The CTX-M β-lactamase pandemic

Incidence of Extended Spectrum β-Lactamase Genes (ESBLs) among community and health care infection in Mansoura University Hospital, Egypt

BACKGROUND

Multidrug-resistant (MDR) Gram-negative bacteria pose a significant challenge due to their limited treatment options. The production of extended-spectrum β-lactamases (ESBLs) is an important mechanism of resistance. This study aimed to identify the incidence and characteristics of ESBL-encoding genes (blaCTX-M, blaTEM, blaSHV, and blaOXA) in MDR isolates.

MATERIALS AND METHODS

A cross-sectional study was conducted from September 2022 to May 2023. ESBL-producing isolates (n = 105) out of 412 were recovered from hospitalized and outpatient settings and analyzed. Standard microbiological methods were used for isolates identification, susceptibility testing, and phenotypic ESBL detection. Additionally, blaCTX-M, blaTEM, blaSHV, and blaOXA genes were identified using conventional PCR.

RESULTS

Molecular profiling of β-lactamase determinants was conducted via PCR targeting blaCTX-M, blaTEM, blaSHV, and blaOXA genes. Among phenotypically confirmed (100%) ESBL producers, 98% harbored one or more target genes, with blaCTX-M predominant (81%), followed by blaSHV (70.4%), blaTEM (62%), and blaOXA (30.4%). Carbapenem resistance was higher in ESBL-producing strains compared to non-ESBL strains. Extensively drug-resistant (XDR) isolates were the most common across hospital departments and outpatients.

DISCUSSION

This study highlights the significant prevalence of ESBL genes and multidrug resistance among Gram-negative bacteria. The dominance of blaCTX-M and the existence of multiple resistance genes raise concerns about limited treatment options. The findings emphasize the need for stricter antibiotic stewardship and infection control measures to curb the spread of MDR pathogens.

CONCLUSION

This study provides valuable insights into the alarming incidence of ESBL genes and MDR in Mansoura, Egypt. Continuous surveillance and implementation of effective control strategies are crucial to combat this growing public health threat.

Houseflies as Vectors of ESBL-Producing Enterobacterales: Insights from Hospital Settings in a Low- to Middle-Income Country

The spread of extended-spectrum beta-lactamase-producing Enterobacterales (ESBL-E) in communities has been facilitated by direct contact with humans or animal carriers and insects such as houseflies. Houseflies may have an increased risk of human exposure to antimicrobial-resistant pathogens, including ESBL-E. In this study, we determined the presence of ESBL-E in houseflies and ready-to-eat food samples from selected food vending sites in five health care facilities in Greater Accra, Ghana. Sixty (60) food vending sites were included in this study. Flies (10) were pooled, and food (5 g) was macerated and homogenized aseptically in brain-heart infusion agar. Suspensions were cultured on MacConkey agar supplemented with 4 µg/mL cefotaxime for ∼18 h. Phenotypic and molecular characterization of ESBL-E was performed using a combination disk diffusion method, multiplex polymerase chain reaction, and direct nucleotide sequencing. Of the 60 food vending sites, 62% (37) of the food vendors had flies within their premises that carried ESBL-E, and 15% (9) of the food samples collected from the vendors were contaminated with ESBL-E. The most predominant ESBL-producing Enterobacterales from housefly samples was Proteus vulgaris (54%) and that of food samples were P. vulgaris (22.5%) and Escherichia coli (22.5%). All Enterobacterales from flies and food samples harbored an ESBL gene with blaCTX-M, mostly blaCTX-M-15, being the predominant gene and gene type, respectively. Houseflies may be potential contributors to the spread of ESBL-producing Enterobacterales in Ghana.

Whole-genome analysis of five Escherichia coli strains isolated from focal duodenal necrosis in laying hens reveals genetic similarities to the E. coli O25:H4 ST131 strain

Focal duodenal necrosis (FDN) is an intestinal disease causing significant economic losses in the table-egg industry due to reduced egg production in laying hens. Its etiology and pathogenesis remain poorly understood. Between 2021 and 2023, 111 Escherichia coli isolates were collected from FDN lesions and screened for the presence of virulence genes using PCR panels. Five strains-FDN-4, FDN-9, FDN-11, FDN-24, and FDN-50-were selected for whole-genome sequencing due to their high virulence gene content. Core-genome analyses found that the five FDN E. coli belong to different phylogroups and strain types (ST), but they all share multiple complete operons involved in key pathogenic functions, including host cell adhesion and invasion, iron acquisition, motility, biofilm formation, and acid resistance. Comparative genomic analyses identified FDN-4 as the most genetically distinct strain, closely resembling EC958, an O25b:H4 ST131 uropathogenic E. coli (UPEC) commonly associated with extended-spectrum beta-lactamase production. FDN-4 and EC958 share unique chromosomal virulence genes absent in the other FDN strains, all located within genomic islands. This study provides the first complete genomic characterization of E. coli isolated from FDN lesions and highlights FDN-4 as a genetically distinct strain with similarities to O25b:H4 ST131 UPEC.IMPORTANCEThis study presents the first complete genomic characterization of Escherichia coli isolated from focal duodenal necrosis (FDN) lesions. Notably, FDN-4 is the first E. coli strain from a poultry disease (FDN) to show significant similarity to O25b:H4 ST131 strains, commonly classified as uropathogenic E. coli and often associated with extended-spectrum beta-lactamase production. However, caution is warranted when attributing direct transmission routes between poultry and humans.

Rapid screening of cefotaxime resistance in Escherichia coli isolates by liquid chromatography with absorbance detection

The clinical outcome of bacterial infection relies on proper and timely diagnosis of antibiotic susceptibility. We demonstrate that liquid chromatography (LC) with diode-array absorbance detection (DAD) accurately diagnoses antimicrobial resistance by measuring cefotaxime recovery following incubation with bacterial isolates either positive or negative for the cefotaximase (CTX-M) family of serine-β-lactamases. Reversed phase, high-performance liquid chromatography with absorbance detection was employed for cefotaxime analysis. A total of 43 blaCTX-M-producing and 5 blaCTX-M-negative Escherichia coli isolates were incubated with 0.5 mg/mL of cefotaxime at 37 °C for 1 and 2 h. Remarkably, after 2 h of incubation, the median ± median absolute deviation percentage of cefotaxime recovery was zero (0 %) for blaCTX-M producing and cefotaxime-resistant E. coli isolates compared to the cefotaxime recovery in blaCTX-M negative (61 ± 5.38 %) and cefotaxime-susceptible (70.68 ± 6.25 %) E. coli isolates. This result allows facile sorting of organism resistance status after only 1-2 h with near-perfect performance. The diagnostic sensitivity (Se) and specificity (Sp) of the chromatographic approach were comparable to widely used phenotypic (Epsilometer test, E-test) and genotypic assays (Whole Genome Sequencing, WGS), but chromatography reduces diagnostic time by >10-fold. Additionally, the optical absorption measurement is fully compatible with microfluidic platforms, suggesting the development of low-cost, high-throughput sensors based on this measurement principle is possible. We conclude LC-DAD is suitable and reliable to determine the cefotaxime resistance status of E. coli isolates with a turn-around time of only 1-2 h.

The spread of CTX-M-type extended-spectrum beta-lactamases in China: Epidemiology and evolutionary analyses

CTX-M-type extended-spectrum beta-lactamases (ESBLs) have shown a high level of global transmission, with limited systematic understanding of their epidemic patterns in China. A comprehensive analysis covering 1974-2023 identified 133 (3.2%) blaCTX-Ms-producing strains among 4146 strains from 25 Chinese cities across 82 genera were performed. Integrating with public database strains (n=431), the study comprised 564 blaCTX-Ms-positive isolates sourced from 19 provinces (1986-2022) including 300 (53.2%) clinical and 228 (40.4%) environmental blaCTX-Ms. The most frequent sources of infection were diarrhea (44%), upper respiratory tract infection (22.2%) and urinary tract infection (14%). Phylogenetic studies indicated CTX-M-1 and CTX-M-9 emerged as the predominant subgroups. Lineages exhibited diverse mutation sites without being restricted by geographical conditions. Ka/Ks ratio distribution varied significantly among lineages (P<0.05). Lineages 1 (L1) and L2 were characterized by neutral or purifying selection, whereas L3 was mainly under purifying selection. Adaptive evolution was noted at different loci within each lineage. The influence of geographic distance on phylogeny varied distinctly across different lineages. Notably, for Lineage L3, there was a remarkably strong correlation observed, which implies that human activities exerted a more substantial influence on genetic distances compared to geography. This research provides valuable insights into the epidemiology, genotypic diversity, and evolutionary traits of blaCTX-Ms in China, supporting health risk assessment for early warning systems.

Whole-genome characterization and global phylogenetic comparison of cefotaxime-resistant Escherichia coli isolated from broiler chickens

Antimicrobial resistance (AMR) poses a serious threat to public health, with the emergence of extended-spectrum beta-lactamases (ESBLs) in Enterobacteriaceae, particularly Escherichia coli, raising significant concerns. This study aims to elucidate the drivers of antimicrobial resistance, and the global spread of cefotaxime-resistant E. coli (CREC) strains. Whole-genome sequencing (WGS) was performed to explore genome-level characteristics, and phylogenetic analysis was conducted to compare twenty CREC strains from this study, which were isolated from broiler chicken farms in Bangladesh, with a global collection (n = 456) of CREC strains from multiple countries and hosts. The MIC analysis showed over 70% of strains isolated from broiler chickens exhibiting MIC values ≥ 256 mg/L for cefotaxime. Notably, 85% of the studied farms (17/20) tested positive for CREC by the end of the production cycle, with CREC counts increasing from 0.83 ± 1.75 log10 CFU/g feces on day 1 to 5.24 ± 0.72 log10 CFU/g feces by day 28. WGS revealed the presence of multiple resistance genes, including blaCTX-M, which was found in 30% of the strains. Phylogenetic comparison showed that the Bangladeshi strains were closely related to strains from diverse geographical regions and host species. This study provides a comprehensive understanding of the molecular epidemiology of CREC. The close phylogenetic relationships between Bangladeshi and global strains demonstrate the widespread presence of cefotaxime-resistant bacteria and emphasize the importance of monitoring AMR in food-producing animals to mitigate the spread of resistant strains.

Beta-lactamase-producing Escherichia coli in migratory geese at West Texas recreational parks

This study aimed to determine the prevalence, and the genomic characteristics of beta-lactamase-Resistant Escherichia coli isolated from the feces of migratory geese at one health interface in West Texas. A descriptive study was conducted. We collected geese feces (n = 165), water (n = 118), and soil (n = 74) from 22 recreational parks in West Texas. We used Chromogenic agar to isolate extended-spectrum beta-lactamase (ESBL)-Resistant-E. coli. We used the whole genome sequencing (WGS) method to determine the genomic characteristics of selected E. coli isolates. Among 357 samples, 12.61 % (95 %CI: 9.34-16.50) were positive for ESBL- Resistant-E. coli. From WGS of 20 E. coli isolates, 19 isolates harbored at least 1 beta-lactamase gene including blaCTX-M-1, blaCTX-M-65, blaCTX-M-14, blaCTX-M-15, blaCTX-M-27, blaCTX-M-55, blaCTX-M-32, blaTEM-1A, blaTEM-1B. Most of the isolates carried genes conferring resistance to tetracyclines-(tet(A), tet(B)), aminoglycosides-(aac(3)-IIa, aph(6)-Id, aph(3')-Ia, aadA1), sulfonamides-(sul1,sul2), amphenicol-(floR), trimethoprim-(dfrA1, dfrA14, dfrA17) and streptogramin-B(MLSB) agent-(mph(A)). 13 isolates showed chromosomal mutations in the promoter region G of the ampC beta-lactamase gene. We detected sixteen incompatibility plasmid groups and 60 virulence genes, which are related to adherence, exotoxin, invasion, and nutrition/metabolic factors. Genome analysis showed that all isolates were genetically similar to human E. coli isolates. The study showed that migratory geese at recreational parks can be reservoirs of resistant bacteria with diverse serotypes and sequence types of E. coli isolates. Based on the findings, the detection of a multidrug-resistant E. coli strain reinforces the importance of adequate hygiene practices for humans and pet animals after visiting recreational parks.

Extended spectrum β-lactamase (ESβL)-producing E. coli causing urinary tract infection among pregnant women and pediatric patients in public hospitals in northern Jordan

BACKGROUND

Urinary tract infections (UTI's) imply the invasion and multiplication of bacteria in the individual's urinary tract, the incidence of UTI's is mainly determined by sex and age being the highest in pregnant females. E. coli is the most frequently encountered causative agent of UTI's and recent data depict an increase in antimicrobial resistance.

OBJECTIVES

This study aims to identify the most common pathogens associated with UTI's in pregnant women and children and to reveal the resistance patterns, and effective treatments and to detect resistance genes in E. coli.

METHODS

This study was conducted in public-teaching Hospitals in northern Jordan during the period from the 1st of March 2024 to the 5th of April 2024. Urine samples were collected in a sterile urine container or using a special tube for pediatric samples. Each sample was cultivated on MacConkey, blood and mannitol salt agar plates, all plates were incubated aerobically at 37°C for 24 hours and identified using standard microbiological protocols. All isolates were tested for antimicrobial susceptibility. Polymerase chain reaction was performed to confirm all E. coli isolates by the detection of universal stress protein (uspA) gene and to detect ESβL genes TEM, SHV CTX-M.

RESULTS

Eight bacterial species were identified, 75% (6/8) Gram Negative, 25% (2/8) Gram Positive). Escherichia coli was the most frequently isolated species 71.4% (50/70) followed by Klebsiella pneumoniae 10% (7/70), Enterobacter cloacae 5.7% (4/70, Proteus mirabilis 4.3% (3/70), Enterococcus faecalis 2.9% (3/70), Acinetobacter baumannii 2.9% (3/70), Lelliottia amnigena 1.4% (1/70) and Streptococcus agalactiae 1.4% (1/70). All 50 biochemically confirmed E. coli isolates were also confirmed using uspA gene. Three resistance genes TEM, SHV and CTX-M were detected using polymerase chain reaction.

CONCLUSION

E. coli was the most frequently isolated species followed by K. pneumoniae, this result may indicate that K. pneumoniae is becoming increasingly common as an etiological agent of UTI. A high resistance toward Amoxicillin- Clavulanic Acid was found among E. coli isolates, while multiple antibiotic/drug resistance was 62%. These results highlight the need to adhere to the therapeutic guidelines in treating UTI's and other infections and not overuse antibiotics to prevent the emergence of multidrug-resistant bacteria.

Evolution of β-Lactam Antibiotic Resistance in Proteus Species: From Extended-Spectrum and Plasmid-Mediated AmpC β-Lactamases to Carbapenemases

The management of infectious diseases has proven to be a daunting task for clinicians worldwide, and the rapid development of antibiotic resistance among Gram-negative bacteria is making it even more challenging. The first-line therapy is empirical, and it most often comprises β-lactam antibiotics. Among Gram-negative bacteria, Proteus mirabilis, an important community and hospital pathogen associated primarily with urinary tract and wound infection, holds a special place. This review's aim was to collate and examine recent studies investigating β-lactam resistance phenotypes and mechanisms of Proteus species and the global significance of its β-lactam resistance evolution. Moreover, the genetic background of resistance traits and the role of mobile genetic elements in the dissemination of resistance genes were evaluated. P. mirabilis as the dominant pathogen develops resistance to expanded-spectrum cephalosporins (ESC) by producing extended-spectrum β-lactamases (ESBL) and plasmid-mediated AmpC β-lactamases (p-AmpC). β-lactamase-mediated resistance to carbapenems in Enterobacterales, including Proteus spp., is mostly due to expression of carbapenemases of class A (KPC); class B (metallo-β-lactamases or MBLs of IMP, VIM, or NDM series); or class D or carbapenem-hydrolyzing oxacillinases (CHDL). Previously, a dominant ESBL type in P. mirabilis was TEM-52; yet, lately, it has been replaced by CTX-M variants, particularly CTX-M-14. ESC resistance can also be mediated by p-AmpC, with CMY-16 as the dominant variant. Carbapenem resistance in Proteus spp. is a challenge due to its intrinsic resistance to colistin and tigecyclin. The first carbapenemases reported belonged to class B, most frequently VIM-1 and NDM-5. In Europe, predominantly France and Belgium, a clonal lineage positive for OXA-23 CHDL spreads rapidly undetected, due to its low-level resistance to carbapenems. The amazing capacity of Proteus spp. to accumulate a plethora of various resistance traits is leading to multidrug or extensively drug-resistant phenotypes.

Pandemic one health clones of Escherichia coli and Klebsiella pneumoniae producing CTX-M-14, CTX-M-27, CTX-M-55 and CTX-M-65 ESβLs among companion animals in northern Ecuador

From a One Health perspective, dogs and cats have begun to be recognized as important reservoirs for clinically significant multidrug-resistant bacterial pathogens. In this study, we investigated the occurrence and genomic features of ESβL producing Enterobacterales isolated from dogs, in the province of Imbabura, Ecuador. We identified four isolates expressing ESβLs from healthy and diseased animals. In this regard, two Escherichia coli strains producing CTX-M-55-like or CTX-M-65 ESβLs belonged to the international ST10 and ST162, whereas two Klebsiella pneumoniae producing CTX-M-14 or CTX-M-27 belonged to ST35 and ST661. Phylogenomic analysis clustered (95-105 SNP differences) CTX-M-55/ST10 E. coli from companion animal with food and human E. coli strains of ST10 isolated in 2016, in Australia and Cambodia, respectively; whereas CTX-M-27-positive K. pneumoniae ST661 was clustered (201-216 SNP differences) with human strains identified in Italy, in 2013 and 2017, respectively. In summary, we report the presence and genomic data of global human-associated clones of CTX-M-producing E. coli and K. pneumoniae in dogs, in Ecuador. The implementation of a national epidemiological surveillance program is necessary to establish future strategies to control the dissemination of antibiotic-resistant priority pathogens using a One Health approach.

Transmission and control strategies of antimicrobial resistance from the environment to the clinic: A holistic review

The environment serves as a significant reservoir of antimicrobial resistance (AMR) microbes and genes and is increasingly recognized as key source of clinical AMR. Modern human activities impose an additional burden on environmental AMR, promoting its transmission to clinical setting and posing a serious threat to human health and welfare. Therefore, a comprehensive review of AMR transmission from the environment to the clinic, along with proposed effective control strategies, is crucial. This review systematically summarized current research on the transmission of environmental AMR to clinical settings. Furthermore, the transmission pathways, horizontal gene transfer (HGT) mechanisms, as well as the influential drivers including triple planetary crisis that may facilitate AMR transfer from environmental species to clinical pathogens are highlighted. In response to the growing trend of AMR transmission, we propose insightful mitigation strategies under the One Health framework, integrating advanced surveillance and tracking technologies, interdisciplinary knowledge, multisectoral interventions, alongside multiple antimicrobial use and stewardship approaches to tacking development and spread of AMR.

Characterization and application of LysSGF2 and HolSGF2 as potential biocontrol agents against planktonic and biofilm cells of common pathogenic bacteria

Antimicrobial resistance represents a global health emergency, necessitating the introduction of novel antimicrobial agents. In the present study, lysozyme and holin from Shigella flexneri 1.1868 phage SGF2, named LysSGF2 and HolSGF2, respectively, were cloned, expressed, and characterized. LysSGF2 and HolSGF2 showed lytic activities against S. flexneri 1.1868 cells at 4-55 °C and pH 3.1-10.3. LysSGF2 exhibited antimicrobial activity against five gram-negative and two gram-positive bacteria. HolSGF2 showed antimicrobial activity against four gram-negative and one gram-positive species. The antibacterial activities of LysSGF2 and HolSGF2 were determined in liquid beverages, including bottled water and milk. The relative lytic activity of LysSGF2 combined with HolSGF2 against the tested bacteria was approximately 46-77 % in water. Furthermore, the combination markedly decreased the viable counts of tested bacteria by approximately 3-5 log CFU/mL. LysSGF2 and HolSGF2 could efficiently remove biofilms on polystyrene, glass, and stainless-steel. The efficacy of the LysSGF2 and HolSGF2 combination against the tested bacteria on polystyrene was 58-71 %. Combination treatment effectively killed biofilm cells formed on stainless-steel and glass by 1-4 log CFU/mL. ese results indicate that LysSGF2 and HolSGF2 can successfully control both the planktonic and biofilm cells of common pathogenic bacteria, suggesting that the combined or single use of LysSGF2 and HolSGF2 may be of great value in food processing.

Expanding the β-Lactamase Family in the Human Microbiome

β-lactams, the most common antibiotics globally, have resistance primarily determined by β-lactamases. Human microbiota and β-lactams influence mutually; however, β-lactamase variety and abundance in the human microbiome remain partially understood. This study aimed to elucidate the diversity, abundance, and substrate spectrum of β-lactamases. 1369 characterized β-lactamases and 16 204 putative sequences are collected from protein databases. Upon clustering analysis and biochemical assays, nine proteins exhibiting less than 35% identity to those previously characterized are confirmed as β-lactamases. These newly identified β-lactamases originated from eight distinct clusters comprising 1163 β-lactamases. Quantifying healthy participants (n = 2394) across 19 countries using functionally confirmed clusters revealed that Japan have the highest gut β-lactamase abundance (log2[reads per million (RPM)] = 6.52) and Fiji have the lowest (log2[RPM] = 2.31). The β-lactamase abundance is correlated with β-lactam consumption (R = 0.50, p = 0.029) and income (R = 0.51, p = 0.024). Comparing individuals with ailments with healthy participants, β-lactamase abundance in the gut is increased significantly in patients with colorectal cancer, cardiovascular diseases, breast cancer, and epilepsy. These outcomes provide insights into investigating antibiotic resistance, antibiotic stewardship, and gut microbiome-antibiotic interactions.

Re-updating the taxonomy of Kluyvera genus for a better understanding of CTX-M β-lactamase origin

The taxonomic definitions within the Kluyvera genus are still unclear, as several deposits might belong to misidentified species or genus or genome assemblies comprehend large indeterminate nucleotide zones. In this study, we performed a comparative phylogenomic analysis of Kluyvera chromosomes and other selected Enterobacterales. We also included the genomic analysis of chromosomal blaCTX-M/KLU from Kluyvera isolates and assigned the plasmid-encoded blaCTX/M genes. The study allowed us to propose a new Kluyvera genomospecies and to better define Kluyvera genomosp. 5. Two new CTX-M sub-groups could also be suggested. Even if no chromosomal blaCTX-M/KLU gene can be found in K. intermedia and Kluyvera genomosp. 6, accurate identification can be achieved by using these gene sequences in the remaining strains.IMPORTANCEThe use of whole-genome sequencing (WGS) accelerated the identification of new Kluyvera species proposals, but a rigorous analysis of these sequences is needed for a better definition, including preexisting, and even established species. Kluyvera genomosp. 5 could be more clearly defined, and, among isolates that do not produce a chromosome-encoded CTX-M enzyme, true K. intermedia should be kept within the genus as well as a new genomospecies (Kluyvera genomosp. 6) different from K. intermedia. We could clean up true Kluyvera from those that deserved transfer to other genera, and some deposits as K. ascorbata, K. cryocrescens, K. georgiana, and several Kluyvera sp. to the real species. Two new sub-groups of CTX-M enzymes could be proposed. The accurate identification of the chromosome-encoded blaCTX-M/KLU gene in Kluyvera isolates could be a useful taxonomic tool to guide the species classification.

A novel chicken-origin colistin-resistant Klebsiella pneumoniae ST5982 Co-harboring mcr-3.11 and CTX-M-27

Klebsiella pneumoniae (K. pneumoniae) is an important zoonotic opportunistic pathogen of Enterobacteriaceae that has become one of the most common infectious diseases causing Enterobacteriaceae after Escherichia coli. In this study, we identified a colistin-resistant, multidrug-resistant ST5982 K. pneumoniae strain of broiler origin. The isolate carried 35 resistance genes of 10 antibiotics classes, detected by whole genome sequencing (WGS); 11.4 % (4/35) of the resistance genes were distributed in the chromosome, and 88.6 % (31/35) of the resistance genes were located in four different resistance plasmids. Among the four plasmids, we found for the first time that CTX-M-27 and mcr-3.11 simultaneously coexisted in K. pneumoniae, and a resistance plasmid of IncI1 carrying a combination of mcr-3.11 and qnrS1 was identified. We successfully transferred mcr-3.11, qnrS1 and CTX-M-27 genes into E. coli J53 through conjugation experiments. In the present study, the co-occurrence of CTX-M-27 and mcr-3.11 in multidrug-resistant K. pneumoniae strain ST5982 was detected for the first time; its drug resistance was evaluated, and the risk of its transmission was assessed to provide a reference for further prevention and treatment of K. pneumoniae.

Understanding the Evolution and Transmission Dynamics of Antibiotic Resistance Genes: A Comprehensive Review

Antibiotic resistance poses a formidable challenge to global public health, necessitating comprehensive understanding and strategic interventions. This review explores the evolution and transmission dynamics of antibiotic resistance genes, with a focus on Bangladesh. The indiscriminate use of antibiotics, compounded by substandard formulations and clinical misdiagnosis, fuels the emergence and spread of resistance in the country. Studies reveal high resistance rates among common pathogens, emphasizing the urgent need for targeted interventions and rational antibiotic use. Molecular assessments uncover a diverse array of antibiotic resistance genes in environmental reservoirs, highlighting the complex interplay between human activities and resistance dissemination. Horizontal gene transfer mechanisms, particularly plasmid-mediated conjugation, facilitate the exchange of resistance determinants among bacterial populations, driving the evolution of multidrug-resistant strains. The review discusses clinical implications, emphasizing the interconnectedness of environmental and clinical settings in resistance dynamics. Furthermore, bioinformatic and experimental evidence elucidates novel mechanisms of resistance gene transfer, underscoring the dynamic nature of resistance evolution. In conclusion, combating antibiotic resistance requires a multifaceted approach, integrating surveillance, stewardship, and innovative research to preserve the efficacy of antimicrobial agents and safeguard public health.

Decoding the origins, spread, and global risks of mcr-9 gene

BACKGROUND

The global spread of the plasmid-mediated mcr (mobilized colistin resistance) gene family presents a significant threat to the efficacy of colistin, a last-line defense against numerous Gram-negative pathogens. The mcr-9 is the second most prevalent variant after mcr-1.

METHODS

A dataset of 698 mcr-9-positive isolates from 44 countries is compiled. The historical trajectory of the mcr-9 gene is reconstructed using Bayesian analysis. The effective reproduction number is used innovatively to study the transmission dynamics of this mobile-drug-resistant gene.

FINDINGS

Our investigation traces the origins of mcr-9 back to the 1960s, revealing a subsequent expansion from Western Europe to the America and East Asia in the late 20th century. Currently, its transmissibility remains high in Western Europe. Intriguingly, mcr-9 likely emerged from human-associated Salmonella and exhibits a unique propensity for transmission within the Enterobacter. Our research provides a new perspective that this host preference may be driven by codon usage biases in plasmids. Specifically, mcr-9-carrying plasmids prefer the nucleotide C over T compared to mcr-1-carrying plasmids among synonymous codons. The same bias is seen in Enterobacter compared to Escherichia (respectively as their most dominant genus). Furthermore, we uncovered fascinating patterns of coexistence between different mcr-9 subtypes and other resistance genes. Characterized by its low colistin resistance, mcr-9 has used this seemingly benign feature to silently circumnavigate the globe, evading conventional detection methods. However, colistin-resistant Enterobacter strains with high mcr-9 expression have emerged clinically, implying a strong risk of mcr-9 evolving into a global "true-resistance-gene".

INTERPRETATION

This study explores the mcr-9 gene, emphasizing its origin, adaptability, and dissemination potential. Given the high mcr-9 expression colistin-resistant strains was observed in clinically the prevalence of mcr-9 poses a significant challenge to drug resistance prevention and control within the One Health framework.

FUNDING

This work was partially supported by the National Natural Science Foundation of China (Grant No. 32141001 and 81991533).

Molecular Characterization of Carbapenem and Colistin Resistance in Klebsiella pneumoniae Isolates Obtained from Clinical Samples at a University Hospital Center in Algeria

The current study aimed to determine the molecular mechanisms of carbapenem and colistin resistance among the clinical isolates of Klebsiella pneumoniae from hospitalized patients admitted to a university hospital in Eastern Algeria. In total, 124 non-duplicate isolates of K. pneumoniae were collected from September 2018 to April 2019. Bacterial identification was performed using MALDI-TOF MS. The presence of extended spectrum β-lactamase (ESBL) genes, carbapenemase genes, chromosomal mutation and mcr genes in colistin-resistant K. pneumoniae were evaluated by PCR. ESBLs represented a rate of 49.1% and harbored blaCTX-M, blaTEM and blaSHV genes. Concerning carbapenems, 12 strains (9.6%) were resistant to ertapenem (MIC: 1-32 μg/mL), of which one strain (0.8%) was also resistant to imipenem (MIC: 32 μg/mL). Among these strains, nine (75%) harbored blaOXA-48 gene. Seven strains (5.6%) expressed resistance to colistin (MIC: 2-32 μg/mL), of which two harbored mcr-8 and mgrB genes simultaneously. The existence of a double resistance to colistin in the same strain is new in Algeria, and this could raise concerns about the increase in levels of resistance to this antibiotic (MIC: 32 μg/mL). The mgrB gene alone was observed in five isolates (71.4%), including two strains harboring blaOXA-48. This is the first report revealing the presence of K. pneumoniae strains carrying the blaOXA-48 gene as well as a mutation in the mgrB gene. Large-scale surveillance and effective infection control measures are also urgently needed to prevent the outbreak of various carbapenem- and colistin-resistant isolates.

Molecular epidemiology of extended-spectrum beta-lactamase-producing-Klebsiella species in East Tennessee dairy cattle farms

Introduction

The rising prevalence of Extended-Spectrum Beta-Lactamase (ESBL)-producing Klebsiella species (spp.) poses a significant threat to human and animal health and environmental safety. To address this pressing issue, a comprehensive study was undertaken to elucidate the burden and dissemination mechanisms of ESBL-Klebsiella spp. in dairy cattle farms.

Methods

Fifty-seven Klebsiella species were isolated on CHROMagar™ ESBL plates and confirmed with MADLI-TOF MS and whole genome sequenced from 14 dairy farms.

Results and discussion

Six families of beta-lactamase (bla) (bla CTX-M, bla SHV, bla TEM, bla OXY, bla OXA, and bla SED) were detected in ESBL-Klebsiella spp. genomes. Most (73%) of isolates had the first three types of beta-lactamase genes, with bla SHV being the most frequent, followed by bla CTX-M. Most (93%) isolates harbored two or more bla genes. The isolates were genotypically MDR, with 26 distinct types of antibiotic resistance genes (ARGs) and point mutations in gyrA, gyrB, and parC genes. The genomes also harbored 22 different plasmid replicon types, including three novel IncFII. The IncFII and Col440I plasmids were the most frequent and were associated with bla CTXM-27 and qnrB19 genes, respectively. Eighteen distinct sequence types (STs), including eight isolates with novel STs of K. pneumoniae, were detected. The most frequently occurring STs were ST353 (n = 8), ST469 (n = 6), and the novel ST7501 (n = 6). Clusters of ESBL-Klebsiella strains with identical STs, plasmids, and ARGs were detected in multiple farms, suggesting possible clonal expansion. The same ESBL variant was linked to identical plasmids in different Klebsiella STs in some farms, suggesting horizontal spread of the resistance gene. The high burden and dual spread mechanism of ESBL genes in Klebsiella species, combined with the emergence of novel sequence types, could swiftly increase the prevalence of ESBL-Klebsiella spp., posing significant risks to human, animal, and environmental health. Immediate action is needed to implement rigorous surveillance and control measures to mitigate this risk.

Antimicrobial resistance profile and associated factors of hospital-acquired gram-negative bacterial pathogens among hospitalized patients in northeast Ethiopia

BACKGROUND

Antimicrobial resistance is a major global public health issue. Infections caused by resistant species are associated with higher mortality rates, longer hospital stays, medication failure, and rising medical costs. The World Health Organisation has declared multidrug resistance-associated infections as an epidemic of public health concern.

OBJECTIVE

This study aimed to evaluate the antimicrobial resistance profile and associated factors of hospital-acquired Gram-negative bacterial pathogens among hospitalized patients in Northeast Ethiopia.

MATERIALS AND METHODS

A health facility-based cross-sectional study was conducted among hospitalized patients from March 2021 to February 2022. About 810 clinical specimens were collected, transported, and processed from admitted patients following the standard bacteriological procedures. The clinical samples were inoculated onto blood agar, MacConkey agar, and chocolate agar. Furthermore, the species identification was done using gram reactions, colony morphology, and color and biochemical tests. Antimicrobial susceptibility tests, extended-spectrum beta-lactamase, and carbapenemase production were performed as per the clinical laboratory standard institute guidelines. For analysis, the information was entered into Epi-data and exported to SPSS. A P value of < 0.05 with a 95% confidence interval was considered as a statistically significant association.

RESULTS

Out of 810 clinical specimens, 285/810 (35.2%) developed bacterial infections. From the isolated bacteria, E. coli was the predominant bacteria accounting for 78/285 (27.4%) followed by K. pneumoniae, 69/285(24.42%), whereas P. vulgaris accounted for the least, 7/285 (2.5%). Overall, 132/285 (46.3%) and 99/285 (34.7%) of culture-positive patients were infected by extended-spectrum beta-lactamase and carbapenemase-producing bacteria. The overall multidrug resistance rate of the isolated bacteria was 89.4%. The highest antibiotic resistance rates were detected for doxycycline (92.9%), amoxicillin-clavulanic acid (83.9%), and ampicillin (93%). The least antibiotic resistance rate was observed for meropenem at 41.1% and amikacin at 1.7%, respectively.

CONCLUSIONS AND RECOMMENDATIONS

In the study area, significant health concerns include a range of hospital-acquired bacterial infections associated with elevated rates of multidrug resistance, Extended-spectrum beta-lactamase (ESBL), and carbapenemase-producing bacterial pathogens. Consequently, it is recommended to conduct drug-susceptibility testing of isolates and molecular detection at a national level to optimize antibiotic usage for treating prevalent bacterial infections in this area.

Prevalence of CTX-M types among ESBL-producing pathogenic Escherichia coli isolates from foodborne diarrheal patients in Gyeonggi-do, South Korea

Prevalence and characteristics of extended-spectrum β-lactamase (ESBL)-producing pathogenic Escherichia coli from foodborne diarrheal patients were studied. Analysis of 495 E. coli isolates revealed that 80 isolates were ESBL-producing pathogenic E. coli, and enteroaggregative E. coli and enterotoxigenic E. coli were two of the most prevalent pathotypes. In silico Clermont phylo-typing of the 80 ESBL-producing E. coli showed that phylogroup A (49/80) and D (22/80) were the predominant phylogroups. The average nucleotide identity analysis of ESBL-producing E. coli disclosed that they could be grouped into two phylogenetic groups; 25 A and 55 B groups. All strains, except one, harbored the blaCTX-M gene. All CTX-M-15 type ESBL-producing strains also carried qnrS, a plasmid-mediated quinolone resistance gene (PMQR). These results suggest that the diversity of ESBL-producing E. coli is high and that co-existence of blaCTX-M-15 and qnrS genes is widespread, highlighting their high risk of antibiotic-resistance spreading in infectious disease outbreaks.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10068-024-01549-5.

High-throughput microfluidic quantitative PCR system for the simultaneous detection of antibiotic resistance genes and bacterial and viral pathogens in wastewater

Comprehensive data on bacterial and viral pathogens of diarrhea and studies applying culture-independent methods for examining antibiotic resistance in wastewater are lacking. This study aimed to simultaneously quantify antibiotic resistance genes (ARGs), class 1 integron-integrase (int1), bacterial and viral pathogens of diarrhea, 16S rRNA, and other indicators using a high-throughput quantitative PCR (HT-qPCR) system. Thirty-six grab wastewater samples from a wastewater treatment plant in Japan, collected three times a month between August 2022 and July 2023, were centrifuged, followed by nucleic acid extraction, reverse transcription, and HT-qPCR. Fourteen targets were included, and HT-qPCR was performed on the Biomark X9™ System (Standard BioTools). For all qPCR assays, R2 was ≥0.978 and the efficiencies ranged from 90.5% to 117.7%, exhibiting high performance. Of the 36 samples, 20 (56%) were positive for Norovirus genogroup II (NoV-GII), whereas Salmonella spp. and Campylobacter jejuni were detected in 24 (67%) and Campylobacter coli in 13 (36%) samples, with mean concentrations ranging from 3.2 ± 0.8 to 4.7 ± 0.3 log10 copies/L. NoV-GII detection ratios and concentrations were higher in winter and spring. None of the pathogens of diarrhea correlated with acute gastroenteritis cases, except for NoV-GII, suggesting the need for data on specific bacterial infections to validate bacterial wastewater-based epidemiology (WBE). All samples tested positive for sul1, int1, and blaCTX-M, irrespective of season. The less explored blaNDM-1 showed a wide prevalence (>83%) and consistent abundance ranging from 4.3 ± 1.0 to 4.9 ± 0.2 log10 copies/L in all seasons. sul1 was the predominant ARG, whereas absolute abundances of 16S rRNA, int1, and blaCTX-M varied seasonally. int1 was significantly correlated with blaCTX-M in autumn and spring, whereas it showed no correlation with blaNDM-1, questioning the applicability of int1 as a sole indicator of overall resistance determinants. This study exhibited that the HT-qPCR system is pivotal for WBE.

Crystal structure of the class A extended-spectrum β-lactamase CTX-M-96 in complex with relebactam at 1.03 Angstrom resolution

The use of β-lactam/β-lactamase inhibitors constitutes an important strategy to counteract β-lactamases in multidrug-resistant (MDR) Gram-negative bacteria. Recent reports have described ceftazidime-/avibactam-resistant isolates producing CTX-M variants with different amino acid substitutions (e.g., P167S, L169Q, and S130G). Relebactam (REL) combined with imipenem has proved very effective against Enterobacterales producing ESBLs, serine-carbapenemases, and AmpCs. Herein, we evaluated the inhibitory efficacy of REL against CTX-M-96, a CTX-M-15-type variant. The CTX-M-96 structure was obtained in complex with REL at 1.03 Å resolution (PDB 8EHH). REL was covalently bound to the S70-Oγ atom upon cleavage of the C7-N6 bond. Compared with apo CTX-M-96, binding of REL forces a slight displacement of the deacylating water inwards the active site (0.81 Å), making the E166 and N170 side chains shift to create a proper hydrogen bonding network. Binding of REL also disturbs the hydrophobic patch formed by Y105, P107, and Y129, likely due to the piperidine ring of REL that creates clashes with these residues. Also, a remarkable change in the positioning of the N104 sidechain is also affected by the piperidine ring. Therefore, differences in the kinetic behavior of REL against class A β-lactamases seem to rely, at least in part, on differences in the residues being involved in the association and stabilization of the inhibitor before hydrolysis. Our data provide the biochemical and structural basis for REL effectiveness against CTX-M-producing Gram-negative pathogens and essential details for further DBO design. Imipenem/REL remains an important choice for dealing with isolates co-producing CTX-M with other β-lactamases.

Aligning antimicrobial resistance surveillance with schistosomiasis research: an interlinked One Health approach

One Health surveillance involves the analysis of human, animal and environmental samples, recognising their interconnectedness in health systems. Such considerations are crucial to investigate the transmission of many pathogens, including drug-resistant bacteria and parasites. The highest rates of antimicrobial resistance (AMR)-associated deaths are observed in sub-Saharan Africa, where concurrently the waterborne parasitic disease schistosomiasis can be highly endemic in both humans and animals. Although there is growing acknowledgment of significant interactions between bacteria and parasites, knowledge of relationships between schistosomes, microbes and AMR remains inadequate. In addition, newly emergent research has revealed the previously underappreciated roles of animals and the environment in both AMR and schistosomiasis transmission. We consider shared environmental drivers and colonisation linkage in this narrative review, with a focus on extended-spectrum beta-lactamase-mediated resistance among bacteria from the Enterobacteriaceae family, which is exceedingly prevalent and responsible for a high burden of AMR-associated deaths. Then we examine novel findings from Malawi, where the landscapes of AMR and schistosomiasis are rapidly evolving, and make comparisons to other geographic areas with similar co-infection epidemiology. We identify several knowledge gaps that could be addressed in future research, including the need to characterise the impact of intestinal schistosomiasis and freshwater contact on intestinal AMR colonisation, before proposing a rationale for connecting AMR surveillance and schistosomiasis research within a One Health framework.

Molecular Characteristics of Cephalosporin Resistant Escherichia coli and Klebsiella pneumoniae Isolated from Children in a Tertiary Care Centre of Central Kerala, India

Aims:

The study was aimed to determine the molecular characteristics of extended-spectrum beta-lactamases (ESBL) producing cephalosporin-resistant Escherichia coli and Klebsiella pneumoniae isolated from children below ten years of age.

Background:

Geographically diverse variations in the prevalence of ESBL genes were reported. No data were available on the prevalence of ESBL genes in central Kerala, India, among children below 10 years of age.

Methods:

A cross-sectional study was performed to analyze ESBL genes in cephalosporin-re-sistant E. coli and K. pneumoniae strains isolated from samples received in the Microbiology la-boratory of a tertiary care centre during the period between May 2021 and July 2022. The strains showed that ESBL + cephalosporin resistance was subjected to PCR-based genotyping for the genes such as bla (beta-lactamase) CTX-M-1, blaCTX-M-15, blaCTX-M-U, blaTEM, blaPER and SHV.

Results:

Among the total 228 samples analyzed, 136 (60%) had no growth. Ninety-two (40 %) samples showed growth of E. coli and K. pneumoniae. Among the isolates that showed growth, 39 (42%) were sensitive, and the remaining 53 (57%) were resistant to third-generation cephalospor-ins. Among the isolates showed resistance, 22 (42%) were ESBL positive and 31 (58%) were ESBL negative. Among the positive ESBL, nine E. coli strains (60%) were positive for CTX-M-15 and CTX-M-1. CTX-M-15 and CTX-M-U were present in six (85%) K. pneumoniae with ESBL +.

Conclusion:

E. coli and K. pneumoniae isolated from specimens of children below ten years of age showed 41-42% ESBL producers. Prevalent ESBL-producing genes in E. coli were CTX-M-15 and CTX-M-1. CTX-M-15 and CTX-M-U were prevalent in ESBL-producing K. pneumoniae.

Emergence of a clinical Klebsiella pneumoniae harboring an acrAB-tolC in chromosome and carrying the two repetitive tandem core structures for bla KPC-2 and bla CTX-M-65 in a plasmid

Objective

The emergence of clinical Klebsiella pneumoniae strains harboring acrAB-tolC genes in the chromosome, along with the presence of two repetitive tandem core structures for bla KPC-2 and bla CTX-M-65 genes on a plasmid, has presented a significant clinical challenge.

Methods

In order to study the detailed genetic features of K. pneumoniae strain SC35, both the bacterial chromosome and plasmids were sequenced using Illumina and nanopore platforms. Furthermore, bioinformatics methods were employed to analyze the mobile genetic elements associated with antibiotic resistance genes.

Results

K. pneumoniae strain SC35 was found to possess a class A beta-lactamase and demonstrated resistance to all tested antibiotics. This resistance was attributed to the presence of efflux pump genes, specifically acrAB-tolC, on the SC35 chromosome. Additionally, the SC35 plasmid p1 carried the two repetitive tandem core structures for bla KPC-2 and bla CTX-M-65, as well as bla TEM-1 with rmtB, which shared overlapping structures with mobile genetic elements as In413, Tn3, and TnAs3. Through plasmid transfer assays, it was determined that the SC35 plasmid p1 could be successfully transferred with an average conjugation frequency of 6.85 × 10-4.

Conclusion

The structure of the SC35 plasmid p1 appears to have evolved in correlation with other plasmids such as pKPC2_130119, pDD01754-2, and F4_plasmid pA. The infectious strain SC35 exhibits no susceptibility to tested antibioticst, thus effective measures should be taken to prevent the spread and epidemic of this strain.

Antimicrobial resistance and phylogenetic relatedness of extended-spectrum ß-lactamase (ESBL)-producing Escherichia coli in peridomestic rats (Rattus norvegicus and Rattus tanezumi) linked to city areas and animal farms in Hong Kong

Extended-spectrum β-lactamase-producing Escherichia (E.) coli (ESBL-EC) in the clinical setting have emerged as a major threat to public and animal health. Wildlife, including Rattus spp. may serve as reservoirs and spreaders of ESBL-EC in the environment. Peridomestic rats are well adapted to living in proximity to humans and animals in a variety of urban and agricultural environments and may serve as sentinels to identify variations of ESBL-EC within their different habitats. In this study, a set of 221 rats (Rattus norvegicus, R. tanezumi, R. andamanensis, and Niviventer huang) consisting of 104 rats from city areas, 44 from chicken farms, 52 from pig farms, and 21 from stables of horse-riding schools were screened for ESBL-EC. Overall, a total of 134 ESBL-EC were isolated from the caecal samples of 130 (59%) rats. The predominant blaESBL genes were blaCTX-M-14, blaCTX-M-15, blaCTX-M-55, and blaCTX-M-65. Phylogenetic analysis revealed a total of 62 sequence types (STs) and 17 SNP clusters. E. coli ST10 and ST155 were common to ESBL-EC from city areas and chicken farms, and ST44 were found among ESBL-EC from city areas and pig farms. Extra-intestinal pathogenic E. coli (ExPEC) ST69, ST131 and ST1193 were found exclusively among rats from city areas, and avian pathogenic E. coli (APEC) ST177 was restricted to ESBL-EC originating from chicken farms. Phylogenetic analysis showed that the populations of rodent ESBL-EC from city areas, chicken farms and pig farms were genetically different, suggesting a certain degree of partitioning between the human and animal locations. This study contributes to current understanding of ESBL-EC occurring in rats in ecologically diverse locations.

Antimicrobial Resistance in Livestock: A Serious Threat to Public Health

Antimicrobial resistance represents an alarming public health problem; its importance is related to the significant clinical implications (increased morbidity, mortality, disease duration, development of comorbidities, and epidemics), as well as its economic effects on the healthcare sector. In fact, therapeutic options are severely limited by the advent and spread of germs resistant to many antibiotics. The situation worldwide is worrying, especially in light of the prevalence of Gram-negative bacteria-Klebsiella pneumoniae and Acinetobacter baumannii-which are frequently isolated in hospital environments and, more specifically, in intensive care units. The problem is compounded by the ineffective treatment of infections by patients who often self-prescribe therapy. Resistant bacteria also show resistance to the latest generation antibiotics, such as carbapenems. In fact, superbacteria, grouped under the acronym extended-spectrum betalactamase (ESBL), are becoming common. Antibiotic resistance is also found in the livestock sector, with serious repercussions on animal production. In general, this phenomenon affects all members of the biosphere and can only be addressed by adopting a holistic "One Health" approach. In this literature overview, a stock is taken of what has been learned about antibiotic resistance, and suggestions are proposed to stem its advance.

Dissemination of Ceftriaxone-Resistant Salmonella Enteritidis Harboring Plasmids Encoding blaCTX-M-55 or blaCTX-M-14 Gene in China

Salmonella Enteritidis was the primary foodborne pathogen responsible for acute gastroenteritis. The growing ceftriaxone resistance poses a significant threat to public health. Infection with S. Enteritidis has emerged as a major public health concern, particularly in developing countries. However, research on ceftriaxone-resistant S. Enteritidis (CRO-RSE) remains limited, particularly concerning its resistance mechanism, plasmid structure, and transmission characteristics. This study aims to address these gaps comprehensively. We collected 235 S. Enteritidis isolates from Hangzhou First People's Hospital between 2010 and 2020. Among these, 8.51% (20/235) exhibited resistance to ceftriaxone. Whole-genome analysis revealed that 20 CRO-RSE isolates harbored blaCTX-M-55 or blaCTX-M-14 on the plasmid. Moreover, the dissemination of the blaCTX-M-type gene was associated with IS26 and ISEcp1. Plasmid fusion entailing the integration of the p1 plasmid with antibiotic resistance genes and the p2 (pSEV) virulence plasmid was observed in certain CRO-RSE. Additionally, the structural analysis of the plasmids unveiled two types carrying the blaCTX-M-type gene: type A with multiple replicons and type B with IncI1 (Alpha) replicon. Type B plasmids exhibited superior adaptability and stability compared to type A plasmids within Enterobacteriaceae. Interestingly, although the type B (S808-p1) plasmid displayed the potential to spread to Acinetobacter baumannii, it failed to maintain stability in this species.

Multidrug-Resistant Bacteria in Surgical Intensive Care Units: Antibiotic Susceptibility and β-Lactamase Characterization

Multidrug-resistant (MDR) bacteria of the utmost importance are extended-spectrum β-lactamase (ESBL) and carbapenemase-producing Enterobacterales (CRE), carbapenem-resistant Acinetobacter baumannii (CRAB), carbapenem-resistant Pseudomonas aeruginosa (CRPA), methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus spp. (VRE). In this study, an evaluation of MDR bacteria in surgical intensive care units in a tertiary referral hospital was conducted. The study aimed to characterize β-lactamases and other resistance traits of Gram-negative bacteria isolated in surgical intensive care units (ICUs). Disk diffusion and the broth dilution method were used for antibiotic susceptibility testing, whereas ESBL screening was performed through a double disk synergy test and an inhibitor-based test with clavulanic acid. A total of 119 MDR bacterial isolates were analysed. ESBL production was observed in half of the Proteus mirabilis, 90% of the Klebsiella pneumoniae and all of the Enterobacter cloacae and Escherichia coli isolates. OXA-48 carbapenemase, carried by the L plasmid, was detected in 34 K. pneumoniae and one E. coli and Enterobacter cloacae complex isolates, whereas NDM occurred sporadically and was identified in three K. pneumoniae isolates. OXA-48 positive isolates coharboured ESBLs belonging to the CTX-M family in all but one isolate. OXA-23 carbapenemase was confirmed in all A. baumannii isolates. The findings of this study provide valuable insight of resistance determinants of Enterobacterales and A. baumannii which will enhance surveillance and intervention strategies that are necessary to curb the ever-growing carbapenem resistance rates.

Extended-Spectrum Beta-Lactamase-Producing Escherichia coli and Other Antimicrobial-Resistant Gram-Negative Pathogens Isolated from Bovine Mastitis: A One Health Perspective

Antimicrobial resistance (AMR) poses an imminent threat to global public health, driven in part by the widespread use of antimicrobials in both humans and animals. Within the dairy cattle industry, Gram-negative coliforms such as Escherichia coli and Klebsiella pneumoniae stand out as major causative agents of clinical mastitis. These same bacterial species are frequently associated with severe infections in humans, including bloodstream and urinary tract infections, and contribute significantly to the alarming surge in antimicrobial-resistant bacterial infections worldwide. Additionally, mastitis-causing coliforms often carry AMR genes akin to those found in hospital-acquired strains, notably the extended-spectrum beta-lactamase genes. This raises concerns regarding the potential transmission of resistant bacteria and AMR from mastitis cases in dairy cattle to humans. In this narrative review, we explore the distinctive characteristics of antimicrobial-resistant E. coli and Klebsiella spp. strains implicated in clinical mastitis and human infections. We focus on the molecular mechanisms underlying AMR in these bacterial populations and critically evaluate the potential for interspecies transmission. Despite some degree of similarity observed in sequence types and mobile genetic elements between strains found in humans and cows, the existing literature does not provide conclusive evidence to assert that coliforms responsible for mastitis in cows pose a direct threat to human health. Finally, we also scrutinize the existing literature, identifying gaps and limitations, and propose avenues for future research to address these pressing challenges comprehensively.

Evaluation of temocillin efficacy against KPC-2-producing Klebsiella pneumoniae isolates in a hollow-fibre infection model

BACKGROUND

Temocillin is an old antimicrobial that is resistant to hydrolysis by ESBLs but has variable activity against carbapenemase-producing Enterobacteriaceae. The current EUCAST susceptibility breakpoints for Enterobacterales are set at ≤16 mg/L (susceptible with increased exposure) based on a dose of 2 g q8h, but there is limited information on the efficacy of this dose against temocillin-susceptible carbapenemase-producing Klebsiella pneumoniae isolates.

OBJECTIVES

To evaluate the efficacy of this dose using a hollow-fibre infection model (HFIM) against six KPC-2-producing clinical isolates of K. pneumoniae.

METHODS

The isolates were characterized by WGS and temocillin susceptibility was determined using standard and high inoculum temocillin. Mutant frequencies were estimated and temocillin activity was tested in time-kill assays and in the HFIM. At standard conditions, three of the isolates were classified as susceptible (MIC ≤ 16 mg/L) and three as resistant (MIC > 16 mg/L). The HFIM was performed over 3 days to mimic human-like pharmacokinetics of 2 g q8h. Bacterial counts were performed by plating on Mueller-Hinton agar (MHA) and MHA containing 64 mg/L temocillin to detect resistant subpopulations.

RESULTS

All isolates showed a reduction in bacterial population of at least 3 log cfu/mL within the first 8 h of simulated treatment in the hollow-fibre assay. Regrowth was observed for the three resistant isolates and one of the susceptible ones. The MIC value for these isolates was higher by at least two dilutions compared with their initial values.

CONCLUSIONS

These data suggest that an optimized pharmacokinetic regimen may be of clinical interest for the treatment of KPC-2-producing K. pneumoniae susceptible to temocillin. These data showed activity of temocillin against KPC-2-producing K. pneumoniae susceptible to temocillin; however, a dose of 2g q8h administered over 30 min may be inadequate to prevent the emergence of resistant variants.

Causal-ARG: a causality-guided framework for annotating properties of antibiotic resistance genes

MOTIVATION

The crisis of antibiotic resistance, which causes antibiotics used to treat bacterial infections to become less effective, has emerged as one of the foremost challenges to public health. Identifying the properties of antibiotic resistance genes (ARGs) is an essential way to mitigate this issue. Although numerous methods have been proposed for this task, most of these approaches concentrate solely on predicting antibiotic class, disregarding other important properties of ARGs. In addition, existing methods for simultaneously predicting multiple properties of ARGs fail to account for the causal relationships among these properties, limiting the predictive performance.

RESULTS

In this study, we propose a causality-guided framework for annotating properties of ARGs, in which causal inference is utilized for representation learning. More specifically, the hidden biological patterns determining the properties of ARGs are described by a Gaussian Mixture Model, and procedure of causal representation learning is used to derive the hidden features. In addition, a causal graph among different properties is constructed to capture the causal relationships among properties of ARGs, which is integrated into the task of annotating properties of ARGs. The experimental results on a real-world dataset demonstrate the effectiveness of the proposed framework on the task of annotating properties of ARGs.

AVAILABILITY AND IMPLEMENTATION

The data and source codes are available in GitHub at https://github.com/David-WZhao/CausalARG.

Global spread characteristics of CTX-M-type extended-spectrum β-lactamases: A genomic epidemiology analysis

BACKGROUND

Extended-spectrum β-lactamases (ESBLs) producing bacteria have spread worldwide and become a global public health concern. Plasmid-mediated transfer of ESBLs is an important route for resistance acquisition.

METHODS

We collected 1345 complete sequences of plasmids containing CTX-Ms from public database. The global transmission pattern of plasmids and evolutionary dynamics of CTX-Ms have been inferred. We applied the pan-genome clustering based on plasmid genomes and evolution analysis to demonstrate the transmission events.

FINDINGS

Totally, 48 CTX-Ms genotypes and 186 incompatible types of plasmids were identified. The geographical distribution of CTX-Ms showed significant differences across countries and continents. CTX-M-14 and CTX-M-55 were found to be the dominant genotypes in Asia, while CTX-M-1 played a leading role in Europe. The plasmids can be divided into 12 lineages, some of which forming distinct geographical clusters in Asia and Europe, while others forming hybrid populations. The Inc types of plasmids are lineage-specific, with the CTX-M-1_IncI1-I (Alpha) and CTX-M-65_IncFII (pHN7A8)/R being the dominant patterns of cross-host and cross-regional transmission. The IncI-I (Alpha) plasmids with the highest number, were presumed to form communication groups in Europe-Asia and Asia-America-Oceania, showing the transmission model as global dissemination and regional microevolution. Meanwhile, the main kinetic elements of blaCTX-Ms showed genotypic preferences. ISEcpl and IS26 were most frequently involved in the transfer of CTX-M-14 and CTX-M-65, respectively. IS15 has become a crucial participant in mediating the dissemination of blaCTX-Ms. Interestingly, blaTEM and blaCTX-Ms often coexisted in the same transposable unit. Furthermore, antibiotic resistance genes associated with aminoglycosides, sulfonamides and cephalosporins showed a relatively high frequency of synergistic effects with CTX-Ms.

CONCLUSIONS

We recognized the dominant blaCTX-Ms and mainstream plasmids of different continents. The results of this study provide support for a more effective response to the risks associated with the evolution of blaCTX-Ms-bearing plasmids, and lay the foundation for genotype-specific epidemiological surveillance of resistance, which are of important public health implications.

Genomic and epidemiological characterization of a blaCTX-M-27-carrying ST34 Salmonella enterica serotype Typhimurium in China

OBJECTIVES

Consuming contaminated food and water is a leading cause of food poisoning, with Salmonella being one of the primary culprits. The aim of this study is to elucidate the genomic characteristics of a blaCTX-M-27-carrying S. enterica strain recovered from a patient with diarrhoea in China.

METHODS

Antimicrobial susceptibility of S. enterica strain 123 was determined by microdilution broth assay. Whole-genome sequencing was performed using both long-read MinION and short-read Illumina platforms to fully characterize the genetic structure of the blaCTX-M-27-carrying plasmid of the S. enterica 123. In silico multilocus sequence typing (MLST), antimicrobial resistance genes and genomic epidemiological analysis of 69 Salmonella strains carrying the blaCTX-M-27 gene stored in NCBI GenBank were further analysed by BacWGSTdb 2.0 server.

RESULTS

The isolate was resistant to ampicillin, ampicillin/sulbactam, ceftazidime, ceftriaxone, cefepime, aztreonam, azithromycin, but still susceptible to ciprofloxacin, levofloxacin, imipenem, amikacin, trimethoprim-sulfamethoxazole and gentamicin. The complete genome sequence of Salmonella 123 is made up of one chromosome and three plasmids, which could be assigned as sequence type (ST)34. The blaCTX-M-27 gene was found in the 65 644 bp IncFII-type plasmid with IS26 and IS5 exist upstream of blaCTX-M-27 gene, and IS26 and IS1B are located downstream as a truncated fragment. The closest relative of Salmonella 123 was Salmonella strain La89, another ST34 strain recovered in 2011, which differed by only 52 SNPs.

CONCLUSION

This study reports the complete genome of a blaCTX-M-27-carrying S. enterica that can be used for gaining insights into the antimicrobial resistance mechanisms and dissemination patterns of the emerging pandemic lineage ST34.

Long-term gut colonization with ESBL-producing Escherichia coli in participants without known risk factors from the southeastern United States

We evaluated gut carriage of extended spectrum beta lactamase producing Enterobacteriaceae (ESBL-E) in southeastern U.S. residents without recent in-patient healthcare exposure. Study enrollment was January 2021-February 2022 in Athens, Georgia, U.S. and included a diverse population of 505 adults plus 50 child participants (age 0-5). Based on culture-based screening of stool samples, 4.5% of 555 participants carried ESBL-Es. This is slightly higher than reported in studies conducted 2012-2015, which found carriage rates of 2.5-3.9% in healthy U.S. residents. All ESBL-E confirmed isolates (n=25) were identified as Escherichia coli. Isolates belonged to 11 sequence types, with 48% classified as ST131. Ninety six percent of ESBL-E isolates carried a blaCTX-M gene. Isolated ESBL-Es frequently carried virulence genes as well as multiple classes of antibiotic resistance genes. Long-term colonization was common, with 64% of ESBL-E positive participants testing positive when rescreened three months later. One participant yielded isolates belonging to two different E. coli sequence types that carried blaCTX-M-1 genes on near-identical plasmids, suggesting intra-gut plasmid transfer. Isolation of E. coli on media without antibiotics revealed that ESBL-E. coli typically made up a minor fraction of the overall gut E. coli population, although in some cases they were the dominant strain. ESBL-E carriage was not associated with a significantly different stool microbiome composition. However, some microbial taxa were differentially abundant in ESBL-E carriers. Together, these results suggest that a small subpopulation of US residents are long-term, asymptomatic carriers of ESBL-Es, and may serve as an important reservoir for community spread of these ESBL genes.

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.

Tn3-like structures co-harboring of blaCTX-M-65, blaTEM-1 and blaOXA-10 in the plasmids of two Escherichia coli ST1508 strains originating from dairy cattle in China

The purpose of this study was to determine the level of horizontal transmission of the blaCTX-M-65 gene and the role of its associated mobile genetic elements (MGEs) in the bovine-derived Escherichia coli. After PCR identification, two plasmids carrying blaCTX-M-65 were successfully transferred to the recipient E. coli J53 Azr through conjugation assays and subsequently selected for Whole-Genome sequencing (WGS) analysis. The resistance profiles of these two positive strains and their transconjugants were also determined through antimicrobial susceptibility tests. Whole genome data were acquired using both the PacBio sequencing platform and the Illumina data platform. The annotated results were then submitted to the Genbank database for accession number recording. For comparison, the genetic environment of plasmids carrying the resistance gene blaCTX-M-65 was mapped using the Easyfig software. WGS analysis revealed Tn3-like composite transposons bearing blaCTX-M-65, blaTEM-1, and blaOXA-10 in the IncHI2-type plasmids of these two E. coli ST1508 strains. A phylogenetic tree was generated from all 48 assembled E. coli isolates blaCTX-M-65, blaTEM-1, and blaOXA-10 from the NCBI Pathogen Detection database with our two isolates, showing the relationships and the contribution of SNPs to the diversity between genetic samples. This study suggests that the transmissibility of blaCTX-M-65 on Tn3-like composite transposons contributes to an increased risk of its transmission in E. coli derived from dairy cattle.

Multidrug-resistant Escherichia coli isolated from patients and surrounding hospital environments in Bangladesh: A molecular approach for the determination of pathogenicity and resistance

Extended spectrum β-lactamase producing Escherichia coli (ESBL E. coli) is a primary concern for hospital and community healthcare settings, often linked to an increased incidence of nosocomial infections. This study investigated the characteristics of ESBL E. coli isolated from hospital environments and clinical samples. In total, 117 ESBL E. coli isolates were obtained. The isolates were subjected to molecular analysis for the presence of resistance and virulence genes, antibiotic susceptibility testing, quantitative adherence assay, ERIC-PCR for phylogenetic analysis and whole genome sequencing of four highly drug resistant isolates. Out of the 117 isolates, 68.4% were positive for blaCTX-M, 39.3% for blaTEM, 30.8% for blaNDM-1, 13.7% for blaOXA and 1.7% for blaSHV gene. Upon screening for diarrheagenic genes, no isolates were found to harbour any of the tested genes. In the case of extraintestinal pathogenic E. coli (ExPEC) virulence factors, 7.6%, 11%, 5.9%, 4.3% and 21.2% of isolates harbored the focG, kpsMII, sfaS, afa and iutA genes, respectively. At a temperature of 25°C, 14.5% of isolates exhibited strong biofilm formation with 21.4% and 28.2% exhibiting moderate and weak biofilm formation respectively, whereas 35.9% were non-biofilm formers. On the other hand at 37°C, 2.6% of isolates showed strong biofilm formation with 3.4% and 31.6% showing moderate and weak biofilm formation respectively, whereas, 62.4% were non-biofilm formers. Regarding antibiotic susceptibility testing, all isolates were found to be multidrug-resistant (MDR), with 30 isolates being highly drug resistant. ERIC-PCR resulted in 12 clusters, with cluster E-10 containing the maximum number of isolates. Hierarchical clustering and correlation analysis revealed associations between environmental and clinical isolates, indicating likely transmission and dissemination from the hospital environment to the patients. The whole genome sequencing of four highly drug resistant ExPEC isolates showed the presence of various antimicrobial resistance genes, virulence factors and mobile genetic elements, with isolates harbouring the plasmid incompatibility group IncF (FII, FIB, FIA). The sequenced isolates were identified as human pathogens with a 93.3% average score. This study suggests that ESBL producing E. coli are prevalent in the healthcare settings of Bangladesh, acting as a potential reservoir for AMR bacteria. This information may have a profound effect on treatment, and improvements in public healthcare policies are a necessity to combat the increased incidences of hospital-acquired infections in the country.

Antimicrobial resistance profiles of salmonella spp. and escherichia coli isolated from fresh nile tilapia (oreochromis niloticus) fish marketed for human consumption

BACKGROUND

Salmonella spp. and pathogenic strains of Escherichia coli are among the major foodborne zoonotic pathogens. These bacterial pathogens cause human illnesses characterized by hemorrhagic colitis, vomiting, nausea, and other agent-related symptoms. The increasing occurrence of antimicrobial resistance in these pathogens is also a serious public health concern globally. Regular surveillance of phenotypes and genotypes of Salmonella spp. and Escherichia coli from animal-derived foods is necessary for effective reduction and control of these foodborne pathogens. This study was conducted to assess the occurrence, antimicrobial resistance, virulence genes and genetic diversity of Salmonella spp. and E. coli isolates from fresh Nile tilapia obtained from retail markets in Nairobi, Kenya.

METHODS

A total of 68 fresh Nile tilapia fish samples were collected from retail markets and used for isolation of Salmonella spp. and E. coli. Antimicrobial susceptibilities of the isolates weretested by Kirby-Bauer agar disc diffusion method. According to the antimicrobial resistance profiles, the multi-drug resistant isolates were identified by 16 S rRNA sequencing and phylogenetic analysis using the Bayesian inference method. The MDR Salmonella spp. and E. coli isolates were subjected to PCR-based screening for the detection virulence and antibiotic resistance genes.

RESULTS

The prevalence of contamination of the fish samples with Salmonella spp. and E.coli was 26.47% and 35.29% respectively. Overall phenotypic resistance among the Salmonella spp. ranged from 5.5% for ceftazidime, chloramphenicol, meropenem, nitrofurantoin and streptomycin and 22.2% for penicillin-G. For E. coli phenotypic resistance ranged from 4.2% for ceftazidime and chloramphenicol and 25% for rifampicin. Multi-drug resistance was observed in three Salmonella spp. and two E. coli isolates. Results of 16 S rRNA sequences, sequence alignment and phylogenic trees confirmed the identified MDR isolates as S. typhymurium WES-09, S. typhymurium MAK-22, S. typhimurium EMB-32 and E. coli MAK-26 and E. coli LAN-35. The presence of antibiotic-resistance genes belonging to β-lactamases, tetracycline, sulfonamide, trimethoprim and aminoglycosides-resistant genes were detected in all the identified MDR isolates.

CONCLUSIONS

The findings from this study indicate that Nile tilapia (Oreochromis niloticus) sold in retail markets can acts as reservoirs of Salmonella spp. and E. coli pathogens linked to human disease, some of which were multidrug resistance to critically important antimicrobials. Both microorganisms are of zoonotic significance and represent a significant public health risk to the society.

Detection of Extended-Spectrum β-Lactamase (ESBL) E. coli at Different Processing Stages in Three Broiler Abattoirs

The European Food Safety Authority (EFSA) identified extended-spectrum β-lactamase/AmpC β-lactamase (ESBL/AmpC)-producing E. coli as one of the main priority hazards for poultry. Different studies detected ESBL-producing E. coli at broiler fattening farms and in abattoirs, concluding that poultry meat is a potential source of human infection. Broiler breast skin samples taken in three abattoirs with different scalding techniques were examined for ESBL-producing Escherichia (E.) coli and their phylogenetic groups. A total of 307 ESBL-producing E. coli isolates were found, and the abattoir with conventional immersion scalding with thermal treatment of the water had the lowest incidence. Phylogroups D/E and B1 were mostly detected, while phylogroups C, D, and E were not detected. Phylogroup B2 was detected in low proportions. The phylogroups B2 and D are important as they have been associated with urinary tract infections in humans, but were only detected in low proportions at different processing stages in this study. Since the risk for the consumer of being infected via chicken meat with ESBL-producing E. coli and E. coli of highly pathogenic phylogroups cannot be excluded, good kitchen hygiene is of great importance.

The role of the plasmid-mediated fluoroquinolone resistance genes as resistance mechanisms in pediatric infections due to Enterobacterales

Introduction

Fluoroquinolones (FQs) are not commonly prescribed in children, yet the increasing incidence of multidrug-resistant (MDR) Enterobacterales (Ent) infections in this population often reveals FQ resistance. We sought to define the role of FQ resistance in the epidemiology of MDR Ent in children, with an overall goal to devise treatment and prevention strategies.

Methods

A case-control study of children (0-18 years) at three Chicago hospitals was performed. Cases had infections by FQ-susceptible, β-lactamase-producing (bla) Ent harboring a non- or low-level expression of PMFQR genes (PMFQS Ent). Controls had FQR infections due to bla Ent with expressed PMFQR genes (PMFQR Ent). We sought bla genes by PCR or DNA (BD Max Check-Points assay®) and PMFQR genes by PCR. We performed rep-PCR, MLST, and E. coli phylogenetic grouping. Whole genome sequencing was additionally performed on PMFQS Ent positive isolates. Demographics, comorbidities, and device, antibiotic, and healthcare exposures were evaluated. Predictors of infection were assessed.

Results

Of 170 β-lactamase-producing Ent isolates, 85 (50%) were FQS; 23 (27%) had PMFQR genes (PMFQS cases). Eighty-five (50%) were FQR; 53 (62%) had PMFQR genes (PMFQR controls). The median age for children with PMFQS Ent and PMFQR Ent was 4.3 and 6.2 years, respectively (p = NS). Of 23 PMFQS Ent, 56% were Klebsiella spp., and of 53 PMFQR Ent, 76% were E. coli. The most common bla and PMFQR genes detected in PMFQS Ent were bla SHV ESBL (44%) and oqxAB (57%), and the corresponding genes detected in PMFQR Ent were bla CTX-M-1-group ESBL (79%) and aac(6')-Ib-cr (83%). Whole genome sequencing of PMFQS Ent revealed the additional presence of mcr-9, a transferable polymyxin resistance gene, in 47% of isolates, along with multiple plasmids and mobile genetic elements propagating drug resistance. Multivariable regression analysis showed that children with PMFQS Ent infections were more likely to have hospital onset infection (OR 5.7, 95% CI 1.6-22) and isolates containing multiple bla genes (OR 3.8, 95% CI 1.1-14.5). The presence of invasive devices mediated the effects of healthcare setting in the final model. Differences in demographics, comorbidities, or antibiotic use were not found.

Conclusions

Paradoxically, PMFQS Ent infections were often hospital onset and PMFQR Ent infections were community onset. PMFQS Ent commonly co-harbored multiple bla and PMFQR genes, and additional silent, yet transferrable antibiotic resistance genes such as mcr-9, affecting therapeutic options and suggesting the need to address infection prevention strategies to control spread. Control of PMFQS Ent infections will require validating community and healthcare-based sources and risk factors associated with acquisition.

Carbapenem resistance in Enterobacterales from agricultural, environmental and clinical origins: South Africa in a global context

Carbapenem agents are regarded as last-resort antibiotics, however, bacterial resistance towards carbapenems has been reported in both clinical and agricultural settings worldwide. Carbapenem resistance, defined as the resistance of a bacteria towards one or more carbapenem drugs, can be mediated in either of, or a combination of, three mechanisms-although, the mechanism mediated through the production of carbapenemases (β-lactamases that are able to enzymatically degrade carbapenems) is of most significance. Of particular concern is the occurrence of carbapenemase producing Enterobacterales (CPE), with literature describing a dramatic increase in resistance globally. In South Africa, increases of carbapenemase activity occurring in Enterobacter species, Klebsiella pneumoniae, Acinetobacter baumannii and Pseudomonas aeruginosa have recently been reported. CPE can also be found in agricultural environments, as global studies have documented numerous instances of CPE presence in various animals such as pigs, cattle, seafood, horses and dogs. However, most reports of CPE occurrence in agricultural settings come from Northern America, Europe and some parts of Asia, where more extensive research has been conducted to understand the CPE phenomenon. In comparison to clinical data, there are limited studies investigating the spread of CPE in agricultural settings in Africa, highlighting the importance of monitoring CPE in livestock environments and the food chain. Further research is necessary to uncover the true extent of CPE dissemination in South Africa. This review will discuss the phenomenon of bacterial antibiotic resistance (ABR), the applications of the carbapenem drug and the occurrence of carbapenem resistance globally.

Multidrug-resistant Enterobacter spp. in wastewater and surface water: Molecular characterization of β-lactam resistance and metal tolerance genes

Among the ESKAPE group pathogens, Enterobacter spp. is an opportunistic Gram-negative bacillus, widely dispersed in the environment, that causes infections. In the present study, samples of hospital wastewater, raw and treated urban wastewater, as well as surface receiving water, were collected to assess the occurrence of multidrug-resistant (MDR) Enterobacter spp. A molecular characterization of β-lactam antibiotic resistance and metal tolerance genes was performed. According to identification by MALDI-TOF MS, 14 isolates were obtained: 7 E. bugandensis, 5 E. kobei, and 2 E. cloacae. The isolates showed resistance mainly to β-lactam antibiotics, including those used to treat infections caused by MDR bacteria. Multiple antibiotic resistance index was calculated for all isolates. It allowed verify whether sampling points showed a high risk due to antibiotic resistant Enterobacter spp., as well as to determine if the isolates have been in environments with a frequent antibiotic use. Twelve isolates showed β-lactam antibiotic resistance gene, being the blaKPC widely detected. Regarding metal tolerance, 13 isolates showed at least two genes that encode metal tolerance mechanisms. Overall, metal tolerance mechanisms to silver, copper, mercury, arsenic and tellurium were found. New data on metal tolerance mechanisms dispersion and antibiotic-resistance characterization of the E. bugandensis and E. kobei species were here provided. The occurrence of MDR Enterobacter spp. in analyzed samples draws attention to an urgent need to put control measures into practice. It also evidences waterborne spread of clinically important antibiotic-resistant bacteria recognized as critical priority pathogens.

Antimicrobial Resistance and Extended-Spectrum Beta-Lactamase Genes in Enterobacterales, Pseudomonas and Acinetobacter Isolates from the Uterus of Healthy Mares

Antibiotic-resistant bacteria are a growing concern for human and animal health. The objective of this study was to determine the antimicrobial resistance and extended-spectrum beta-lactamase genes in Enterobacterales, Pseudomonas spp. and Acinetobacter spp. isolates from the uterus of healthy mares. For this purpose, 21 mares were swabbed for samples, which were later seeded on blood agar and MacConkey agar. The isolates were identified using MALDI-TOF and the antimicrobial susceptibility test was performed using the Kirby-Bauer technique. To characterize the resistance genes, a polymerase chain reaction (PCR) scheme was performed. Of the isolates identified as Gram-negative, 68.8% were Enterobacterales, represented by E. coli, Enterobacter cloacae, Citrobacter spp., and Klebsiella pneumoniae; 28.1% belonged to the genus Acinetobacter spp.; and 3.1% to Pseudomonas aeruginosa. A 9.3% of the isolates were multidrug-resistant (MDR), presenting resistance to antibiotics from three different classes, while 18.8% presented resistance to two or more classes of different antibiotics. The diversity of three genes that code for ESBL (blaTEM, blaCTX-M and blaSHV) was detected in 12.5% of the strains. The most frequent was blaSHV, while blaTEM and blaCTX-M were present in Citrobacter spp. and Klebsiella pneumoniae. These results are an alarm call for veterinarians and their environment and suggest taking measures to prevent the spread of these microorganisms.

Performance and Hypothetical Impact on Joint Infection Management of the BioFire Joint Infection Panel: a Retrospective Analysis

Pathogen identification is key in septic arthritis. Culture-based techniques are challenging, especially when patients have been pretreated with antibiotics or when difficult-to-culture bacteria are encountered. The BioFire joint infection assay (BJA) is a multiplex PCR panel which detects 31 of the most prevalent bacterial and fungal pathogens causing septic arthritis. Here, 123 cryoconserved contemporary synovial fluid samples from 120 patients underwent BJA analysis. Results were compared to those of culture-based diagnostics (standard of care [SOC]). Clinical data were collected, and the possible impact of the molecular diagnostic application on patient management was evaluated. Fifteen of 123 synovial fluid cultures grew bacterial pathogens. All on-panel pathogens (9/15) were correctly identified by the BJA. The BJA identified four additional bacterial pathogens in four SOC-negative cases. BJA sensitivity and specificity were 100% (95% confidence interval [CI], 69.2% to 100%) and 100% (95% CI, 96.8% to 100%), respectively. Compared to the SOC, the BJA would have resulted in faster provision of species identification and molecular susceptibility data by 49 h and 99 h, respectively. Clinical data analysis indicates that in BJA-positive cases, faster species ID could have led to timelier optimization of antibiotic therapy. This retrospective study demonstrates high sensitivity and specificity of the BJA to detect on-panel organisms in bacterial arthritis. The usefulness of the BJA in prosthetic-joint infections is limited, as important pathogens (i.e., coagulase negative staphylococci and Cutibacterium acnes) are not covered. Evidence from patient data analysis suggests that the assay might prove valuable for optimizing patient management in acute arthritis related to fastidious organisms or for patients who received antibiotics prior to specimen collection.

Prevalence of antibiotic-resistant Gram-negative bacteria having extended-spectrum β-lactamase phenotypes in polluted irrigation-purpose wastewaters from Indian agro-ecosystems

Antibiotic resistance in bacteria has emerged as a serious public health threat worldwide. Aquatic environments including irrigation-purpose wastewaters facilitate the emergence and transmission of antibiotic-resistant bacteria and antibiotic resistance genes leading to detrimental effects on human health and environment sustainability. Considering the paramount threat of ever-increasing antibiotic resistance to human health, there is an urgent need for continuous environmental monitoring of antibiotic-resistant bacteria and antibiotic resistance genes in wastewater being used for irrigation in Indian agro-ecosystems. In this study, the prevalence of antibiotic resistance in Gram-negative bacteria isolated from irrigation-purpose wastewater samples from Sirmaur and Solan districts of Himachal Pradesh was determined. Bacterial isolates of genera Escherichia, Enterobacter, Hafnia, Shigella, Citrobacter, and Klebsiella obtained from 11 different geographical locations were found to exhibit resistance against ampicillin, amoxyclav, cefotaxime, co-trimoxazole, tobramycin, cefpodoxime and ceftazidime. However, all the isolates were sensitive to aminoglycoside antibiotic gentamicin. Enterobacter spp. and Escherichia coli showed predominance among all the isolates. Multidrug-resistance phenotype was observed with isolate AUK-06 (Enterobacter sp.) which exhibited resistant to five antibiotics. Isolate AUK-02 and AUK-09, both E. coli strains showed resistant phenotypes to four antibiotics each. Phenotypic detection revealed that six isolates were positive for extended-spectrum β-lactamases which includes two isolates from Enterobacter spp. and E. coli each and one each from Shigella sp. and Citrobacter sp. Overall, the findings revealed the occurrence of antibiotic resistant and ESBL-positive bacterial isolates in wastewaters utilized for irrigation purpose in the study area and necessitate continuous monitoring and precautionary interventions. The outcomes of the study would be of significant clinical, epidemiological, and agro-environmental importance in designing effective wastewater management and environmental pollution control strategies.

Comparative Genetic Characterization of CTX-M-Producing Escherichia coli Isolated from Humans and Pigs with Diarrhea in Korea Using Next-Generation Sequencing

Pathogenic E. coli causes intra- and extraintestinal diseases in humans and pigs and third-generation cephalosporins are the primary option for the treatment of these diseases. The objective of this study was to investigate the characteristics and correlation between CTX-M-producing E. coli from humans and pigs regarding CTX-M-producing E. coli using next-generation sequencing and bioinformatic tools. Among the 24 CTX-M-producing E. coli, three types of CTX-M genes (CTX-M-12, CTX-M-14, and CTX-M-15) were detected in humans and four types of CTX-M genes (CTX-M-14, CTX-M-15, CTX-M-55, and CTX-M-101) were detected in pigs. A total of 24 CTX-M-producing E. coli isolates also showed the following antimicrobial resistance genes: other B-Lactam resistance gene (75.0%); aminoglycoside resistance genes (75.0%); phenicol resistance genes (70.8%); tetracycline resistance genes (70.8%); sulfonamide resistance genes (66.7%); quinolone resistance genes (62.5%); trimethoprim resistance genes (54.2%); and fosfomycin resistance genes (8.3%). FII (92.3%) and FIB (90.9%) were the most common plasmid replicon in humans and pigs, respectively. A total of thirty-eight different genes associated with virulence 24 CTX-M-producing E. coli and all isolates contained at least more than one virulence gene. A total of 24 CTX-M-producing E. coli isolates showed 15 diverse sequence types (STs): thirteen isolates from human belonged to 6 different STs, and 11 isolates from pig belonged to 9 different STs. The presence of virulence genes in E. coli together with antimicrobial resistance genes (including CTX-M genes) emphasizes the necessity of comprehensive surveillance and persistent monitoring of the food chain to avoid all types of bacterial contamination, regardless of human or pig origin.

The Impact of COVID-19 Pandemic on ESBL-Producing Enterobacterales Infections: A Scoping Review

Several studies have reported an increased frequency of colonization and/or infection with antibiotic-resistant bacteria (ARB) during the COVID-19 pandemic. Extended-spectrum beta-lactamase-producing Enterobacterales (ESBL-PE) are a group of bacteria with intrinsic resistance to multiple antibiotics, including penicillins, cephalosporins, and monobactams. These pathogens are easy to spread and can cause difficult-to-treat infections. Here, we summarize the available evidence on the impact of the COVID-19 pandemic on infections caused by ESBL-PE. Using specific criteria and keywords, we searched PubMed, MEDLINE, and EMBASE for articles published up to 30 March 2023 on potential changes in the epidemiology of ESBL-E since the beginning of the COVID-19 pandemic. We identified eight studies that documented the impact of COVID-19 on ESBL-E. Five studies were focused on assessing the frequency of ESBL-PE in patient-derived specimens, and three studies investigated the epidemiological aspects of ESBL-PE infections in the context of the COVID-19 pandemic. Some of the studies that were focused on patient specimens reported a decrease in ESBL-PE positivity during the pandemic, whereas the three studies that involved patient data (1829 patients in total) reported a higher incidence of ESBL-PE infections in patients hospitalized for COVID-19 compared with those with other conditions. There are limited data on the real impact of the COVID-19 pandemic on the epidemiology of ESBL-PE infections; however, patient-derived data suggest that the pandemic has exacerbated the spread of these pathogens.

Allele distribution and phenotypic resistance to ciprofloxacin and gentamicin among extended-spectrum β-lactamase-producing Escherichia coli isolated from the urine, stool, animals, and environments of patients with presumptive urinary tract infection in Tanzania

Background

Additional antimicrobial resistance to extended-spectrum β-lactamase (ESBL)-producing E. coli exhausts treatment options. We investigated allele distribution and resistance to ciprofloxacin and gentamicin among ESBL-producing E. coli isolates from the urine, stool, animals, and environments of presumptive urinary tract infection (UTI) patients, in order to gain a crucial insight toward devising prevention and control measures and treatment guidelines.

Methods

Archived ESBL-producing E. coli isolates from the urine, stool, animals, and surrounding environments of presumptive UTI patients were retrieved. Antimicrobial susceptibility profiles for ciprofloxacin and gentamicin were done followed by multiplex Polymerase chain reaction (PCR) for blaCTX-M , blaTEM , and blaSHV , to determine ESBL allele distribution. Data were analyzed using STATA version 17.

Results

A total of 472 confirmed ESBL-producing E. coli isolates from Mwanza 243 (51.5%), Kilimanjaro 143 (30.3%), and Mbeya 86 (18.2%) were analyzed. Of these, 75 (15.9%) were from urine, 199 (42.2%) from stool, 58 (12.3%) from rectal/cloaca swabs of animals, and 140 (29.7%) from surrounding environments. Out of the 472 ESBL-producing E. coli, 98.9% (467) had at least one ESBL allele. The most frequent allele was blaCTX-M , which was detected in 88.1% (416/472) of isolates, followed by the blaTEM allele, which was detected in 51.5% (243/472) of isolates. A total of 40.7% (192/472) of isolates harbored dual blaCTX-M  + blaTEM alleles and only 0.2% (1/472) of isolates had dual blaCTX-M  + blaSHV alleles, whereas 2.3% (11/472) of isolates had a combination of all three alleles (blaCTX-M  + blaTEM  + blaSHV ). None of the isolates harbored a combination of blaTEM  + blaSHV only. Resistance to ciprofloxacin and gentamicin was observed in 70.8% (334/472) and 46.0% (217/472) of isolates, respectively. There was a significant difference in the distribution of resistance to ciprofloxacin as well as gentamicin among ESBL-producing E. coli isolated from various sources (p-value < 0.001 and 0.002, respectively).

Conclusion

Almost all ESBL-producing E. coli isolates carry blaCTX-M , blaTEM , and blaSHV either alone or in combination, with the most common allele being blaCTX-M. The resistance to ciprofloxacin and gentamicin, which are frontline antibiotics for UTIs among ESBL-producing E. coli, is high. This implies the need to continually revise the local guidelines used for optimal empirical therapy for UTIs, and for continual research and surveillance using one health approach.