Plasmid-mediated colistin resistance and ESBL production in Escherichia coli from clinically healthy and sick pigs

Unravelling the advances of CRISPR-Cas9 as a precise antimicrobial therapy: A systematic review

Antimicrobial resistance is a critical public health threat, compromising treatment effectiveness. The spread of resistant pathogens, facilitated by genetic variability and horizontal gene transfer, primarily through plasmids, poses significant challenges to health systems.

OBJECTIVE

This review explores the potential of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) technology and Cas9 nucleases in combating antimicrobial resistance.

METHODS

The literature review followed the PRISMA guidelines using PubMed, Embase, and Scopus databases until July 2023.

RESULTS

The Enterobacterales family, particularly Escherichia coli, was the main focus. The resistance genes targeted were mainly associated with β-lactam antibiotics, specifically bla genes, and colistin resistance linked to the mcr-1 gene. Plasmid vectors have been the primary delivery method for the CRISPR-Cas9 system, with conjugative plasmids resensitizing bacterial strains to various antimicrobials. Other delivery methods included electroporation, phage-mediated delivery, and nanoparticles. The efficacy of the CRISPR-Cas9 system in resensitizing bacterial strains ranged from 4.7% to 100%.

CONCLUSIONS

Despite challenges in delivery strategies and clinical application, studies integrating nanotechnology present promising approaches to overcome these limitations. This review highlights new perspectives for the clinical use of CRISPR-Cas9 as a specific and efficient antimicrobial agent, potentially replacing traditional broad-spectrum antimicrobials in the future.

Tracking Extended-spectrum β-lactamase-Producing and Colistin-Resistant Escherichia Coli in Pig Abattoirs: Impacts on Food Safety

The ongoing increase in antimicrobial resistance (AMR) in Escherichia coli, particularly the emergence of extended-spectrum β-lactamase (ESBL)-producing and colistin-resistant strains in livestock, is a significant public health concern. The effectiveness of pig abattoir management, specifically through Hazard Analysis and Critical Control Points (HACCP) protocols, in reducing antimicrobial-resistant contamination continues to be scrutinized. This study investigated the prevalence, characteristics, and critical contamination points of ESBL-producing E. coli (ESBL-Ec) and colistin-resistant ESBL-Ec across the slaughtering processes in two pig abattoirs in Thailand-one operating under HACCP standards and the other certified solely under Good Manufacturing Practices. A higher prevalence of ESBL-Ec was found in the non-HACCP facility (67.98%) compared with the HACCP facility (52.04%), especially in pig carcasses. Skin and carcass washing in HACCP facilities effectively decreased bacterial contamination. Conversely, non-HACCP facilities should implement measures such as cleaning skin with disinfectants at the lairage, regularly monitoring and adjusting the final washing protocol, and strict sterilization of chopping plates to effectively control contamination points. Most ESBL-Ec isolates were multidrug-resistant and carried blaCTX-M group 1 or group 9 genes. Additionally, 12.6% of these isolates were resistant to colistin, with the mcr-1 gene predominantly identified. ST10 was the dominant clone of mcr-carrying ESBL-Ec across various slaughtering stages and sample types. These findings highlight the importance of implementing HACCP protocols to reduce contamination, enhance food safety, and mitigate public health risks. Ongoing AMR monitoring to find critical points along the slaughtering process is essential to reduce sources of AMR transmission to consumers.

Resistome and plasmidome genomic features of mcr-1.1-harboring Escherichia coli: a One Health approach

AIMS

This study evaluated the phenotypic and genotypic traits of mcr-1.1-harboring Escherichia coli isolates from chickens, pigs, humans, and farm environments. The resistome and the mobile genetic elements associated with the spread of mcr-1.1 in Southern Brazil were also characterized.

METHODS AND RESULTS

The 22 mcr-1.1-harboring E. coli isolates from different origins were selected for antimicrobial susceptibility testing and whole genome sequencing for characterization of the resistome, plasmids, and sequence types. All isolates presented several resistance genes and harbored the mcr-1.1 gene in a highly similar IncX4 plasmid. Furthermore, the mcr-1.1 gene co-occurred with the mcr-3.12 gene in a multidrug-resistant isolate from the farm environment.

CONCLUSIONS

These findings demonstrate that the mcr-1.1 gene in E. coli isolates from Brazil is spreading mainly by horizontal transfer of the IncX4 plasmid. The co-occurrence of mcr-1.1 and mcr-3.12 highlights pig farming as an important reservoir of colistin resistance.

Detection and Characterisation of Colistin-Resistant Escherichia coli in Broiler Meats

The irrational use of antimicrobials has led to the emergence of resistance, impacting not only pathogenic bacteria but also commensal bacteria. Resistance against colistin, a last-resort antibiotic, mediated by globally disseminated plasmid-borne mobile colistin resistance (mcr) genes, has raised significant global concerns. This cross-sectional study aimed to investigate the antimicrobial resistance patterns of colistin-resistant Escherichia coli (E. coli) and mobilised colistin resistance (mcr 1-5) genes from broiler meat. A total of 570 broiler samples (285 liver and 285 muscle) were collected from 7 supermarkets and 11 live bird markets (LBMs) in Chattogram metropolitan areas of Bangladesh. The isolation and identification of E. coli were carried out using standard bacteriological and molecular techniques. Antimicrobial susceptibility testing (AST) was performed using the Kirby-Bauer disc diffusion method, and colistin's minimum inhibitory concentration (MIC) was determined by the broth microdilution (BMD) method. Colistin-resistant isolates were further tested for the presence of mcr (1-5) genes using polymerase chain reaction (PCR). Out of the 570 samples, 311 (54.56%; 95% confidence interval: 50.46-58.60) were positive for E. coli. AST results showed the highest resistance to sulphamethoxazole-trimethoprim (89.39%), while the highest susceptibility was observed for cefalexin (62.70%). A total of 296 isolates (95.18%) were found to be multidrug-resistant (MDR), with the multiple antibiotic resistance (MAR) index ranging from 0.38 to 1. Additionally, 41 isolates (13.18%) exhibited resistance to five antimicrobial classes, with resistance patterns of CIP + SXT + AMP + DO + TE + CT. A total of 233 isolates (74.92%) were resistant to colistin (MIC > 2 mg/L). A strong correlation between colistin resistance and the presence of the mcr-1 gene was observed (r = 1). All phenotypic colistin-resistant E. coli isolates carried the mcr-1 gene, while no isolates were positive for mcr (2-5). The detection of mcr genes in E. coli strains from poultry sources poses a significant risk, as these resistance genes can be transferred to humans through the food chain. The prevalence of multidrug-resistant Escherichia coli and the mcr-1 gene in poultry products in Bangladesh presents a significant public health and food safety concern.

Characteristics of the extended-spectrum-β-lactamase-producing Escherichia coli isolated from diseased livestock and poultry in Taiwan

A total of 297 Escherichia coli isolates from diseased livestock with diarrhea and 269 isolates from poultry affected by colibacillosis were assessed for extended-spectrum-β-lactamase (ESBL) production. In livestock, 36 isolates (12.1%) were ESBL-producing, with pigs (52.8%), cattle (30.5%), and goats (16.7%) being the most affected. Poultry exhibited 22 ESBL-producing strains (8.6%), with distribution among species: chicken (36.3%), duck (22.7%), goose (22.7%), and others (18.2%). ESBL-producing E. coli demonstrated higher drug resistance, except for amoxicillin/clavulanic acid, while all isolates were susceptible to imipenem. The blaCTX-M-55 gene, from the blaCTX-M-1 group, was prevalent in the ESBL-producing E. coli from livestock and poultry. Multilocus sequence typing (MLST) identified distinct sequence types (STs) for 58 ESBL-producing E. coli, except for ST162 and ST1196, detected in both sources. Livestock yielded one ST10 and two ST38 isolates, while poultry exhibited two ST69 and one ST617 isolates, recognized as common extraintestinal pathogenic E. coli (ExPEC) types. In conjugation assays, all ESBL-producing E. coli successfully transferred bla genes to the recipient E. coli J53 strain. The findings underscore food-producing animals as significant ESBL reservoirs, emphasizing the crucial role of judicious antimicrobial use on farms.

PmrB Y358N, E123D amino acid substitutions are not associated with colistin resistance but with phylogeny in Escherichia coli

Colistin resistance in Escherichia coli is of public health significance for its use to treat multidrug-resistant Gram-negative infections. Amino acid variations in PmrB have been implicated in colistin resistance in E. coli. In this cross-sectional study, 288 generic E. coli isolates from surveillance of broiler chicken and feedlot cattle feces, retail meat, wastewater, and well water were whole-genome sequenced. Phylogroup designation and screening for two amino acid substitutions in PmrB putatively linked to colistin resistance (Y358N, E123D) were performed in silico. Three additional data sets of publicly available E. coli assemblies were similarly scrutinized: (i) E. coli isolates from studies identifying the Y358N or E123D substitutions, (ii) colistin-susceptible E. coli isolates reported in the literature, and (iii) a random sampling of 14,700 E. coli assemblies available in the National Center for Biotechnology Information public database. Within all data sets, ≥95% of phylogroup B1 and C isolates have the PmrB Y358N variation. The PmrB E123D amino acid substitution was only identified in phylogroup B2 isolates, of which 94%-100% demonstrate the substitution. Both PmrB amino acid variations were infrequent in other phylogroups. Among published colistin susceptible isolates, colistin minimum inhibitory concentrations (MICs) were not higher in isolates bearing the E123D and Y358N amino acid variations than in isolates without these PmrB substitutions. The E123D and Y358N PmrB amino acid substitutions in E. coli appear strongly associated with phylogroup. The previously observed associations between Y358N and E123D amino acid substitutions in PmrB and colistin resistance in E. coli may be spurious.

IMPORTANCE

Colistin is a critical last-resort treatment for extensively drug-resistant Gram-negative infections in humans. Therefore, accurate identification of the genetic mechanisms of resistance to this antimicrobial is crucial to effectively monitor and mitigate the spread of resistance. Examining over 16,000 whole-genome sequenced Escherichia coli isolates, this study identifies that PmrB E123D and Y358N amino acid substitutions previously associated with colistin resistance in E. coli are strongly associated with phylogroup and are alone not sufficient to confer a colistin-resistant phenotype. This is a critical clarification, as both substitutions are identified as putative mechanisms of colistin resistance in many publications and a common bioinformatic tool. Given the potential spurious nature of initial associations of these substitutions with colistin resistance, this study's findings emphasize the importance of appropriate experimental design and consideration of relevant biological factors such as phylogroup when ascribing causal mechanisms of resistance to chromosomal variations.

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.

Phenotypic and molecular characterization of multidrug-resistant Enterobacterales isolated from clinical samples in Palestine: a focus on extended-spectrum β-lactamase- and carbapenemase-producing isolates

BACKGROUND

Infections resulting from multidrug-resistant Enterobacterales (MDR-E) pose a growing global threat, presenting challenges in treatment and contributing significantly to morbidity and mortality rates. The main objective of this study was to characterize phenotypically and genetically extended-spectrum β-lactamase- and carbapenemase- producing Enterobacterales (ESBLE and CPE respectively) isolated from clinical samples in the West Bank, Palestine.

METHODS

A cross sectional study was conducted in October 2023 on clinical bacterial isolates collected from five governmental hospitals in the West Bank, Palestine. The isolates obtained from the microbiology laboratories of the participating hospitals, underwent identification and antibiotic susceptibility testing (AST) using the VITEK® 2 Compact system. ESBL production was determined by the Vitek2 Compact system. A modified carbapenem inactivation method (mCIM) was employed to identify carbapenemase-producing Enterobacterales (CPE). Resistance genes were detected by real-time PCR.

RESULTS

Out of the total 1380 collected isolates, we randomly selected 600 isolates for analysis. Our analysis indicated that 287 (47.83%) were extended-spectrum beta-lactamase producers (ESBLE), and 102 (17%) as carbapenem-resistant Enterobacterales (CRE) isolates. A total of 424 isolates (70.67%) were identified as multidrug-resistant Enterobacterales (MDRE). The most prevalent ESBL species were K. pneumoniae (n = 124; 43.2%), E. coli (n = 119; 41.5%) and E. cloacae (n = 31; 10.8%). Among the CRE isolates, 85 (83.33%) were carbapenemase-producing Enterobacterales (CPE). The most frequent CRE species were K. pneumoniae (n = 63; 61.7%), E. coli (n = 25; 24.5%) and E. cloacae (n = 13; 12.8%). Additionally, 47 (7.83%) isolates exhibited resistance to colistin (CT), with 38 (37.62%) being CT-resistant CRE and 9 (3.14%) being CT-resistant ESBLE while sensitive to carbapenems. We noticed that 11 isolates (6 Klebsiella pneumoniae and 5 Enterobacter cloacae complex) demonstrated sensitivity to carbapenems by phenotype but carried silent CPE genes (1 blaOXA48, and 6 blaNDM, 4 blaOXA48, blaNDM). ESBL-producing Enterobacterales strains exhibited varied resistance patterns across different antibiotic classes. E. coli isolates showed notable 48% resistance to trimethoprim/sulfamethoxazole. K. pneumoniae isolates displayed a significant resistance to trimethoprim/sulfamethoxazole, nitrofurantoin, and fosfomycin (54%, 90%, and 70% respectively). E. cloacae isolates showed complete resistance to nitrofurantoin and fosfomycin. P. mirabilis isolates exhibited high resistance against fluoroquinolones (83%), and complete resistance to trimethoprim/sulfamethoxazole, nitrofurantoin and fosfomycin.

CONCLUSION

This study showed the high burden of the ESBLE and CRE among the samples collected from the participating hospitals. The most common species were K. pneumoniae and E. coli. There was a high prevalence of blaCTXm. Adopting both conventional and molecular techniques is essential for better surveillance of the emergence and spread of antimicrobial-resistant Enterobacterales infections in Palestine.

Metagenomic insights into isolable bacterial communities and antimicrobial resistance in airborne dust from pig farms

This study aims to investigate bacterial communities and antimicrobial resistance (AMR) in airborne dust from pig farms. Airborne dust, pig feces and feed were collected from nine pig farms in Thailand. Airborne dust samples were collected from upwind and downwind (25 meters from pig house), and inside (in the middle of the pig house) of the selected pig house. Pig feces and feed samples were individually collected from the pen floor and feed trough from the same pig house where airborne dust was collected. A direct total bacteria count on each sampling plate was conducted and averaged. The ESKAPE pathogens together with Escherichia coli, Salmonella, and Streptococcus were examined. A total of 163 bacterial isolates were collected and tested for MICs. Pooled bacteria from the inside airborne dust samples were analyzed using Metagenomic Sequencing. The highest bacterial concentration (1.9-11.2 × 103 CFU/m3) was found inside pig houses. Staphylococcus (n = 37) and Enterococcus (n = 36) were most frequent bacterial species. Salmonella (n = 3) were exclusively isolated from feed and feces. Target bacteria showed a variety of resistance phenotypes, and the same bacterial species with the same resistance phenotype were found in airborne dust, feed and fecal from each farm. Metagenomic Sequencing analysis revealed 1,652 bacterial species across all pig farms, of which the predominant bacterial phylum was Bacillota. One hundred fifty-nine AMR genes of 12 different antibiotic classes were identified, with aminoglycoside resistance genes (24%) being the most prevalent. A total of 251 different plasmids were discovered, and the same plasmid was detected in multiple farms. In conclusion, the phenotypic and metagenomic results demonstrated that airborne dust from pig farms contained a diverse array of bacterial species and genes encoding resistance to a range of clinically important antimicrobial agents, indicating the significant role in the spread of AMR bacterial pathogens with potential hazards to human health. Policy measurements to address AMR in airborne dust from livestock farms are mandatory.

Prevalence and characteristics of ESBL-producing Escherichia coli in clinically healthy pigs: implications for antibiotic resistance spread in livestock

AIM

This study aimed to compare and characterize the resistance profile and the presence of extended-spectrum beta-lactamase (ESBL) related genes in Escherichia coli isolated from healthy finishing pigs fed with or without antibiotics in their diets.

METHODS AND RESULTS

A total of 27 ceftiofur-resistant E. coli isolates were obtained from 96 healthy pigs. The antibiotic resistance profile was tested, and all 27 isolates were classified as multidrug-resistant (MDR). A high proportion of isolates were resistant to cephalosporins, ampicillin, ciprofloxacin, and tetracyclines. The ESBL production was observed in 85% of isolates by double-disc synergy test. The MDR-E. coli isolates harbored ESBL genes, such as blaTEM, blaCTX-M-1, blaCTX-M-2, and blaCTX-M-8,25. In addition, other antibiotics resistance genes (ARGs) were also detected, such as sul2, ant(3″)-I, tetA, and mcr-1. The mobilization of the blaCTX-M gene was confirmed for nine E. coli isolates by conjugation assays. The presence of blaCTX-M on mobile genetic elements in these isolates was demonstrated by Southern blot hybridization, and the resistance to cephalosporins was confirmed in the transconjugants. Our results indicate the prevalence of CTX-M-producing E. coli strains harboring mobile genetic elements in the normal microbiota of healthy pigs.

CONCLUSIONS

These findings highlight the significance of ESBL genes as a global health concern in livestock and the potential spread of antimicrobial resistance to other members of the gastrointestinal tract microbiota.

Occurrence and molecular characteristics of antimicrobial resistance, virulence factors, and extended-spectrum β-lactamase (ESBL) producing Salmonella enterica and Escherichia coli isolated from the retail produce commodities in Bangkok, Thailand

The incidence of antimicrobial resistance (AMR) in the environment is often overlooked and leads to serious health threats under the One Health paradigm. Infection with extended-spectrum β-lactamase (ESBL) producing bacteria in humans and animals has been widely examined, with the mode of transmission routes such as food, water, and contact with a contaminated environment. The purpose of this study was to determine the occurrence and molecular characteristics of resistant Salmonella enterica (S. enterica) (n = 59) and Escherichia coli (E. coli) (n = 392) isolated from produce commodities collected from fresh markets and supermarkets in Bangkok, Thailand. In this study, the S. enterica isolates exhibited the highest prevalence of resistance to tetracycline (11.9%) and streptomycin (8.5%), while the E. coli isolates were predominantly resistant to tetracycline (22.5%), ampicillin (21.4%), and sulfamethoxazole (11.5%). Among isolates of S. enterica (6.8%) and E. coli (15.3%) were determined as multidrug resistant (MDR). The prevalence of ESBL-producing isolates was 5.1% and 1.0% in S. enterica and E. coli, respectively. A minority of S. enterica isolates, where a single isolate exclusively carried blaCTX-M-55 (n = 1), and another isolate harbored both blaCTX-M-55 and blaTEM-1 (n = 1); similarly, a minority of E. coli isolates contained blaCTX-M-55 (n = 2) and blaCTX-M-15 (n = 1). QnrS (11.9%) and blaTEM (20.2%) were the most common resistant genes found in S. enterica and E. coli, respectively. Nine isolates resistant to ciprofloxacin contained point mutations in gyrA and parC. In addition, the odds of resistance to tetracycline among isolates of S. enterica were positively associated with the co-occurrence of ampicillin resistance and the presence of tetB (P = 0.001), while the E. coli isolates were positively associated with ampicillin resistance, streptomycin resistance, and the presence of tetA (P < 0.0001) in this study. In summary, these findings demonstrate that fresh vegetables and fruits, such as cucumbers and tomatoes, can serve as an important source of foodborne AMR S. enterica and E. coli in the greater Bangkok area, especially given the popularity of these fresh commodities in Thai cuisine.

Extended-Spectrum β-Lactamases (ESBL) Producing Bacteria in Animals

Animals have been identified as potential reservoirs and vectors of resistance genes, with studies showing that Gram-negative bacteria can acquire resistance through the horizontal transmission of resistance genes on plasmids. It is important to understand the distribution of antimicrobial-resistant bacteria and their drug-resistant genes in animals. Previous review articles mostly focused on a single bacterium or a single animal. Our objective is to compile all ESBL-producing bacteria isolated from various animals in recent years and provide a comprehensive viewpoint. Using a thorough PubMed literature search spanning from 1 January 2020 to 30 June 2022, studies exploring extended-spectrum beta-lactamase (ESBL) producing bacteria in animals were included. ESBL-producing bacteria are present in animals from various countries around the world. The most common sources of these bacteria were farm animals, and the most frequently isolated bacteria were Escherichia coli and Klebsiella pneumoniae. The most detected ESBL genes were blaTEM, blaSHV, and blaCTX-M. The presence of ESBL-producing bacteria in animals highlights the importance of the One Health approach to address the issue of antibiotic resistance. Further research is needed to better understand the epidemiology and mechanisms of the spread of ESBL-producing bacteria in animal populations and their potential impact on human and animal health.

Extended-spectrum β-lactamase- and AmpC β-lactamase-producing Enterobacterales associated with urinary tract infections in the New Zealand community: a case-control study

OBJECTIVES

To assess whether having a pet in the home is a risk factor for community-acquired urinary tract infections associated with extended-spectrum β-lactamase (ESBL)- or AmpC β-lactamase (ACBL)- producing Enterobacterales.

METHODS

An unmatched case-control study was conducted between August 2015 and September 2017. Cases (n = 141) were people with community-acquired urinary tract infection (UTI) caused by ESBL- or ACBL-producing Enterobacterales. Controls (n = 525) were recruited from the community. A telephone questionnaire on pet ownership and other factors was administered, and associations were assessed using logistic regression.

RESULTS

Pet ownership was not associated with ESBL- or ACBL-producing Enterobacterales-related human UTIs. A positive association was observed for recent antimicrobial treatment, travel to Asia in the previous year, and a doctor's visit in the last 6 months. Among isolates with an ESBL-/ACBL-producing phenotype, 126/134 (94%) were Escherichia coli, with sequence type 131 being the most common (47/126).

CONCLUSIONS

Companion animals in the home were not found to be associated with ESBL- or ACBL-producing Enterobacterales-related community-acquired UTIs in New Zealand. Risk factors included overseas travel, recent antibiotic use, and doctor visits.