Extended-spectrum β-lactamases producing multidrug resistance Escherichia coli, Salmonella and Klebsiella pneumoniae in pig population of Assam and Meghalaya, India

In Silico Detection of Integrons and Their Relationship with Resistance Phenotype of Salmonella Isolates from a Brazilian Pork Production Chain

The pork production chain is an important reservoir of antimicrobial resistant bacteria. This study identified and characterized integrons in Salmonella isolates from a Brazilian pork production chain and associate them with their antibiotic resistance pattern. A total of 41 whole-genome sequencing data of nontyphoidal Salmonella were analyzed using PlasmidSPAdes and IntegronFinder software. Nine isolates (21.9%) had some integrons identified (complete and/or incomplete). Six complete class 1 integrons were found, with streptomycin resistance genes (aadA1, aadA2) alone or downstream of a trimethoprim resistance gene (dfrA1, dfrA12), and some also containing resistance genes for sulfonamides (sul1, sul3) and chloramphenicol (cmlA1). Class 2 integron was detected in only one isolate, containing dfrA1-sat2-aadA1 gene cassettes. Five isolates harbored CALINs-clusters attC but lacking integrases-with antimicrobial resistance genes typically found in integron structures. In all, integrons were observed among four serotypes: Derby, Bredeney, Panama, and monophasic var. Typhimurium I 4,[5],12:i:-. The association of integrons with antibiotic resistance phenotype showed that these elements were predominantly identified in multidrug resistance isolates, and six of the seven gentamicin-resistant isolates had integrons. So, surveillance of integrons in Salmonella should be performed to identify the potential for the spread of antimicrobial resistance genes among bacteria.

A Duplex PCR Assay for Rapid Detection of Klebsiella pneumoniae and Chryseobacterium in Large Yellow Croaker Fish

Both Klebsiella pneumoniae and Chryseobacterium cause an increasing number of diseases in fish, resulting in great economic losses in aquaculture. In addition, the disease infected with Klebsiella pneumoniae or Chryseobacterium exhibited the similar clinical symptoms in aquatic animals. However, there is no effective means for the simultaneous detection of co-infection and discrimination them for these two pathogens. Here, we developed a duplex polymerase chain reaction (PCR) method based on the outer membrane protein A (ompA) gene of Klebsiella pneumoniae and Chryseobacterium. The specificity and validity of the designed primers were confirmed experimentally using simplex PCR. The expected amplicons for Klebsiella pneumoniae and Chryseobacterium had a size of 663 and 1404 bp, respectively. The optimal condition for duplex PCR were determined to encompass a primer concentration of 0.5 μM and annealing temperature of 57°C. This method was analytical specific with no amplification being observed from the genomic DNA of Escherichia coli, Vibrio harveyi, Pseudomonas plecoglossicida, Aeromonas hydrophila and Acinetobacter johnsonii. The limit of detection was estimated to be 20 fg of genomic DNA for Chryseobacterium and 200 fg for Klebsiella pneumoniae, or 100 colony-forming units (CFU) of bacterial cells in both cases. The duplex PCR was capable of simultaneously amplifying target fragments from genomic DNA extracted from the bacteria and fish liver. For practical validation of the method, 20 diseased fish were collected from farms, among which 4 samples were PCR-positive for Klebsiella pneumoniae and Chryseobacterium. The duplex PCR method developed here is time-saving, specific, convenient, and may prove to be an invaluable tool for molecular detection and epidemiological investigation of Klebsiella pneumoniae and Chryseobacterium in the field of aquaculture.

Development and application of an indirect ELISA and nested PCR for the epidemiological analysis of Klebsiella pneumoniae among pigs in China

Introduction

Klebsiella pneumoniae (K. pneumoniae) is an important opportunistic and zoonotic pathogen which is associated with many diseases in humans and animals. However, the pathogenicity of K. pneumoniae has been neglected and the prevalence of K. pneumoniae is poorly studied due to the lack of rapid and sensitive diagnosis techniques.

Methods

In this study, we infected mice and pigs with K. pneumoniae strain from a human patient. An indirect ELISA was established using the KHE protein as the coating protein for the detection of K. pneumoniae specific antibody in clinical samples. A nested PCR method to detect nuclei acids of K. pneumoniae was also developed.

Results

We showed that infection with K. pneumoniae strain from a human patient led to mild lung injury of pigs. For the ELISA, the optimal coating concentration of KHE protein was 10 µg/mL. The optimal dilutions of serum samples and secondary antibody were 1:100 and 1:2500, respectively. The analytical sensitivity was 1:800, with no cross-reaction between the coated antigen and porcine serum positive for antibodies against other bacteria. The intra-assay and inter-assay reproducibility coefficients of variation are less than 10%. Detection of 920 clinical porcine serum samples revealed a high K. pneumoniae infection rate by established indirect ELISA (27.28%) and nested PCR (19.13%). Moreover, correlation analysis demonstrated infection rate is positively correlated with gross population, Gross Domestic Product (GDP), and domestic tourists.

Discussion

In conclusion, K. pneumoniae is highly prevalent among pigs in China. Our study highlights the role of K. pneumoniae in pig health, which provides a reference for the prevention and control of diseases associated with K. pneumoniae.

Extended-Spectrum β-Lactamases (ESBL): Challenges and Opportunities

The rise of antimicrobial resistance, particularly from extended-spectrum β-lactamase producing Enterobacteriaceae (ESBL-E), poses a significant global health challenge as it frequently causes the failure of empirical antibiotic therapy, leading to morbidity and mortality. The E. coli- and K. pneumoniae-derived CTX-M genotype is one of the major types of ESBL. Mobile genetic elements (MGEs) are involved in spreading ESBL genes among the bacterial population. Due to the rapidly evolving nature of ESBL-E, there is a lack of specific standard examination methods. Carbapenem has been considered the drug of first choice against ESBL-E. However, carbapenem-sparing strategies and alternative treatment options are needed due to the emergence of carbapenem resistance. In South Asian countries, the irrational use of antibiotics might have played a significant role in aggravating the problem of ESBL-induced AMR. Superbugs showing resistance to last-resort antibiotics carbapenem and colistin have been reported in South Asian regions, indicating a future bleak picture if no urgent action is taken. To counteract the crisis, we need rapid diagnostic tools along with efficient treatment options. Detailed studies on ESBL and the implementation of the One Health approach including systematic surveillance across the public and animal health sectors are strongly recommended. This review provides an overview of the background, associated risk factors, transmission, and therapy of ESBL with a focus on the current situation and future threat in the developing countries of the South Asian region and beyond.

Meta-Analysis of the Prevalence of Porcine Zoonotic Bacterial Pathogens in India: A 13-Year (2010-2023) Study

The presence of bacterial pathogens such as Brucella spp., Clostridium spp., E. coli, Listeria monocytogenes, Salmonella spp., Staphylococcus spp., and Streptococcus suis not only hampers pig production but also carries significant zoonotic implications. The present study aims to conduct a comprehensive meta-analysis spanning over 13 years (2010-2023) to ascertain the prevalence of these zoonotic bacterial pathogens in Indian pig populations. The study seeks to synthesize data from diverse geographic regions within India and underscores the relevance of the One Health framework. A systematic search of electronic databases was meticulously performed. Inclusion criteria encompassed studies detailing zoonotic bacterial pathogen prevalence in pigs within India during the specified timeframe. Pertinent information including authors, publication year, geographical location, sampling techniques, sample sizes, and pathogen-positive case counts were meticulously extracted. The meta-analysis of zoonotic bacterial pathogens in Indian pig populations (2010-2023) unveiled varying prevalence rates: 9% Brucella spp., 22% Clostridium spp., 19% E. coli, 12% Listeria monocytogenes, 10% Salmonella spp. and Streptococcus suis, and 24% Staphylococcus spp. The application of random effects further revealed additional variability: 6% Brucella spp., 23% Clostridium spp., 24% E. coli, 14% Listeria monocytogenes, 10% Salmonella spp. and Streptococcus suis, and 35% Staphylococcus spp. Notably, the observed heterogeneity (I2) varied significantly from 87% to 99%. The meta-analysis findings underscore the pervasive nature of these diseases throughout India's pig populations, accentuating the substantial impact of these pathogens on pig health and the potential for zoonotic transmission. The present study reinforces the importance of the adoption of a comprehensive One Health approach that acknowledges the intricate interplay between animal, human and environmental health.

Detection of extended spectrum beta-lactamase genes in strains of Escherichia coli and Klebsiella pneumoniae isolated from recreational water and tertiary hospital waste water in Zaria, Nigeria

Extended spectrum beta-lactamase (ESBL) producing bacteria pose a severe health risk globally. This study focused on detecting ESBL genes in Escherichia coli and Klebsiella pneumoniae isolated from a recreational water source and the waste water from a tertiary hospital in Zaria, Kaduna State, Nigeria. The isolates (twenty-two) were screened phenotypically for extended spectrum beta lactamase production using the double disk synergy test. Of the isolates, 13 (59.1%) were E. coli, while 9 (40.9%) were Klebsiella pneumoniae; 17 (77.3%) were isolated from the waste water and 5 (22.7%) were isolated from the recreational water. Six (27.2%) of them showed ESBL production phenotypically; however, PCR amplification of the ESBL genes showed that only five of them had at least one of the genes. The presence of ESBL bacteria in hospital waste water and surface waters highlights that water matrices are important routes of transmission of antibiotic resistant bacteria.

Antimicrobial, Multi-Drug and Colistin Resistance in Enterobacteriaceae in Healthy Pigs in the Greater Accra Region of Ghana, 2022: A Cross-Sectional Study

There is little published information on antimicrobial resistance (AMR) in animals in Ghana. We determined the prevalence and factors associated with AMR, multi-drug resistance (MDR-resistance to ≥3 antimicrobial classes) and colistin resistance in Enterobacteriaceae in healthy pigs in Accra, Ghana. Rectal swabs obtained from the pigs on 20 farms from January to March 2022, were examined for Escherichia coli, Enterobacter spp. and Klebsiella pneumoniae. AMR was determined using standard microbiological techniques and the mcr-1 gene detected through molecular analysis. Enterobacteriaceae were isolated from 197 of 200 pigs: these comprised 195 E. coli isolates, 38 Enterobacter spp. and 3 K. pneumoniae, either singly or combined. Over 60% of E. coli were resistant to tetracycline, with 27% and 34% being resistant to amoxicillin/clavulanic acid and ampicillin, respectively; 23% of E. coli and 5% of Enterobacter spp. exhibited MDR phenotypes. Phenotypic colistin resistance was found in 8% of E. coli and Enterobacter spp., with the mcr-1 gene detected in half. Our study findings should be incorporated into on-going AMR, MDR and colistin resistance surveillance programs in Ghana. We further advocate for tailored-specific education for pig farmers on animal antimicrobial use and for strengthened regulatory policy on antimicrobial usage and monitoring in the animal production industry.

Antimicrobial Susceptibility and Frequency of bla and qnr Genes in Salmonella enterica Isolated from Slaughtered Pigs

Salmonella enterica is known as one of the most common foodborne pathogens worldwide. While salmonellosis is usually self-limiting, severe infections may require antimicrobial therapy. However, increasing resistance of Salmonella to antimicrobials, particularly fluoroquinolones and cephalosporins, is of utmost concern. The present study aimed to investigate the antimicrobial susceptibility of S. enterica isolated from pork, the major product in Philippine livestock production. Our results show that both the qnrS and the bla_TEM antimicrobial resistance genes were present in 61.2% of the isolates. While qnrA (12.9%) and qnrB (39.3%) were found less frequently, co-carriage of bla_TEM and one to three qnr subtypes was observed in 45.5% of the isolates. Co-carriage of bla_TEM and bla_CTX-M was also observed in 3.9% of the isolates. Antimicrobial susceptibility testing revealed that the majority of isolates were non-susceptible to ampicillin and trimethoprim/sulfamethoxazole, and 13.5% of the isolates were multidrug-resistant (MDR). MDR isolates belonged to either O:3,10, O:4, or an unidentified serogroup. High numbers of S. enterica carrying antimicrobial resistance genes (ARG), specifically the presence of isolates co-carrying resistance to both β-lactams and fluoroquinolones, raise a concern on antimicrobial use in the Philippine hog industry and on possible transmission of ARG to other bacteria.

A One Health Review of Community-Acquired Antimicrobial-Resistant Escherichia coli in India

Antimicrobial resistance (AMR) threatens to undermine nearly a century of progress since the first use of antimicrobial compounds. There is an increasing recognition of the links between antimicrobial use and AMR in humans, animals, and the environment (i.e., One Health) and the spread of AMR between these domains and around the globe. This systematic review applies a One Health approach-including humans, animals, and the environment-to characterize AMR in Escherichia coli in India. E. coli is an ideal species because it is readily shared between humans and animals, its transmission can be tracked more easily than anaerobes, it can survive and grow outside of the host environment, and it can mobilize AMR genes more easily than other intestinal bacteria. This review synthesized evidence from 38 studies examining antimicrobial-resistant E. coli (AR-E) across India. Studies of AR-E came from 18 states, isolated from different sample sources: Humans (n = 7), animals (n = 7), the environment (n = 20), and combinations of these categories, defined as interdisciplinary (n = 4). Several studies measured the prevalence of AMR in relation to last-line antimicrobials, including carbapenems (n = 11), third-generation cephalosporins (n = 18), and colistin (n = 4). Most studies included only one dimension of the One Health framework, highlighting the need for more studies that aim to characterize the relationship of AMR across different reservoirs of E. coli.

Screening of Epidemiologically Significant Mechanisms of Antibiotics to β-Lactams in Enterobacteriaceae - Pathogens of Zoonoses

Among the acquired mechanisms of resistance to antibiotics of microorganisms, the production of beta-lactamases, enzymes that inactivate penicillins, cephalosporins, carbapenems, and monobactams, is widespread. Most often, such beta-lactamases, in particular ESBL (extended-spectrum beta-lactamases), are capable of destroying III and IV generations of cephalosporins. One of the important ESBL producers is Escherichia coli and, to a lesser extent, Salmonella enteritidis, which are clinically significant in animals and humans. The purpose of the study was to screen ESBL DDM using cephalosporin markers and screening of mobile extrachromosomal factors of bacterial heredity – plasmids (potentially dangerous factors of genetic transport) in isolates of E. coli and S. enteritidis, polyresistant to aminoderms, from environmental objects, patho- and biological material, raw materials and products of animal origin. Results of our studies have shown the level of their distribution among animals, poultry, since from 13 field isolates of E. coli isolated from the milk of cows with mastitis and pathological material from pigs, ESBL production was found in 3 strains (23.1%) and from 18 field isolates of S. enteritidis isolated from pathological material from poultry, ESBL production was found in 2 strains (11.1%). Based on the results of molecular genetics studies, the presence of resistance plasmids (R-plasmids) in 9 field E. coli isolates was confirmed, 4 of which produced acquired beta-lactamases, incl. ESBL and 8 field isolates of S. enteritidis, 7 of which confirmed the presence of acquired carbapenemases.

Characterization of Extended-Spectrum Cephalosporin (ESC) Resistance in Salmonella Isolated from Chicken and Identification of High Frequency Transfer of blaCMY-2 Gene Harboring Plasmid In Vitro and In Vivo

Simple Summary

The prevalence of extended-spectrum cephalosporin (ESC)-resistant Salmonella is of great concern, as these strains with the same β-lactamase (bla) genes were found in human and poultry. The objective is to characterize ESC-resistant Salmonella isolated from chicken and to determine the transferability of β-lactamase gene-harboring plasmid in vitro and in vivo. ESC resistance genes in Salmonella isolated from chickens and presented a comprehensive analysis of the highly frequent transfer of the bla_CMY-2 gene in vitro and in vivo. In addition, this study has demonstrated the ease with which a bla_CMY-2 gene-harboring plasmid can be rapidly transferred between Salmonella and pathogenic E. coli within the intestinal tracts of mice, even without antimicrobial selective pressure. Given the potential risk of the frequent transfer of the bla_CMY-2 gene via the food chain to the human digestive tract, the molecular mechanism involved in the dissemination and maintenance of ESC resistance genes should be studied as further research in greater detail, and enhanced surveillance should be implemented to prevent the widespread of ESC resistant strains.

Abstract

A total of 136 Salmonella isolates from chicken feces and meat samples of the top 12 integrated chicken production companies throughout Korea were collected. Among the 17 ESC-resistant Salmonella; bla_CTX-M-15 was the most prevalent gene and two strains carried bla_TEM-1/bla_CTX-M-15 and bla_CMY-2, respectively. The transferable bla_CTX-M-15 gene was carried by IncFII plasmid in three isolates and the bla_CMY-2 gene carried by IncI1 plasmid in one isolate. bla_CMY-2 gene-harboring strain was selected as the donor based on the high frequency of bla_CMY-2 gene transfer in vitro and its transfer frequencies were determined at 10⁻³ transconjugants per recipient. The transfer of bla_CMY-2 gene-harboring plasmid derived from chicken isolate into a human pathogen; enteroinvasive Escherichia coli (EIEC), presented in mouse intestine with about 10⁻¹ transfer frequency without selective pressure. From the competition experiment; bla_CMY-2 gene-harboring transconjugant showed variable fitness burden depends on the parent strains. Our study demonstrated direct evidence that the bla_CMY-2 gene harboring Salmonella from chicken could frequently transfer its ESC-resistant gene to E. coli in a mouse intestine without antimicrobial pressure; resulting in the emergence of multidrug resistance in potentially virulent EIEC isolates of significance to human health; which can increase the risk of therapeutic inadequacy or failures.

Higher prevalence of multidrug-resistant extended-spectrum β-lactamases producing Escherichia coli in unorganized pig farms compared to organized pig farms in Mizoram, India

Aim

The present study was conducted to record the prevalence of multidrug-resistant (MDR), extended-spectrum β-lactamases (ESBLs) producing Escherichia coli from pig population of organized and unorganized farms of Mizoram and to record the presence of ESBLs, non-ESBLs, and integrons.

Materials and Methods

Fecal samples were collected from pigs under organized (n=40) and unorganized (n=58) farms of Mizoram. Samples were processed for isolation and identification of E. coli by conventional techniques, BD Phoenix™ automated bacterial system, and polymerase chain reaction (PCR) based confirmatory test. All the isolates were subjected to antimicrobial sensitivity test by disk diffusion assay and ESBLs production by double-disk synergy test (DDST). The ESBLs producing isolates were subjected to PCR for determination of ESBLs genes and all the isolates were screened for non-ESBLs genes and integrons by PCR.

Results

A total of 258 E. coli was isolated and identified from organized (n=120) and unorganized farms (n=138). Majority of the E. coli isolates exhibited high level of resistance against amoxicillin (Ax) (81.78%), cefalexin (85.42%), co-trimoxazole (50.78%), sulfafurazole (69.38%), tetracycline (65.89%), and trimethoprim (TR) (51.94%). Statistically highly significant (p<0.01) variations in resistance among the isolates from organized and unorganized farms were recorded in case of Ax, ampicillin, cephalexin, ciprofloxacin, co-trimoxazole, gentamicin, piperacillin, and TR. By DDST, 65.89% isolates were recorded as ESBLs producer, of which 82/120 (68.33%) and 88/138 (63.77%) were from organized and unorganized farms, respectively. A total of 29/258 (11.24%) isolates were positive for at least one ESBLs gene. bla_TEM was most frequently (9.69%) gene, followed by bla_CTX -M (5.04%) and bla_CMY (0.78%). Altogether, 6 (5.00%), 4 (3.33%), and 2 (1.67%) isolates from the organized farms were positive for bla_CTX-M , bla_TEM , and bla_CMY genes, respectively. Similarly, 21 (15.22%) and 7 (5.07%) isolates from the unorganized farms were positive for bla_TEM and bla_CTX-M genes, respectively. None of them were positive for bla_SHV genes. Altogether 57 (22.09%), 9 (3.49%), 66 (25.58%), 78 (30.23%), 21 (8.14%), and 18 (6.98%) isolates were positive for tetA, tetB, sul1, sul2, aadA, and dfrla genes, respectively. The prevalence of non-ESBLs genes was higher in the E. coli isolates from the unorganized farms than organized farms.

Conclusion

MDR and ESBLs producing E. coli are circulating among the pigs and their environment in Mizoram. Pigs under unorganized farms exhibited higher level of resistance against majority of the antimicrobials, including third-generation cephalosporins, which might be an indication of overuse or misuse of antibiotics under the unorganized piggery sectors in Mizoram.

Presence and Transfer of Antimicrobial Resistance Determinants in Escherichia coli in Pigs, Pork, and Humans in Thailand and Lao PDR Border Provinces

This study aimed to investigate antimicrobial resistance (AMR) characteristics of Escherichia coli isolates from pig origin (including pigs, pig carcass, and pork) and humans in Thailand and Lao People's Democratic Republic (PDR) border provinces. The majority of the E. coli isolates from Thailand (69.7%) and Lao PDR (63.3%) exhibited multidrug resistance. Class 1 integrons with resistance gene cassettes were common (n = 43), of which the most predominant resistance gene cassette was aadA1. The percentage of extended-spectrum beta-lactamase (ESBL) producers was 3.4 in Thailand and 3.2 in Lao PDR. The ESBL genes found were bla_CTX-M14, bla_CTX-M27, and bla_CTX-M55, of which bla_CTX-M55 was the most common (58.6%). Ser-83-Leu and Asp-87-Asn were the predominant amino acid changes in GyrA of ciprofloxacin-resistant isolates. Twenty-two percent of all isolates were positive for qnrS. Class 1 integrons carrying aadA1 from pigs (n = 1) and ESBL genes (bla_CTX-M55 and bla_CTX-M14) from pigs (n = 2), pork (n = 1), and humans (n = 7) were located on conjugative plasmids. Most plasmids (29.3%) were typed in the IncFrepB group. In conclusion, AMR E. coli are common in pig origin and humans in these areas. The findings confirm AMR as One Health issue, and highlight the need for comprehensive and unified collaborations within and between sectors on research and policy.