Prevalence, antimicrobial resistance and detection of virulence genes of Escherichia coli and Salmonella spp. isolated from white-lipped peccaries and collared peccaries

Salmonella spp. and Escherichia coli are implicated in human and animal infections and require antimicrobial treatment in many situations. Faecal samples of healthy white-lipped peccaries (Pecari tajacu) (n = 30) and collared peccaries (Tayassu pecari ) (n = 60) obtained in three farms located in the Midwest Brazil. The antimicrobial profiles of commensal E. coli from P. tajacu and T. pecari from commercial herds in Brazil were isolated and analyzed and virulence genes were detected. Among 90 healthy animals, no Salmonella spp. were isolated. However, 30 samples (27%) tested positive for E. coli, with 18 isolates from P. tajacu and 12 from T. pecari, representing frequencies of 58.0% and 38.7%, respectively. Additionally, other Enterobacteriaceae family bacteria were detected but not included in this analysis. However, individual samples from 30 animals tested positive for E. coli, of which 16 were isolated from P. tajacu presenting multidrug resistance and six were isolated from T. pecari presenting a similar pattern. The E. coli virulence genes detected were papC (pilus-associated pyelonephritis) in five isolates, tsh (temperature-sensitive hemagglutinin) in one isolate, and eae (enteric attachment and effacement) in one isolate. The serum resistance gene, iss (increased serum survival), was detected in four isolates. An association between these genes and the presence of hemolysin was also observed in one isolate. Thus, T. pecari and P. tajacu are potential reservoirs of pathogenic and multidrug-resistant and E. coli. Faecal E. coli of healthy P. tajacu and T. pecari could act as a possible reservoir of antimicrobial resistance genes in environment.

Longitudinal Monitoring Reveals Persistence of Colistin-Resistant Escherichia coli on a Pig Farm Following Cessation of Colistin Use

Colistin-resistant bacteria harboring plasmid-mediated mcr genes are of concern as they may be a cause of serious nosocomial infections. It is hypothesized that cessation of colistin use as a feed additive for pigs will reduce the occurrence and distribution of mcr genes in farms. The aim of this study was to investigate this hypothesis by longitudinal monitoring and characterizing of mcr positive Escherichia coli (MCRPE) isolates after colistin was withdrawn on a central Thailand pig farm that previously had a high frequency of MCRPE. Colistin use ceased at the beginning of 2017, and subsequently 170 samples were collected from farrowing sows and suckling piglets (n = 70), wastewater (n = 50) and farm workers (n = 50) over a 3.5-year period. Bacteria were identified by MALDI-TOF mass spectrometry and minimal inhibitory concentrations were determined by broth microdilution. The antibiogram of mcr positive E. coli isolates was determined using the Vitek2 automated susceptibility machine, and multiplex and simplex PCRs were performed for mcr-1-8 genes. MCRPE containing either mcr-1 or mcr-3 were isolated from pigs throughout the investigation period, but with a declining trend, whereas MCRPE isolates were recovered from humans only in 2017. MCRPE were still being recovered from wastewater in 2020. Most MCRPE isolates possessed the virulence genes Stap, Stb, or Stx2e, reflecting pathogenic potential in pigs, and showed high rates of resistance to ampicillin, gentamicin and tetracycline. Pulsed-field gel electrophoresis and multi-locus sequence typing showed that diverse MCRPE clones were distributed on the farm. The study identified a decline of pathogenic MCRPE following withdrawal of colistin, with pigs being the primary source, followed by wastewater. However, short-term therapeutic usage of other antibiotics could enhance the re-occurrence of mcr-carrying bacteria. Factors including the environment, management, and gene adaptations that allow maintenance of colistin resistance require further investigation, and longer-term studies are needed.

Genotypic and phenotypic situation of antimicrobial drug resistance of Escherichia coli in water and manure between biogas and non-biogas swine farms in central Thailand

Currently, Thai livestock is rapidly expanding, especially the production of ruminants, chicken, and swine. The improper use of antibiotics will probably lead to an antimicrobial resistance problem. It has long been suspected that wastewater released from swine farms is a crucial aspect of the spread of antimicrobial resistance to the environment. Biogas systems are wastewater treatment systems commonly used on swine farms; however, little is known about the roles they play in the occurrence and transmission of resistant bacteria between biogas and non-biogas systems. This study collected pooled water, wastewater, and feces samples from five biogas farms and three non-biogas farms in Central Thailand. The samples were isolated to hemolytic E. coli (HEC) and non-hemolytic E. coli (NHEC) to test the drug resistance by using VITEK® 2 Compact (BioMérieux, USA) and detect resistant genes by using the polymerase chain reaction (PCR) technique to correlate the determined phenotypic and genotypic patterns. The results demonstrated that enumeration levels of E. coli ranged from 20.1 to 70.4 (MPN/100 ml), 10⁵ to 10⁷ (cfu/ml), and 10⁵ to 10⁹ (cfu/g), while they were 0-148.7 (MPN/100 ml), 10⁵ to 10⁷ (cfu/ml) and 10⁵ to 10⁹ (cfu/g) for water, wastewater and manure from biogas and non-biogas swine farms, respectively. The amount of E. coli in the sow feces samples was higher than the samples of nursery piglets on biogas farms at a 0.05 significant level (p < 0.05). The antimicrobial resistance indicated the relevant resistance characteristics of E. coli: the highest antimicrobial resistance was for ampicillin (AMP), followed by amoxicillin (AMX), tetracyclines (TET), chloramphenicol (C), and piperacillin (PIP), respectively. Multidrug resistance (MDR) of E. coli was 15 drugs: AMP-AMX-AMC-PIP-CEX-CEV-CPD-XNL-GM-IMP-SXT-C-TE (11.9%) and AMP-AMX-AMC-PIP-CEX-CEV-CPD-XNL-GM-IMP-SXT-C-ENR-MBR-TE (18.55%), which were the most commonly found in biogas and non-biogas swine farms, respectively. The bla_TEM, tetA, sul2, and sul3 were dominantly resistant genes isolated from the water from both types of farm; while, bla_TEM, aadA1, tetA, dfrA12, sul2, sul3, and cmlA were isolated from feces. The amount of E. coli in the final effluent from biogas swine farms was higher than the non-biogas swine farms; however, it was not significantly different at (p > 0.05). Furthermore, the findings of study found that genotypic characteristic of HEC showed similarity 100%. Thus, it was concluded that the levels of E. coli were accelerated in biogas wastewater treatment systems, and isolated E. coli demonstrated multidrug resistance. Even though E. coli was found in different locations, it showed relevant resistance characteristics. Therefore, regular monitoring of antimicrobial resistance on livestock farms is necessary for efficient management and drug uses on farms.

Multidrug Resistance and Virulence Factors of Escherichia coli Harboring Plasmid-Mediated Colistin Resistance: mcr-1 and mcr-3 Genes in Contracted Pig Farms in Thailand

The presence of the plasmid-mediated colistin resistance encoding mcr gene family in the Enterobacteriaceae is one of the crucial global concerns. The use of colistin in livestock rearing is believed to be the cause of mcr gene spreading and is of impact to public health. The objective of this research was to detect the frequency and virulent genes of mcr-positive Escherichia coli (MCRPE) in fecal samples from healthy pigs in a contract farming system across Thailand. A total of 696 pooled samples were derived from 80 farms, located in 49 provinces across six regions of Thailand. The colistin-resistant E. coli were identified by MALDI-TOF mass spectrometry and antimicrobial susceptibility testing by broth microdilution. The antibiogram was determined using an automated susceptibility machine, and the genetic characteristics were investigated for mcr-1–5 genes, phylogenetic group, replicon types, and virulent genes. In total, 31 of 696 samples were positive, with E. coli containing mcr-1 or combination of mcr-1 and mcr-3 with incidence of 4.45 and 0.43%. Phylogenetic groups A and B1 and the IncF and IncFIB replicon types were predominantly found in the MCRPE located in the central area, with multidrug-resistant traits against 3–14 types of antimicrobials. Additionally, 19 of 31 isolates identified as enterotoxigenic E. coli were with the stap and stb (enterotoxin-encoding genes). In conclusion, a low carriage rate of mcr-positive E. coli was detected in the large-scale farming of healthy pigs. The association between multidrug-resistant MCRPE and their pathogenic potential should be of concern.

In Vitro Selective Growth-Inhibitory Activities of Phytochemicals, Synthetic Phytochemical Analogs, and Antibiotics against Diarrheagenic/Probiotic Bacteria and Cancer/Normal Intestinal Cells

A desirable attribute of novel antimicrobial agents for bacterial diarrhea is decreased toxicity toward host intestinal microbiota. In addition, gut dysbiosis is associated with an increased risk of developing intestinal cancer. In this study, the selective growth-inhibitory activities of ten phytochemicals and their synthetic analogs (berberine, bismuth subsalicylate, ferron, 8-hydroxyquinoline, chloroxine, nitroxoline, salicylic acid, sanguinarine, tannic acid, and zinc pyrithione), as well as those of six commercial antibiotics (ceftriaxone, ciprofloxacin, chloramphenicol, metronidazole, tetracycline, and vancomycin) against 21 intestinal pathogenic/probiotic (e.g., Salmonella spp. and bifidobacteria) bacterial strains and three intestinal cancer/normal (Caco-2, HT29, and FHs 74 Int) cell lines were examined in vitro using the broth microdilution method and thiazolyl blue tetrazolium bromide assay. Chloroxine, ciprofloxacin, nitroxoline, tetracycline, and zinc pyrithione exhibited the most potent selective growth-inhibitory activity against pathogens, whereas 8-hydroxyquinoline, chloroxine, nitroxoline, sanguinarine, and zinc pyrithione exhibited the highest cytotoxic activity against cancer cells. None of the tested antibiotics were cytotoxic to normal cells, whereas 8-hydroxyquinoline and sanguinarine exhibited selective antiproliferative activity against cancer cells. These findings indicate that 8-hydroxyquinoline alkaloids and metal-pyridine derivative complexes are chemical structures derived from plants with potential bioactive properties in terms of selective antibacterial and anticancer activities against diarrheagenic bacteria and intestinal cancer cells.

Escherichia coli aggravates endoplasmic reticulum stress and triggers CHOP-dependent apoptosis in weaned pigs

Intestinal cells can sense the presence of pathogens and trigger many important signaling pathways to maintain tissue homeostasis and normal function. Escherichia coli and lipopolysaccharides (LPS) are the main pathogenic factors of intestinal disease in pigs. However, the roles of endoplasmic reticulum stress (ERS) and its mediated apoptosis in intestinal malfunction induced by E. coli or LPS remain unclear. In the present study, we aimed to evaluate whether ERS could be activated by E. coli fed to piglets and whether the underlying mechanisms of this disease process could be exploited. Eighteen weaned pigs (21 days old) were randomly assigned to one of two treatment groups (n = 9 per group). After pre-feeding for 1 week, the diets of the piglets in one group were supplemented with E. coli (W25 K, 10⁹ cells kg^-1 diet) for 7 days. At the end of the experiment, all piglets were slaughtered to collect jejunum and ileum samples. Western blotting and immunofluorescence experiments were used to determine the expression levels and histological locations of ERS and its downstream signaling proteins. The intestinal porcine epithelial cell line J2 (IPEC-J2) was used as in vitro model to investigate the possible mechanism. The results showed that E. coli supplementation in the diet increased the GRP78 expression in the jejunum and ileum, especially in the jejunal epithelium and ileac germinal center, and elevated the expression levels of CHOP (in both the jejunum and ileum) and caspase-11 (in the ileum), indicating that ERS and CHOP-caspase-11 dependent apoptosis were activated in the porcine small intestine. Moreover, as demonstrated by in vitro experiments, the CHOP inhibitor 4-phenylbutyrate alleviated the damage to IPEC-J2 cells induced by LPS derived from E. coli. Taken together, these data strongly suggest that ERS can be triggered in the small intestine by dietary supplementation with E. coli and that CHOP-caspase-11 dependent apoptosis may play a key role in maintaining normal homeostasis of the intestine in response to pathogenic factors.

Routine Prophylactic Antimicrobial Use Is Associated with Increased Phenotypic and Genotypic Resistance in Commensal Escherichia coli Isolates Recovered from Healthy Fattening Pigs on Farms in Thailand

This study examined antimicrobial resistance (AMR) profiles in commensal Escherichia coli derived from healthy fattening pigs in Thai farms that used prophylactic antimicrobials (in-feed tiamulin fumarate and amoxicillin) [PAs], therapeutic antimicrobials (injectable enrofloxacin or gentamicin) [TAs], or no antimicrobials [NAs]. Commensal E. coli were used as a proxy for overall AMR on the farms. There was a high level of multidrug resistance in all three categories of farm, with isolates showing resistance to β-lactams (amoxicillin, ampicillin, and piperacillin) and tetracyclines (tetracycline), and commonly possessing tetA, bla_TEM, and plasmid replicons FIB and F. On the other hand, isolates with an extended-spectrum beta-lactamase phenotype (ESBLP) and with resistance to aminoglycosides, chloramphenicol, fluoroquinolones, nitrofurantoin, tiamulin, and trimethoprim/sulfamethoxazole were significantly more common among the PA farms (p < 0.05) than in the other two farm categories. In the PA farms, ESBLP E. coli commonly contained the bla_CTX-M-1 group, bla_CTX-M-9 group, or both gene groups, and were shown to transfer bla_CTX-M genes in a conjugation experiment. E. coli containing N, FIC and A/C replicons were found only in PA farms. In summary, although E. coli isolates from all farms contained a core set of resistance to β-lactams and tetracyclines, the routine use of PA increased resistance rates to other important antimicrobials.

Antimicrobial Usage and Antimicrobial Resistance in Animal Production in Southeast Asia: A Review

Southeast Asia is an area of great economic dynamism. In recent years, it has experienced a rapid rise in the levels of animal product production and consumption. The region is considered to be a hotspot for infectious diseases and antimicrobial resistance (AMR). We reviewed English-language peer-reviewed publications related to antimicrobial usage (AMU) and AMR in animal production, as well as antimicrobial residues in meat and fish from 2000 to 2016, in the region. There is a paucity of data from most countries and for most bacterial pathogens. Most of the published work relates to non-typhoidal Salmonella (NTS), Escherichia coli (E. coli), and Campylobacter spp. (mainly from Vietnam and Thailand), Enterococcus spp. (Malaysia), and methicillin-resistant Staphylococcus aureus (MRSA) (Thailand). However, most studies used the disk diffusion method for antimicrobial susceptibility testing; breakpoints were interpreted using Clinical Standard Laboratory Institute (CSLI) guidelines. Statistical models integrating data from publications on AMR in NTS and E. coli studies show a higher overall prevalence of AMR in pig isolates, and an increase in levels of AMR over the years. AMU studies (mostly from Vietnam) indicate very high usage levels of most types of antimicrobials, including beta-lactams, aminoglycosides, macrolides, and quinolones. This review summarizes information about genetic determinants of resistance, most of which are transferrable (mostly plasmids and integrons). The data in this review provide a benchmark to help focus research and policies on AMU and AMR in the region.

Colistin use and colistin resistance in bacteria from animals

Colistin has been used in veterinary medicine for decades, mainly for the prevention and treatment of Enterobacteriaceae infections. However, data regarding colistin resistance in bacteria from animals and food of animal origin are relatively scarce, partly because there are methodological difficulties hampering the analysis of susceptibility to colistin. Most data regarding clinical isolates are related to enteropathogenic Escherichia coli and Salmonella. The resistance percentages are sometimes high for pathogenic strains, and the mcr-1 gene has been detected in pathogenic E. coli isolates from pigs, cattle and poultry in different countries. The prevalence of colistin resistance in Salmonella from healthy animals is usually low but depends on the proportion of intrinsically colistin-resistant serotypes. For indicator E. coli, the resistance levels are often very low, although higher levels have been observed in Asia. The mcr-1 gene has been detected in indicator E. coli from pigs, cattle, poultry and their products. Thus, there is an urgent need to re-assess the use of colistin in livestock throughout the world to ensure a global strategy for preserving this last-resort antimicrobial.

Prevalence and characterization of verotoxigenic-Escherichia coli isolates from pigs in Malaysia

Background

Postweaning diarrhea caused by pathogenic Escherichia coli, in particular verotoxigenic E. coli (VTEC), has caused significant economic losses in the pig farming industry worldwide. However, there is limited information on VTEC in Malaysia. The objective of this study was to characterize pathogenic E. coli isolated from post-weaning piglets and growers with respect to their antibiograms, carriage of extended-spectrum beta-lactamases, pathotypes, production of hemolysins and fimbrial adhesins, serotypes, and genotypes.

Results

PCR detection of virulence factors associated with different E. coli pathotypes (ETEC, EPEC, EHEC, and VTEC) revealed that VTEC was the only pathotype identified from six swine farms located at north-western Peninsular Malaysia. A low prevalence rate of VTEC was found among the swine samples (n = 7/345) and all 7 VTEC isolates were multidrug resistant. Five of these isolates from different hosts raised in the same pen were likely to be of the same clone as they shared identical sero-pathotypes (O139:H1, VT2e/α-hly/F18), resistance profiles and DNA fingerprinting profiles. Two other serotypes, O130: H26 (n = 1) and O168: H21 (n = 1) carrying virulence factors were also identified. O168: H21 is possibly a new serotype as this has not been previously reported.

Conclusions

The occurrence of VTEC with infrequently encountered serotypes that are multidrug resistant and harbouring virulence factors may be of public health concern. The detection of possible clones in this study also showed that the combination of different typing tools including phenotyping and genotyping methods is useful for molecular epidemiologic surveillance and studies.

In vitro susceptibility of Mycoplasma hyopneumoniae field isolates and occurrence of fluoroquinolone, macrolides and lincomycin resistance

A total of 159 Thai isolates of Mycoplasma hyopneumoniae isolated from pneumonic lungs of pigs during 2006-2011 were investigated for their in vitro susceptibility to 12 antimicrobial agents. Low activity of chlortetracycline was indicated by the MIC range from 3.12-100 μg/ml and MIC90 of 50 μg/ml. Seventy-six isolates showed resistance to enrofloxacin, whereas 2 isolates showed resistance to macrolides and lincomycin. In addition, a point mutation at A2058G was revealed by sequence analysis of 23S ribosomal RNA in both isolates. The present results confirmed the rapid increase of resistant M. hyopneumoniae isolates against chlortetracycline, enrofloxacin, macrolides and lincomycin in Thailand. Selection of drugs to control swine diseases in Thailand must be done more prudently in consideration of reducing the antimicrobial resistance.