Extended-spectrum Beta-lactams Research Articles

The microbiological quality, shelf-life, and multidrug-resistant Salmonella contamination rates assessment in chicken giblets purchased from live poultry shops

The objective of the current study was to assess the shelf-life durations and hygienic standards of chicken giblets purchased from Egyptian live poultry outlets compared to the Egyptian Standardization Organization criteria. Salmonella prevalence and antibiotic-resistance profiles were also described. On the first day, forty-five giblet samples were randomly collected and evaluated for aerobic plate count (APC), coliform, Escherichia coli, Staphylococcus and Staphylococcus aureus, and multidrug-resistant Salmonella contamination rates using culturing methods, matrix-assisted laser desorption ionization-time of flight mass spectrometry, and the VITEK® −2 system. Four- and five-day shelf-life durations were assessed. All chicken giblets had acceptable APC levels below the 6 log cfu/g on the collection day, but 27 % were contaminated with Salmonella Enteritidis, rendering them unfit. More than 2-log CFU/gm of Escherichia coli and Staphylococcus aureus contamination was identified in 64 % and 58 % of the giblets, respectively. All targeted indices surpassed maximum authorized requirements after four and five days of chilling at 4 °C, coupled with the detection of obvious greenish discoloration and off odor. All twelve Salmonella Enteritidis were vulnerable to carbapenems, cefepime, and piperacillin/tazobactam, but 83 % were multidrug-resistant (MDR), with four demonstrating extended-spectrum beta-lactam resistance. This could be the first Egyptian report identifying such a high prevalence rate of Salmonella and MDR to key antibiotics in chicken giblets. The current study encourages Egyptian authorities to reevaluate laws governing live poultry outlets to reduce the risk of disease exposure, including the National Egyptian Food Safety Authority's direct supervision over these outlets to establish a stringent safety program.

A Review of the effects Al-Madinah Al-Munawwarah Ajwa dates on several of E. coli producing extended spectrum beta-lactam

Urinary tract infection (UTI) is the second most common disease after respiratory problems, it's also the most common infectious disease on a global scale in the field of health. The emergence of extended-spectrum beta-lactamase (ESBL)-producing E. coli (E. coli) resistance has led to a significant increase in urinary tract infections (UTIs) globally, this has posed a significant challenge. As a result, numerous investigations have been conducted with the goal of exploring botanical approaches to addressing the effects of antibiotic resistance in bacteria that cause diseases. Antibiotic resistance presents a formidable and pressing global challenge, requiring urgent and pivotal interventions to mitigate the spread of antibiotic-resistant bacterial strains. Date palms (Phoenix dactylifera L.) produce fruits that are popular throughout the world and are a significant part of the dietary culture in the Middle East. In the Kingdom of Saudi Arabia, dates have a significant role as a crop that's integral to the country's culture and heritage. The Ajwa date variety is distinguished by its elevated sugar content and large amount of dietary fiber, minerals, and vitamines. Its unique chemical composition that exhibits the potential to address multiple microorganisms that are resistant to antibiotics. Al-Madinah Al-Munawwarah is renowned for its production of rare dates exclusive to the region. Among the most famous types of date fruits found in Al-Madinah are Ajwah, Amberah, Majdool, and Safawi. These varieties are highly sought after for their distinct flavors and exceptional quality, contributing to the city's reputation as a hub for premium date production. The purpose of this review was to Study the effect of extracts from Ajwa date seeds on Extended-spectrum beta-lactamase of E. coli strains.

Antimicrobial susceptibility profile and detection of extended spectrum β-lactamase resistance genes in pseudomonas aeruginosa isolated from post-operative wounds

The spread of Pseudomonas aeruginosa is difficult to control with disinfectants and antibiotics due to the resistance found in P. aeruginosa isolates. The study investigated the susceptibility profile and detect extended spectrum β-lactamase (ESBL) resistance genes in the Pseudomonas aeruginosa isolated from post-operative wound infection. Wound swabs were cultured on MacConkey and sub-cultured on Cetrimide agar. The isolates were identified base on their macroscopic and microscopic characteristics as well as 16SrRNA. Disc diffusion technique was used to check the susceptibility profile of the isolates and the extended spectrum beta-lactam (ESBL) producers were determined by growing the isolates on Mueller Hinton agar plate in the presence of amoxyclav. 40 positive isolates were recovered in the study with 21 isolates been multi-drug resistance (MDR). Before plasmid curing, Streptomycin, ceftazidime, Augmentin, and Gentamicin has the highest resistance rate of 80% (n=32), 60% (n=24), 60% (n=24) and 60% (n=24) respectively. However, after plasmid curing, the result showed reduction in resistance rates. Streptomycin and ceftazidime showed high reduction in resistance from 80% to 25% and from 60 to 12.7% respectively indicating that resistance was plasmid-mediated. Pseudomonas aeruginosa F23 and Pseudomonas aeruginosa S15 isolates shown to possess both the plcH and bla PER genes with bands amplicons size of 307bp and 520bp respectively. Antibiotic susceptibility pattern after plasmid curing showed that 45% of the isolates produces beta-lactamase enzymes i.e., 18 out of 40 isolates were inactive to all beta-lactam group of antibiotics.

Evaluation of phage—antibiotic combinations in the treatment of extended-spectrum β-lactamase-producing Salmonella enteritidis strain PT1

Foodborne infections caused by Salmonella spp. are among the most common foodborne diseases in the world. We isolated a lytic phage against extended-spectrum beta-lactam producing S. Enteritidis strain PT1 derived from chicken carcass. Results from electronmicrography indicated that phiPT1 belonged to the family, Siphoviridae, in the order, Caudovirales. Phage phiPT1 was stable at temperatures from 4 °C to 60 °C and inactivated at 90 °C. phiPT1 retained a high titer from pH 4 to pH 10 for at least 1 h. Nevertheless, it displayed a significant decrease (p < 0.05) in titer at pH 11 and 12, with phage titers of 5.5 and 2.4 log10 PFU/mL, respectively. The latent time and burst size of phiPT1 were estimated to be 30 min and 252 PFU/infected cell, respectively. The virulence of phage phiPT1 was evaluated against S. Enteritidis strain PT1 at different MOIs. phiPT1 reduced Salmonella proliferation relative to the negative control (MOI 0) at all MOIs (P < 0.05). However, there is no significant difference among the MOIs (P > 0.05). The phage-antibiotic combination analysis (PAS) indicated that synergism was not detected at higher phiPT1 titer (1012 PFU/mL) with all tested antibiotics at all subinhibitory concentrations. However, synergistic activities were recorded at 0.25 × MIC of four tested antibiotics: cefixime, gentamicin, ciprofloxacin, and aztreonam in combination with phage at 104, 106 and 108 PFU/mL (ΣFIC ≤0.5). Synergism was detected for all antibiotics (0.1 × MIC) except meropenem and colistin in combination with phiPT1 at 104, 106 and 108 PFU/mL (ΣFIC ≤0.5). Synergism also displayed at the lowest concentrations of all antibiotics (0.01 MIC) in combination with phiPT1 at all titers except 1012 PFU/mL. Such characteristic features make phiPT1 to be a potential candidate for therapeutic uses.

413. Cost effectiveness of rectal screening for ESBL producing organism in preventing urosepsis following transrectal prostate biopsy

Abstract Background Urosepsis following transrectal ultrasound guided prostate biopsy (TRUS PB) occurs in 0.3-3.1% of patients. Our center gives ciprofloxacin and ceftriaxone prophylaxis. With rise in urinary pathogens resistant to fluoroquinolones or producing extended spectrum beta lactam (ESBL+), prophylactic regimen might need changing. Studies have highlighted cost effectiveness of rectal screening for ESBL+ organism prior to TRUS PB to determine target antibiotic. We compare our center’s incidence of urosepsis admissions following TRUS PB to the expected rate and calculate cost-effectiveness of pre-procedure screening to prevent urosepsis admissions. Methods All patients with CPT billing code 55700 (biopsy, prostate; needle or punch, single or multiple, any approach) from January 2020 through January 2021 were identified retrospectively. Charts were queried for emergency department or urgent care visits and hospital admissions within two weeks of TRUS PB and admissions reviewed for evidence of urosepsis and ESBL+ cultures. Hospitalization cost was compared to the extrapolated cost of doing pre-procedural rectal swabs. Cost of rectal swab and culture was estimated at $39.02 per swab, and identification and susceptibility at $67 per isolate. Results 33 of 1593 patients presented to our institution within 2 weeks of TRUS PB over a 13 month period. 3 were admitted for urosepsis post TRUS PB (2 with ESBL+ infection, 1 with no growth on culture), 12 had ED visits relating to their TRUS PB without urosepsis, (2 due to UTI with other organisms) and 18 visits were unrelated to TRUS PB. Our urosepsis admission rate was 0.19% (for ESBL+ 0.13%). Cost of the 3 hospitalizations was $37,910.92 ($27,063.76 for 2 ESBL+ infections). Rectal swabs would in theory have prevented 2 admissions. Cost of swab and culture would be $62,158.86. 50% of the swabs would need further testing to identify ESBL+ organism, for an additional cost of $53,365.50. Conclusion Given lower than expected urosepsis admission rates at our institution after TRUS PB, pre-procedure rectal swabs would not be cost effective, especially since some admissions may be unavoidable. The cost analysis is an underestimate as a visit some days prior to procedure would be scheduled and the staff resource utilization to collect the swab is not accounted for. Disclosures All Authors: No reported disclosures.

Detection and Dissemination of Extented-Spectrum Beta-Lactamases Genes (CTX-M-15 and SHV-187) Isolated in Multi-Drug Resistant Uropathogenic Klebsiella pneumoniae and Escherichia coli in Cote D'ivoire

Enterobacteriaceae are ubiquitous commensal bacteria of humans that have become major causative agents of hospital infections. The objective of the study was to characterized the extended-spectrum beta-lactam resistance genes from multi-drug uropathogenic clinical strains in Côte d'Ivoire. Bacterial strains isolated from various biological products were collected from January 2011 to June 2016 at the Observatoire de la résistance des micro-organismes aux anti-infectieux en Côte d'ivoire (ORMICI). Two hundred and sixty six (266) enterobacterial strains were collected during this study. Antibacterial susceptibility and the presence of bla genes were determined by the solid-state diffusion method and by PCR, respectively. The presence of ESBL was confirmed by the double disc synergy test method and Sequencing was performed. Of the strains collected, the most isolated were Escherichia coli 53 (39.25%) and Klebsiella pneumoniae 36 (26.66%). Antibiotic resistance of more than 50% was observed for gentamicin, norfloxacin, third generation cephalosporins and tobramicin in E coli. Only imipenem had a low resistance rate of 5.6%. However, apart from norfloxacin, the Klebsiella pneumoniae strains tested expressed resistance to aztreonam and second generation cephalosporins in excess of 50%. The rate of resistance to aztreonam and cefotaxin was statistically different between E. coli and Klebsiella pneumoniae strains (p-value ₌ 0,008 and p-value ₌ 0,032 respectively). The genes blaCTX-M, blaSHV, blaTEM, qnr B and a class I integron were detected. After sequencing, the SHV-1, SHV-28, SHV-187 and CTX-M15 variants were detected. Although these results are of low proportions, this may be considered critical for the future, hence the need for a better antibiotic surveillance strategy in Abidjan.

Molecular Analysis of Ndm-1 Positive Klebsiella pneumoniae Strains Isolated From Patients With Bacteremia Due to Urinary System Infection

Introduction: Health concerns about Klebsiella pneumoniae, which causes urinary tract infections (UTIs) and sepsis, are increasing worldwide. In addition, New Delhi metallo-ß-lactamase (NDM) carrier K. pneumoniae and other Gram-negative bacteria appear to cause serious clinical problems. This study aimed to reveal NDM-1 positive K. pneumoniae carrier status, molecular properties, and antibiotic resistance differences of patients who have bacteremia due to urinary system infections. Methods: Blood culture, biochemical tests, Vitek2, polymerase chain reaction, sequencing, phylogenetic analysis, and multilocus sequence typing (MLST) methods were used for the microbiological analysis of K. pneumoniae strains. Results: Overall, 146 K. pneumoniae strains were obtained from the cultures, 16 of which were found to be NDM-1 positive. Although these strains were discovered to have resistance to the authorized antibiotics, they were sensitive to gentamicin (CN), colistin (CT), and trimethoprim/sulfamethoxazole (SXT). Furthermore, it was found that the resistance rates of carbapenem (ertapenem (Etp), imipenem (Ipm), and meropenem (Mem)) were high. All K. pneumoniae strains represented extended-spectrum beta-lactam resistance. It was found that the phylogenetic affinities of K. pneumoniae strains were higher with Asian strains. Five and eleven K. pneumoniae isolates were determined to be ST17 and ST147 type variations, respectively, as a conclusion of the MLST study. Conclusions: It was observed that the presence of NDM-1-positive K. pneumoniae may pose a serious problem in patients with bacteremia caused by UTI. It has been demonstrated that it is important to develop preventive and control measures in the hospital by considering NDM-1-positive K. pneumoniae strains with multi-drug resistance.

Surviving White-out: How to Manage Severe Noninfectious Acute Lung Allograft Dysfunction of Unknown Etiology.

Surviving White-out: How to Manage Severe Noninfectious Acute Lung Allograft Dysfunction of Unknown Etiology.

Four new N-phenethylbenzamide derivatives from the stems of piper betle and their antimicrobial activity

Four new N-phenethylbenzamide derivatives, named piperbetamides A-D (1–4), and six allylbenzene derivatives (5–10) were isolated from the stems of Piper betle L. Their structures were determined by HR-ESI-MS and NMR spectroscopic methods. Compounds 1–10 were evaluated for their inhibitory effects on the growth of nine microorganisms including five Gram-negative (Escherichia coli, Salmonella enterica serovar Typhimurium, Shigella flexneri, Pseudomonas aeruginosa, and Extended-spectrum beta-lactam resistant Klebsiella pneumoniae), three Gram-positive (Listeria monocytogenes, Methicilin-resistant Staphylococcus aureus, Vancomycin-resistant Enterococcus faecalis), and one yeast (Candida albicans) strains. Compounds 1, 3, 4, 6 and 10 exhibited potential antimicrobial activity against S. flexneri, L. monocytogenes, methicillin-resistant S. aureus and vancomycin-resistant E. faecalis with minimum inhibitory concentration (MIC) values in the range of 16–32 µg/mL.

Characterization of plasmid-mediated quinolone resistance genes and extended-spectrum beta-lactamases in non-typhoidal Salmonella enterica isolated from broiler chickens.

Background and Aim:Antibiotic-resistant Salmonella is a public health concern. Fluoroquinolones and extended-spectrum beta-lactams are widely used for the treatment of Salmonella infections. This study focused on the detection of plasmid-mediated quinolone resistance (PMQR) and extended-spectrum beta-lactamase (ESBL) genes among multidrug-resistant (MDR) Salmonella enterica isolated from broilers.Materials and Methods:A total of 40 non-typhoidal S. enterica isolates were collected from 28 broiler chicken farms in four Iraqi Governorates. These isolates were examined for their susceptibility to 10 antimicrobial agents by disk-diffusion method followed by polymerase chain reaction assay for the detection of PMQR determinants and ESBLs genes.Results:Salmonella strains revealed high levels of resistance to the following antibiotics: Nalidixic acid 100%, levofloxacin (LEV) 97.5%, amoxicillin-clavulanic acid 95.0%, tetracycline 92.5%, and nitrofurantoin 80.0%. Otherwise, all isolates were susceptible to cefotaxime and ceftriaxone. All isolates were MDR, with 15 different profiles observed. Among 38 amoxicillin/clavulanic acid-resistant Salmonella isolates, 20 (52.6%) had the blaTEM gene, while blaSHV, blaCTX-M, and blaOXA genes were not detected. Only 5 (12.8%) out of 39 LEV-resistant isolates were positive for qnrB, three of which had blaTEM. No qnrC or qnrD, qnrS, aac(6`)-Ib-cr, qunA, and oqxAB genes were found in any of the tested isolates.Conclusion:This study demonstrates that broiler chickens may be considered a potential source for spreading MDR non-typhoidal Salmonella and ESBL traits in poultry production. Therefore, it is important to continuously monitor ESBL and PMQR genes to avoid the spread of resistant strains in the food chain and impact public health.

Molecular Detection of blaSHV-la Gene in Klebsiella pneumonia Isolated from Urinary Tract Infections, Najaf, Iraq.

Klebsiella pneumoniae is a gram-negative bacterium that causes serious illnesses, including pneumonia, liver abscess, meningitis, bloodstream infections, and urinary tract infections (UTIs). This study aimed to isolate and diagnose K. pneumoniae from clinical specimens of urine from patients with UTIs and perform molecular detection of the blaSHV-la gene in K. pneumonia in the Najaf Province, Iraq. The study included 100 clinical specimens from October 2021 to March 2022. As an initial diagnosis, K. pneumoniae isolates were diagnosed based on culture and biochemical features. Apart from the usage of polymerase chain reaction (PCR) technology to identify the blaSHV-la gene, the final diagnostic was achieved by the automated Vitek-2 compact system. The biochemical findings revealed that 40 out of every 100 isolates tested positive for K. pneumoniae. These results were validated by Vitek, which revealed that 40/100 of the samples tested positive for K. pneumoniae, and by PCR utilizing the blaSHV-la gene, which showed that 13/40 of the samples tested positive for K. pneumoniae isolated from the urine of patients with UTIs. In conclusion, the results indicated that the use of the Vitek-2 technique was required to confirm the accurate identification of the pathogen. Klebsiella pneumoniae clinical isolates showed multidrug resistance to antibiotics commonly used to treat UTIs. The blaSHV gene encoded for Extended-spectrum beta-lactam antibiotic was found almost in K. pneumoniae isolates.

Cost of care and impact on quality of life of upper urinary tract infections in South India with a focus on diabetics and extended-spectrum beta-lactam producing organisms

Cost of care and impact on quality of life of upper urinary tract infections in South India with a focus on diabetics and extended-spectrum beta-lactam producing organisms

Molecular Study of Escherichia albertii in Pediatric Urinary Tract Infections

Background: There are insufficient data about the presence of E. albertii as a causative organism in urinary tract infection in pediatric patients. Objective: The present study aimed to detect E. albertii by polymerase chain reaction (PCR) for detection of uidA, mdh, and lysP genes among isolated E.coli from children with urinary tract infection. Methods: The present study was a cross-sectional retrograde study which was carried out on 100 isolates of phenotypically confirmed E.coli detected in urine samples of children suffering from urinary tract infection. The isolates were subjected to molecular identification by PCR for uidA, mdh, and lysP genes. Results: E. albertii was identified by PCR in 7% of the isolates and E.coli was identified in 93% of the isolates. Two mdh and lysP genes were detected for E. albertii and the uidA gene for E. coli. E. albertii isolates had marked resistance to gentamicin (71.4%), followed by resistance to ciprofloxacin (57.1%), meropenem and imipenem (42.9% each) and ESBL activity by double discs method was reported in 57.1% of the isolates. However, none of the isolates had shown resistance to nalidixic acid and only one isolate had resistance to norfloxacin. There was a statistically insignificant difference between resistance to the used antibiotics such as aztreonam (P=0.083), ampicillin/clavulanate (P=0.5), ciprofloxacin (P=0.69), gentamicin (P=0.3) and ceftazidime (P=1.00). Conclusion: The present study highlights the emergence of E. albertii as a pathogen associated with urinary tract infections in children. There is marked antibiotic resistance of this pathogen, especially toward extended spectrum beta-lactams antibiotics. The identification method depends mainly on genetic studies. Further longitudinal studies with large number of patients are required to verify the accurate prevalence of this bacterium.

Genome Sequencing Identifies Previously Unrecognized Klebsiella pneumoniae Outbreaks in Neonatal Intensive Care Units in the Philippines.

Background Klebsiella pneumoniae is a critically important pathogen in the Philippines. Isolates are commonly resistant to at least 2 classes of antibiotics, yet mechanisms and spread of its resistance are not well studied.MethodsA retrospective sequencing survey was performed on carbapenem-, extended spectrum beta-lactam-, and cephalosporin-resistant Klebsiella pneumoniae isolated at 20 antimicrobial resistance (AMR) surveillance sentinel sites from 2015 through 2017. We characterized 259 isolates using biochemical methods, antimicrobial susceptibility testing, and whole-genome sequencing (WGS). Known AMR mechanisms were identified. Potential outbreaks were investigated by detecting clusters from epidemiologic, phenotypic, and genome-derived data.ResultsPrevalent AMR mechanisms detected include blaCTX-M-15 (76.8%) and blaNDM-1 (37.5%). An epidemic IncFII(Yp) plasmid carrying blaNDM-1 was also detected in 46 isolates from 6 sentinel sites and 14 different sequence types (STs). This plasmid was also identified as the main vehicle of carbapenem resistance in 2 previously unrecognized local outbreaks of ST348 and ST283 at 2 different sentinel sites. A third local outbreak of ST397 was also identified but without the IncFII(Yp) plasmid. Isolates in each outbreak site showed identical STs and K- and O-loci, and similar resistance profiles and AMR genes. All outbreak isolates were collected from blood of children aged < 1 year.ConclusionWGS provided a better understanding of the epidemiology of multidrug resistant Klebsiella in the Philippines, which was not possible with only phenotypic and epidemiologic data. The identification of 3 previously unrecognized Klebsiella outbreaks highlights the utility of WGS in outbreak detection, as well as its importance in public health and in implementing infection control programs.

Prospective antibacterial behavior of some essential aromatic oils against new Escherichia coli strain of extended-spectrum Beta-lactam

Aim: To evaluate the antimicrobial activities of some aromatic essential oils against a new pathogenic Escherichia coli strain with extended-spectrum beta-lactamase (ESBL) activity. Methodology: A total of 66 enteric bacteria were isolated from 250 urine samples that had been collected from human patients at different hospitals in Cairo, Egypt. Virulence factors of pathogenic isolates were determined, and the antibacterial activities of cinnamon bark oil and clove oil against E. coli EMH-542017 were estimated using the VITEK 2 system; this strain was confirmed as E. coli based on its 16S rRNA gene sequence, which was deposited in NCBI GenBank. Finally, modification of the bacterial cell wall following treatment with essential oil was observed with transmission electron microscopy (TEM). Results: The results confirmed that E. coli EMH-542017 was capable of producing hydroxamate siderophores and was resistant to 11 antibiotics, which were significantly observed with different grades. Nevertheless, screening by the combination disc method showed that 20 isolates were ESBL producers. Polymerase chain reaction analysis confirmed that the selected isolate EMH-542017 was positive for both ESBL blaCTX-M-9 genes. The addition of cinnamon and clove oils at levels of 12.5, 25, and 50 mg ml-1 was revealed to have high bactericidal effects on bacterial growth, and a change in bacterial cell morphology was detected by TEM, in which the cell wall seemed to be damaged and the flagella were lost following essential oil treatments, demonstrating that essential oil treatments are an effective means of suppressing multidrug-resistant E. coli. Interpretation: Despite these results, there is an urgent need to identify effective, safe, and economical treatments to reduce and protect against urinary tract infections in Egyptian patients.

Use of critically important antimicrobial classes early in life may adversely impact bacterial resistance profiles during adult years: potential co-selection for plasmid-borne fluoroquinolone and macrolide resistance via extended-spectrum beta-lactam use in dairy cattle.

The transfer of antimicrobial resistance genes commonly occurs via vertical and horizontal gene transfer, as such genes are often found on the same mobile genetic element. This occurrence can lead to the co-selection of resistance to antimicrobials without their application. Dairy cattle located in the south-western United States were enrolled in a matched-pair longitudinal study to evaluate the effects of a two-dose ceftiofur treatment for metritis on levels of third-generation cephalosporin resistance among faecal Escherichia coli temporally. Escherichia coli chosen for further investigation were isolated on selective media, harboured extended-spectrum beta-lactam, fluoroquinolone and macrolide resistance genes. This combination has previously been unreported; importantly, it included genes encoding for resistance to antibiotics that can only be used in dairy cattle less than 20months of age. Fluoroquinolones, macrolides and third and higher generation cephalosporins are considered critically important and highest priority for human medicine by the World Health Organization.

High relatedness of invasive multi-drug resistant non-typhoidal Salmonella genotypes among patients and asymptomatic carriers in endemic informal settlements in Kenya.

Invasive Non-typhoidal Salmonella (iNTS) disease is a major public health challenge, especially in Sub-Saharan Africa (SSA). In Kenya, mortality rates are high (20–25%) unless prompt treatment is instituted. The most common serotypes are Salmonella enterica serotype Typhimurium (S. Typhimurium) and Salmonella enterica serotype Enteritidis (S. Enteritidis). In a 5 year case-control study in children residing in the Mukuru informal settlement in Nairobi, Kenya, a total of 4201 blood cultures from suspected iNTS cases and 6326 fecal samples from age-matched controls were studied. From the laboratory cultures we obtained a total of 133 S. Typhimurium isolates of which 83(62.4%) came from cases (53 blood and 30 fecal) and 50(37.6%) from controls (fecal). A total of 120 S. Enteritidis consisted of 70(58.3%) from cases (43 blood and 27 fecal) and 50(41.7%) from controls (fecal).The S. Typhimurium population fell into two distinct ST19 lineages constituting 36.1%, as well as ST313 lineage I (27.8%) and ST313 lineage II (36.1%) isolates. The S. Enteritidis isolates fell into the global epidemic lineage (46.6%), the Central/Eastern African lineage (30.5%), a novel Kenyan-specific lineage (12.2%) and a phylogenetically outlier lineage (10.7%). Detailed phylogenetic analysis revealed a high level of relatedness between NTS from blood and stool originating from cases and controls, indicating a common source pool. Multidrug resistance was common throughout, with 8.5% of such isolates resistant to extended spectrum beta lactams. The high rate of asymptomatic carriage in the population is a concern for transmission to vulnerable individuals and this group could be targeted for vaccination if an iNTS vaccine becomes available.

Whole-genome sequencing resolves a polyclonal outbreak by extended-spectrum beta-lactam and carbapenem-resistant Klebsiella pneumoniae in a Portuguese tertiary-care hospital.

Klebsiella pneumoniae has emerged as an important nosocomial pathogen, with whole-genome sequencing (WGS) significantly improving our ability to characterize associated outbreaks. Our study sought to perform a genome-wide analysis of multiclonal K. pneumoniae isolates (n=39; 23 patients) producing extended spectrum beta-lactamases and/or carbapenemases sourced between 2011 and 2016 in a Portuguese tertiary-care hospital. All isolates showed resistance to third-generation cephalosporins and six isolates (five patients) were also carbapenem resistant. Genome-wide-based phylogenetic analysis revealed a topology representing ongoing dissemination of three main sequence-type (ST) clades (ST15, ST147 and ST307) and transmission across different wards, compatible with missing links that can take the form of undetected colonized patients. Two carbapenemase-coding genes were detected: blaKPC-3 , located on a Tn4401d transposon, and blaGES-5 on a novel class 3 integron. Additionally, four genes coding for ESBLs (blaBEL-1 , blaCTX-M-8 , blaCTX-M-15 and blaCTX-M-32 ) were also detected. ESBL horizontal dissemination across five clades is highlighted by the similar genetic environments of blaCTX-M-15 gene upstream of ISEcp1 on a Tn3-like transposon. Overall, this study provides a high-resolution genome-wide perspective on the epidemiology of ESBL and carbapenemase-producing K. pneumoniae in a healthcare setting while contributing for the adoption of appropriate intervention and prevention strategies.

Escherichia coli ST302: Genomic Analysis of Virulence Potential and Antimicrobial Resistance Mediated by Mobile Genetic Elements.

aEPEC are associated with persistent diarrhea, and diarrheal outbreaks in both humans and animals worldwide. They are differentiated from typical EPEC by the lack of bundle-forming pili, and from EHEC by the lack of phage-mediated stx toxins. However, phylogenetic analyses often associate aEPEC with EHEC, promoting the hypothesis that aEPEC are the progenitors of EHEC, which is supported by aEPEC conversion to EHEC by stx-carrying phages. While aEPEC can cause disease outright, the potential to acquire stx, one of the most potent bacterial toxins known, merits close monitoring. Escherichia coli ST302 (O108:H9, O182:H9, O45:H9) are aEPEC that have been isolated from diarrheic human, pig and rabbit hosts, as well as in healthy pigs, however, no study to date has focused on E. coli ST302 strains. Through WGS and hybrid assembly we present the first closed chromosome, and two circularized plasmids of an ST302 strain - F2_18C, isolated from a healthy pig in Australia. A phylogenetic analysis placed E. coli ST302 strains in proximity to EHEC ST32 (O145:H28) strains. Public databases were interrogated for WGSs of E. coli ST302 strains and short-read gene screens were used to compare their virulence-associated gene (VAG) and antimicrobial resistance gene (ARG) cargo. E. coli ST302 strains carry diverse VAGs, including those that typically associated with extraintestinal pathogenic E. coli (ExPEC). Plasmid comparisons showed that pF2_18C_FIB shared homology with EHEC virulence plasmids such as pO103 while pF2_18C_HI2 is a large multidrug resistance IncHI2:ST3 plasmid. A comparison of 33 HI2:ST3 plasmids demonstrated that those of Australian origin have not acquired resistances to extended-spectrum beta-lactams, colistin, fosfomycin or rifampicin, unlike those originating from Asia. F2_18C was shown to carry two additional pathogenicity islands – ETT2, and the STEC-associated PAICL3, plasmid-associated heavy metal resistance genes, as well as several unoccupied stx-phage attachment sites. This study sheds light on the virulence and AMR potential of E. coli ST302 strains and informs AMR genomic surveillance.

Exploration of antibiotic resistance risks in a veterinary teaching hospital with Oxford Nanopore long read sequencing.

The Oxford Nanopore MinION DNA sequencing device can produce large amounts of long sequences, typically several kilobases, within a few hours. This long read capacity was exploited to detect antimicrobial resistance genes (ARGs) in a large veterinary teaching hospital environment, and to assess their taxonomic origin, genetic organisation and association with mobilisation markers concurrently. Samples were collected on eight occasions between November 2016 and May 2017 (inclusive) in a longitudinal study. Nanopore sequencing was performed on total DNA extracted from the samples after a minimal enrichment step in broth. Many ARGs present in the veterinary hospital environment could potentially confer resistance to antimicrobials widely used in treating infections of companion animals, including aminoglycosides, extended-spectrum beta-lactams, sulphonamides, macrolides, and tetracyclines. High-risk ARGs, defined here as single or multiple ARGs associated with pathogenic bacterial species or with mobile genetic elements, were shared between the intensive care unit (ICU) patient cages, a dedicated laundry trolley and a floor cleaning mop-bucket. By contrast, a floor surface from an office corridor without animal contact and located outside the veterinary hospital did not contain such high-risk ARGs. Relative abundances of high-risk ARGs and co-localisation of these genes on the same sequence read were higher in the laundry trolley and mop bucket samples, compared to the ICU cages, suggesting that amplification of ARGs is likely to occur in the collection points for hospital waste. These findings have prompted the implementation of targeted intervention measures in the veterinary hospital to mitigate the risks of transferring clinically important ARGs between sites and to improve biosecurity practices in the facility.