Antibiotic Resistance Profiles and Molecular Characteristics of Extended-Spectrum Beta-Lactamase (ESBL)-Producing Escherichia coli and Klebsiella pneumoniae Isolated From Shrimp Aquaculture Farms in Kerala, India

High prevalence and genetic diversity of multidrug-resistant and extended-spectrum ß-lactamase-producing Escherichia coli and Klebsiella pneumoniae in mothers and neonates in a Cameroonian labor ward

BACKGROUND

Escherichia coli and Klebsiella pneumoniae rank among the primary bacterial culprits in neonatal infections and fatalities in sub-Saharan Africa. This study characterized the phenotypic and genotypic features of E coli and K pneumoniae in a labor ward in Yaoundé, Cameroon.

METHODS

A prospective and cross-sectional study spanning 5months, from February 21, 2022 to June 30, 2022. Rectovaginal swabs were obtained from expectant mothers, and nasopharyngeal swabs were collected from their babies. Hand swabs of health care workers and environmental samples were also collected. The samples were cultured on eosin methylene blue agar. Extended-spectrum ß-lactamase (ESBL) production was assessed using CHROMAgar ESBL and the double-disk synergy test. A polymerase chain reaction was employed to detect ß-lactamase genes.

RESULTS

A total of 93 mothers and 90 neonates were collected. Almost all pregnant women (90%) were colonized by one or more multidrug-resistant (MDR) isolates with 58% being concomitantly ESBL producers. Altogether, 14 of 22 (64%) neonates were colonized by MDR isolates, while out of the 5 workers positive to Enterobacterales, all were colonized by MDR isolates. E coli predominated in pregnant women (55%) and neonates (73%), while K pneumoniae (83%) predominated in health care workers. The blaCTX-M (75%) was the leading ß-lactamase gene detected.

CONCLUSIONS

Our study suggests that drug-resistant E coli and K pneumoniae are circulating at high prevalence in the labor ward in Yaoundé and emphasizes the necessity for effective infection prevention and control along with antimicrobial stewardship measures.

Review: Antimicrobial resistance of Klebsiella pneumoniae isolated from poultry, cattle and pigs

Klebsiella pneumoniae, common pathogenic bacteria, cause dangerous infectious diseases in animals and humans. Klebsiella pneumoniae have numerous resistance mechanisms to antibacterials and the frequency of resistant K. pneumoniae isolates increases, making treatment of K. pneumoniae-induced infections difficult. Farm animals are a possible source of antibacterial resistant K. pneumoniae. The aim of this literature review (2018-2024) was to evaluate the antibacterial resistance of K. pneumoniae isolated from poultry, cattle and pigs in various countries. The analysis shows that farm animals are an important source of antibacterial-resistant and multidrug-resistant K. pneumoniae and that resistance patterns differ among antibacterial groups, animals and locations. In poultry, high resistance to penicillins (91%), III and IV generation cephalosporins (> 50%) occurred, and low to carbapenems (5%) and polymyxins (6%). In cattle, high resistance to sulphonamides (76%), IV generation cephalosporins, macrolides and lincosamides, and penicillins occurred (> 50%), and low to carbapenems (10%) and polymyxins (1%). Isolates from pigs showed high resistance to I and II-generation cephalosporins, I-generation fluoroquinolones, macrolides and lincosamides, tetracyclines (> 50%) and carbapenems (> 20%), and low to polymyxins (5%). The highest resistance rates to most antibacterial groups occurred in pigs, and in Africa and Asia, while the lowest in cattle, and in North and South America. Particularly, the relatively high resistance of K. pneumoniae to carbapenems and polymyxins in Africa poses a threat to animal and human health as these antibiotics are the last resort therapeutics used to treat severe infections. Different rates of K. pneumoniae resistance to antibacterials among isolates from farm animals probably result from differences in the treatment of each animal group with various antibacterial agents and different regimes of their use in various locations.

Analysis of Antibiotic Resistance Genes (ARGs) across Diverse Bacterial Species in Shrimp Aquaculture

There is little information available on antibiotic resistance (ABR) within shrimp aquaculture environments. The aim of this study was to investigate the presence of antibiotic resistance genes (ARGs) in shrimp farming operations in Atacames, Ecuador. Water samples (n = 162) and shrimp samples (n = 54) were collected from three shrimp farming operations. Samples were cultured and a subset of isolates that grew in the presence of ceftriaxone, a third-generation cephalosporin, were analyzed using whole-genome sequencing (WGS). Among the sequenced isolates (n = 44), 73% of the isolates contained at least one ARG and the average number of ARGs per isolate was two, with a median of 3.5 ARGs. Antibiotic resistance genes that confer resistance to the β-lactam class of antibiotics were observed in 65% of the sequenced isolates from water (20/31) and 54% of the isolates from shrimp (7/13). We identified 61 different ARGs across the 44 sequenced isolates, which conferred resistance to nine antibiotic classes. Over half of all sequenced isolates (59%, n = 26) carried ARGs that confer resistance to more than one class of antibiotics. ARGs for certain antibiotic classes were more common, including beta-lactams (26 ARGs); aminoglycosides (11 ARGs); chloramphenicol (three ARGs); and trimethoprim (four ARGs). Sequenced isolates consisted of a diverse array of bacterial orders and species, including Escherichia coli (48%), Klebsiella pneumoniae (7%), Aeromonadales (7%), Pseudomonadales (16%), Enterobacter cloacae (2%), and Citrobacter freundii (2%). Many ARGs were shared across diverse species, underscoring the risk of horizontal gene transfer in these environments. This study indicated the widespread presence of extended-spectrum β-lactamase (ESBL) genes in shrimp aquaculture, including blaCTX-M, blaSHV, and blaTEM genes. Increased antibiotic resistance surveillance of shrimp farms and identification of aquaculture operation-level risk factors, such as antibiotic use, will likely be important for mitigating the spread of ARGs of clinical significance.

Prevalence of opportunistic pathogens and anti-microbial resistance in urban aquaculture ponds

Bacterial antimicrobial resistance (AMR) has emerged as a significant concern worldwide. The microbial community profile and potential AMR level in aquaculture ponds are often undervalued and attract less attention than other aquatic environments. We used amplicon and metagenomic shotgun sequencing to study microbial communities and AMR in six freshwater polyculture ponds in rural and urban areas of Bangladesh. Amplicon sequencing revealed different community structures between rural and urban ponds, with urban ponds having a higher bacterial diversity and opportunistic pathogens including Streptococcus, Staphylococcus, and Corynebacterium. Despite proteobacterial dominance, Firmicutes was the most interactive in the community network, especially in the urban ponds. Metagenomes showed that drug resistance was the most common type of AMR found, while metal resistance was only observed in urban ponds. AMR and metal resistance genes were found mainly in beta and gamma-proteobacteria in urban ponds, while AMR was found primarily in alpha-proteobacteria in rural ponds. We identified potential pathogens with a high profile of AMR and metal resistance in urban aquaculture ponds. As these ponds provide a significant source of protein for humans, our results raise significant concerns for the environmental sustainability of this food source and the dissemination of AMR into the food chain.

Skin and soft tissue infection suspiciously caused by Klebsiellapneumoniae in an aquaculture worker: A case report

Skin and soft tissue infections (SSTIs), which are mainly caused by Gram-positive cocci existing on the skin surface, are more common than those caused by Gram-negative bacteria; however, the role of Gram-negative bacteria as emerging pathogens in SSTIs cannot to be ignored. Klebsiella pneumoniae is an opportunistic pathogenic bacterium that mainly inhabits the respiratory and intestinal tracts of humans and animals, as well as the environment, including aquaculture farms. This bacterium can cause multiple infections in humans and animals. The present study reports the case of a SSTI which was suspected to be caused by Klebsiella pneumoniae in a 74-year-old farmer with venous thrombosis. The patient had exposed his four bare limbs to the farmed shrimps and shrimp pond routinely. Pustule and skin ulcers were observed on both the legs of the patient. After receiving anti-infection therapy, the SSTI was almost completely resolved on day 9 and the patient was then discharged.

Whole-Genome Sequence Analysis of Antibiotic Resistance, Virulence, and Plasmid Dynamics in Multidrug-Resistant E. coli Isolates from Imported Shrimp

We analyzed antimicrobial resistance and virulence traits in multidrug-resistant (MDR) E. coli isolates obtained from imported shrimp using whole-genome sequences (WGSs). Antibiotic resistance profiles were determined phenotypically. WGSs identified key characteristics, including their multilocus sequence type (MLST), serotype, virulence factors, antibiotic resistance genes, and mobile elements. Most of the isolates exhibited resistance to gentamicin, streptomycin, ampicillin, chloramphenicol, nalidixic acid, ciprofloxacin, tetracycline, and trimethoprim/sulfamethoxazole. Multilocus sequence type (MLST), serotype, average nucleotide identity (ANI), and pangenome analysis showed high genomic similarity among isolates, except for EC15 and ECV01. The EC119 plasmid contained a variety of efflux pump genes, including those encoding the acid resistance transcriptional activators (gadE, gadW, and gadX), resistance-nodulation-division-type efflux pumps (mdtE and mdtF), and a metabolite, H1 symporter (MHS) family major facilitator superfamily transporter (MNZ41_23075). Virulence genes displayed diversity, particularly EC15, whose plasmids carried genes for adherence (faeA and faeC-I), invasion (ipaH and virB), and capsule (caf1A and caf1M). This comprehensive analysis illuminates antimicrobial resistance, virulence, and plasmid dynamics in E. coli from imported shrimp and has profound implications for public health, emphasizing the need for continued surveillance and research into the evolution of these important bacterial pathogens.

Antibacterial effectiveness of trans-cinnamaldehyde against foodborne Enterobacteriaceae and its adjuvant effect with gentamicin

The Enterobacteriaceae family is recognized as a primary group of Gram-negative pathogens responsible for foodborne illnesses and is frequently associated with antibiotic resistance. The present study explores the natural-based compound trans-cinnamaldehyde (TC) against drug-resistant Enterobacteriaceae and its synergism with gentamicin (GEN) to address this issue. The research employs three strains of Escherichia coli, Klebsiella pneumoniae, and Enterobacter cloacae, previously isolated from shrimp. The antibacterial activity was evaluated by the disk diffusion method, microdilution test, kinetics of growth, and time-kill curve. In addition, the synergistic effect between TC/GEN was investigated by checkerboard assay. All strains showed sensitivity to TC with an inhibition zone diameter > 35 mm. The TC showed inhibitory and bactericidal action in the most tested bacteria around 625 μg/mL. Sub-inhibitory amounts (1/2 and 1/4 MIC) of TC interfered with the growth kinetics by lag phase extension and decreased the log phase. Time-kill curves show a reduction of viable cells after the first hour of TC treatment at bactericidal concentrations. The synergistic effect between TC/GEN was observed for E. coli and E. cloacae strains with FICi ranging from 0.15 to 0.50. These findings, therefore, suggest TC as a promising alternative in the fight against drug-resistant Enterobacteriaceae that can cause foodborne illnesses.

The CRISPR/Cas system as an antimicrobial resistance strategy in aquatic ecosystems

With the growing population, demand for food has dramatically increased, and fisheries, including aquaculture, are expected to play an essential role in sustaining demand with adequate quantities of protein and essential vitamin supplements, employment generation, and GDP growth. Unfortunately, the incidence of emerging/re-emerging AMR pathogens annually occurs because of anthropogenic activities and the frequent use of antibiotics in aquaculture. These AMR pathogens include the WHO's top 6 prioritized ESKAPE pathogens (nosocomial pathogens: Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.), extended-spectrum beta lactases (ESBLs) and carbapenemase-producing E. coli, which pose major challenges to the biomagnification of both nonnative and native antibiotic-resistant bacteria in capture and cultured fishes. Although implementing the rational use of antibiotics represents a promising mitigation measure, this approach is practically impossible due to the lack of awareness among farmers about the interplay between antimicrobial use and the emergence of antimicrobial resistance (AMR). Nevertheless, to eradicate these 'superbugs,' CRISPR/Cas (clustered regularly interspersed short palindromic repeats/CRISPR associate protein) has turned out to be a novel approach owing to its ability to perform precise site-directed targeting/knockdown/reversal of specific antimicrobial resistance genes in vitro and to distinguish AMR-resistant bacteria from a plethora of commensal aquatic bacteria. Along with highlighting the importance of virulent multidrug resistance genes in bacteria, this article aims to provide a holistic picture of CRISPR/Cas9-mediated genome editing for combating antimicrobial-resistant bacteria isolated from various aquaculture and marine systems, as well as insights into different types of CRISPR/Cas systems, delivery methods, and challenges associated with developing CRISPR/Cas9 antimicrobial agents.

Prevalence of antimicrobial resistance, biofilm formation, efflux pump activity, and virulence capabilities in multi-drug-resistant Klebsiella pneumoniae isolated from freshwater fish farms

The present study aimed to determine the antibiotic resistance, underlying mechanisms, antibiotic residues, and virulence genes involved in 32 multi-drug-resistant Klebsiella pneumoniae isolates from freshwater fishes in Andhra Pradesh, India. Antibiogram studies revealed that all isolates were multi-drug-resistant, harbored tetA (96.8%), tetC (59.3%), tetD (71.9%), nfsA (59.3%), nfsB (53.1%), sul2 (68.7%), qnrC (43.7%), qnrD (50%), blaSHV (75%), blaTEM (68.7%), and blaCTX-M (93.7%) genes. Multiple antibiotic resistance index was calculated as 0.54. Sixteen isolates were confirmed to be hyper-virulent and harbored magA and rmpA genes. In total, 46.9, 31.2, and 21.9% of the isolates were categorized as strong, moderate, or weak biofilm formers, respectively. All isolates possessed an active efflux pump and harbored acrA, acrB, acrAB, and tolC genes in 94% of the isolates, followed by mdtK (56.2%). Porins such as ompK35 and ompK36 were detected in 59.3 and 62.5% of the isolates, respectively. Virulence genes fimH-1, mrkD, and entB were present in 84.3, 81.2, 87.5% of the isolates, respectively. These findings imply a potential threat that multi-drug-resistant bacterial pathogens could transmit to surrounding environments and humans through contaminated water and the aquaculture food chain.

Snapshot of resistome, virulome and mobilome in aquaculture

Aquaculture environments can be hotspots for resistance genes through the surrounding environment. Our objective was to study the resistome, virulome and mobilome of Gram-negative bacteria isolated in seabream and bivalve molluscs, using a WGS approach. Sixty-six Gram-negative strains (Aeromonadaceae, Enterobacteriaceae, Hafniaceae, Morganellaceae, Pseudomonadaceae, Shewanellaceae, Vibrionaceae, and Yersiniaceae families) were selected for genomic characterization. The species and MLST were determined, and antibiotic/disinfectants/heavy metals resistance genes, virulence determinants, MGE, and pathogenicity to humans were investigated. Our study revealed new sequence-types (e.g. Aeromonas spp. ST879, ST880, ST881, ST882, ST883, ST887, ST888; Shewanella spp. ST40, ST57, ST58, ST60, ST61, ST62; Vibrio spp. ST206, ST205). >140 different genes were identified in the resistome of seabream and bivalve molluscs, encompassing genes associated with β-lactams, tetracyclines, aminoglycosides, quinolones, sulfonamides, trimethoprim, phenicols, macrolides and fosfomycin resistance. Disinfectant resistance genes qacE-type, sitABCD-type and formA-type were found. Heavy metals resistance genes mdt, acr and sil stood out as the most frequent. Most resistance genes were associated with antibiotics/disinfectants/heavy metals commonly used in aquaculture settings. We also identified 25 different genes related with increased virulence, namely associated with adherence, colonization, toxins production, red blood cell lysis, iron metabolism, escape from the immune system of the host. Furthermore, 74.2 % of the strains analysed were considered pathogenic to humans. We investigated the genetic environment of several antibiotic resistance genes, including blaTEM-1B, blaFOX-18, aph(3″)-Ib, dfrA-type, aadA1, catA1-type, tet(A)/(E), qnrB19 and sul1/2. Our analysis also focused on identifying MGE in proximity to these genes (e.g. IntI1, plasmids and TnAs), which could potentially facilitate the spread of resistance among bacteria across different environments. This study provides a comprehensive examination of the diversity of resistance genes that can be transferred to both humans and the environment, with the recognition that aquaculture and the broader environment play crucial roles as intermediaries within this complex transmission network.

High prevalence of multidrug-resistant Escherichia coli in retail aquatic products in China and the first report of mcr-1-positive extended-spectrum β-lactamase-producing E. coli ST2705 and ST10 in fish

Contamination of food by multidrug-resistant (MDR) bacteria is a potential threat to consumers. Aquatic products are increasingly consumed due to their high value and rich nutrient. Nevertheless, the prevalence of multi-drug resistant (MDR) E. coli in retail aquatic products has not been systematically investigated in China. In this study, we conducted a national investigation on the prevalence of E. coli and MDR E. coli in retail aquatic products and the characteristics of the MDR E. coli isolates. A total of 849 samples consisting of 680 fish, 143 shrimp, and 26 shellfish were purchased from markets in 39 cities in China and investigated for the presence of E. coli. Overall, 340 (40.0 %) and 169 (19.9 %) samples were contaminated with E. coli and MDR E. coli, indicating poor hygiene conditions of retail aquatic products. A total of 190 MDR E. coli were isolated, which were recovered from 38.5 % shellfish, 20.1 % shrimp, and 19.0 % fish. Thirty-two ESBL-producing E. coli were identified from 3.5 % fish, 3.5 % shrimp, and 3.8 % shellfish. The MDR E. coli isolates showed a high prevalence of resistance to tetracycline (93.7 %), trimethoprim-sulfamethoxazole (78.9 %), ampicillin (78.4 %), chloramphenicol (72.1 %), nalidixic acid (73.2 %), cephalothin (65.3 %), and streptomycin (65.8 %). Resistances to kanamycin (42.1 %), gentamicin (37.9 %), ciprofloxacin (42.6 %), and norfloxacin (45.8 %) were also common. Further, 15.3 % and 8.4 % of the isolates were resistant to cefotaxime and ceftazidime, respectively. Four isolates were resistant to colistin. More than 85.0 % of the isolates were resistant to 5-15 antibiotics. Of the antibiotic resistance genes, TEM-1, tetA, strA/B, sul2, aadA, floR, and qnrS were the most prevalent, followed by sul1, aac(6')-Ib, oqxA/B, cmlA and aphA1. Six CTX-M-types were found, among which CTX-M-55 and CTX-M-14 were predominant. All 4 colistin-resistant isolates carried the mcr-1 gene, of which three were ESBL strains. WGS indicated that the mcr-1 gene was located on two types of plasmids (IncHI2 and IncX4). Conjugation experiments showed the mcr-1 gene could be transferred to E. coli C600. To our knowledge, this is the first report of mcr-1-positive ESBL E. coli (ST10 and ST2705) in retail aquatic products. The emergence of such strains poses a serious threat to consumers, with the potential to spread resistance genes to humans. Our results indicate that retail aquatic products are important reservoirs of MDR E. coli and facilitate the dissemination of the resistance genes. Continuous surveillance and interventions of restricting antibiotic use in aquatic environments should also be applied to reduce the prevalence of MDR bacteria.

"One Health" perspective on prevalence of co-existing extended-spectrum β-lactamase (ESBL)-producing Escherichia coli and Klebsiella pneumoniae: a comprehensive systematic review and meta-analysis

BACKGROUND

The Escherichia coli (E. coli) and Klebsiella pneumoniae (K. pneumoniae) bacterial isolates that produce extended-spectrum β-lactamases (ESBLs) contribute to global life-threatening infections. This study conducted a systematic review and meta-analysis on the global prevalence of ESBLs in co-existing E. coli and K. pneumoniae isolated from humans, animals and the environment.

METHODS

The systematic review protocol was registered in the International Prospective Register of Systematic Reviews (PROSPERO) [ID no: CRD42023394360]. This study was carried out following the preferred reporting items for systematic reviews and meta-analyses (PRISMA) guidelines. One hundred and twenty-six eligible studies published on co-existing antibiotic resistance in E. coli and K. pneumoniae between 1990 and 2022 were included.

RESULTS

The pooled prevalence of ESBL-producing E. coli and K. pneumoniae was 33.0% and 32.7% for humans, 33.5% and 19.4% for animals, 56.9% and 24.2% for environment, 26.8% and 6.7% for animals/environment, respectively. Furthermore, the three types of resistance genes that encode ESBLs, namely blaSHVblaCTX-M,blaOXA, and blaTEM, were all detected in humans, animals and the environment.

CONCLUSIONS

The concept of "One-Health" surveillance is critical to tracking the source of antimicrobial resistance and preventing its spread. The emerging state and national surveillance systems should include bacteria containing ESBLs. A well-planned, -implemented, and -researched alternative treatment for antimicrobial drug resistance needs to be formulated.

Bidirectional Interaction between Tetracyclines and Gut Microbiome

The escalating misuse of antibiotics, particularly broad-spectrum antibiotics, has emerged as a pivotal driver of drug resistance. Among these agents, tetracyclines are widely prescribed for bacterial infections, but their indiscriminate use can profoundly alter the gut microbiome, potentially compromising both their effectiveness and safety. This review delves into the intricate and dynamic interplay between tetracyclines and the gut microbiome, shedding light on their reciprocal influence. By exploring the effects of tetracyclines on the gut microbiome and the impact of gut microbiota on tetracycline therapy, we seek to gain deeper insights into this complex relationship, ultimately guiding strategies for preserving antibiotic efficacy and mitigating resistance development.

Extended Spectrum β-Lactamase-Producing Enterobacterales of Shrimp and Salmon Available for Purchase by Consumers in Canada-A Risk Profile Using the Codex Framework

The extended-spectrum β-lactamase (ESBL)-producing Enterobacterales (ESBL-EB) encompass several important human pathogens and are found on the World Health Organization (WHO) priority pathogens list of antibiotic-resistant bacteria. They are a group of organisms which demonstrate resistance to third-generation cephalosporins (3GC) and their presence has been documented worldwide, including in aquaculture and the aquatic environment. This risk profile was developed following the Codex Guidelines for Risk Analysis of Foodborne Antimicrobial Resistance with the objectives of describing the current state of knowledge of ESBL-EB in relation to retail shrimp and salmon available to consumers in Canada, the primary aquacultured species consumed in Canada. The risk profile found that Enterobacterales and ESBL-EB have been found in multiple aquatic environments, as well as multiple host species and production levels. Although the information available did not permit the conclusion as to whether there is a human health risk related to ESBLs in Enterobacterales in salmon and shrimp available for consumption by Canadians, ESBL-EB in imported seafood available at the retail level in Canada have been found. Surveillance activities to detect ESBL-EB in seafood are needed; salmon and shrimp could be used in initial surveillance activities, representing domestic and imported products.

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.

Antimicrobial Resistance and Clonal Lineages of Escherichia coli from Food-Producing Animals

Escherichia coli are one of the most important pathogenic bacteria readily found in the livestock and widely studied as an indicator that carries drug-resistant genes between humans, animals, and the environment. The use of antimicrobials in the food chain, particularly in food-producing animals, is recognized as a significant contributor to the development and spread of antimicrobial resistance (AMR) and resistance genes can be transferred from the farm through the food-chain. The objective of this review is to highlight the background of the antimicrobials use in food-producing animals, more specifically, to study clonal lineages and the resistance profiles observed in E. coli, as well as in extended spectrum beta-lactamases (ESBL) producing E. coli, in a set of food-production animals with greater relevance in food consumption, such as pigs, poultry, cattle, fish farming and rabbits. Regarding the prevalence of ESBL-producing E. coli among farm animals, high-to-moderate prevalence was observed, and the highest resistance rates to tetracycline and ampicillin was detected in different farms in all geographic regions. Worldwide pandemic clones and high-risk zoonotic E. coli clones have been identified in most food-producing animals, and some of these clones are already disseminated in different niches, such as the environment and humans. A better understanding of the epidemiology of E. coli and ESBL-producing E. coli in livestock is urgently needed. Animal production is one of the major causes of the antibiotic resistance problem worldwide and a One Health approach is needed.

Resistance profiles and genotyping of extended-spectrum beta-lactamase (ESBL) -producing and non-ESBL-producing E. coli and Klebsiella from retail market fishes

Studies on antimicrobial resistance (AMR) profiles and epidemiological affirmation for AMR transmission are limited in fisheries and aquaculture settings. Since 2015, based on Global Action Plan on AMR by World Health Organization (WHO) and World Organization for Animal Health (OIE), several initiatives have been under taken to enhance the knowledge, skills and capacity to establish AMR trends through surveillance and strengthening of epidemiological evidence. The focus of this study was to determine the prevalence of antimicrobial resistance (AMR), its resistance profiles and molecular characterization with respect to phylogroups, antimicrobial resistance genes (ARGs), virulence genes (VGs), quaternary ammonium compounds resistance (QAC) genes and plasmid typing in retail market fishes. Pulse field gel electrophoresis (PFGE) to understand the genetic lineage of the two most important Enterobacteriaceae members, E. coli and Klebsiella sp. was performed. 94 fish samples were collected from three different sites viz., Silagrant (S1), Garchuk (S2) and North Guwahati Town Committee (NGTC) Region (S3) in Guwahati, Assam. Out of the 113 microbial isolates from the fish samples, 45 (39.82%) were E. coli; 23 (20.35%) belonged to Klebsiella genus. Among E. coli, 48.88% (n = 22) of the isolates were alerted by the BD Phoenix M50 instrument as ESBL, 15.55% (n = 7) as PCP and 35.55% (n = 16) as non-ESBL. E. coli (39.82%) was the most prevalent pathogen among the Enterobacteriaceae members screened and showed resistance to ampicillin (69%) followed by cefazoline (64%), cefotaxime (49%) and piperacillin (49%). In the present study, 66.66% of E. coli and 30.43% of Klebsiella sp. were categorized as multi drug resistance (MDR) bacteria. CTX-M-gp-1, with CTX-M-15 variant (47%), was the most widely circulating beta-lactamase gene, while other ESBL genes bla_TEM (7%), bla_SHV (2%) and bla_OXA-1-like (2%) were also identified in E. coli. Out of the 23 isolates of Klebsiella, 14(60.86%) were ampicillin (AM)-resistant (11(47.82%) K. oxytoca, 3(13.04%) K. aerogenes), whereas 8(34.78%) isolates of K. oxytoca showed intermediate resistance to AM. All Klebsiella isolates were susceptible to AN, SCP, MEM and TZP, although two K. aerogenes were resistant to imipenem. DHA and LAT genes were detected, respectively, in 7(16%) and 1(2%) of the E. coli strains while a single K. oxytoca (4.34%) isolate carried MOX, DHA and bla_CMY-2 genes. The fluoroquinolone resistance genes identified in E. coli included qnrB (71%), qnrS (84%), oqxB (73%) and aac(6)-Ib-cr (27%); however, in Klebsiella, these genes, respectively, had a prevalence of 87%, 26%, 74% and 9%. The E. coli isolates belonged to phylogroup A(47%), B1(33%) and D(14%). All of the 22(100%) ESBL E. coli had chromosome-mediated disinfectant resistance genes viz., ydgE, ydgF, sugE(c), mdfA while 82% of ESBL E. coli had emrE. Among the non-ESBL E. coli isolates, 87% of them showed the presence of ydgE, ydgF and sugE(c) genes, while 78% of the isolates had mdfA and 39% had emrE genes respectively. 59% of the ESBL and 26% of the non-ESBL E. coli had showed the presence of qacEΔ1. The sugE(p) was present in 27% of the ESBL-producing E. coli and in 9% of non-ESBL isolates. Out of the 3 ESBL-producing Klebsiella isolates, 2(66.66%) K. oxytoca isolates were found harboring plasmid-mediated qacEΔ1 gene while one (33.33%) K. oxytoca isolate had sugE(p) gene. IncFI was the most prevalent plasmid type detected in the isolates studied, with A/C (18%), P (14%), X, Y (9% each) and I1-Iγ (14%, 4%). 50% (n = 11) of the ESBL and 17% (n = 4) of the non-ESBL E. coli isolates harboured IncFIB and 45% (n = 10) ESBL and one (4.34%) non-ESBL E. coli isolates harboured IncFIA. Dominance of E. coli over other Enterobacterales and diverse phylogenetic profiles of E. coli and Klebsiella sp. suggests the possibility of contamination and this may be due to compromised hygienic practices along the supply chain and contamination of aquatic ecosystem. Continuous surveillance in domestic markets must be a priority in addressing antimicrobial resistance in fishery settings and to identify any unwarranted epidemic clones of E. coli and Klebsiella that can challenge public health sector.

A scoping review of the distribution and frequency of extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae in shrimp and salmon

Antimicrobial-resistant (AMR) bacteria are a threat to public health as they can resist treatment and pass along genetic material that allows other bacteria to become drug-resistant. To assess foodborne AMR risk, the Codex Guidelines for Risk Analysis of Foodborne AMR provide a framework for risk profiles and risk assessments. Several elements of a risk profile may benefit from a scoping review (ScR). To contribute to a larger risk profile structured according to the Codex Guidelines, our objective was to conduct a ScR of the current state of knowledge on the distribution, frequency and concentrations of extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae in salmon and shrimp. Articles were identified via a comprehensive search of five bibliographic databases. Two reviewers screened titles and abstracts for relevance and characterised full-text articles with screening forms developed a priori. Sixteen relevant studies were identified. This review found that there is a lack of Canadian data regarding ESBL-producing Enterobacteriaceae in salmon and shrimp. However, ESBL- producing Escherichia coli, Klebsiella pneumoniae and other Enterobacteriaceae have been isolated in multiple regions with a history of exporting seafood to Canada. The literature described herein will support future decision-making on this issue as research/surveillance and subsequent assessments are currently lacking.

Aeromonas species isolated from aquatic organisms, insects, chicken, and humans in India show similar antimicrobial resistance profiles

Aeromonas species are Gram-negative bacteria that infect various living organisms and are ubiquitously found in different aquatic environments. In this study, we used whole genome sequencing (WGS) to identify and compare the antimicrobial resistance (AMR) genes, integrons, transposases and plasmids found in Aeromonas hydrophila, Aeromonas caviae and Aeromonas veronii isolated from Indian major carp (Catla catla), Indian carp (Labeo rohita), catfish (Clarias batrachus) and Nile tilapia (Oreochromis niloticus) sampled in India. To gain a wider comparison, we included 11 whole genome sequences of Aeromonas spp. from different host species in India deposited in the National Center for Biotechnology Information (NCBI). Our findings show that all 15 Aeromonas sequences examined had multiple AMR genes of which the Ambler classes B, C and D β-lactamase genes were the most dominant. The high similarity of AMR genes in the Aeromonas sequences obtained from different host species point to interspecies transmission of AMR genes. Our findings also show that all Aeromonas sequences examined encoded several multidrug efflux-pump proteins. As for genes linked to mobile genetic elements (MBE), only the class I integrase was detected from two fish isolates, while all transposases detected belonged to the insertion sequence (IS) family. Only seven of the 15 Aeromonas sequences examined had plasmids and none of the plasmids encoded AMR genes. In summary, our findings show that Aeromonas spp. isolated from different host species in India carry multiple AMR genes. Thus, we advocate that the control of AMR caused by Aeromonas spp. in India should be based on a One Health approach.

Determination of antibiotic resistance and biofilm formation in Klebsiella strains isolated from bovine mastitis cases

Mastitis is diseases of dairy cows with a high economic impact. Bovine mastitis is caused by a wide range of bacterial pathogens. As one of the major environmental pathogens Klebsiella ssp. was investigated in this study by some phenotypic characteristics like antibiotic resistance patterns and biofilm formation properties. A number of 483 cows by dairy farms around the Konya were examined by California Mastitis Test (CMT) producing 36 positive in terms of subclinical mastitis. A further 19 samples from clinical mastitic udders were also collected. Samples were inoculated onto Trypticase Soy Agar medium enriched with sheep blood and incubated aerobicaly for 24-48 hours at 37 °C. By morphological, biochemical and cultural charcateristics 14 isolates out of 37 coliform were identified as Klebsiella ssp. The double disc synergy method and Congo Red Agar test were used to perform antibiotic susceptibility and in vitro slime forming properties, respectively. Resistances to the antibiotics Ampicillin, Carbenicillin, Cephotaxime, Chloramphenicol, Erythromycin, Gentamicin, Neomycin, Oxytetracycline, Sulphamethoxazole/Trimpethoprim, Amoxicillin-Clavulanate and Imipenem were 78.5%, 78.5%, 35.7%, 42.8%, 100%, 7%, 7%, 50%, 14%, 21% and 7%, respectively. Three of the total isolets produced biofilm only. This appears to the first report on ESBL producing Klebsiella ssp from subclinical cases of bovine mastitis in Konya, Türkiye. Presently, two numbers of antimicrobial combinations to treat bovine cases are recommended by this work. In conclusion, because of costly challange nature of Klebsiella caused bovine mastitis implemantation of an effective mastitis control program should be used in local farms from Konya.

Whole genome sequencing and characteristics of extended-spectrum beta-lactamase producing Escherichia coli isolated from poultry farms in Banaskantha, India

Worldwide dissemination of extended-spectrum -lactamase (ESBL)-producing Escherichia coli constitutes an emerging global health issue, with animal food products contributing as potential reservoirs. ESBL E. coli infection is associated with the high mortality and mobility rate in developing countries due to less susceptibility to antibiotics. The present study aimed to elucidate the molecular characteristics and sequence-based analysis of ESBL E. coli in the Gujarat state of India. This study included 108 E. coli strains were isolated from different poultry farms (broiler and layer) in the Banaskantha District. PCR was employed to identify genotypic ESBL-producing antimicrobial resistance genes. Overall, a high occurrence of ESBL genes was found in poultry farms due to the high usage of antimicrobials. The PCR analysis revealed that 79.62% of isolates were detected positive with one or more ESBL genes. Among them, bla_TEM (63.88%) was found to be the predominant genotype, followed by bla_SHV (30.55%) and bla_OXA (28.70%). In the bla_CTX-M group, a higher occurrence was observed in bla_CTX-M-9 (23.14%), followed by bla_CTX-M-2 (24.07%) and bla_CTX-M-1 (22.22%). We used the whole-genome sequencing (WGS) method to evaluate the antimicrobial resistance genes, virulence factors, single nucleotide polymorphisms (SNPs), plasmid replicons, and plasmid-mediated AMR genes of one ESBL E. coli isolated. We examined the genetic relatedness of a human pathogenic E. coli strain by comparing its sequence with the broad geographical reference E. coli sequences. Escherichia coli ST 681 was determined using multi-locus sequence typing. We compared our findings to the reference sequence of Escherichia coli str. K- 12 substr. MG1655. We found 24,937 SNPs with 21,792 in the genic region, 3,145 in the intergenic region, and six InDels across the genome. The WGS analysis revealed 46 antimicrobial resistance genes and seven plasmid-mediated AMR genes viz., tetA, qnrS1, dfrA14, sul2, aph(3”)-lb, aph(6)-ld, and Aph(3’)-la. The ST 681 was found to have Cib, traT, and terC virulence factors and two plasmid replicons, IncFII(pHN7A8) and IncI1-I(Alpha). This study revealed a higher occurrence of ESBL E. coli detected in poultry.

Presence of Extended Spectrum Beta Lactamase, Virulence Genes and Resistance Determinants in Biofilm Forming Klebsiella pneumoniae Isolated from Food Sources: A Potent Risk to the Consumers

Foodborne diseases and infection caused by associated pathogens is a public health concern. Majority of the investigations focus on common foodborne pathogens like Vibrio parahaemolyticus, Escherichia coli, Listeria monocytogenes, Shigella, Salmonella and Staphylococcus aureus. Limited knowledge has been accounted on Klebsiella pneumoniae. Presence of multidrug-resistant K. pneumoniae in the food supply is disturbing. Hence, this study assessed the presence of K. pneumoniae isolates from food samples (fresh vegetables and chicken), ascertained the presence of drug-resistant phenotypes, extended spectrum beta lactamase production, antibiotic resistance determinants, genes associated with virulence and their ability to form biofilm. Resistance towards ceftazidime and tetracycline was noted among all the isolates in the study, while they exhibited sensitivity to chloramphenicol and co-trimoxazole. All the isolates were potent ESBL producers carrying at least one ESBL encoding genes. Plasmid mediated quinolone resistance gene was detected in one isolate each from onion and chicken respectively. The isolates marked the absence of tetracycline and chloramphenicol resistance genes. Multiple virulence genes (ureA, khe, fimH, mrkD, wabG, uge and elt) were possessed by each of the isolates. K. pneumoniae from chicken and cucumber were moderate biofilm formers and those from tomato exhibited weak biofilm formation. Increased expression of the mrkA gene and reduction in the expression of the biofilm forming gene fimH gene was observed among the biofilm formers. One of the moderate and non-biofilm formers exhibited increased mrkD gene expression. The results from our study stipulate, that raw vegetables and meat serve as dormant source of drug-resistant and virulent K. pneumoniae.

Characterization and Comparative Genomics Analysis of lncFII Multi-Resistance Plasmids Carrying bla CTX - M and Type1 Integrons From Escherichia coli

This research aimed to investigate the presence and transferability of the extended-spectrum β-lactamase resistance genes to identify the genetic context of multi-drug resistant (MDR) loci in two Escherichia coli plasmids from livestock and poultry breeding environment. MICs were determined by broth microdilution. A total of 137 E. coli resistant to extended-spectrum β-lactam antibiotics were screened for the presence of the ESBL genes by PCR. Only two E. coli out of 206 strains produced carbapenemases, including strain 11011 that produced enzyme A, and strain 417957 that produced enzyme B. The genes were bla_KPC and bla_NDM, respectively. The plasmids containing bla_CTX–M were conjugatable, and the plasmids containing carbapenem resistance gene were not conjugatable. Six extended-spectrum β-lactamase resistance genes were detected in this research, including bla_TEM, bla_CTX–M, bla_SHV, bla_OAX–1, bla_KPC, and bla_NDM, and the detection rates were 94.89% (130/137), 92.7% (127/137), 24.81% (34/137), 20.43% (28/137), 0.72% (1/137), and 0.72% (1/137), respectively. Two conjugative lncFII multi-resistance plasmids carrying bla_CTX–M, p11011-fosA and p417957-CTXM, were sequenced and analyzed. Both conjugative plasmids were larger than 100 kb and contained three accessory modules, including MDR region. The MDR region of the two plasmids contained many antibiotic resistance genes, including bla_CTX–M, mph (A), dfrA17, aadA5, sul1, etc. After transfer, both the transconjugants displayed elevated MICs of the respective antimicrobial agents. A large number of resistance genes clusters in specific regions may contribute to the MDR profile of the strains. The presence of mobile genetic elements at the boundaries can possibly facilitate transfer among Enterobacteriaceae through inter-replicon gene transfer. Our study provides beta-lactam resistance profile of bacteria, reveals the prevalence of β-lactamase resistance genes in livestock and poultry breeding environment in Zhejiang Province, and enriches the research on IncFII plasmids containing bla_CTX–M.