Third-generation Cephalosporin Resistance Research Articles

Estimating the subnational prevalence of antimicrobial resistant Salmonella enterica serovars Typhi and Paratyphi A infections in 75 endemic countries, 1990-2019: a modelling study.

Enteric fever, a systemic infection caused by Salmonella enterica serovars Typhi and Paratyphi A, remains a major cause of morbidity and mortality in low-income and middle-income countries. Enteric fever is preventable through the provision of clean water and adequate sanitation and can be successfully treated with antibiotics. However, high levels of antimicrobial resistance (AMR) compromise the effectiveness of treatment. We provide estimates of the prevalence of AMR S Typhi and S Paratyphi A in 75 endemic countries, including 30 locations without data. We used a Bayesian spatiotemporal modelling framework to estimate the percentage of multidrug resistance (MDR), fluoroquinolone non-susceptibility (FQNS), and third-generation cephalosporin resistance in S Typhi and S Paratyphi A infections for 1403 administrative level one districts in 75 endemic countries from 1990 to 2019. We incorporated data from a comprehensive systematic review, public health surveillance networks, and large multicountry studies on enteric fever. Estimates of the prevalence of AMR and the number of AMR infections (based on enteric fever incidence estimates by the Global Burden of Diseases study) were produced at the country, super-region, and total endemic area level for each year of the study. We collated data from 601 sources, comprising 184 225 isolates of S Typhi and S Paratyphi A, covering 45 countries over 30 years. We identified a decline of MDR S Typhi in south Asia and southeast Asia, whereas in sub-Saharan Africa, the overall prevalence increased from 6·0% (95% uncertainty interval 4·3-8·0) in 1990 to 72·7% (67·7-77·3) in 2019. Starting from low levels in 1990, the prevalence of FQNS S Typhi increased rapidly, reaching 95·2% (91·4-97·7) in south Asia in 2019. This corresponded to 2·5 million (1·5-3·8) MDR S Typhi infections and 7·4 million (4·7-11·3) FQNS S Typhi infections in endemic countries in 2019. The prevalence of third-generation cephalosporin-resistant S Typhi remained low across the whole endemic area over the study period, except for Pakistan where prevalence of third-generation cephalosporin resistance in S Typhi reached 61·0% (58·0-63·8) in 2019. For S Paratyphi A, we estimated low prevalence of MDR and third-generation cephalosporin resistance in all endemic countries, but a drastic increase of FQNS, which reached 95·0% (93·7-96·1; 3·5 million [2·2-5·6] infections) in 2019. This study provides a comprehensive and detailed analysis of the prevalence of MDR, FQNS, and third-generation cephalosporin resistance in S Typhi and S Paratyphi A infections in endemic countries, spanning the last 30 years. Our analysis highlights the increasing levels of AMR in this preventable infection and serves as a resource to guide urgently needed public health interventions, such as improvements in water, sanitation, and hygiene and typhoid fever vaccination campaigns. Fleming Fund, UK Department of Health and Social Care; Wellcome Trust; and Bill and Melinda Gates Foundation.

Genomic epidemiology reveals geographical clustering of multidrug-resistant Escherichia coli ST131 associated with bacteraemia in Wales

Antibiotic resistance is a significant global public health concern. Uropathogenic Escherichia coli sequence type (ST)131, a widely prevalent multidrug-resistant clone, is frequently associated with bacteraemia. This study investigates third-generation cephalosporin resistance in bloodstream infections caused by E. coli ST131. From 2013-2014 blood culture surveillance in Wales, 142 E. coli ST131 genomes were studied alongside global data. All three major ST131 clades were represented across Wales, with clade C/H30 predominant (n = 102/142, 71.8%). Consistent with global findings, Welsh strains of clade C/H30 contain β-lactamase genes from the blaCTX-M-1 group (n = 65/102, 63.7%), which confer resistance to third-generation cephalosporins. Most Welsh clade C/H30 genomes belonged to sub-clade C2/H30Rx (58.3%). A Wales-specific sub-lineage, named GB-WLS.C2, diverged around 1996-2000. An introduction to North Wales around 2002 led to a localised cluster by 2009, depicting limited genomic diversity within North Wales. This investigation emphasises the value of genomic epidemiology, allowing the detection of genetically similar strains in local areas, enabling targeted and timely public health interventions.

Genomic epidemiology of third-generation cephalosporin-resistant Escherichia coli from Argentinian pig and dairy farms reveals animal-specific patterns of co-resistance and resistance mechanisms.

Little is known about the ecology of critically important antibiotic resistance among bacteria with the potential to be opportunistic human pathogens (e.g., Escherichia coli) on South American farms. By studying 70 pig and dairy cattle farms in central-eastern Argentina, we identified that third-generation cephalosporin resistance (3GC-R) in E. coli was mediated by mechanisms seen more often in certain species and that 3GC-R pig E. coli were more likely to be co-resistant to florfenicol and amoxicillin/clavulanate. This suggests that on-farm antibiotic usage is key to selecting the types of E. coli present on these farms. 3GC-R E. coli and 3GC-R plasmids were diverse, suggestive of long-term circulation in this region. We identified the de novo mobilization of the resistance gene blaROB from pig pathogens into E. coli on a novel mobile genetic element, which shows the importance of surveying poorly studied regions for antibiotic resistance that might impact human health.

Clonal and plasmidic dissemination of critical antimicrobial resistance genes through clinically relevant ExPEC and APEC-like lineages (ST) in the dairy cattle population of Québec, Canada.

Antimicrobial resistance can be effectively limited by improving the judicious use of antimicrobials in food production. However, its effect on the spread of AMR genes in animal populations is not well described. In the province of Québec, Canada, a new legislation implemented in 2019 has led to an unprecedented reduction in the use of critical antimicrobials in dairy production. We aimed to investigate the potential link between ESBL/AmpC E. coli isolated before and after legislation and to determine the presence of plasmids carrying genes responsible for critical AMR. We collected fecal samples from calves, cows, and manure pit from 87 Québec dairy farms approximately 2 years before and 2 years after the legislation came into effect. The whole genomes of 183 presumptive ESBL/AmpC E. coli isolated after cefotaxime enrichment were sequenced. Their phylogenetic characteristics (MLST, serogroup, cgMLST) and the presence of virulence and resistance genes and replicons were examined. A maximum likelihood phylogenetic tree was constructed based on single nucleotide polymorphism (SNPs). We identified 10 clonal lineages (same cgMLST) and 7 clones (SNPs ≤ 52). Isolates belonging to these clones could be found on different farms before and after the legislation, strongly suggesting a clonal spread of AMR genes in the population during this 4-year period. All isolates were multidrug resistant (MDR), with clone 2 being notable for the presence of macrolide, fluoroquinolone, and third-generation cephalosporin resistance genes. We also identified clinically relevant ExPEC (ST10) and APEC-like lineages (ST117, ST58, ST88) associated with the presence of ExPEC and APEC virulence genes, respectively. Our data also suggests the presence of one epidemic plasmid belonging to the IncY incompatibility group and carrying qnrs1 and blaCTX-M-15. We demonstrated that AMR genes spread through farms and can persist over a 4-year period in the dairy cattle population through both plasmids and E. coli clones, despite the restriction of critical antimicrobial use. MDR ExPEC and APEC-like STs are present in the normal microbiota of cattle (more frequently in calves). These data increase our knowledge on gene dissemination dynamics and highlight the fact that biosecurity measures should be enhanced in this industry to limit such dissemination.

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.

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.

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.

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.

Asymptomatic gastrointestinal carriage of multidrug-resistant carbapenemase-producing Enterobacteriaceae among children under five years in a Kenyan hospital

ObjectivesAsymptomatic gastrointestinal carriage of carbapenem-resistant Enterobacteriaceae (CRE) is a threat to global health in developing countries with inadequate safe drinking water, poor hygiene, and weak antimicrobial stewardship; however, epidemiological data to guide CRE infection prevention and control is limited in these settings. We assessed asymptomatic CRE and carbapenem-producing Enterobacteriaceae (CPE) fecal carriage rates and associated risk factors among hospitalized children aged under 5 years. MethodsWe adopted a cross-sectional study at Mama Lucy Kibaki Hospital in Nairobi-City County, Kenya, between June and September 2022. We collected demographic and clinical characteristics using a structured questionnaire and clinical reports and analyzed stool/rectal swab samples by standard and automated bacteriological methods. ResultsAsymptomatic CRE and CPE fecal carriage rate was 2.25% (6/267), with six isolates recovered, predominated by Escherichia coli (33.33%) and Enterobacter cloacae subsp dissolvens (33.33%). Third-generation cephalosporin and ciprofloxacin resistance were highest in Citrobacter farmer and E. cloacae subsp cloacae. All CRE and CPE were multidrug-resistant, and except E. cloacae subsp cloacae, were 100% colistin-resistant. ConclusionsAsymptomatic gastrointestinal carriage of multidrug-resistant-CRE among hospitalized children under 5 years, presents a substantial public health threat. This calls for continuous surveillance including molecular characterization of isolates, to inform infection prevention and antimicrobial stewardship adherence in line with local and global plans on AMR.

Doxycycline post exposure prophylaxis could select for cross-resistance to other antimicrobials in various pathogens: An in silico analysis.

A number of randomized controlled trials have found that doxycycline post exposure prophylaxis (PEP) can reduce the incidence of gonorrhoea, chlamydia and syphilis in men who have sex with men (MSM). If tetracycline resistance is associated with resistance to other antimicrobials in a range of bacterial species, then doxycycline PEP could have the unintended effect of selecting for resistance to other antimicrobials in these bacterial species. Antimicrobial susceptibility data were retrieved from two sources: pubMLST (https://pubmlst.org/) and Pathogenwatch (https://pathogen.watch/) for the following bacterial pathogens: Klebsiella pneumoniae, Salmonella enterica subsp. Enterica serovar Typhi, Campylobacter jejuni, Staphylococcus aureus, Streptococcus pneumoniae and Streptococcus pyogenes. We assessed if tetracycline resistance was associated with resistance to six relevant antimicrobials. We found evidence of cross resistance to various antimicrobials in all six bacterial species assessed. Cross resistance was found in 4 of 5 antimicrobials for K. pneumoniae, 1 of 2 for C. jejuni, 3 of 5 for S. enterica subsp. Enterica serovar Typhi, 5 of 5 for S. aureus, 5 of 6 for S. pneumoniae and 2 of 3 for S. pyogenes. These associations include a higher prevalence of methicillin resistance in tetracycline resistant S. aureus, penicillin resistance in S. pneumoniae, macrolide and clindamycin resistance in S. pyogenes, fluoroquinolone resistance in S. enterica subsp. Enterica serovar Typhi and third-generation cephalosporin resistance in K. pneumoniae. These results suggest that studies evaluating the effects of doxycycline PEP should include the effects of doxycycline on resistance not only to doxycycline but also to other antimicrobials and in a broader array of bacterial species than has been included in doxycycline PEP studies thus far.

Mortality associated with third-generation cephalosporin resistance in Enterobacterales bloodstream infections at eight sub-Saharan African hospitals (MBIRA): a prospective cohort study

Bacteria of the order Enterobacterales are common pathogens causing bloodstream infections in sub-Saharan Africa and are frequently resistant to third-generation cephalosporin antibiotics. Although third-generation cephalosporin resistance is believed to lead to adverse outcomes, this relationship is difficult to quantify and has rarely been studied in this region. We aimed to measure the effects associated with resistance to third-generation cephalosporins in hospitalised patients with Enterobacterales bloodstream infection in Africa. We conducted a prospective, matched, parallel cohort study at eight hospitals across sub-Saharan Africa. We recruited consecutive patients of all age groups with laboratory-confirmed Enterobacterales bloodstream infection and matched them to at least one patient without bloodstream infection on the basis of age group, hospital ward, and admission date. Date of infection onset (and enrolment) was defined as the day of blood sample collection for culturing. Patients infected with bacteria with a cefotaxime minimum inhibitory concentration of 1 mg/L or lower were included in the third-generation cephalosporin-susceptible (3GC-S) cohort, and the remainder were included in the third-generation cephalosporin-resistant (3GC-R) cohort. The primary outcomes were in-hospital death and death within 30 days of enrolment. We used adjusted multivariable regression models to first compare patients with bloodstream infection against matched patients within the 3GC-S and 3GC-R cohorts, then compared estimates between cohorts. Between Nov 1, 2020, and Jan 31, 2022, we recruited 878 patients with Enterobacterales bloodstream infection (221 [25·2%] to the 3GC-S cohort and 657 [74·8%] to the 3GC-R cohort) and 1634 matched patients (420 [25·7%] and 1214 [74·3%], respectively). 502 (57·2%) bloodstream infections occurred in neonates and infants (age 0-364 days). Klebsiella pneumoniae (393 [44·8%] infections) and Escherichia coli (224 [25·5%] infections) were the most common Enterobacterales species identified. The proportion of patients who died in hospital was higher in patients with bloodstream infection than in matched controls in the 3GC-S cohort (62 [28·1%] of 221 vs 22 [5·2%] of 420; cause-specific hazard ratio 6·79 [95% CI 4·06-11·37] from Cox model) and the 3GC-R cohort (244 [37·1%] of 657 vs 115 [9·5%] of 1214; 5·01 [3·96-6·32]). The ratio of these cause-specific hazard ratios showed no significant difference in risk of in-hospital death in the 3GC-R cohort versus the 3GC-S cohort (0·74 [0·42-1·30]). The ratio of relative risk of death within 30 days (0·82 [95% CI 0·53-1·27]) also indicated no difference between the cohorts. Patients with bloodstream infections with Enterobacterales bacteria either resistant or susceptible to third-generation cephalosporins had increased mortality compared with uninfected matched patients, with no differential effect related to third-generation cephalosporin-resistance status. However, this finding does not account for time to appropriate antibiotic treatment, which remains clinically important to optimise. Measures to prevent transmission of Enterobacterales could reduce bloodstream infection-associated mortality from both drug-resistant and drug-susceptible bacterial strains in Africa. Bill & Melinda Gates Foundation.

Comparative genetic characterisation of third-generation cephalosporin-resistant Escherichia coli isolated from integrated and conventional pig farm in Korea

Pig-farming systems consist of integrated or conventional farms, and many antimicrobials are used to treat bacterial infections. The objective of this study was to compare characteristics of third-generation cephalosporin resistance and extended-spectrum β-lactamase (ESBL)/pAmpC β-lactamase-producing Escherichia coli between integrated and conventional farms. Third-generation cephalosporin-resistant E. coli was collected from integrated and conventional pig farms from 2021 to 2022. Polymerase chain reaction and DNA sequencing were performed for the detection of β-lactamase-encoding genes, molecular analysis, and identification of genetic relationships. To determine the transferability of β-lactamase genes, conjugation assays were conducted. Antimicrobial resistance rates were higher in conventional farms than in integrated farms; ESBL- and pAmpC-lactamase-producing E. coli rates were higher in conventional farms (9.8%) than in integrated farms (3.4%). Fifty-two (6.5%) isolates produced ESBL/pAmpC β-lactamase genes. Isolates from integrated farms harboured CTX-15 (3 isolates), CTX-55 (9 isolates), CTX-229 (1 isolate), or CMY-2 (1 isolate) genes; isolates from conventional farms harboured CTX-1 (1 isolate), CTX-14 (6 isolates), CTX-15 (2 isolates), CTX-27 (3 isolates), CTX-55 (14 isolates), CTX-229 (1 isolate), and CMY-2 (11 isolates) genes. Of the 52 ESBL/pAmpC β-lactamase-producing E. coli isolates, class 1 integrons with 11 different gene cassette arrangements were detected in 39 (75.0%) isolates, and class 2 integrons were detected in 3 isolates. The most common sequence type in both integrated and conventional farms was ST5229, followed by ST101, and then ST10. Third-generation cephalosporin-resistant patterns and molecular characteristics differed between integrated and conventional farms. Our findings suggest that continuous monitoring of third-generation cephalosporin resistance on pig farms is necessary to prevent the dissemination of resistant isolates.

Detection of blaCTX-M genes in ESBL-producing Klebsiella isolates from animals in Croatia.

This study investigated the frequency of third-generation cephalosporin resistance in Klebsiella spp. isolated from animals in Croatia and the presence of blaCTX-M genes. A total of 711 enteric bacteria were isolated from clinical samples, and Klebsiella spp. isolates accounted for 6.9% (n = 49). Thirteen Klebsiella isolates (26.5%) were ESBL producers, nine isolates from the Klebsiella pneumoniae species complex (69.2%), and four (30.8%) Klebsiella oxytoca isolates. All carried the blaCTX-M-15 gene, and antimicrobial susceptibility testing revealed them as multidrug resistant. All were resistant to all tested cephalosporins, fluoroquinolones, aminoglycosides and aztreonam, 92.3% showed resistance to tetracycline, 84.6% to trimethoprim-sulfamethoxazole and 69.2% to nitrofurantoin. No isolate showed resistance to imipenem and meropenem. It can be concluded that ESBL-producing Klebsiella expressing the blaCTX-M gene are not rare among Klebsiella isolates from animals in Croatia.

Molecular epidemiology of enterically colonizing Escherichia coli with resistance against third-generation cephalosporins isolated from stool samples of European soldiers with concomitant diarrhea on deployment in Western African Mali.

Extended spectrum beta-lactamases (ESBL) are frequently found in Enterobacterales isolates from Western Africa. However, information on the molecular epidemiology of regional ESBL-positive Enterobacterales strains is scarce. In order to provide epidemiological information, ESBL-positive Escherichia coli isolates from stool samples of European soldiers with diarrhea deployed to a field camp in Mali were subjected to whole-genome sequencing (Illumina MiSeq and Oxford Nanopore MinION) and antimicrobial susceptibility testing. With two exemptions, sequence-based analysis suggested an absence of transmission events between soldiers as indicated by a high genetic diversity of isolates and sequence types, confirming previous rep-PCR results. Third-generation cephalosporin resistance was associated with the presence of blaCTX-M-15 genes with (n = 14) and without (n = 5) co-occurring blaTEM-1b genes. Between 0 and 6 virulence and resistance plasmids per isolate were recorded. The detected resistance plasmids could be categorized into five types, which, in turn, share different sequence-identical segments, representing particular antimicrobial resistance gene-associated mobile genetic elements (MGEs). Phenotypic resistance rates within the 19 assessed isolates that showed distinguishable colony morphologies were 94.7% (18/19) against ampicillin-sulbactam and trimethoprim/sulfamethoxazole, 68.4% (13/19) against moxifloxacin, 31.6% (6/19) against ciprofloxacin, 42.1% (8/19) against gentamicin, 31.6% (6/19) against tobramycin, and 21.1% (4/19) against piperacillin-tazobactam and fosfomycin. Virulence-associated genes mediating infectious gastroenteritis were rarely detected. The gene aggR, which is characteristic for enteroaggregative E. coli, was only detected in one single isolate. In summary, we found a variety of different strains and clonal lineages of ESBL-carrying E. coli. Transmission either between soldiers or from common contaminated sources was demonstrated in two cases and played only a minor role in this military field camp, while there were indications that resistance gene bearing MGEs had been exchanged between antimicrobial resistance gene-(ARG-)carrying plasmids.

Investigating Possible Interspecies Communication of Plasmids Associated with Transfer of Third-Generation Cephalosporin, Quinolone, and Colistin Resistance Between Simultaneously Isolated Escherichia Coli and Klebsiella Pneumoniae.

The coinfection process producing multiple species of pathogens provides a specific ecological niche for the exchange of genetic materials between pathogens, in which plasmids play a vital role in horizontal gene transfer, especially for drug resistance, but the underlying transfer pathway remains unclear. Interspecies communication of the plasmids associated with the transfer of third-generation cephalosporins, quinolones, and colistin resistance has been observed in simultaneously isolated Escherichia coli and Klebsiella pneumoniae from abdominal drainage following surgery. The MICs of antimicrobial agents were determined by the broth microdilution method. The complete chromosome and plasmid sequences were obtained by combining Illumina paired-end short reads and MinION long reads. S1-PFGE, southern blot analysis and conjugation assay confirmed the transferability of the mcr-1-harboring plasmid. Both the E. coli isolate EC15255 and K. pneumoniae isolate KP15255 from the same specimen presented multidrug resistance. Each of them harbored one chromosome and three plasmids, and two plasmids and their mediated resistance could be transferred to the recipient by conjugation. Comparison of their genome sequences suggested that several genetic communication events occurred between species, especially among their plasmids, such as whole-plasmid transfer, insertion, deletion, amplification, or inversion. Exchange of plasmids or the genetic elements they harbor plays a critical role in antimicrobial resistance gene transmission and poses a substantial threat to nosocomial infection control, necessitating the continued surveillance of multidrug resistant pathogens, especially during coinfection. IMPORTANCE The genome sequence of bacterial pathogens commonly provides a detailed clue of genetic communication among clones or even distinct species. The intestinal microecological environment is a representative ecological niche for genetic communication. However, it is still difficult to describe the details of horizontal gene transfer or other genetic events within them because the evidence in the genome sequence is incomplete and limited. In this study, the simultaneously isolated Escherichia coli and Klebsiella pneumoniae from a coinfection process provided an excellent example for observation of interspecies communication between the two genomes and the plasmids they harbor. A complete genome sequence acquired by combining the Illumina and MinION sequencing platforms facilitated the understanding of genetic communication events, such as whole-plasmid transfer, insertion, deletion, amplification, or inversion, which contribute to antimicrobial resistance gene transmission and are a substantial threat to nosocomial infection control.

Changing Trends in Antimicrobial Susceptibility Patterns of Bloodstream Infection (BSI) in Secondary Care Hospitals of India.

Introduction Bloodstream infection (BSI) and subsequent sepsis are life-threatening medical conditions. The onset of antimicrobial resistance and subsequent multi-drug resistant organisms (MDRO) significantly increase healthcare-associated expenditure with adverse clinical outcomes. The present study was undertaken to identify the trends of BSI in community settings in secondary care hospitals (smaller private hospitals and district hospitals) in the state of Madhya Pradeshin Central India with the support of the Indian Council of Medical Research (ICMR) and National Health Mission, Madhya Pradesh. Methodology The present study was a prospective, longitudinal observational chart review type of study. The study was carried out at 10 secondary care hospitals (eight smaller private hospitals and two government district hospitals) nominated by the State Government as part of the ICMR Antimicrobial Resistance Surveillance and Research Network (AMRSN). The hospitals were nominated depending on the availability of a microbiology laboratory and a full-time microbiologist. Result A total of 6202 blood samples were received from patients with suspected BSI, out of which 693 samples were positive for aerobic culture. Among these, 621 (89.6%) showed bacterial growth and 72 (10.3%) grew Candida species (spp). Out of the 621 bacterial growth samples, Gram-negative bacteria were 406 (65.3%) and Gram-positive bacteria were 215 (34.6%). Among the Gram-negative isolates (406), the predominant isolate was Escherichia coli (115; 28.3%) followed by Klebsiella pneumoniae(109; 26.8%), Pseudomonas aeruginosa(61; 15%), Salmonella spp. (52; 12.8%), Acinetobacter spp. (47; 11.6%) and the other Enterobacter spp. (22; 5.4%). Among the Gram-positive isolates (215), the predominant isolate was Staphylococcus aureus(178; 82.8%) followed by Enterococcus spp. (37; 17.2%). Among the Escherichia coli, third-generation cephalosporin resistance was identified in 77.6%, piperacillin-tazobactam resistance in 45.2%, carbapenem resistance in 23.5% and colistin resistance in 16.5% of cases. Among the Klebsiella pneumoniae, third-generation cephalosporin resistance was identified in 80.7%, piperacillin-tazobactam resistance in 72.8%, carbapenem resistance in 63.3% and colistin resistance in 14% of cases. Among the Pseudomonas aeruginosa, ceftazidime resistance was identified in 61.2%, piperacillin-tazobactam resistance in 55%, carbapenem resistance in 32.8%, and colistin resistance in 38.3% of cases. Among the Acinetobacter spp., piperacillin-tazobactam resistance was identified in 72.7%, carbapenem resistance in 72.3%, and colistin resistance in 9.3% cases. While analyzing the antibiogram for Staphylococcus aureus isolates, methicillin resistance (MRSA) was seen in 70.3% of cases, followed by vancomycin resistance (VRSA) in 8% of cases and linezolid resistance in 8.1%. Among the Enterococcus spp. isolates, linezolid resistance was found in 13.5%, vancomycin resistance (VRE) in 21.6%, and teicoplanin resistance in 29.7% of cases. Conclusion In conclusion, the first-ever study to identify the risk of high-end antibiotics causing significant drug resistance in secondary and tertiary care settings has highlighted the urgent need for more randomized control studies and proactive measures from healthcare authorities and serves as a beacon for future research efforts and underscores the importance of implementing antibiograms to combat the growing threat of antibiotic resistance.

Description of Antimicrobial-Resistant Escherichia coli and Their Dissemination Mechanisms on Dairy Farms.

Despite its importance in veterinary medicine, there is little information about antimicrobial resistance (AMR) and its transmission in dairy cattle. The aim of this work is to compare AMR phenotypes and genotypes in resistant Escherichia coli and to determine how the resistance genes spread among the E. coli population on dairy farms in Québec, Canada. From an existing culture collection of E. coli isolated from dairy manure, a convenient selection of the most resistant isolates (a high level of multidrug resistance or resistance to broad-spectrum β-lactams or fluoroquinolones) was analyzed (n = 118). An AMR phenotype profile was obtained for each isolate. Whole genome sequencing was used to determine the presence of resistance genes, point mutations, and mobile genetic elements. In addition, a subset of isolates from 86 farms was taken to investigate the phylogenetic relationship and geographic distribution of the isolates. The average agreement between AMR phenotypes and genotypes was 95%. A third-generation cephalosporin resistance gene (blaCTX-M-15), a resistance gene conferring reduced susceptibility to fluoroquinolones (qnrS1), and an insertion sequence (ISKpn19) were detected in the vicinity of each other on the genome. These genes were harbored in one triplet of clonal isolates from three farms located >100 km apart. Our study reveals the dissemination of resistant E. coli clones between dairy farms. Furthermore, these clones are resistant to broad-spectrum β-lactam and fluoroquinolone antimicrobials.

Nationwide analysis of antimicrobial resistance in pathogenic Escherichia coli strains isolated from diseased swine over 29 years in Japan.

Pathogenic Escherichia coli strains are important causes of several swine diseases that result in significant economic losses worldwide. In Japan, the use of antimicrobials in swine is much higher than that in other farm animals every year. Antimicrobial resistance in pathogenic E. coli strains also heavily impacts the swine industry due to the limited treatment options and an increase in the potential risk of the One Health crisis. In 2016, we investigated 684 Japanese isolates of swine pathogenic E. coli belonging to four major serogroups and reported the emergence and increase in the highly multidrug-resistant serogroups O116 and OSB9 and the appearance of colistin-resistant strains. In the present study, by expanding our previous analysis, we determined the serotypes and antimicrobial resistance of 1,708 E. coli strains isolated from diseased swine between 1991 and 2019 in Japan and found recent increases in the prevalences of multidrug-resistant strains and minor serogroup strains. Among the antimicrobials examined in this study that have been approved for animal use, a third-generation cephalosporin was found to be effective against the most isolates (resistance rate: 1.2%) but not against highly multidrug-resistant strains. We also analyzed the susceptibilities of the 1,708 isolates to apramycin and bicozamycin, both which are available for treating swine in Japan, and found that the rates of resistance to apramycin and bicozamycin were low (6.7% and 5.8%, respectively), and both antimicrobials are more effective (resistance rates: 2.7% and 5.4%, respectively) than third-generation cephalosporins (resistance rate: 16.2%) against highly multidrug-resistant strains.

Central line-associated Rhizobium radiobacter bloodstream infection in two allogeneic hematopoietic cell transplant recipients.

Rhizobium radiobacter is a gram-negative, opportunistic phytopathogen that rarely causes human infections. We report two cases of Rhizobium radiobacter central line-associated bloodstream infection (CLABSI) in allogeneic hematopoietic cell transplantation (alloHCT) recipients. We review previous reports and common microbiological characteristics associated with this organism. Two adult males developed R. radiobacter CLABSIs at day +81 and day +77 post-alloHCT. Patient one was asymptomatic on presentation while patient two was febrile. One patient had a polymicrobial infection, which has not been previously described. The presence of high-level ceftazidime resistance in both patients suggests third-generation cephalosporin resistance may be more common than previously recognized. For both patients, microbiologic clearance was achieved through peripherally inserted central catheter removal and initiation of intravenous cefepime. Antibiotic therapy was narrowed to oral levofloxacin for a total 14-day course from the time of first negative blood culture. There has been no subsequent recurrence of R. radiobacter infection at 12 and 5 months of follow-up for patients one and two, respectively. These two cases add to the scant literature characterizing R. radiobacter infection following alloHCT. Immunosuppressive agents for graft-versus-host disease prophylaxis may have predisposed these patients to R. radiobacter infection. Our reports, and previously reported cases, suggest R. radiobacter exhibits low virulence, mild symptom burden, and does not confer a high mortality risk. In the alloHCT setting, further accumulation of cases is needed to aid in understanding clinical features and characteristics of R. radiobacter infection.

SG-APSIC1157: The attributable mortality and excess length of stay associated with third-generation cephalosporin-resistant Enterobacterales bloodstream infections—A prospective cohort study in Suva, Fiji

Objectives: Although antimicrobial resistance (AMR) disproportionately affects low- and middle-income countries (LMICs), primary clinical data on AMR burden from LMICs are lacking, particularly from the Pacific Islands. We adapted recent World Health Organization methodology to measure the impact of third-generation cephalosporin (3GC) resistance on mortality and excess length of hospital stay among inpatients with Enterobacterales bloodstream infection (BSI) in Fiji. Methods: We conducted a prospective cohort study of inpatients with Enterobacterales BSIs at Colonial War Memorial Hospital in Suva. We collected demographic, clinical, and microbiological data, and we stored bacterial isolates for confirmatory testing and molecular genomics in Melbourne, Australia. We employed cause-specific Cox proportional hazards models to estimate the effect of 3GC-resistance on hazard of in-hospital mortality and discharge alive (competing outcomes), and we used multistate modelling to estimate the excess length of hospital stay associated with 3GCR. Results: From July 2020 to February 2021, we identified 162 consecutive Enterobacterales BSIs, and 66 (40.7%) were 3GC resistant. The crude mortality rates for patients with 3GC-susecptible and 3GC-resistant BSIs were 16.7% (16 of 96) and 30.3% (20 of 66), respectively. Also, 3GC resistance was not associated with either in-hospital mortality (aHR, 1.67; 95% CI, 0.80–3.49) or discharge alive (aHR, 0.75; 95% CI, 0.50–1.12). However, patient comorbidities and acuity of illness were associated with in-hospital mortality. Furthermore, 3GC-resistance was associated with an increased length of stay of 2.6 days (95% CI, 2.5–2.8). Overall, 3GC-resistance was more common among patients with hospital-associated than community-acquired infection, but genomics did not identify clonal transmission. Conclusions: Among patients with Enterobacterales BSIs, mortality was relatively high, and 3GC resistance was common. Also, 3GC resistance was associated with increased hospital length of stay but not with in-hospital mortality after adjusting for potential confounders. Accurate estimates of the burden of AMR are important, especially from LMICs. Such knowledge can inform policy decisions, guide allocation of limited resources, and assist the evaluation of future interventions to address AMR.