Cephalosporin Resistance Research Articles

Study of the resistance to quaternary Ammonium-based disinfectants in Escherichia coli and Staphylococcus aureus strains carrying third-generation cephalosporin resistance

Multidrug-resistant bacteria pose a significant public health challenge, with the effectiveness of biocides in their eradication proving occasionally inadequate. This ineffectiveness highlights concerns over the potential correlation between biocide utilization and the rise in antibiotic resistance. Accordingly, this study is designed to examine the effectiveness of specific quaternary ammonium compound-based disinfectants against Escherichia coli and Staphylococcus aureus strains that are resistant to third-generation cephalosporins, particularly CTX-M type. The evaluation is based on performing antibiograms, followed by subjecting these strains to escalating concentrations of disinfectants with quaternary ammonium components. Additionally, the study involves screening for resistance genes to deepen our understanding of these resistance mechanisms. The outcomes revealed that the strains under scrutiny were resistant to a multitude of antibiotics. The Escherichia coli strains in question also displayed markedly reduced susceptibility to the biocides being studied. Conversely, the Staphylococcus aureus strains were inhibited at notably low concentrations of biocides. Notably, the qacΔE1 gene was detected in two Escherichia coli strains. We have identified instances of cross-resistance between certain disinfectants and antibiotics. Specifically, certain E. coli strains demonstrated diminished susceptibility to the first biocidal agent. This resistance was supported by the presence of the qacΔE1 gene in these same strains.

Analysis of the presence of the blaCTX-M genes in Escherichia coli isolated from downstream of the Bekasi River

Antimicrobial resistance (AMR) is a global public health threat caused by antibiotic resistance genes (ARGs), such as blaCTX-M. The blaCTX-M is one of the most common ARGs that confers cephalosporin resistance. This study aimed to investigate the concentrations of cefotaxime-resistant Escherichia coli (E. coli) and the presence of the blaCTX-M in E. coli isolated from downstream of the Bekasi River. The results of this study provided some information on AMR in reservoir environmental bacteria. This study used polymerase chain reaction (PCR) to amplify DNA and gel electrophoresis to visualize the target genes. The results are downstream of the Bekasi River had an average concentration of non-selective E. coli (2,3 ± 0,4) × 104 CFU/100mL and the average concentration of cefotaxime-resistant E. coli (2,1 ± 0,6) × 103 CFU/100 mL. The ratio of antibiotic-resistant E. coli to non-selective E. coli was 9.4%. The blaCTX-M genes were detected in 80% of E. coli isolates, with blaCTX-M group 1 genes predominating, which includes the blaCTX-M -1, blaCTX-M-3, and blaCTX-M-15 genes.

Genotypic Characterization of Uropathogenic Escherichia coli from Companion Animals: Predominance of ST372 in Dogs and Human-Related ST73 in Cats.

Extraintestinal pathogenic Escherichia coli (ExPEC) account for over 80% and 60% of bacterial urinary tract infections (UTIs) in humans and animals, respectively. As shared uropathogenic E. coli (UPEC) strains have been previously reported among humans and pets, our study aimed to characterize E. coli lineages among UTI isolates from dogs and cats and to assess their overlaps with human UPEC lineages. We analysed 315 non-duplicate E. coli isolates from the UT of dogs (198) and cats (117) collected in central Germany in 2019 and 2020 utilizing whole genome sequencing and in silico methods. Phylogroup B2 (77.8%), dog-associated sequence type (ST) 372 (18.1%), and human-associated ST73 (16.6%), were predominant. Other STs included ST12 (8.6%), ST141 (5.1%), ST127 (4.8%), and ST131 (3.5%). Among these, 58.4% were assigned to the ExPEC group and 51.1% to the UPEC group based on their virulence associated gene (VAG) profile (ExPEC, presence of ≥VAGs: papAH and/or papC, sfa/focG, afaD/draBC, kpsMTII, and iutA; UPEC, additionally cnf1 or hlyD). Extended-spectrum cephalosporin (ESC) resistance mediated by extended-spectrum β-lactamases (ESBL) and AmpC-β-lactamase was identified in 1.9% of the isolates, along with one carbapenemase-producing isolate and one isolate carrying a mcr gene. Low occurrence of ESC-resistant or multidrug-resistant (MDR) isolates (2.9%) in the two most frequently detected STs implies that E. coli isolated from UTIs of companion animals are to a lesser extent associated with resistance, but possess virulence-associated genes enabling efficient UT colonization and carriage. Detection of human-related pandemic lineages suggests interspecies transmission and underscores the importance of monitoring companion animals.

Azithromycin susceptibility testing for salmonella enterica isolates: Comparing disk diffusion results with MIC gradient strips

Background: Enteric fever remains an imperative public health problem in developing countries. After the emergence of cephalosporin resistance in Salmonella enterica subsp. enterica serovar Typhi, azithromycin is increasingly being used for oral treatment of enteric fever. Reports of sporadic azithromycin resistance have been reported across the country, additionally, misuse of azithromycin during the COVID-19 pandemic has concerns regarding emerging azithromycin resistance. This study evaluated the reliability of the disc diffusion method as a screening test for detecting azithromycin resistance by comparing it with the minimum inhibitory concentrations (MIC) gradient strip results, in 231 typhoidal salmonellae. Material and Methods: This prospective study was conducted in the Section of microbiology of the Shaukat Khanum Memorial Cancer Hospital and Research Centre, Lahore from March 2022 to March 2023. Isolates recovered from blood cultures of patients, suffering from enteric fever were selected. Azithromycin susceptibility testing was performed both by disk diffusion and as well as gradient strips and their results were compared. Results: Among typhoidal salmonellae, a significant portion consisted of extensively drug resistant Salmonella Typhi (61.9%). Only one XDR S. Typhi was found to be resistant to azithromycin both by disk diffusion method and MIC gradient strip method, with a MIC value of 64µg/ml. The study found no discrepancy between the disk diffusion and gradient strip methods. Conclusion: The current study found no discordance between disk diffusion and gradient strip test methods for evaluating azithromycin susceptibility among typhoidal salmonellae. Keywords: Azithromycin, disk diffusion testing, enteric fever, Minimum inhibitory concentration, Salmonella Typhi

Cephalosporin resistance, tolerance, and approaches to improve their activities.

Cephalosporins comprise a β-lactam antibiotic class whose first members were discovered in 1945 from the fungus Cephalosporium acremonium. Their clinical use for Gram-negative bacterial infections is widespread due to their ability to traverse outer membranes through porins to gain access to the periplasm and disrupt peptidoglycan synthesis. More recent members of the cephalosporin class are administered as last resort treatments for complicated urinary tract infections, MRSA, and other multi-drug resistant pathogens, such as Neisseria gonorrhoeae. Unfortunately, there has been a global increase in cephalosporin-resistant strains, heteroresistance to this drug class has been a topic of increasing concern, and tolerance and persistence are recognized as potential causes of cephalosporin treatment failure. In this review, we summarize the cephalosporin antibiotic class from discovery to their mechanisms of action, and discuss the causes of cephalosporin treatment failure, which include resistance, tolerance, and phenomena when those qualities are exhibited by only small subpopulations of bacterial cultures (heteroresistance and persistence). Further, we discuss how recent efforts with cephalosporin conjugates and combination treatments aim to reinvigorate this antibiotic class.

Genomic characterization of Salmonella isolated from retail chicken and humans with diarrhea in Qingdao, China.

Salmonella, especially antimicrobial resistant strains, remains one of the leading causes of foodborne bacterial disease. Retail chicken is a major source of human salmonellosis. Here, we investigated the prevalence, antimicrobial resistance (AMR), and genomic characteristics of Salmonella in 88 out of 360 (24.4%) chilled chicken carcasses, together with 86 Salmonella from humans with diarrhea in Qingdao, China in 2020. The most common serotypes were Enteritidis and Typhimurium (including the serotype I 4,[5],12:i:-) among Salmonella from both chicken and humans. The sequence types were consistent with serotypes, with ST11, ST34 and ST19 the most dominantly identified. Resistance to nalidixic acid, ampicillin, tetracycline and chloramphenicol were the top four detected in Salmonella from both chicken and human sources. High multi-drug resistance (MDR) and resistance to third-generation cephalosporins resistance were found in Salmonella from chicken (53.4%) and humans (75.6%). In total, 149 of 174 (85.6%) Salmonella isolates could be categorized into 60 known SNP clusters, with 8 SNP clusters detected in both sources. Furthermore, high prevalence of plasmid replicons and prophages were observed among the studied isolates. A total of 79 antimicrobial resistant genes (ARGs) were found, with aac(6')-Iaa, blaTEM-1B, tet(A), aph(6)-Id, aph(3″)-Ib, sul2, floR and qnrS1 being the dominant ARGs. Moreover, nine CTX-M-type ESBL genes and the genes blaNMD-1, mcr-1.1, and mcr-9.1 were detected. The high incidence of MDR Salmonella, especially possessing lots of mobile genetic elements (MGEs) in this study posed a severe risk to food safety and public health, highlighting the importance of improving food hygiene measures to reduce the contamination and transmission of this bacterium. Overall, it is essential to continue monitoring the Salmonella serotypes, implement the necessary prevention and strategic control plans, and conduct an epidemiological surveillance system based on whole-genome sequencing.

Investigation of Cephalosporin and Heavy Metal Resistance of Aeromonas hydrophila and Pseudomonas aeruginosa Strains Isolated from Hospital Sewage in Türkiye

In this study, 89 strains of Aeromonas hydrophila and 88 strains of Pseudomonas aeruginosa were isolated from the sewage of a university hospital in Turkey. The resistance of these bacterial isolates to 11 different cephalosporin classes’ antibiotics belonging to four generations and to 4 heavy metals was investigated. Cadmium, lead, manganese, and zinc are the heavy metals employed. There was a high incidence of resistance to cefazolin (98.9%), cefaclor (98.9%), and cefprozil (97.8%) among the A. hydrophila isolates. Lower resistance to cefoxitin (30.3%), cefepime (30.3%), and ceftazidime (31.4%) were found. Cefazolin, cefuroxime, cefaclor, and cefoxitin resistance was found to be (100%) among the P. aeruginosa isolates. Moreover, resistance rates to cefprozil (98.9%), cefixime (96.6%), and ceftizoxime (85.2%) were detected. No isolates of P. aeruginosa were showed resistance to ceftazidime, cefepime and cefpirome. Multiple antibiotic resistance (MAR) indexes ranged from 0.27 to 1.0 among A. hydrophila isolates and from 0.46 to 0.72 among P. aeruginosa isolates. All of the A. hydrophila and P. aeruginosa isolates showed resistance to cadmium. A. hydrophila and P. aeruginosa isolates showed low resistance to lead of 6.7% and 2.2% respectively. Results indicate that both species are easily recovered in hospital sewage and these species gained resistance to different generations of cephalosporins and heavy metals.

Effect of rapid cefpodoxime disk screening for early detection of third-generation cephalosporin resistance in Escherichia coli and Klebsiella pneumoniae bacteremia

BackgroundSeveral methods have been reported for detecting resistance genes or phenotypic testing on the day of positive blood culture in Escherichia coli or Klebsiella pneumoniae bacteremia. However, some facilities have not introduced these methods because of costs or other reasons. Toyota Kosei Hospital introduced cefpodoxime (CPDX) rapid screening on May 7, 2018, to enable early detection of third-generation cephalosporin resistance. In this study, we aimed to evaluate the effects of intervention with an Antimicrobial Stewardship Team using CPDX rapid screening.MethodsCefotaxime (CTX)-resistant E. coli or K. pneumoniae bacteremia cases were selected retrospectively and divided into two groups: the pre-CPDX screening (June 1, 2015, to May 6, 2018) and CPDX screening groups (July 7, 2018, to August 31, 2021). The primary outcome was the proportion of cases in which modifications were made to the administration of susceptible antimicrobial agents within 24 h of blood culture-positive reports.ResultsOverall, 63 patients in the pre-CPDX screening group and 84 patients in the CPDX screening group were eligible for analysis. The proportion of patients who modified to susceptible antimicrobial agents within 24 h of blood culture-positive reports was significantly increased in the CPDX screening group compared to that in the pre-CPDX screening group (6.3% vs. 22.6%, p = 0.010).ConclusionThe results demonstrated that in CTX-resistant E. coli or K. pneumoniae bacteremia, CPDX rapid screening increased the proportion of early initiation of appropriate antimicrobial agents.

Secrets of getting started: Regulation of the first committed step of peptidoglycan synthesis by protein phosphorylation in Enterococcus and other Gram-positive bacteria.

Regulation of the first committed step of peptidoglycan precursor synthesis by MurA-enzyme homologs has recently taken center stage in many different bacteria. In different low-GC Gram-positive bacteria, regulation of this step has been shown to be regulated by phosphorylation of homologs of the IreB/ReoM regulatory protein by PASTA-domain Ser/Thr-protein kinases. In this issue, Mascari, Little, and Kristich determine this regulatory pathway and its links to resistance to cephalosporin β-lactam antibiotics in the major human pathogen, Enterococcus faecalis (Efa). Unbiased genetic selections identified MurAA (MurA-family homolog) as the downstream target of IreB regulation in the absence of the IreK Ser/Thr-protein kinase. Physiological and biochemical approaches, including determination of MICs to ceftriaxone, Western blotting of MurAA cellular amounts, isotope incorporation into peptidoglycan sacculi, and thermal-shift binding assays of purified proteins, demonstrated that unphosphorylated IreB, together with proteins MurAB (MurZ-family homolog), and ReoY(Efa) negatively regulate MurAA stability and cellular amount by the ClpCP protease. Importantly, this paper supports the idea that ceftriaxone stimulates phosphorylation of IreB, which leads to increased cellular MurAA amount and precursor pathway flux required for E. faecalis cephalosporin resistance. Overall, findings in this paper significantly contribute to understanding variations of this central regulatory pathway in other low-GC Gram-positive bacteria.

Performance of CHROMagar ESBL media for the surveillance of extended-spectrum cephalosporin-resistant Enterobacterales (ESCrE) from rectal swabs in Botswana.

Introduction. Lack of laboratory capacity hampers consistent national antimicrobial resistance (AMR) surveillance. Chromogenic media may provide a practical screening tool for detection of individuals colonized by extended-spectrum beta-lactamase (ESBL)-producing organisms.Hypothesis. CHROMagar ESBL media represent an adequate screening method for the detection of extended-spectrum cephalosporin-resistant Enterobacterales (ESCrE), isolated from rectal swabs.Aim. To evaluate the performance of CHROMagar ESBL media to accurately identify ESCrE isolates from rectal swab samples attained from hospitalized and community participants.Methodology. All participants provided informed consent prior to enrolment. Rectal swabs from 2469 hospital and community participants were inoculated onto CHROMagar ESBL. The performance of CHROMagar ESBL to differentiate Escherichia coli and Klebsiella spp., Enterobacter spp. and Citrobacter spp. (KEC spp.) as well as select for extended-spectrum cephalosporin resistance were compared to matrix-assisted laser desorption/ionization-time-of-flight MS (MALDI-TOF-MS) and VITEK-2 automated susceptibility testing.Results. CHROMagar ESBL had a positive and negative agreement of 91.2 % (95 % CI, 88.4-93.3) and 86.8 % (95 % CI, 82.0-90.7) for E. coli and 88.1 % (95 % CI 83.2-92.1) and 87.6 % (95 % CI 84.7-90.2) for KEC spp. differentiation, respectively, when compared to species ID by MALDI-TOF-MS. When evaluated for phenotypic susceptibilities (VITEK-2), 88.1 % (714/810) of the isolates recovered on the selective agar exhibited resistance to third-generation cephalosporins.Conclusion. The performance characteristics of CHROMagar ESBL media suggest that they may be a viable screening tool for the identification of ESCrE from hospitalized and community participants and could be used to inform infection prevention and control practices in Botswana and potentially other low-and middle-income countries (LMICs). Further studies are required to analyse the costs and the impact on time-to-result of the media in comparison with available laboratory methods for ESCrE surveillance in the country.

Pattern of cephalosporin and carbapenem-resistant Pseudomonas aeruginosa: a retrospective analysis

ObjectivesDespite its financial cost on the world's health care system, Pseudomonas aeruginosa antibiotic resistance has been increasing. Therefore, the goal of this study was to assess the level of antimicrobial resistance to anti-pseudomonas medicines, specifically β-lactam medications such as cephalosporin and carbapenems. In addition, we evaluate the prevalence of multi-drug resistance to P. aeruginosa, particularly during the years of the COVID-19 pandemic. MethodsThis retrospective analysis covered the period from January 2019 to December 2022 and included cephalosporin- and carbapenem-resistant P. aeruginosa isolates. The real-time polymerase chain reaction Genexpert test (CARBA-R kit) was used for the detection of genes responsible for carbapenemase resistance. ResultsDuring the time of the study, 1815 clinical isolates of P. aeruginosa were identified and 160 (9%) were resistant to carbapenems and cephalosporins. The resistance rates were 32.5% (13/597) in 2019, 11.2% (44/393) in 2020, 7% (26/369) in 2021, and 11% (50/456) in 2022. Of those isolates, multidrug-resistant rates were 6.7%, 86.3%, 57.7%, and 56%, per year over the study period. Using Genexpert test, 88 (93.6%) of multidrug-resistant P. aeruginosa were negative for carbapenemase genes. ConclusionThis study emphasizes the alarming patterns of carbapenem and cephalosporin resistance among P. aeruginosa clinical isolates. Furhter surviellance from different centers and different regions is required.

From farm to fork: Spread of a multidrug resistant Salmonella Infantis clone encoding blaCTX-M-1 on pESI-like plasmids in Central Italy

Salmonella enterica subsp. enterica serovar Infantis (S. Infantis) is one of the “top five Salmonella serovars” of clinical significance in the European Union (EU). Antimicrobial resistant and extended spectrum β-lactamase (ESBL) AmpC-producing S. Infantis have been described in food production systems and human clinical samples in Italy. Recently, an increase of MDR S. Infantis carrying blaCTX-M genes involved in 3rd generation cephalosporin resistance was noticed in the EU, including Italy, mainly due to the spread of S. Infantis harboring a pESI-like plasmid.The aim of this study was to investigate the occurrence of the S. Infantis pESI-like plasmid among antibiotic resistant S. Infantis strains isolated at different points of the food chain, and to provide a phylogenetic analysis to gain further insight on their transmission pathways from ‘farm to fork’.MDR S. Infantis strains (n. 35) isolated from 2016 to 2021 at different stages of the food chain (animals, food, food-related environments, and humans) were investigated with in depth molecular characterization using real-time PCR, S1 nuclease pulsed-field gel electrophoresis (S1-PFGE) and whole genome sequencing (WGS).Our study reported the occurrence of S. Infantis strains harboring pESI-like plasmids, carrying blaCTX-M-1 genes, in Central Italy, at different sampling points along the food chain. Results confirmed the presence of a plasmid with a molecular size around 224–310 kb, thus consistent with the pESI-like, in 97 % of the 35 samples investigated. Two variants of S. Infantis pESI-like IncFIB(K)_1_Kpn3 were detected, one associated with the European clone carrying blaCTX-M-1 (21 isolates) and the other associated with U.S. isolates carrying blaCTX-M-65 (2 isolates, pESI-like U.S. variant). The majority was resistant to 3rd generation cephalosporins but none of the strains tested positive for the carbapenemase encoding genes. A total of 118 virulence genes were identified in isolates harboring the pESI-like plasmid. cgMLST and SNP-based analysis revealed the presence of one main cluster, composed by strains isolated from the environment, animals, food and humans.The results of this investigation underline the importance of phylogenetic studies to monitor and understand pathogen and AMR spread in a One Health approach.

Two-Dose Ceftiofur Treatment Increases Cephamycinase Gene Quantities and Fecal Microbiome Diversity in Dairy Cows Diagnosed with Metritis.

Antimicrobial resistance is a significant concern worldwide; meanwhile, the impact of 3rd generation cephalosporin (3GC) antibiotics on the microbial communities of cattle and resistance within these communities is largely unknown. The objectives of this study were to determine the effects of two-dose ceftiofur crystalline-free acid (2-CCFA) treatment on the fecal microbiota and on the quantities of second-and third-generation cephalosporin, fluoroquinolone, and macrolide resistance genes in Holstein-Friesian dairy cows in the southwestern United States. Across three dairy farms, 124 matched pairs of cows were enrolled in a longitudinal study. Following the product label regimen, CCFA was administered on days 0 and 3 to cows diagnosed with postpartum metritis. Healthy cows were pair-matched based on lactation number and calving date. Fecal samples were collected on days 0, 6, and 16 and pooled in groups of 4 (n = 192) by farm, day, and treatment group for community DNA extraction. The characterization of community DNA included real-time PCR (qPCR) to quantify the following antibiotic resistance genes: blaCMY-2, blaCTX-M, mphA, qnrB19, and the highly conserved 16S rRNA back-calculated to gene copies per gram of feces. Additionally, 16S rRNA amplicon sequencing and metagenomics analyses were used to determine differences in bacterial community composition by treatment, day, and farm. Overall, blaCMY-2 gene copies per gram of feces increased significantly (p ≤ 0.05) in the treated group compared to the untreated group on day 6 and remained elevated on day 16. However, blaCTX-M, mphA, and qnrB19 gene quantities did not differ significantly (p ≥ 0.05) between treatment groups, days, or farms, suggesting a cephamycinase-specific enhancement in cows on these farms. Perhaps unexpectedly, 16S rRNA amplicon metagenomic analyses showed that the fecal bacterial communities from treated animals on day 6 had significantly greater (p ≤ 0.05) alpha and beta diversity than the untreated group. Two-dose ceftiofur treatment in dairy cows with metritis elevates cephamycinase gene quantities among all fecal bacteria while paradoxically increasing microbial diversity.

Prevalence and Transmission of Extended-Spectrum Cephalosporin (ESC) Resistance Genes in Escherichia coli Isolated from Poultry Production Systems and Slaughterhouses in Denmark.

The emergence of extended-spectrum cephalosporin (ESC)-resistant Escherichia coli is a global concern. This study aimed to assess the prevalence and transmission of ESC-resistant E. coli in the Danish broiler production system. Samples from two vertically integrated Production Systems (1 and 2) and two slaughterhouses (A and B) were analyzed (n = 943) for the occurrence of ESC-resistant E. coli from 2015 to 2018. ESC-resistant E. coli isolates were whole-genome sequenced (WGS) for characterization of the multi-locus sequence type (MLST), antibiotic resistance genes, virulence genes, and plasmid replicon types. An ad hoc core genome (cg) MLST based on 2513 alleles was used to examine the genetic relatedness among isolates. The prevalence of ESC-resistant E. coli in the conventional Production System 1 was 2.7%, while in Production System 2 the prevalence was 26.7% and 56.5% for samples from the conventional and organic production, respectively. The overall prevalence of ESC-resistant E. coli in broiler thigh and fecal samples ranged from 19.3% in Slaughterhouse A to 22.4% in Slaughterhouse B. In total, 162 ESC-resistant E. coli were isolated and shown to belong to 16 different sequence types (STs). The most prevalent STs were ST2040 (n = 85) and ST429 (n = 22). Seven ESC resistance genes were detected: blaCMY-2 (n = 119), blaTEM-52B (n = 16), blaCTX-M-1 (n = 5), blaTEM-52C (n = 3), blaCTX-M-14 (n = 1), blaSHV-12 (n = 1), and up-regulation of ampC (n = 16), with an unknown resistance gene in one isolate (n = 1). The carriage of blaCMY-2 in 119 isolates was primarily associated with IncI1 (n = 87), and IncK plasmids (n = 31). Highly similar blaCMY-2 carrying E. coli isolates from ST429 were found in production systems as well as in slaughterhouses. In conclusion, findings from this study indicate that ESC-resistant E. coli are transferred vertically from farms in the production systems to slaughterhouses with the potential to enter the food supply.

Multiple drug resistant enterobacteria from biofilms in some tap water supplies in a Nigerian university

Tap outlets have been found to contain biofilms, which are a consortium of bacteria, fungi, viruses and protozoa. These microorganisms, especially Gram negative bacteria, could be pathogenic and highly resistant to antibiotics, leading to an increase in the prevalence of diseases worldwide. The university community depends on water from boreholes for consumption and domestic uses; as such, the need to identify the Gram negative bacteria is expedient. The main objective of this research is to determine the potability of the water released from the taps, and ultimately reduce the incidence of biofilm-related water infections. Water samples were collected from five boreholes and five tap outlets were swabbed with a sterile swab stick. Coliforms were estimated from the water samples using the Most Probable Number (MPN) technique. Gram negative bacteria were isolated and identified from the swabbing using standard bacteriological and biochemical tests. The antibiotic resistance patterns of the isolates were also determined, and the genes responsible for the multiple antibiotic resistance were identified using the DNA extraction and Polymerase Chain Reaction (PCR) methods. Bacterial counts of the samples ranged from 6.0×105cfu/mL to 1.4×106cfu/mL. MPN values of the tap water samples ranged from 4 to 1100+cfu/100mL, which exceeded the WHO standards of water quality. A total of 31 bacteria were isolated, of which 8 (25.8%) were Pseudomonas sp, 7 (22.6%) were Proteus sp, 4 (12.9%) were Klebsiella sp, 4 (12.9%) were Escherichia coli, 3 (9.7%) were Enterobacter sp, 3 (9.7%) were Citrobacter sp and 2 (6.5%) were Salmonella sp. All the bacteria showed multiple drug resistance to different antibiotics used, especially the cephalosporins. The gene found to be responsible for the cephalosporin resistance was the TEM - 445. Tap swabbing and water samples were found to contain a high value of coliforms (4 – 1100cfu/100mL), showing heavy faecal pollution, many of which could be pathogenic microorganisms that renders the water unfit for human consumption. The presence of these multidrug resistant microorganisms in the tap outlets could pose a serious threat to public health.

Application of Precision Medicine Concepts in Ambulatory Antibiotic Management of Acute Pyelonephritis.

Acute pyelonephritis (APN) is a relatively common community-acquired infection, particularly in women. The early appropriate antibiotic treatment of this potentially life-threatening infection is associated with improved outcomes. The international management guidelines for complicated urinary tract infections and APN recommend using oral antibiotics with <10% resistance among urinary pathogens. However, increasing antibiotic resistance rates among Escherichia coli and other Enterobacterales to fluoroquinolones, trimethoprim-sulfamethoxazole (TMP-SMX), and beta-lactams has left patients without reliable oral antibiotic treatment options for APN. This narrative review proposes using precision medicine concepts to improve empirical antibiotic therapy for APN in ambulatory settings. Whereas resistance rates to a particular antibiotic class may exceed 10% at the population-based level, the predicted antibiotic resistance rates based on patient-specific risk factors fall under 10% in many patients with APN on the individual level. The utilization of clinical tools for the prediction of fluoroquinolones, TMP-SMX, and third-generation cephalosporin resistance improves the ambulatory antibiotic management of APN. It may also reduce the need to switch antibiotic therapy later based on the in vitro antibiotic susceptibility testing results of bacterial isolates in urinary cultures. This approach may mitigate the burden of increasing antibiotic resistance in the community by ensuring that the initial antibiotic prescribed has the highest likelihood of treating APN appropriately.

ANTIBIOTIC RESISTANCE INDUCED BY EXTENDED-SPECTRUM BETA-LACTAMASES AND COVID-19

Antibacterial resistance, particularly that resulted from by extended-spectrum betalactamases (ESBLs), is increasing at an alarming pace as a direct consequence of extensive antibiotic usage, leading to an increase in the number of infections that are difficult to be eradicated.. Klebsiella pneumoniae and Staphylococcus epidermidis were the most common pathogens grown from 156 (18.5%) samples. Escherichia coli AmpC-producing ESBL due to worldwide Escherichia coli proliferation, researchers tested 10,780 clinical strains for decreased susceptibility. Nevertheless, genes and multilocus sequences varied widely among nations. CTX-M enzymes caused ESBL to rise 53% from 2012 to 2017. Levofloxacin, cefepime, piperacillintazobactam, and meropenem may detect ESBL-E bacteremia risk. During the COVID-19 pandemic, Acinetobacter baumannii had the most resistant strains, followed by Klebsiella pneumonia, Escherichia coli, and Pseudomonas aeruginosa. To combat the epidemic's spread, a statewide community lockdown was implemented, confining nursing home patients and prohibiting outside contact and movement. This study found that donor screening for fecal microbiota transplantation is likely to fail due to a high frequency of extended-spectrum beta-lactamase positive bacteria in feces, poor adherence to regular fecal donation, increased social isolation, travel restrictions, and decreased antibiotic use. Conventional lactamase antagonists may decrease ESBLs, which cause cephalosporin resistance in certain bacteria. Extended-spectrum beta-lactamase-producing Klebsiella pneumoniae strains are increasing, and the COVID-19 pandemic triggered a critical care unit pandemic. This study found that gram-negative antibiotic resistance was 1.11-fold higher among those without documented attempts to improve infection prevention, treatment, or prescription safety. More efforts need to be made to prevent infections, offer treatments, and monitor medication resistance. These activities are all vital.

Study Gene Expression of OXA-48and CTX-M-1 Genes Cephalosporin resistance in Escherichia coli isolated from urinary tract infections in Baghdad hospitals

Escherichia coli are a normal flora in the human. It is pathogenic in patients with immune system disorders and is the leading cause of enteritis, urinary tract infection, septicemia and other medical infections. E. coli is the most common cause of community and hospital-acquired urinary tract infections (UTIs). It is responsible for &gt;80% of all cases of UTI. These study samples were taken from Al-Karama Teaching Hospital and Al-Yarmouk Teaching Hospital in Baghdad. This study aimed to determine the Minimum Inhibition concentration (MIC) of Ceftazidim. As well as comparing the effect of antibiotics and without antibiotics on beta-lactam genes (OXA-48 –CTXM-1) resistance to Cephalosporin where there is an overexpression of gene expression in the antibiotic between (125-64) µg/ml. Bacteria produce beta-lactam enzymes that break down the beta-lactam ring in the antibiotic, which reduces the effectiveness of antibiotics. This mechanism is one of the mechanisms of resistance in bacteria. The presence of both genes increases the resistance of this species to Cephalosporin. The results of gene expression when treated with antibiotics for the OXA-48 gene in his sample were 1.4, and the highest value was 14.5, as well as for the CTX-M-1 gene, where the results ranged between the lowest value of 1.3 and the highest value of 7.3 when compared to the control samples, we notice an overexpression of gene. It was concluded that the resistance of E. coli to Ceftazidim was related to the genes blaOXA45 and CTXM-1, but the primary role may be due to blaOXA45. Keywords: Gene Expression, OXA-48 Gene, CTX-M-1 Gene, Cephalosporin, Escherichia coli.

Association of cephalosporin resistance in intraoperative biliary cultures with surgical site infections in patients undergoing pancreaticoduodenectomy. A retrospective cohort study

BackgroundThe aim of this study was to assess the incidence of bacterobilia at the time of a pancreaticoduodenectomy (PD) and the association of resistant bacteria in bile to surgical site infections (SSI). MethodsThis was a retrospective cohort study including patients undergoing PD in a single center between May 2016 and October 2020. Data of preoperative biliary drainage (PBD), intraoperative biliary cultures (IBC) and postoperative complications were analysed to assess the risk factors for resistant bacteria in IBC and SSIs. ResultsOf 361 patients included, 254 (70%) had undergone PBD. Second-generation cephalosporin resistant bacteria were found in IBC of 183 (64%) of all the patients. PBD was the only risk factor for second-generation cephalosporin resistance. The risk for second-generation cephalosporin resistance was more than 20-fold in patients with PBD [n = 170/254 (67%) (OR 22.58 (95% CI, 9.61–53.01), p < 0.001)] compared to patients who did not have PBD (n = 13/107 (12%)). Also, if the time between PBD and surgery was 2 months or more the second-generation cephalosporin resistance in IBC increased the risk for SSIs (OR 4.14 (95% CI, 1.18–14.51), p = 0.027). ConclusionThe second-generation cephalosporin resistance in IBC is common in patients who have undergone PBD. Broad-spectrum antibiotics in prophylaxis may be beneficial for these patients.

Genetic determinants underlying the progressive phenotype of β-lactam/β-lactamase inhibitor resistance in Escherichia coli.

Currently, whole-genome sequencing (WGS) data have not shown strong concordance with Escherichia coli susceptibility profiles to the commonly used β-lactam/β-lactamase inhibitor (BL/BLI) combinations: ampicillin-sulbactam (SAM), amoxicillin-clavulanate (AMC), and piperacillin-tazobactam (TZP). Progressive resistance to these BL/BLIs in the absence of cephalosporin resistance, also known as extended-spectrum resistance to BL/BLI (ESRI), has been suggested to primarily result from increased copy numbers of blaTEM variants, which is not routinely assessed in WGS data. We sought to determine whether addition of gene amplification could improve genotype-phenotype associations through WGS analysis of 147 E. coli bacteremia isolates with increasing categories of BL/BLI non-susceptibility ranging from ampicillin (AMP) susceptibility to being fully resistant to all three BL/BLIs. Consistent with a key role of blaTEM in ESRI, 112/134 strains (84%) with at least ampicillin non-susceptibility encoded blaTEM. Evidence of blaTEM amplification (i.e., blaTEM gene copy number estimates > 2×) was present in 40/112 (36%) strains. There were positive correlations between blaTEM copy numbers with minimum inhibitory concentrations of AMC and TZP (P < 0.05) but not for SAM (P = 0.09). The diversity of β-lactam resistance mechanisms, including non-ceftriaxone hydrolyzing blaCTX-M variants, blaOXA-1, and ampC and blaTEM strong promoter mutations, was greater in AMC- and TZP-non-susceptible strains but rarely observed within SAM- and AMP-non-susceptible isolates. Our study indicates that comprehensive analysis of WGS data, including β-lactamase-encoding gene amplification, can help categorize E. coli with AMC or TZP non-susceptibility but that discerning the transition from SAM susceptibility to SAM non-susceptibility using genetic data requires further refinement. IMPORTANCE The increased feasibility of whole-genome sequencing has generated significant interest in using such molecular diagnostic approaches to characterize difficult-to-treat, antimicrobial-resistant (AMR) infections. Nevertheless, there are current limitations in the accurate prediction of AMR phenotypes based on existing AMR gene database approaches, which primarily correlate a phenotype with the presence/absence of a single AMR gene. Our study utilized a large cohort of cephalosporin-susceptible Escherichia coli bacteremia samples to determine how increasing the dosage of narrow-spectrum β-lactamase-encoding genes in conjunction with other diverse β-lactam/β-lactamase inhibitor (BL/BLI) genetic determinants contributes to progressively more severe BL/BLI phenotypes. We were able to characterize the complexity of the genetic mechanisms underlying progressive BL/BLI resistance including the critical role of β-lactamase encoding gene amplification. For the diverse array of AMR phenotypes with complex mechanisms involving multiple genomic factors, our study provides an example of how composite risk scores may improve understanding of AMR genotype/phenotype correlations.