Mobile Colistin Resistance (mcr) Gene-Containing Organisms in Poultry Sector in Low- and Middle-Income Countries: Epidemiology, Characteristics, and One Health Control Strategies

Structural insights into the advancements of mobile colistin resistance enzymes

The plasmid-encoded mobile colistin resistance enzyme (MCR) is challenging the clinical efficacy of colistin as a last-resort antibiotic against multidrug-resistant bacteria. This transferase catalyzes the addition of positively charged phosphoethanolamine to lipid A, and its catalytic domain in the periplasm has been elucidated. To date, there are many works on the catalytic domain and function of this enzyme class. However, the roles of unreported soluble or inter-membrane domains remain undefined, which might cause an inaccurate or even incorrect understanding of substrate recognition and binding. In this review, MCR-1 is first compared and analyzed from the perspective of the full-length alpha-fold MCR-1. Specifically, some disputed issues, especially in its architecture and catalytic mechanism are discussed independently. Meanwhile, the structure-based insights into MCRs variants, their evolutions, and the balance between colistin-resistance and survival costs, are also critically analyzed. Importantly, by comparing it with the full-length MCR-1, several potential pockets for drug design have been re-identified. Finally, recent advancements in inhibitors targeting MCR-1 are also in-depth summarized. These details offer a new perspective on MCRs and serve as a valuable foundation for drug development.

Commercial Day-Old Chicks in Nigeria Are Potential Reservoirs of Colistin- and Tigecycline-Resistant Potentially Pathogenic Escherichia coli

Background: Frequent use of colistin (COL) and tetracyclines in the Nigerian poultry sector potentially triggers bacterial resistance against COL and tigecycline (TIG), which are last-line antibiotics used to treat multidrug-resistant infections. Aim/Objectives: This study aimed to isolate COL- and TIG-resistant E. coli from commercial day-old chicks distributed to poultry farmers in Nsukka Southeastern Nigeria, assess the production of extended-spectrum β-lactamase (ESBL) and carbapenemase by the isolates, and establish their pathogenic potentials. Materials and Methods: Non-duplicate cloacal swabs were systematically collected from 250 randomly selected day-old chicks. MacConkey agar with 1 µg/mL of COL and 16 µg/mL of tetracycline was used for the isolation of putative COL- and tetracycline-resistant E. coli, respectively. E. coli isolates were confirmed biochemically using the API20E Gram-negative identification kit and molecularly by polymerase chain reaction targeting the uidA gene. Phenotypic COL resistance was established using COL agar and COL disc elution tests, while TIG insusceptibility was determined with disc diffusion. ESBL and carbapenemase production was assessed by double-disc synergy and modified carbapenem inactivation methods, respectively. Pathogenic potentials were determined using phenotypic methods. Results: COL- and TIG-resistant E. coli was recovered from 95 (38.0%) and 62 (24.8%) swabs from the 250 chicks, respectively. None of the isolates were potential ESBL or carbapenemase producers. The COL-resistant isolates displayed pathogenic potentials such as biofilm formation, haemagglutination, cell surface hydrophobicity, surface layer, and gelatinase activities at rates of 30.7%, 8.4%, 33.7%, 23.5%, and 17.6%, respectively. Meanwhile, the TIG-resistant isolates exhibited their respective potentials at rates of 47.0%, 21.0%, 35.5%, 58.1%, and 43.6%. Red, dry, and rough (RDAR) was the predominant curli fimbriae, and the cellulose morphotype portrayed by both the COL- and TIG-unsusceptible potential biofilm-producing isolates. Conclusions: This study demonstrates that a significant percentage of commercial day-old chicks distributed to farmers in Nsukka, southeastern Nigeria, are colonized by potentially pathogenic COL- and TIG-resistant E. coli, which could spread to humans and the environment.

Investigating the role of PmrB mutation on Colistin antibiotics drug resistance in Klebsiella Pneumoniae

Klebsiella pneumoniae, a member of the Enterobacteriaceae family, naturally resides in the digestive tracts of both healthy animals and humans. Carbapenem-resistant Klebsiella pneumoniae (CRKP) poses a significant health risk for hospitalized patients worldwide, greatly reducing the effectiveness of commonly used antibiotics. This leaves healthcare providers with limited treatment options, often relying on colistin. PmrB is important for the survival of Klebsiella pneumonia and, a mutation in the PmrB protein is accountable for the development of colistin antibiotic resistance in Klebsiella pneumonia. This is especially important because colistin is a fundamental component in the treatment of pneumonia. Three mutated residues-T157P, G207D, and T246A-are responsible for colistin resistance. The structural alterations and underlying mechanisms in the PmrB protein that cause resistance owing to mutation remain unclear. As a result, this study is focused to the exploration of the putative mechanism of resistance resulting from these mutations, as well as the structure modification of normal and mutant PmrB proteins, using molecular docking and molecular dynamics simulations analysis. Our results demonstrated that the interaction paradigm for the mutants has been altered and thus showing a significant effect upon the hydrogen bonding network. Interestingly, the binding of Colistin with the three mutant demonstrate unstable behavior as compared with WT+Colistin. The proposed drug-resistance mechanism will help to guide the development of PmrB drugs. These finding may give a new framework for developing novel drugs against the mutant version of PmrB.

Aeromonas and mcr-3: A Critical Juncture for Transferable Polymyxin Resistance in Gram-Negative Bacteria

Polymyxin antibiotics B and colistin are considered drugs of last resort for the treatment of multi-drug and carbapenem-resistant Gram-negative bacteria. With the emergence and dissemination of multi-drug resistance, monitoring the use and resistance to polymyxins imparted by mobilised colistin resistance genes (mcr) is becoming increasingly important. The Aeromonas genus is widely disseminated throughout the environment and serves as a reservoir of mcr-3, posing a significant risk for the spread of resistance to polymyxins. Recent phylogenetic studies and the identification of insertion elements associated with mcr-3 support the notion that Aeromonas spp. may be the evolutionary origin of the resistance gene. Furthermore, mcr-3-related genes have been shown to impart resistance in naïve E. coli and can increase the polymyxin MIC by up to 64-fold (with an MIC of 64 mg/L) in members of Aeromonas spp. This review will describe the genetic background of the mcr gene, the epidemiology of mcr-positive isolates, and the relationship between intrinsic and transferable mcr resistance genes, focusing on mcr-3 and mcr-3-related genes.

Validation of Recombinase Polymerase Amplification with In-House Lateral Flow Assay for mcr-1 Gene Detection of Colistin Resistant Escherichia coli Isolates

BACKGROUND/OBJECTIVES

The emergence of the mobilized colistin resistance 1 (mcr-1) gene, which causes colistin resistance, is a serious concern in animal husbandry, particularly in pigs. Although antibiotic regulations in many countries have prohibited the use of colistin in livestock, the persistence and dissemination of this plasmid-mediated gene require effective and rapid monitoring. Therefore, a rapid, sensitive, and specific method combining recombinase polymerase amplification (RPA) with an in-house lateral flow assay (LFA) for the mcr-1 gene detection was developed.

METHODS

The colistin agar test and broth microdilution were employed to screen 152 E. coli isolates from pig fecal samples of five antibiotic-used farms. The established RPA-in-house LFA was validated with PCR for mcr-1 gene detection.

RESULTS

The RPA-in-house LFA was completed within 35 min (20 min of amplification and 5-15 min on LFA detection) at 37 °C. The sensitivity, specificity, and accuracy were entirely 100% in concordance with PCR results. No cross-reactivity was detected with seven common pathogenic bacteria or other mcr gene variants.

CONCLUSIONS

Therefore, the in-house RPA-LFA serves as a point-of-care testing tool that is rapid, simple, and portable, facilitating effective surveillance of colistin resistance in both veterinary and clinical settings, thereby enhancing health outcomes.

A Systematic Review and Comprehensive Analysis of mcr Gene Prevalence in Bacterial Isolates in Arab Countries

BACKGROUND

The resurgence of colistin has become critical in combating multidrug-resistant Gram-negative bacteria. However, the emergence of mobilized colistin resistance (mcr) genes presents a crucial global challenge, particularly in the Arab world, which includes regions with unique conditions and ongoing conflicts in some parts.

METHODS

To address this issue, a systematic review was conducted using multiple databases, including Cochrane, PubMed, Scopus, Web of Science, and Arab World Research Source.

RESULTS

A total of 153 studies were included, revealing substantial heterogeneity in the prevalence of mcr genes across 15 Arab countries, with notable findings indicating that Egypt and Lebanon reported the highest number of cases. The analysis indicated that the most prevalent sequence types were ST10, ST101, and ST1011, all of which are Escherichia coli strains linked to significant levels of colistin resistance and multiple antimicrobial resistance profiles.

CONCLUSIONS

By analyzing the diverse findings from different Arab countries, this review lays a critical foundation for future research and highlights the necessity for enhanced surveillance and targeted interventions to address the looming threat of colistin resistance in the region.

SYSTEMATIC REVIEW REGISTRATION

PROSPERO CRD42024584379.

A Health Threat from Farm to Fork: Shiga Toxin-Producing Escherichia coli Co-Harboring blaNDM-1 and mcr-1 in Various Sources of the Food Supply Chain

The dissemination of resistant pathogens through food supply chains poses a significant public health risk, spanning from farm to fork. This study analyzed the distribution of Shiga toxin-producing Escherichia coli (STEC) across various sources within the animal-based food supply chain. A total of 500 samples were collected from livestock, poultry, the environment, fisheries, and dairy. Standard microbiological procedures were employed to isolate and identify E. coli isolates, which were further confirmed using MALDI-TOF and virulence-associated genes (VAGs) such as stx1, stx2, ompT, hylF, iutA, fimH, and iss. The phenotypic resistance patterns of the isolates were determined using the disc diffusion method, followed by molecular identification of antibiotic resistance genes (ARGs) through PCR. STEC were subjected to PCR-based O typing using specific primers for different O types. Overall, 154 (30.5%) samples were confirmed as E. coli, of which 77 (50%) were multidrug-resistant (MDR) E. coli. Among these, 52 (67.53%) isolates exhibited an array of VAGs, and 21 (40.38%) were confirmed as STEC based on the presence of stx1 and stx2. Additionally, 12 out of 52 (23.07%) isolates were identified as non-O157 STEC co-harbouring mcr-1 and blaNDM-1. O26 STEC was found to be the most prevalent among the non-O157 types. The results suggest that the detection of STEC in food supply chains may lead to serious health consequences, particularly in developing countries with limited healthcare resources.

A review of the mechanisms that confer antibiotic resistance in pathotypes of E. coli

The dissemination of antibiotic resistance in Escherichia coli poses a significant threat to public health worldwide. This review provides a comprehensive update on the diverse mechanisms employed by E. coli in developing resistance to antibiotics. We primarily focus on pathotypes of E. coli (e.g., uropathogenic E. coli) and investigate the genetic determinants and molecular pathways that confer resistance, shedding light on both well-characterized and recently discovered mechanisms. The most prevalent mechanism continues to be the acquisition of resistance genes through horizontal gene transfer, facilitated by mobile genetic elements such as plasmids and transposons. We discuss the role of extended-spectrum β-lactamases (ESBLs) and carbapenemases in conferring resistance to β-lactam antibiotics, which remain vital in clinical practice. The review covers the key resistant mechanisms, including: 1) Efflux pumps and porin mutations that mediate resistance to a broad spectrum of antibiotics, including fluoroquinolones and aminoglycosides; 2) adaptive strategies employed by E. coli, including biofilm formation, persister cell formation, and the activation of stress response systems, to withstand antibiotic pressure; and 3) the role of regulatory systems in coordinating resistance mechanisms, providing insights into potential targets for therapeutic interventions. Understanding the intricate network of antibiotic resistance mechanisms in E. coli is crucial for the development of effective strategies to combat this growing public health crisis. By clarifying these mechanisms, we aim to pave the way for the design of innovative therapeutic approaches and the implementation of prudent antibiotic stewardship practices to preserve the efficacy of current antibiotics and ensure a sustainable future for healthcare.

Epidemiology of multidrug-resistant zoonotic E. coli from beef processing and retail points in Delta State, Nigeria: Public health implications

Some sorbitol non-fermenting E. coli (SN-F E. coli) and all E. coli O157 are zoonotic. Contamination of beef with zoonotic E. coli at the processing or retail point is a significant public health problem. Despite the public health importance of these organisms, there is no published data on the prevalence and antimicrobial resistance (AMR) of zoonotic E. coli from Delta State, Nigeria. Consequently, this study determined the prevalence and AMR of SN-F E. coli and E. coli O157 isolates from meat contact surfaces at the processing and retail points in the study area. The isolation, biochemical and serological characterisations and AMR status of the isolates were performed following standard microbiological methods. Overall prevalence of SN-F E. coli and E. coli O157 were 13.8% (56/406) and 1.5% (6/406), respectively. Majority of the 56 SN-F E. coli (64.3%, 36/56) and all the six E. coli O157 (10.7%, 6/56) detected in this study were found at the meat processing points. Most of the SN-F E. coli were isolated at the slaughterhouse floor (31%), meat hooks (17.2%) and meat sellers' knives (17.2%). The SN-F E. coli exhibited greater AMR to ampicillin (67.9%), gentamycin (64.3%) and tetracycline (50%) than other antimicrobial agents tested. No isolate was resistant to aztreonam. All six E. coli O157 isolates were resistant to enrofloxacin. Overall, 23 AMR patterns, comprised 14 from meat processing points and nine from meat retailing points, were observed from the 56 antimicrobial-resistant SN-F E. coli isolates. All the six E. coli O157 and 73.2% (41/56) of the SN-F E. coli isolates were multidrug-resistant. An overall mean multiple antimicrobial resistance index of 0.6 was recorded. Multidrug-resistant zoonotic E. coli were detected at meat processing and retail points in Delta State, Nigeria. The findings warrant the adoption of One Health control approach, "farm to fork" principle of food safety and prudent use of antimicrobial agents in animal agriculture. These may help to limit beef contamination with multidrug-resistant zoonotic E. coli at the processing and retailing points, for public health safety.

Isolation, Genomic Characterization of Shigella prophage fPSFA that effectively infects multi-drug resistant Shigella isolates from the Indian Poultry Sector

Because of uncontrolled use of antibiotics, emergence of multidrug-resistant Shigella species poses a huge potential of zoonotic transfer from poultry sector. With increasing resistance to current antibiotics, there is a critical need to explore antibiotic alternatives. Using a Shigella flexneri reference strain, we isolated a novel fPSFA phage after inducing with mitomycin C. The phage was found to be stable for wide ranges of temperature -20 °C-65 °C and pH 3 to 11. fPSFA shows a latent period that ranges from 20 to 30 min and generation times of 50-60 min. The genome analysis of phage reveals two major contigs of 23788 bp and 23285 bp with 50.16 % and 39.33 % G + C content containing a total of 80 CDS and 2 tRNA genes. The phage belongs to Straboviridae family and lacks any virulence or antimicrobial resistance gene, thus making it a suitable candidate for treatment of drug-resistant infections. To confirm lytic ability of novel phage, we isolated 54 multidrug-resistant Shigella species from thirty-five poultry fecal samples that shows multiple antibiotic resistance index ranging from 0.15 to 0.75 (from 3 Indian states). The fPSFA showed lytic activity against multidrug-resistant Shigella isolates (73.08 %) (MARI≥0.50). The wide host ranges of fPSFA phage demonstrate its potential to be used as a biocontrol agent.

Detection of multidrug-resistant Campylobacter species from food-producing animals and humans in Nigeria: Public health implications and one health control measures

Antimicrobial-resistant thermophilic Campylobacter species (TCS) pose tremendous public health problems because they are zoonotic, difficult to treat and usually harboured by food-producing animals (FPAs). This study ascertained the phenotypic antimicrobial resistance (AMR) in 56 phenotypically identified TCS from slaughtered cattle, poultry, and humans in Enugu State, Nigeria. The presence of selected AMR and virulence genes harboured by the animal and human isolates were also detected and compared in 36 PCR-confirmed Campylobacter species. All the 56 TCS were multidrug-resistant as none were susceptible to ampicillin, penicillin-G, amoxicillin-clavulanic acid, cephalothin and metronidazole. The isolates were 92.9 %, 62.5 %, 92.9 %, 42.9 %, 26.8 %, 25 %, 28.6 %, 53.7 %, 30.1 %, 32.1 % and 55.4 % resistant to ceftriaxone, nalidixic acid, cefotaxime, enrofloxacin, ciprofloxacin, streptomycin, gentamycin, erythromycin, azithromycin, chloramphenicol and tetracycline, respectively. The top four most effective classes of antimicrobials were aminoglycosides > macrolides > amphenicol > fluoroquinolones. The AMR genes detected and the percentage of the isolates that harboured them were: aadE-1 (33.3 %), aphA-3-1 (36.1 %), tetO (44.4%), Blaoxa-61 (61.1 %) and the multidrug efflux pump, cmeB (86.1%). Virulence genes detected and the corresponding percentage of TCS that harboured them were: cdtB (61.1 %), flaA (47.2 %), ciaB (38.9 %), and pldA (38.9 %). The cmeB was significantly detected in animal isolates (p = 0.018, OR = 5.1, CI = 0.7-6.6) while BlaOXA-61 predominated in human isolates (p = 0.019, OR = 6.2). Likewise, ciaB virulence gene was mostly detected (p = 0.019, OR = 6.4, CI = 1.3-25) in animal isolates. The findings underscore the roles of FPAs in the zoonotic dissemination of Campylobacter-associated AMR and virulence genes in the study area. This warrants the adoption of One Health control strategies to limit spread of the multidrug-resistant zoonotic Campylobacter species.

Prevalence of Salmonella species and factors associated with contamination of mechanically recovered poultry meat imported into South Africa, 2016-2017

Background and Aim

Mechanically recovered meat (MRM) products have been linked to outbreaks of human salmonellosis. However, no studies have investigated the prevalence of Salmonella species in MRM products in South Africa despite the products being imported. Therefore, this study aimed to estimate the prevalence and factors associated with Salmonella spp. contamination of mechanically recovered poultry meat (MRPM) imported into South Africa.

Materials and Methods

This study used secondary data of MRPM consignments imported through a port entry into South Africa from May 2016 to December 2017. Crude and factor-specific proportions of Salmonella positive MRPM and their 95% confidence intervals were calculated. A logistic regression model was used to assess the association among country, season, importer, year, and MRPM Salmonella status.

Results

A total of 8127 MRPM consignments were imported. Seventeen percentages (17.18%, 985/5733) of consignments tested positive for Salmonella species and only 364 isolates were serotyped. Salmonella Heidelberg (73.90%, 269/364) was the most common serotype followed by Salmonella Infantis (6.59%, 24/364), Salmonella Salamae (4.67%, 17/364), and Salmonella Schwarzengrund (3.57%, 13/364). The odds of a consignment testing positive for Salmonella spp. was higher among consignments from country-B (Odds Ratio [OR]: 3.958, p < 0.0001) compared to "All others." The odds of testing positive for Salmonella were also higher among consignments imported in autumn (OR: 1.488, p < 0.0001) but lower among those imported in spring (OR: 0.767, p = 0.0004) and summer (OR: 0.843, p < 0.0001) when compared to the winter season. Consignments imported in 2016 compared to 2017 were 1.563 times (p < 0.0001) as likely to test positive for a Salmonella species.

Conclusion

Salmonella species were reported in MRPM consignments in this study with Salmonella Heidelberg being the most common serotype. Furthermore, some Salmonella serotypes reported in this study have been implicated in foodborne disease outbreaks. Country of origin, season, and year of importation were significantly associated with the odds of a consignment testing positive for Salmonella species.