Prevalence and Molecular Characterization of Extended-Spectrum β-Lactamases and AmpC β-lactamase-Producing Enterobacteriaceae among Human, Cattle, and Poultry

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.

Prevalence and molecular characterization of ESBL/pAmpC producing faecal Escherichia coli strains with widespread detection of CTX-M-15 isolated from healthy poultry flocks in Eastern Algeria

The intensification of livestock farming has led to the widespread use of massive amounts of antibiotics worldwide. Poultry production, including white meat, eggs and the use of their manure as fertiliser, has been identified as one of the most crucial reservoirs for the emergence and spread of resistant bacteria, including E. coli in poultry as an important opportunistic pathogen representing the greatest biological hazard to human and wildlife health. Thus, this study aimed to analyse E. coli in the faecal carriage of healthy poultry flocks and to investigate the phenotypic and genotypic characteristics of antimicrobial resistance, including integrons genes and phylogenetic groups. A total of 431 cloacal swabs from apparently healthy poultry from four regions in Eastern Algeria from December 2021 to October 2022. 360 E. coli were isolated; from broilers (n = 151), broiler breeders (n = 91), laying hens (n = 72), and breeding hens (n = 46). Among this, 281 isolates exhibited multidrug resistance (MDR) phenotype, 17 of the 360 E. coli isolates exhibited ESBL, and one isolate exhibited both ESBL/pAmpC. A representative collection of 183 among 281 MDR E. coli was selected for further analysis by PCR to detect genes encoding resistance to different antibiotics, and sequencing was performed on all positive PCR products of blaCTX-M and blaCMY-2 genes. Phylogenetic groups were determined in 80 E. coli isolates (20 from each of the four kinds of poultry). The blaCTX-M gene was found in 16 (94.11 %) ESBL-producing E. coli isolates within 11 strains co-expressing the blaSHV gene and 8 strains co-expressing the blaTEM gene. Sequence analysis showed frequent diversity in CTX-M-group-1, with blaCTX-M-15 being the most predominant (n = 11), followed by blaCTX-M-1 (n = 5). The blaCMY-2 gene was detected only in one ESBL/pAmpC isolate. Among the 183 tested isolates, various antimicrobial resistance genes were found (number of strains) blaTEM (n = 121), blaSHV (n = 12), tetA (n = 100), tetB (n = 29), sul1(n = 67), sul2 (n = 32), qnrS (n = 45), qnrB (n = 10), qnrA (n = 1), catA1(n = 13), aac-(6')-Ib (n = 3). Furthermore, class 1 and class 2 integrons were found in 113 and 2 E. coli, respectively. The isolates were classified into multiple phylogroups, including A (35 %), B1 (27.5 %), B2 and D each (18.75 %). The detection of integrons and different classes of resistance genes in the faecal carriage of healthy poultry production indicates that commensal E. coli could potentially act as a reservoir for antimicrobial resistance, posing a significant One Health challenge encompassing the interconnected domains of human, animal health and the environment. Here, we present the first investigation to describe the diversity of blaCTX-M producing E. coli isolates with widespread detection of CTX-M-15 and CTX-M-1 in healthy breeders (Broiler and breeding hens) in Eastern Algeria.

Extended-spectrum β-lactamase-producing Escherichia coli from poultry: A review

Extended-spectrum β-lactamases (ESBLs) are β-lactamase enzymes produced by Gram-negative bacterial pathogens that harbor the ESBL genes. In addition, most ESBL genes are plasmid-mediated and usually encode a broader spectrum of antimicrobial resistance, especially to penicillins, first-generation, second-generation, and third-generation cephalosporins, as well as monobactam, such as aztreonam. Escherichia coli has become an opportunistic pathogen, especially in poultry, and has been implicated in zoonotic diseases that can be transmitted to humans, resulting in public health problems. Poultry can act as carriers of ESBL-producing E. coli (ESBL-EC) bacteria to humans through poultry meat that is contaminated by waste products, feces, and excretions. The ESBL gene CTX-M type was identified as the main cause of infection in humans and was detected in poultry as a cause of infection accompanied by clinical symptoms. Several studies have also shown a link between E. coli and ESBL gene transfer from birds to humans. Controlling the spread of ESBL-EC involves maintaining the cleanliness of poultry products, especially meat, and eliminating contaminant sources from poultry. Likewise, maintaining the environmental cleanliness of poultry slaughterhouses and poultry farms must be taken as a precautionary measure to curtail the increasing spread of ESBL-EC into the environment. This review aimed to explain the spread of ESBL-producing E. coli in poultry.

The Global Rise of ESBL-Producing Escherichia coli in the Livestock Sector: A Five-Year Overview

β-lactam antibiotics are a key element in the treatment of bacterial infections. However, the excessive use of these antibiotics has contributed to the emergence of β-lactam-resistant enterobacteria, including Escherichia coli. One of the main challenges facing the public health sector is antibacterial resistance (ABR), mainly due to limited options in its pharmacological treatment. Currently, extended-spectrum β-lactamases (ESBLs) present an alarming situation, as there is an increase in morbidity and mortality rates, prolonged hospital stays, and increased costs for sanitary supplies, which involve not only humans but also the environment and animals, especially animals destined for food production. This review presents an analysis of the prevalence of ESBL-producing E. coli and its distribution in different animal sources throughout the world, providing an understanding of the association with resistance and virulence genes, as well as perceiving the population structure of E. coli.

Monitoring viruses and beta-lactam resistance genes through wastewater surveillance during a COVID-19 surge in Suwon, South Korea

The present study reports data on a long-term campaign for monitoring SARS-CoV-2, norovirus, hepatitis A virus, and beta-lactam resistance genes in wastewater samples from a wastewater treatment plant during COVID-19 surge in Suwon, South Korea. Real-time digital PCR (RT-dPCR) assays indicated 100 % occurrence of all but hepatitis A virus and blaNDM gene in influent wastewater samples. CDC-N1 assay detected SARS-CoV-2 in all influent samples with an average log-transformed concentration of 5.1 ± 0.39 and the highest level at 6.02 gene copies/L. All samples were also positive for norovirus throughout the study with a mean concentration 5.67 ± 0.65 log10 gene copies/L. On the contrary, all treated wastewater (effluent) tested negative for both viruses' genetic materials. Furthermore, plasmid-mediated AmpC β-lactamases (PABLs) genes blaDHA, blaACC, and blaFOX, extended-spectrum β-lactamases (ESBLs) genes blaTEM and blaCTX, and Klebsiella pneumoniae carbapenemase (blaKPC) gene were measured at average concentrations of 7.05 ± 0.26, 5.60 ± 0.35, 7.82 ± 0.43, 8.38 ± 0.20, 7.64 ± 0.29, and 7.62 ± 0.41 log10 gene copies/L wastewater, respectively. Beta-lactam resistance genes showed strong correlations (r), the highest being 0.86 for blaKPC - blaFOX, followed by 0.82 for blaTEM - blaCTX and 0.79 for blaTEM - blaDHA. SARS-CoV-2 RNA occurrence in the wastewater was strongly associated (r = 0.796) with COVID-19 cases in the catchment during the initial study period of six months. A positive association of the SARS-CoV-2 RNA with the prevalence of COVID-19 cases showed a promising role of community-scale monitoring of pathogens to provide considerable early signals of infection dynamics. High concentrations of beta-lactam resistance genes in wastewater indicated a high concern for one of the biggest global health threats in South Korea and the need to find control measures. Moreover, antibiotic-resistance genes in treated wastewater flowing through water bodies and agricultural environments indicate further dissemination of antibiotic resistance traits and increasing microbial antibiotic resistance.

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.

Antimicrobial Resistance Patterns and Risk Factors Associated with ESBL-Producing and MDR Escherichia coli in Hospital and Environmental Settings in Lusaka, Zambia: Implications for One Health, Antimicrobial Stewardship and Surveillance Systems

Antimicrobial resistance (AMR) is a public health problem threatening human, animal, and environmental safety. This study assessed the AMR profiles and risk factors associated with Escherichia coli in hospital and environmental settings in Lusaka, Zambia. This cross-sectional study was conducted from April 2022 to August 2022 using 980 samples collected from clinical and environmental settings. Antimicrobial susceptibility testing was conducted using BD PhoenixTM 100. The data were analysed using SPSS version 26.0. Of the 980 samples, 51% were from environmental sources. Overall, 64.5% of the samples tested positive for E. coli, of which 52.5% were from clinical sources. Additionally, 31.8% were ESBL, of which 70.1% were clinical isolates. Of the 632 isolates, 48.3% were MDR. Most clinical isolates were resistant to ampicillin (83.4%), sulfamethoxazole/trimethoprim (73.8%), and ciprofloxacin (65.7%) while all environmental isolates were resistant to sulfamethoxazole/trimethoprim (100%) and some were resistant to levofloxacin (30.6%). The drivers of MDR in the tested isolates included pus (AOR = 4.6, CI: 1.9-11.3), male sex (AOR = 2.1, CI: 1.2-3.9), and water (AOR = 2.6, CI: 1.2-5.8). This study found that E. coli isolates were resistant to common antibiotics used in humans. The presence of MDR isolates is a public health concern and calls for vigorous infection prevention measures and surveillance to reduce AMR and its burdens.

Extended-Spectrum β-Lactamase-Producing Escherichia coli Isolated from Food-Producing Animals in Tamaulipas, Mexico

Extended-spectrum β-lactamase (ESBL)-producing E. coli has become an important global problem for the public health sector. This study aims to investigate the E. coli antimicrobial resistance profile among living food-producing animals in Tamaulipas, Mexico. A total of 200 fecal samples were collected from bovines, pigs, chickens and sheep. A total of 5.0% of the strains were phenotypically confirmed as ESBL producers. A high percentage of phenotypic antimicrobial resistance was observed against gentamicin (93.3%), tetracycline (86.6%) and streptomycin (83.3%). The gentamicin-resistant strains showed MDR, distributed among 27 resistance patterns to different antimicrobials. The antimicrobial resistance gene tet(A) was detected in 73.3% of isolates, aadA1 in 60.0% and sul2 in 43.3% of strains. The bla_CTX-M gene was found in 23.3% of strains. The virulence gene hlyA was detected in 43.3% of isolates; stx1 and stx2 were not detected in any strain. The phylotyping indicated that the isolates belonged to groups A (33.3%), B1 (16.6%), B2 (40.0%) and D (10.0%). These results show that food-producing animals might be a reservoir of ESBL-producing bacteria and may play a role in their spread.

Multidrug-Resistant ESBL-Producing E. coli in Clinical Samples from the UK

Globally, cephalosporin therapy failure is a serious problem for infection control. One causative agent of cephalosporin-resistant infections is multidrug-resistant (MDR) E. coli producing extended-spectrum β-lactamases (ESBLs) and/or plasmid-encoded AmpC (pAmpC) β-lactamases. We evaluated the occurrence of ESBL/pAmpC genetic determinants in phenotypically MDR E. coli isolated from clinical samples of blood, faeces, ear effusion, urine and sputum from a UK hospital. Phenotypic resistance profiling for 18 antibiotics (from seven classes) showed that 32/35 isolates were MDR, with resistance to 4-16 of the tested antibiotics. Of the isolates, 97.1% showed resistance to ampicillin, 71.4% showed resistance to co-amoxiclav, cefotaxime, ceftazidime and ceftiofur, and 68.5% showed resistance to cefquinome. blaCTX-M, blaTEM and blaOXA-1 genes were detected in 23, 13 and 12 strains, respectively, and Intl1 was detected in 17 isolates. The most common subtypes among the definite sequence types were CTX-M-15 (40%) and TEM-1 (75%). No E. coli isolates carried pAmpC genes. Significant correlations were seen between CTX-M carriage and cefotaxime, ceftiofur, aztreonam, ceftazidime and cefquinome resistance; between blaCTX-M, blaTEM and blaOXA-1 carriage and ciprofloxacin resistance; and between Intl1 carriage and trimethoprim/sulfamethoxazole resistance. Thus, MDR phenotypes may be conferred by a relatively small number of genes. The level and pattern of antibiotic resistance highlight the need for better antibiotic therapy guidelines, including reduced use and improved surveillance.

Prevalence of Extended-Spectrum β-Lactamase-Resistant Genes in Escherichia coli Isolates from Central China during 2016-2019

The emergence and dissemination of Escherichia coli (E. coli) strains that produce extended-spectrum beta-lactamases (ESBLs) represents a major public health threat. The present study was designed to evaluate the prevalence and characteristics of ESBL-producing Escherichia coli isolates from chickens in central China during 2016-2019. A total of 407 E. coli strains isolated from 581 chicken swabs were identified conventionally and analyzed for various cephalosporin susceptibility by disk-diffusion assay. ESBL-producing strains were screened using the double=disk synergy test and ESBL-encoding genes were carried out by PCR/sequencing. A total of 402 E. coli isolates exhibited strong resistance to first- to fourth-generation cephalosporins and monobactam antibiotics, especially cefazolin (60.69%), cefuroxime (54.05%), cefepime (35.14%), ceftriaxone (54.30%), and aztreonam (40.29%). Piperacillin/tazobactam (1.72%) was the most effective drug against the strains, but the resistance rates increased each year. Among the isolates, 262 were identified as ESBL producers and the isolation rates for the ESBL producers increased from 63.37% to 67.35% over the four years. CTX-M (97.33%) was the most prevalent type, followed by TEM (76.72%) and SHV (3.05%). The most common ESBL genotype combination was bla_TEM + bla_CTX-M (74.46%), in which the frequency of carriers increased steadily, followed by bla_CTX-M + bla_SHV (3.05%). In addition, the most predominant specific CTX-M subtypes were CTX-M-55 (48.47%) and CTX-M-1 (17.94%), followed by CTX-M-14 (11.01%), CTX-M-15 (8.02%), CTX-M-9 (6.11%), CTX-M-65 (4.58%), and CTX-M-3 (1.15%). Moreover, a novel multiplex qPCR assay was developed to detect bla_CTX-M, bla_TEM, and bla_SHV, with limits of detection of 2.06 × 10¹ copies/μL, 1.10 × 10¹ copies/μL, and 1.86 × 10¹ copies/μL, respectively, and no cross-reactivity with other ESBL genes and avian pathogens. The assays exhibited 100% sensitivity and specificities of 85%, 100%, and 100% for bla_CTX-M, bla_TEM, and bla_SHV, respectively. In conclusion, our findings indicated that ESBL-producing E.coli strains isolated from chickens in central China were highly resistant to cephalosporins and frequently harbored diversity in ESBL-encoding genes. These isolates can pose a significant public health risk. The novel multiplex qPCR method developed in this study may be a useful tool for molecular epidemiology and surveillance studies of ESBL genes.