborne pathogens globally, and it remains a major public health concern with the increasing concern of the emergence and spread of antimicrobial-resistant strains. In Ethiopia, the information on the prevalence of Salmonella is scarce in export abattoirs.ObjectiveTo estimate the magnitude and antimicrobial susceptibility profile of Salmonella recovered from export abattoirs located in East Shewa, Ethiopia.MethodsA cross-sectional study was conducted from January to October 2020. In the study, 345 samples were collected from five export abattoirs using a systematic random sampling method. There were 150 carcass swabs (100 from goats and 50 from sheep), 60 goat skin swabs, 60 knife swabs, and 75 human stools. The isolates were identified and characterized using standard bacteriological procedures and confirmed using Salmonella genus-specific primer by polymerase chain reaction. Isolates were subjected to antimicrobial susceptibility to 14 antibiotics using the Kirby–Bauer disk diffusion method, and the results were assessed by using Clinical and Laboratory Standards Institute 2018.ResultsOf the 345 samples, 21 (6.08%; 95% CI 4.9–11.2%) were positive for Salmonella. The specific prevalence of Salmonella in carcass, skin, and knife swabs were 10 (6.67%; 95% CI 3.5–11.19%), 7 (11.67%; 95% CI 5.70–23.00%), and 4 (6.67%; 95% CI 2.50–16.64%), respectively. There was no statistically significant difference in the occurrence of Salmonella among export abattoirs and types of samples (P>0.05). In the current study, Salmonella was not isolated from sheep carcass and human stool samples. Among the 21 Salmonella isolates, 7 (33.3%) were resistant to at least 1 of the 14 antimicrobial agents tested and 2 (9.04%) of isolates were resistant to two antibiotics, tetracycline, and streptomycin. All isolates were susceptible to kanamycin, chloramphenicol, cephalothin, gentamycin, and ceftriaxone.ConclusionSalmonella was detected in carcass, skin, and knife samples from export abattoirs, which can have serious public health consequences. Some commonly used drugs in veterinary medicine have developed antimicrobial resistance. Therefore, sufficient sanitation at abattoirs, appropriate cooking of carcasses, and rational drug use is strongly advised. Further in-depth study such as serotyping and antimicrobial-resistant gene identification is recommended.

Prevalence and Antimicrobial Resistance Profile of Different Salmonella serovars Isolated from Food Products of Animal Origin

Salmonella is the major cause of foodborne diseases and a serious public health problem in the world, with an increasing concern for the emergence and spread of antimicrobial-resistant strains. Our study was conducted to assess the prevalence and antimicrobial resistance profiles of Salmonella isolates using standard bacteriological methods. The overall prevalence rate of 11.4% was recorded from the total analyzed food items of animal origin. Salmonella isolates were detected from 5.7% of minced meat, 1.4% of kofta, 1.4% of luncheon, and 2.8% of burger. All Salmonella species recovered were resistant to amoxicillin-clavulanic acid with 100% sensitivity to ciprofloxacin and meropenem. Findings on the multidrug-resistant (MDR) profile showed that a total of 6/8 (75%) of Salmonella Enteritidis were resistant to 3 or more antibiotics. Therefore, our findings provide the prevalence and drug resistance of Salmonella from foods of animal origin and contribute information to scientists as well as public health researchers to minimize the prevalent and resistant foodborne Salmonella species in Egypt.

Phenotypic characterization of antimicrobial drug resistance of Staphylococcus aureus and S. epidermidis strains isolated from various community infections in Oum El Bouaghi city, Algeria

Abstract. Rahmani A, Meradi L, Malawi K, Khanfouf F. 2021. Phenotypic characterization of antimicrobial drug resistance of Staphylococcus aureus and S. epidermidis strains isolated from various community infections in Oum El Bouaghi city, Algeria. Biodiversitas 22: 2665-2671. In Algeria most community infections caused by Staphylococcus epidermidis and Staphylococcus aureus present resistance to several antibiotics and induce therapeutic failures. The aim of this study is the characterization and the comparison of antimicrobial resistance of Staphylococcus strains isolated from community infection in Oum El Bouaghi city, Algeria. Species identification was realized by conventional biochemical tests and the determination of antibiotics susceptibility pattern was realized by using the agar disk diffusion method, according to the recommendations of the French Society for Microbiology (FSM, 2019). A total of 102 Staphylococci strains were obtained from clinical samples, with a frequency of isolation of 57,8% for S. epidermidis and 42,2% for S. aureus, both strains present a resistance for most used antibiotics, the higher resistance was found for oxacillin in both strains with 25,6% for S. aureus and 42,4% for S. epidermidis. Multidrug-Resistance (MDR) phenotype was detected in 37,3% of S. epidermidis and 14% in S. aureus strains. In Algeria, new control policies should be adopted to prevent the further spread of antimicrobial-resistant strains, especially in the community

Escherichia coli O15 : H7 from Food of Animal Origin in Arsi: Occurrence at Catering Establishments and Antimicrobial Susceptibility Profile.

Escherichia coli O157 : H7 (E. coli O157 : H7) has been found to be the major cause of food-borne diseases and a serious public health problem in the world, with an increasing concern for the emergence and spread of antimicrobial-resistant strains. Hitherto, little is known about the carriage of E. coli O157 : H7 and its antimicrobial susceptibility profile in the food of animal origin in Ethiopia. This study aimed to determine the occurrence and multidrug resistance profile of E. coli O157 : H7 from food of animal origin at different catering establishments in the selected study settings of Arsi Zone. One hundred ninety-two animal origin food items, namely, raw/minced meat (locally known as “Kitfo,” “Kurt,” and “Dulet”), raw milk, egg sandwich, and cream cake samples were collected and processed for microbiological detection of E. coli O157 : H7. Out of 192 samples, 2.1% (4/192) were positive for E. coli O157 : H7. Two E. coli O157 : H7 isolates were obtained from “Dulet” (6.3%) followed by “Kurt” (3.1%, 1/32) and raw milk (3.1%, 1/32), whereas no isolate was obtained from “Kitfo,” egg sandwich, and cream cake samples. Of the 4 E. coli O157 : H7 isolates subjected to 10 panels of antimicrobial discs, 3 (75%) were highly resistant to kanamycin, streptomycin, and nitrofurantoin. Besides, all the isolates displayed multidrug resistance phenotypes, 3 to 5 antimicrobial resistance, amid kanamycin, streptomycin, nitrofurantoin, tetracycline, and chloramphenicol. The occurrence of multidrug-resistant E. coli O157 : H7 isolates from foods of animal origin sampled from different catering establishments reveals that the general sanitary condition of the catering establishments, utensils used, and personnel hygienic practices did not comply with the recommended standards. Thus, this finding calls for urgent attention toward appropriate controls and good hygienic practices in different catering establishments dealing with consuming raw/undercooked foods of animal origin.

Modeling the Antimicrobial Resistance of Enterobacteria Responsible for Urinary Tract Infections in Benin: Another Way to Control Antimicrobial Resistance

Background: Infectious diseases are serious public health issue both in developing countries and industrialized nations. In developing countries, they are the main cause of high mortality rates. In the second group, existing resistance strains to antibiotics is developing and growing at an alarming rate. The purpose of this study was to produce data of national interest to implement sustainable control program against the spread of antimicrobial resistance strains in Benin.
 Methods: One hundred and ninety (190) urine samples were collected in selected hospitals in Benin from patients with urinary tract infection. After getting the informed consent from the patients, samples collections were performed under aseptic conditions and cultured for further analysis in the laboratory. The resistance profile of the bacterial strains was established. The search for beta-lactamase production by the isolates was performed using the synergy test for amoxicillin/clavulanic acid and cephalosporins. Mathematical modeling for predicting the development of resistance of the strains by the year 2024 was carried out employing the compartmental deterministic models.
 Results: Two hundred and thirty (230) strains were identified from the urine samples. Male individuals were the most affected by urinary tract infections. Individuals between the ages of 21-30 were predominantly infected. E. coli was the most isolated species (32.43%) in the urine samples, followed by K. pneumoniae (26.85%) and E. cloacae (25.92%). The susceptibility testing of isolates showed a high resistance to amoxicillin (91.82%). Whereas the lowest resistance was to imipenem (2%). The beta-lactamase was produced by 24.03% of the strains. Escherichia coli (32.43%) was the most productive of broad spectrum beta-lactamase, followed by K. pneumoniae (31.03%). The mathematical modeling revealed a rampant rise in resistance development of the strains to the tested antibiotics.
 Conclusions: These results provide important data for developing new preventive strategies against the evolution of bacterial resistance to antibiotics. It therefore, further deserves a constructive advocacy so that more actions are taken against the rampant spread of antimicrobial resistance strains in our health facilities as well as in the communities.

Emergence of Almost Identical F36:A-:B32 Plasmids Carryingbla NDM-5andqepAinEscherichia colifrom Both Pakistan and Canada.

The New Delhi Metallo-β-lactamase (NDM) producing Enterobacteriaceae is spreading worldwide. Although the blaNDM gene has been identified in animal associated Enterobacteriaceae isolates in many countries, little is known about its occurrence in animal products in Pakistan. In this study, 13 Escherichia coli isolates were collected from chicken meat samples in Pakistan. Two isolates, 15978 and C4109, exhibited reduced susceptibility (MIC ≥1 μg/mL) to imipenem, and carried blaNDM-5 and blaNDM-7 gene, respectively. Whole-genome sequencing and Oxford Nanopore MinION sequencing revealed that 15978 and C4109 belonged to ST156 and ST167, respectively. blaNDM-7 was carried by an IncX3 plasmid that has disseminated worldwide, whereas blaNDM-5 was located on an F36: A-: B32 plasmid, which shared high identity with two plasmids carried by E. coli isolates from other countries (one from a patient in Canada). To the best of our knowledge, this is the first report characterizing blaNDM-carrying plasmids from chicken meat samples in Pakistan. The dissemination of almost identical blaNDM-5-bearing F36:A-:B32 and blaNDM-7-bearing IncX3 plasmids in different countries highlights the importance of international trade and travel in the spread of antimicrobial resistance strains and plasmids worldwide.

Antimicrobial resistance (AMR) and molecular characterization of Neisseria gonorrhoeae in Ghana, 2012-2015

Neisseria gonorrhoeae antimicrobial resistance (AMR) surveillance is essential for tracking the emergence and spread of AMR strains in local, national and international populations. This is crucial for developing or refining treatment guidelines. N. gonorrhoeae multiantigen sequence typing (NG-MAST) is beneficial for describing the molecular epidemiology of gonococci at national and international levels. Elucidation of AMR determinants to β-lactam drugs, is a means of monitoring the development of resistance. In Ghana, little is known about the current gonococcal AMR prevalence and no characterization of gonococcal isolates has been previously performed. In this study, gonococcal isolates (n = 44) collected from five health facilities in Ghana from 2012 to 2015, were examined using AMR testing, NG-MAST and sequencing of penA. High rates of resistance were identified to tetracycline (100%), benzylpenicillin (90.9%), and ciprofloxacin (81.8%). One isolate had a high cefixime MIC (0.75 μg/ml). Twenty-eight NG-MAST sequence types (STs) were identified, seventeen of which were novel. The isolate with the high cefixime MIC contained a mosaic penA-34 allele and belonged to NG-MAST ST1407, an internationally spreading multidrug-resistant clone that has accounted for most cefixime resistance in many countries. In conclusion, AMR testing, NG-MAST, and sequencing of the AMR determinant penA, revealed high rates of resistance to tetracycline, benzylpenicillin, and ciprofloxacin; as well as a highly diverse population of N. gonorrhoeae in Ghana. It is imperative to continue with enhanced AMR surveillance and to understand the molecular epidemiology of gonococcal strains circulating in Ghana and other African countries.

Antibacterial activities of trans-cinnamaldehyde, caprylic acid, and β-resorcylic acid against catfish pathogens

Bacterial pathogens such as Edwardsiella ictaluri, Flavobacterium columnare, and virulent Aeromonas hydrophila have a significant economic impact on farm-raised catfish in the United States. Due to the limited number of licensed vaccines, and regulations with antimicrobials usage, there is need to find alternative therapeutics for sustainable aquaculture. Therefore, the antibacterial activities of trans-cinnamaldehyde (TC), caprylic acid (CA), and β-resorcylic acid (BA) were assessed against E. ictaluri 93–146, F. columnare 94–081, and A. hydrophila ML09–119 using broth microdilutions, and the capacity of TC to prevent E. ictaluri infection was evaluated during a challenge trial. Results demonstrated that TC inhibited growth of E. ictaluri, F. columnare, and A. hydrophila at 40, 20, and 80 μg/ml. Scanning electron microscopy (SEM) and transmission electron microscopy (TEM) of E. ictaluri, F. columnare, and A. hydrophila after incubation with TC revealed cell wall lysis, leakage of cytoplasmic contents, and pleomorphism in the bacterial shape with rupture of outer membranes. By the histological analysis, no abnormal changes were observed in the catfish intestines as a result of supplementation of TC. Moreover, an increasing number of goblet cells was observed in catfish received TC compared to control. In the E. ictaluri challenge trial, significantly higher survival was found in catfish that received TC at the levels of 15 and 20 mg/kg compared to control group (49.12% and 65.52% survival vs 11.11% survival). Bacterial concentrations in spleen and anterior kidney were significantly (P < .05) lower in fish fed with TC (20 mg/kg diet) compared to control at 5-day post-infection. Results indicate that supplementation of catfish feed with TC reduces E. ictaluri infection. A safe and efficacious alternative to antimicrobials will reduce the emergence and spread of antimicrobial resistant strains.

Antimicrobial resistance prediction and phylogenetic analysis of Neisseria gonorrhoeae isolates using the Oxford Nanopore MinION sequencer

Antimicrobial resistance (AMR) in Neisseria gonorrhoeae is common, compromising gonorrhoea treatment internationally. Rapid characterisation of AMR strains could ensure appropriate and personalised treatment, and support identification and investigation of gonorrhoea outbreaks in nearly real-time. Whole-genome sequencing is ideal for investigation of emergence and dissemination of AMR determinants, predicting AMR, in the gonococcal population and spread of AMR strains in the human population. The novel, rapid and revolutionary long-read sequencer MinION is a small hand-held device that generates bacterial genomes within one day. However, accuracy of MinION reads has been suboptimal for many objectives and the MinION has not been evaluated for gonococci. In this first MinION study for gonococci, we show that MinION-derived sequences analysed with existing open-access, web-based sequence analysis tools are not sufficiently accurate to identify key gonococcal AMR determinants. Nevertheless, using an in house-developed CLC Genomics Workbench including de novo assembly and optimised BLAST algorithms, we show that 2D ONT-derived sequences can be used for accurate prediction of decreased susceptibility or resistance to recommended antimicrobials in gonococcal isolates. We also show that the 2D ONT-derived sequences are useful for rapid phylogenomic-based molecular epidemiological investigations, and, in hybrid assemblies with Illumina sequences, for producing contiguous assemblies and finished reference genomes.

Human Campylobacteriosis in Italy: Emergence of Multi-Drug Resistance to Ciprofloxacin, Tetracycline, and Erythromycin.

Campylobacter spp. is one of the main cause of bacterial gastroenteritis in the world. The increase of antibiotic resistance in this species is a threat to public health. A Campylobacter spp. surveillance study was performed in Italy in the 2013–2016 period by the Enter-Net Italia network. The most prevalent Campylobacter species identified causing gastroenteritis was Campylobacter jejuni (73.4%) and 45% of all the annual cases of campylobacteriosis were reported in the summer period. High rates of ciprofloxacin and tetracycline resistance in Campylobacter spp. have been observed. An increasing percentage of Campylobacter coli strains simultaneously resistant to ciprofloxacin, tetracycline and erythromycin has been found. Molecular mechanisms of resistance have been investigated and the role of efflux pumps evaluated. Antibiotic resistance in Campylobacter spp. is an increasing serious threat that requires coordinated action to minimize the emergence and spread of antimicrobial resistant strains from animals to humans throughout the food chain.

Prevalence and Antimicrobial Resistance of Salmonella Isolated from Animal-Origin Food Items in Gondar, Ethiopia.

Salmonella has been found to be the major cause of foodborne diseases and a serious public health problem in the world, with an increasing concern for the emergence and spread of antimicrobial-resistant strains. A cross-sectional study was conducted between February 2014 and December 2015 on food items of animal origin to assess the prevalence and antimicrobial resistance profiles of Salmonella isolates using standard bacteriological methods. The overall prevalence rate of 5.5% was recorded from the total analyzed food items of animal origin. Salmonella isolates were detected from 12% of raw meat, 8% of minced meat, 2.9% of burger samples, 18% of raw eggs, and 6% of raw milk. Furthermore, antimicrobial susceptibility test identified 47.6% resistant Salmonella isolates, 28.6% intermediately sensitive isolates, and 23.8% susceptible isolates. Among Salmonella isolates tested, 42.6%, 28.6%, and 14.3% were found to be relatively resistant to tetracycline, sulfamethoxazole-trimethoprim, and ampicillin, respectively, while 9.5%–19% were intermediately resistant to tetracycline, amoxicillin, ampicillin, cephalothin, and nitrofurantoin. Therefore, our findings provide the prevalence and drug resistance of Salmonella from foods of animal origin and contribute information to scientists as well as public health researchers to minimize the prevalent and resistant foodborne Salmonella species in Ethiopia.

PERFIL DE USO DE ANTIMICROBIANOS E SUAS INTERAÇÕES MEDICAMENTOSAS EM UMA UTI ADULTO DO RIO GRANDE DO SUL

Justification and objective: In hospitals, especially in ICUs, there is a greater chance of selection and spread of antimicrobial resistant strains, due to the overuse of antibiotics and poor compliance with protocols. Therefore, the objective of this study was to analyze the antibiotics used, the indication, the treatment period, the identification of potential drug interactions between these drugs and others used by patients. Method: Sectional and descriptive study in a hospital level IV of Rio Grande do Sul, was conducted from drug prescriptions in the Intensive Care Unit for the period April-May 2011, who received at least one antibiotic during hospitalization. Since all the prescriptions were assessed every day. Results: The majority (54%) patients were female. The average age was 61.8 years. Most patients (63%) were discharged from the ICU. The average number of drugs prescribed per patient was 12.5 ± 3.6. The most commonly prescribed antibiotics were vancomycin, piperacillin + tazobactam and cefepime. Among the possible interactions, the most serious were: haloperidol and levofloxacin and levofloxacin x Regular insulin. Conclusions: Although not all drug interactions can be prevented, the spread of knowledge among health professionals through the pharmacist, as the main risk factors for drug interactions, is one of the main instruments for the prevention of drug interactions. Keywords: Anti-infective agents. Drug Interactions. Intensive Care Units.

Species-wide whole genome sequencing reveals historical global spread and recent local persistence in Shigella flexneri.

Shigella flexneri is the most common cause of bacterial dysentery in low-income countries. Despite this, S. flexneri remains largely unexplored from a genomic standpoint and is still described using a vocabulary based on serotyping reactions developed over half-a-century ago. Here we combine whole genome sequencing with geographical and temporal data to examine the natural history of the species. Our analysis subdivides S. flexneri into seven phylogenetic groups (PGs); each containing two-or-more serotypes and characterised by distinct virulence gene complement and geographic range. Within the S. flexneri PGs we identify geographically restricted sub-lineages that appear to have persistently colonised regions for many decades to over 100 years. Although we found abundant evidence of antimicrobial resistance (AMR) determinant acquisition, our dataset shows no evidence of subsequent intercontinental spread of antimicrobial resistant strains. The pattern of colonisation and AMR gene acquisition suggest that S. flexneri has a distinct life-cycle involving local persistence.

Safety Evaluation of the Coagulase-Negative Staphylococci Microbiota of Salami: Superantigenic Toxin Production and Antimicrobial Resistance.

The risks of contracting staphylococci food poisoning by the consumption of improperly manufactured salami and the possibility of this food being reservoirs for antibiotic resistance were evaluated. Nineteen coagulase-negative staphylococci (CNS) strains were found in commercial and artisanal salami. The species in commercial salami were S. saprophyticus, S. sciuri, S. xylosus, and S. carnosus. Artisanal salami showed S. succinus, S. epidermidis, and S. hominis but no S. carnosus. Phylogenetic analyses grouped the strains into three major staphylococcal species groups, comprised of 4 refined clusters with similarities superior to 90%. Fifteen strains harbored multiple enterotoxin genes, with high incidence of seb/sec and sea, 57% and 50%, respectively, intermediate incidence of sed/seh/selm and sei/seln/tst-H, 33% and 27%, correspondingly, and low incidence of see/selj/selo and seg, of respectively 13% and 1%. Real time RT-PCR and enzyme-linked-immunosorbent assays confirmed the enterotoxigenicity of the strains, which expressed and produced enterotoxins in vitro. The CNS strains showed multiresistance to several antimicrobials of therapeutic importance in both human and veterinarian medicine, such as β-lactams, vancomycin, and linezolid. The effective control of undue staphylococci in fermented meat products should be adopted to prevent or limit the risk of food poisoning and the spread of antimicrobial-resistant strains.