Detection of class 1 integrons in Salmonella Weltevreden and silent antibiotic resistance genes in some seafood-associated nontyphoidal isolates of Salmonella in south-west coast of India

Possibility of transfer and activation of 'silent' tetracycline resistance genes among Enterococcus faecalis under high-pressure processing

In this study, the tetracycline resistance of Enterococcus faecalis strains isolated from food was determined and molecular analyses of the resistance background were performed by determining the frequency of selected tetracycline resistance genes. In addition, the effect of high-pressure stress (400 and 500 MPa) on the expression of selected genes encoding tetracycline resistance was determined, as well as changes in the frequency of transfer of these genes in isolates showing sensitivity to tetracyclines. In our study, we observed an increase in the expression of genes encoding tetracyclines, especially the tet(L) gene, mainly under 400 MPa pressure. The study confirmed the possibility of transferring genes encoding tetracyclines such as tet(M), tet(L), tet(K), tet(W) and tet(O) by horizontal gene transfer in both control strains and exposed to high-pressure. Exposure of the strains to 400 MPa pressure had a greater effect on the possibility of gene transfer and expression than the application of a higher-pressure. To our knowledge, this study for the first time determined the effect of high-pressure stress on the expression of selected genes encoding tetracycline resistance, as well as the possibility and changes in the frequency of transfer of these genes in Enterococcus faecalis isolates showing sensitivity to tetracyclines and possessing silent genes. Due to the observed possibility of increased expression of some of the genes encoding tetracycline resistance and the possibility of their spread by horizontal gene transfer to other microorganisms in the food environment, under the influence of high-pressure processing in strains phenotypically susceptible to this antibiotic, it becomes necessary to monitor this ability in isolates derived from foods.

Class 1 and 2 integrons and antibiotic resistance profile in Salmonella spp. from San Cristobal River, Laguna, Philippines

Infection with multidrug resistant bacteria is a significant public health concern. Bacteria culture of water samples (n=120) collected in San Cristobal River, Philippines, showed that half (n=60) were positive for Salmonella spp. Screening of all isolates (n=179) for susceptibility to antibiotics showed that most (76.4%; n=113) were positive for class 1 integrons, of which one isolate was also positive for the class 2 integron. The presence of class 1 integrons was associated with resistance to antibiotics (p<0.05). Sequencing of class 1 integron variable regions (VRs) differeciated 11 gene cassettes: dfrA1 or dfrA17; aadA1 or aadA2; blaCTX-M-2 or bla-OXA-1; SmdAB; CmlA1 and aaC 3-Id. However, sequencing of class 2 integron VR differenciated estX, sat2, and aadA1. These results provide insights into evolutionary changes within bacterial multidrug resistant cassettes, more accurately to estimate heath risk associated with the river water.            .

Assessing the mechanisms of multi-drug resistant non-typhoidal Salmonella (NTS) serovars isolated from layer chicken farms in Nigeria

BACKGROUND

In Nigeria, there have been reports of widespread multiple antimicrobial resistance (AMR) amongst Salmonella isolated from poultry. To mitigate the impact of mortality associated with Salmonella on their farms, farmers resort to the use of antimicrobials without sound diagnostic advice. We conducted this study to describe the AMR patterns, mechanisms and genetic similarities within some Salmonella serovars isolated from different layer farms.

METHOD

We determine the AMR profiles of two hundred Salmonella isolates, selected based on frequency, serovar, and geographical and sample type distribution. We also assessed the mechanisms of multi-drug resistance for specific genetic determinants by using PCR protocols and gene sequence analysis. Pulsed-field gel electrophoresis (PFGE) was conducted on seven selected serovars to determine their genetic relatedness.

RESULTS

Of 200 isolates, 97 (48.5%) revealed various AMR profiles, with the multiple antibiotic resistance (MAR) index ranging from 0.07-0.5. Resistance to ciprofloxacin was common in all the multi-drug resistant isolates, while all the isolates were susceptible to cefotaxime, ceftazidime, and meropenem. Genotypic characterization showed the presence of resistance genes as well as mutations in the nucleotide genes with subsequent amino acid substitutions. Fifteen isolates (43%) of S. Kentucky were indistinguishable, but were isolated from four different states in Nigeria (Ogun, n = 9; Kaduna, n = 6; Plateau, n = 3, and: Bauchi, n = 2). PFGE revealed 40 pulsotype patterns (Kentucky, n = 12; Larochelle, n = 9; Virchow, n = 5; Saintpaul, n = 4; Poona, n = 3; Isangi, n = 2, and; Nigeria, n = 2).

CONCLUSION

This study recorded strictly related but diversely distributed Salmonella serovars with high AMR rates in poultry. We recommend strict regulation on antimicrobial use and regular monitoring of AMR trends among bacteria isolated from animals and humans to inform public policy.

Prevalence and Antimicrobial Resistance of Salmonella spp. Isolated From Chilled Chicken Meat Commercialized at Retail in Federal District, Brazil

Salmonella represents one of the most common foodborne pathogens, frequently associated with the contamination of poultry products, constituting a prominent worldwide public health concern. This study determined the prevalence and antimicrobial resistance of Salmonella spp. in chilled chicken meat (115 samples) commercialized at retail in the Federal District, Brazil. Microbiological tests were performed to screen for Salmonella spp. in the chicken meat samples, and the isolated strains were confirmed by the invA gene presence (PCR technique). The strains were evaluated for antimicrobial susceptibility by the disk diffusion technique (Kirby-Bauer method) and tested for the presence of the sul2, blaCTX, and tetB antimicrobial resistance genes. The Salmonella spp. prevalence in chilled chicken meat sold at retail in the Federal District, Brazil, was 46.1% (53 of 115 chicken meat samples analyzed had invA gene-positive strains). Seventy-eight strains of Salmonella spp. isolated from the 53 contaminated samples showed higher resistance to amoxicillin/clavulanic acid (83.3%), followed by sulfonamide (64.1%) and tetracycline (46.2%); 53.8% of the isolates were multidrug-resistant (MDR). The sul2 gene that confers resistance to sulfonamide was found in 53 strains (68.0%), the blaCTX gene that confers resistance to beta-lactams was identified in 39 strains (50.0%), and the tetB gene that confers resistance to tetracycline was identified in 29 strains (37.2%). The high percentage of Salmonella contamination in chicken meat can pose a risk to consumers' health due to the possibility of causing salmonellosis. In addition, many isolates were MDR and carried antimicrobial resistance genes. Public agencies can use these results to develop effective public health policies and strategies to ensure the safety of these food products.

The role of food chain in antimicrobial resistance spread and One Health approach to reduce risks

The incidence of antimicrobial resistance (AMR) is rapidly spreading worldwide. It is depleting the repertoire of antibiotics in use but the pace of development of new antibiotics is stagnant for decades. Annually, millions of people are killed by AMR. This alarming situation urged both scientific and civil bodies to take steps to curb AMR as a top priority. Here we review the various sources of AMR in the environment, especially focusing on the food chain. Food chain inculcates pathogens with AMR genes and serves as a conduit for its transmission. In certain countries, the antibiotics are more used in livestock than in humans. It is also used in agriculture crops of high value products. The indiscriminate use of antibiotics in livestock and agriculture increased rapid emergence of AMR pathogens. In addition, in many countries nosocomial settings are spewing AMR pathogens, which is a serious health hazard. Both the developed and low and middle income countries (LMIC) face the phenomenon of AMR. Therefore, a comprehensive approach for monitoring all sectors of life is required to identify the emerging trend of AMR in environment. AMR genes' mode of action must be understood to develop strategies to reduce risk. The new generation sequencing technologies, metagenomics and bioinformatics capabilities can be resorted to quickly identify and characterize AMR genes. The sampling for AMR monitoring can be done from multiples nodes of the food chain as envisioned and promoted by the WHO, FAO, OIE and UNEP under the One Health approach to overcome threat of AMR pathogens.

Comparative Analysis between Salmonella enterica Isolated from Imported and Chinese Native Chicken Breeds

Salmonella enterica is considered a significant threat to the global poultry industry and public health. In recent decades, antimicrobial resistance in Salmonella enterica has attracted increasing concern throughout the world. However, limited information is available on Salmonella enterica among different breeds of breeder chickens. Thus, this study aimed to compare the prevalence, serotype distribution, emergence of extended-spectrum beta-lactamases (ESBLs), antimicrobial resistance, and genetic resistance mechanisms in Salmonella enterica among different breeds of breeder chickens. A total of 693 samples (dead embryos, cloacal swabs, water, feed, environmental swabs, and meconium of newly hatched chicks) were selected and cultured for Salmonella from four breeder chicken farms in Shandong province, China, representing one imported and three native breeds, and the isolates were further serotyped. Of the Salmonella isolates, susceptibility to 11 antimicrobials of 5 classes, ESBL screening, and the presence of 21 antimicrobial resistance genes were determined in the present study. Overall, 94 (13.6%) isolates were recovered, which were divided into 3 serotypes (Salmonella Pullorum (n = 36), Salmonella Thompson (n = 32), and Salmonella Enteritidis (n = 26)). The results showed that the prevalence of Salmonella enterica isolates from the imported breeds was higher compared with the three domestic breeds. Eight of the ninety-four isolates were ESBL-positive strains, which were recovered from a domestic breed chicken farm. These eight ESBL-producing isolates were serotyped to Pullorum. Surprisingly, Salmonella Enteritidis (S. enteritidis) and S. pullorum were simultaneously isolated from a single dead embryo observed among one native breed. Meanwhile, among the Salmonella isolates, 53.2% (50/94) were multidrug-resistant strains, and 44.7% (42/94) of the isolates presented resistance to at least five antibiotics. Nearly all of the isolates (97.9%, 92/94) were resistant to at least one antimicrobial; one isolate of S. Thompson was resistant to seven antimicrobial agents belonging to four different classes. The carriage rate of three resistance genes (tetA, tetB, and sul1) among isolates from the imported breeds (87%, 70%, and 65.2%) was higher than that in those from domestic breeds (35.2%, 36.6, and 14.1%). To our knowledge, this is the first report of ESBLs-producing Salmonella isolated from a Chinese native breed of breeder chickens. Our results also highlight that a high prevalence of multidrug-resistant Salmonella enterica contamination is widespread among different breeds of breeder chickens, which is a major risk of food-borne diseases and public health.

Molecular characterization of antimicrobial resistance related genes in E. coli, Salmonella and Klebsiella isolates from broilers in the West Region of Cameroon

BACKGROUND

Antibiotic resistance has become an enduring threat to human health. This has prompted extensive research to identify the determinants responsible in a bid to fight the spread of resistance and also develop new antibiotics. However, routine procedures focus on identifying genetic determinants of resistance only on phenotypically resistant isolates. We aimed to characterise plasmid mediated resistance determinants in key Enterobacteriaceae isolates with differential phenotypic susceptibility profiles and evaluated the contribution of resistance genes on phenotypic expression of susceptibility.

METHODS

The study was carried out on 200 Enterobacteriaceae isolates belonging to the genera E. coli, Salmonella, and Klebsiella; 100 resistant and 100 susceptible to quinolones, aminoglycosides, and ESBL-producing as determined by disk diffusion. Reduced susceptibility in susceptible isolates was determined as an increased MIC by broth microdilution. Plasmid-borne resistance genes were sought in all isolates by endpoint PCR. We performed correlations tests to determine the relationship between the occurrence of resistance genes and increased MIC in susceptible isolates. We then used the notion of penetrance to show adequacy between resistance gene carriage and phenotypic resistance as well as diagnostic odds ratio to evaluate how predictable phenotypic susceptibility profile could determine the presence of resistant genes in the isolates.

RESULTS

Reduced susceptibility was detected in 30% (9/30) ESBL negative, 50% (20/40) quinolone-susceptible and 53.33% (16/30) aminoglycoside-susceptible isolates. Plasmid-borne resistance genes were detected in 50% (15/30) of ESBL negative, 65% (26/40) quinolone susceptible and 66.67% (20/30) aminoglycoside susceptible isolates. Reduced susceptibility increased the risk of susceptible isolates carrying resistance genes (ORs 4.125, 8.36, and 8.89 respectively for ESBL, quinolone, and aminoglycoside resistance genes). Resistance gene carriage correlated significantly to reduced susceptibility for quinolone and aminoglycoside resistance genes (0.002 and 0.015 at CI95). Gene carriage correlated with phenotypic resistance at an estimated 64.28% for ESBL, 56.90% for quinolone, and 58.33% for aminoglycoside resistance genes.

CONCLUSIONS

A high carriage of plasmid-mediated genes for ESBL, quinolone, and aminoglycoside resistance was found among the Enterobacteriaceae tested. However, gene carriage was not always correlated with phenotypic expression. This allows us to suggest that assessing genetic determinants of resistance should not be based on AST profile only. Further studies, including assessing the role of chromosomal determinants will shed light on other factors that undermine antimicrobial susceptibility locally.

Effect of NaCl, high iron, iron chelator and antibiotics on growth, virulence gene expression and drug susceptibility in non-typhoidal Salmonella: an in vitro fitness study

Salmonella is one among the most versatile and resilient enteric pathogens that is known to have developed various survival strategies within the host system. The ability of the bacteria to circumvent the physiological parameters as well as dodge the antimicrobial stress environment within the host is one of the most crucial steps in establishing an infection. With an alarming rise in multi-drug resistant serovars of non-typhoidal Salmonella and lack of vaccine for combatting the infections, behaviour of the bacteria in the presence of host physiological conditions (NaCl, high and low iron) and antibiotics will help in understanding the survival strategies as well as mechanisms of resistance. Two multi-drug resistant and two sensitive serovars of Salmonella Weltevreden and Salmonella Newport isolated from poultry and seafood were used for growth kinetics and virulence gene expression study. The results obtained revealed that despite similar resistance pattern, effect of individual class of antibiotics on the growth of serovars varied. On the contrary, no significant difference was observed in growth pattern on exposure to these in vitro experimental conditions. Nevertheless, coupling these conditions with antibiotics drastically reduced the minimum inhibitory concentration (MIC) of antibiotics in resistant strains. A first of its kind study that draws attention on the significant effect of antibiotics and physiological conditions on MIC between resistant and sensitive non-typhoidal Salmonella serovars and expression of virulence genes from Salmonella pathogenicity island (SPI) 1 and 2 (invA, hilC, fliC2, sseA and ssrB).

'To be, or not to be' - the dilemma of 'silent' antimicrobial resistance genes in bacteria

Antimicrobial resistance is a serious threat to public health that dramatically undermines our ability to treat bacterial infections. Microorganisms exhibit resistance to different drug classes by acquiring resistance determinants through multiple mechanisms including horizontal gene transfer. The presence of drug resistance genotypes is mostly associated with corresponding phenotypic resistance against the particular antibiotic. However, bacterial communities harboring silent antimicrobial resistance genes - genes whose presence is not associated with a corresponding resistant phenotype, do exist. Under suitable conditions, the expression pattern of such genes often revert and regain resistance, and could potentially lead to therapeutic failure. We often miss the presence of silent genes, since the current experimental paradigms are focused on resistant strains. Therefore, the knowledge on the prevalence, importance, and mechanism of silent antibiotic resistance genes in bacterial pathogens is very limited. Silent genes, therefore, provide an additional level of complexity in the war against drug-resistant bacteria, reminding us that not only phenotypically resistant strains but also susceptible strains should be carefully investigated. In this review, we discuss the presence of silent antimicrobial resistance genes in bacteria, their relevance, and their importance in public health.

How Do Transposable Elements Activate Expression of Transcriptionally Silent Antibiotic Resistance Genes?

The rapidly emerging phenomenon of antibiotic resistance threatens to substantially reduce the efficacy of available antibacterial therapies. Dissemination of resistance, even between phylogenetically distant bacterial species, is mediated mainly by mobile genetic elements, considered to be natural vectors of horizontal gene transfer. Transposable elements (TEs) play a major role in this process—due to their highly recombinogenic nature they can mobilize adjacent genes and can introduce them into the pool of mobile DNA. Studies investigating this phenomenon usually focus on the genetic load of transposons and the molecular basis of their mobility. However, genes introduced into evolutionarily distant hosts are not necessarily expressed. As a result, bacterial genomes contain a reservoir of transcriptionally silent genetic information that can be activated by various transposon-related recombination events. The TEs themselves along with processes associated with their transposition can introduce promoters into random genomic locations. Thus, similarly to integrons, they have the potential to convert dormant genes into fully functional antibiotic resistance determinants. In this review, we describe the genetic basis of such events and by extension the mechanisms promoting the emergence of new drug-resistant bacterial strains.

Prevalence and antimicrobial resistance profile in <em>Salmonella</em> spp. isolates from swine food chain

The aim of this survey was to examine the prevalence and the antimicrobial resistance (AMR) of Salmonella spp. isolated from swine food chain. A total of 435 samples were collected: 360 from slaughterhouse (150 carcasses, 30 cecal samples, 180 environmental samples) and 75 from Italian traditional pork dry sausages. Thirty-six Salmonella were isolated and identified by Polymerase Chain Reaction (PCR): 13,3% (4/30) in fecal samples, 5,5% (10/180) in environmental samples, 7,3% (11/150) in carcasses, and 14,6% (11/75) in Italian traditional dry sausages. Salmonella serotypes were: S. Typhimurium (44,4%), S. Typhimurium monophasic variant (8,3%), S. Typhi (2,8%), S. Enteritidis (22,2%), S. Rissen (16,6%) and S. Derby (5,5%). Phenotypic and genotypic characterization of AMR Salmonella spp. isolates was executed through automatic system (VITEK 2, bioMèrieux) and PCR assays. Salmonella spp. showed phonotypical and genotypical resistance to at least one or more classes of antibiotic. All Salmonella spp. were resistant to aminoglycoside (amikacin and tobramycin) and gentamicin, 86,1% strains were resistant to tetracycline, 55,5% strains were resistant to ampicillin and piperacillin, 25% strains to trimethoprim, 5,5% strains to chloramphenicol, 2,8% strains to amoxicillin/ clavulanic acid, and nitrofurantoin. Among Salmonella isolates, the most detected AMR genes were catA for chloramphenicol (94,4%), nitrofuran nfsA (77.7%), nfsB (86,1%) and, for fluoroquinolone par C (100%) and gyrA (94,4%). This study reported epidemiological data regarding Salmonella spp. and AMR’s circulation in the swine food chain. This phenomenon (AMR) has critical repercussions on the final consumer health; therefore, it represents a crucial One-Health issue.

Research progress on antibiotic resistance of Salmonella

Antibiotic abuse results in various antibiotic resistance among a number of foodborne bacteria, posing a severe threat to food safety. Antibiotic resistance genes are commonly detected in foodborne pathogens, which has sparked much interest in finding solutions to these issues. Various strategies against these drug-resistant pathogens have been studied, including new antibiotics and phages. Recently, a powerful tool has been introduced in the fight against drug-resistant pathogens, namely, clustered regularly interspaced short palindromic repeats-CRISPR associated (CRISPR-Cas) system aggregated by a prokaryotic defense mechanism. This review summarized the mechanism of antibiotic resistance in Salmonella and resistance to common antibiotics, analysed the relationship between Salmonella CRISPR-Cas and antibiotic resistance, discussed the changes in antibiotic resistance on the structure and function of CRISPR-Cas, and finally predicted the mechanism of CRISPR-Cas intervention in Salmonella antibiotic resistance. In the future, CRISPR-Cas is expected to become an important tool to reduce the threat of antibiotic-resistant pathogens in food safety.

Antibiotics Resistance in Escherichia coli Isolated from Livestock in the Emirate of Abu Dhabi, UAE, 2014–2019

Escherichia coli (E. coli) is a zoonotic pathogen that showed growing resistance to antibiotics. No descriptive analysis highlights the threat of antimicrobial-resistant (AMR) of E. coli among livestock in the United Arab Emirates (UAE). Herein, we conducted phenotypic and genotypic resistance studies on E. coli isolates from livestock samples in the Emirate of Abu Dhabi based on routine diagnosis between the periods 2014–2019. Bacterial culture and disk diffusion methods were used for bacterial isolation and phenotypic resistance analysis. Resistance mechanism was studied by PCR targeting the most commonly resistance genes: ampicillin (blaSHV, blaCMY, and blaTEM-1B), tetracyclines (tetA and tetB), co-trimoxazole [sulfamethoxazole (sul1, sul2, and sul3) + trimethoprim (dfrA1 and dfrA17)], aminoglycosides [aph(3'')-Ia, aph(6)-Id, and aac(3)-IV], and fluoroquinolones (qnrA and aac(6’)-Ib-cr). Analysis of 165 E. coli isolates showed resistant to ampicillin, tetracycline, co-trimoxazole, gentamicin, and enrofloxacin by 157/165 (95.4%), 154/165 (93.6%), 141/165 (86%), 139/165 (85%), and 135/165 (82.7%), respectively. Predominant resistance gene/s detected by PCR were blaCMY (119/160, 72%) and blaTEM-1B (154/160, 96.3%) for ampicillin; tetA (162/164, 98.8%) and tetB (112/164, 68.3%) for tetracyclines; sul2 (156/164, 95%), sul3 (138/164, 84%), and dfra17 (74/164, 44.5%) for co-trimoxazole; aph(3'')-Ia (134/164, 82.1%) and aph(6)-Id (161/164, 98.2%) for aminoglycosides; and aac(6’)-Ib-cr (61/61, 100%) for enrofloxacin. Both phenotypic and genotypic analyses revealed that all E. coli isolates were multidrug-resistant (resistance to 3, 4, and 5 antibiotics classes by 3.6%, 57.6%, and 38.8%, respectively) carrying one or more resistance gene/s for the same antibiotic. PCR profiling confirmed the presence of resistance genes corresponding to their antibiotic profile. Results of the study will highlight the knowledge based on E. coli AMR related to livestock in UAE that may call for interventions.

Analysis of Antimicrobial Resistance in Non-typhoidal Salmonella Collected From Pork Retail Outlets and Slaughterhouses in Vietnam Using Whole Genome Sequencing

Non-typhoidal salmonella (TS) remains a significant health burden worldwide. In Vietnam, pork accounts for 70% of the total meat consumed, and contamination with Salmonella is high. High levels of antimicrobial resistance (AMR) have emerged among porcine NTS and of particular concern is the emergence of colistin resistance, a “last defense” antibioic against multi-drug resistant (MDR) Gram-negative pathogens. This study aimed to investigate the antibiotic susceptibility of 69 NTS isolates collected from the pork retail outlets and slaughterhouses in Vietnam during 2014 a nd 2018/19. Phenotypic testing and whole genome sequencing was used to assess the serotype and AMR gene profiles of the 69 NTS isolates. Seventeen different serotypes were identified, of which S. enterica subsp enterica serotype Typhimurium was the most common followed by S. ser. Rissen, S. ser. London, S. ser. Anatum, and S. ser. Derby. Phenotype AMR was common with 41 (59.4%) isolates deemed MDR. MDR strains were most common in slaughterhouses (83%) and supermarkets (75%) and lowest in traditional markets (38%) and convenience stores (40%). Colistin resistance was identified in 18 strains (15 resistant, three intermediate) with mcr-1 identified in seven isolates (S. ser. Meleagridis, S. Rissen, S. Derby) and mcr-3 in two isolates (S. Typhimurium). This includes the first mcr positive S. Meleagridis to our knowledge. Surprisingly, boutique stores had high levels (60%) of MDR isolates including 5/20 isolates with mcr-1. This study demonstrates that pork from modern retail stores classed as supermarkets or boutique (with pork claiming to be high quality, traceable, environmentally friendly marketed toward higher income consumers) still contained NTS with high levels of AMR.

Overcoming Multidrug Resistance in Salmonella spp. Isolates Obtained From the Swine Food Chain by Using Essential Oils: An in vitro Study

Antimicrobial resistance (AMR) is a global concern, and new approaches are needed to circumvent animal and food-borne resistant pathogens. Among the new strategies, the combination of antibiotics with natural compounds such as essential oils (EOs) could be an alternative to challenge bacterial resistance. The present study evaluates the phenotypic and genotypic antibiotic resistance of 36 Salmonella enterica (16 S. Typhimurium, 3 monophasic variant S. Typhimurium, 8 S. Enteritidis, 6 S. Rissen, 1 S. Typhi, and 2 S. Derby) strains, isolated from the swine production chain. The isolates displayed phenotypic resistance to gentamicin, amikacin, tobramycin, and tetracycline, while the resistance genes most commonly detected were parC, catA, nfsB, nfsA, blaTEM, tetA, and tetB. Then 31/36 Salmonella isolates were chosen to evaluate resistance to tetracycline and Thymus vulgaris, Eugenia caryophyllata, and Corydothymus capitatus EOs by determining minimum inhibitory concentrations (MICs). Finally, the synergistic effect between tetracycline and each EOs was evaluated by the checkerboard method, calculating the fractional inhibitory concentration (FIC) index. Among the EOs, C. capitatus displayed the best bioactivity in terms of MICs, with the lowest values (0.31 and 0.625 μl/ml). On the contrary, the strains showed the ability to grow in the presence of the maximum concentration of tetracycline employed (256 μg/ml). While not displaying a real synergism according to the FIC index, the combination of tetracycline compounds and the three EOs resulted in a significant reduction in the MIC values to tetracycline (4 μg/ml), suggesting a restoration of the susceptibility to the antibiotic in Salmonella spp.

Non-diarrhoeic pigs as source of highly virulent and multidrug-resistant non-typhoidal Salmonella

Food-producing animals act as reservoirs of non-typhoidal Salmonella (NTS) serovars with potential food safety and public health implications. The present cross-sectional study aimed at determining the prevalence of Salmonella serotypes in non-diarrhoeic pigs and characterizing the isolates using molecular tools. Salmonella isolates (n = 22) recovered from faecal samples of 194 randomly selected pigs were characterized for virulence and antimicrobial resistance and subtyped using XbaI-PFGE. The prevalence of Salmonella in apparently healthy non-diarrhoeic pigs was 11.3% (95%CI, 4.3-19.5%), with S. Weltevreden (81.8%) and S. Enteritidis (18.2%) being the serotypes detected. Salmonella isolates harboured virulence genes such as invA (100%), stn (100%), spvR/spvC (86.3%) and fimA (22.7%). Phenotypically, isolates showed sensitivity to chloramphenicol, levofloxacin and ciprofloxacin and resistance to tetracycline and ampicillin (100%), streptomycin (86.4%), amoxicillin-clavulanate (63.6%), cefotaxime (22.7%) and ceftriaxone (9.1%). Notably, 18.2% isolates were multidrug-resistant (≥ 3 antimicrobial class) with multiple antimicrobial resistance (MAR) index of 0.56-0.67 (18.2%), 0.44 (45.5%), 0.33 (31.8%) and 0.22 (4.5%). Genotypically, isolates carried various antibiotic resistance genes: ESBL (bla_TEM and bla_OXA), aminoglycoside (strA, strB and aadA1), sulphonamide (sul1, sul2 and dfrA1), tetracycline (tetA and tetB) and plasmid AmpC beta-lactamase (ACC, FOX, MOX, DHA, CIT and EBC). The present investigation emphasizes the epidemiological significance of PFGE typing in the detection of emerging strains of highly virulent and multidrug-resistant S. Weltevreden and S. Enteritidis in non-diarrhoeic pigs that pose serious public health implications in the pork supply chain environment. More extensive longitudinal study is warranted to provide epidemiological links between environmental reservoirs and animal and human infections in piggery settings.

Silent Genes: Antimicrobial Resistance and Antibiotic Production

Silent genes are DNA sequences that are generally not expressed or expressed at a very low level. These genes become active as a result of mutation, recombination, or insertion. Silent genes can also be activated in laboratory conditions using pleiotropic, targeted genome-wide, or biosynthetic gene cluster approaches. Like every other gene, silent genes can spread through horizontal gene transfer. Most studies have focused on strains with phenotypic resistance, which is the most common subject. However, to fully understand the mechanism behind the spreading of antibiotic resistance, it is reasonable to study the whole resistome, including silent genes.

Presence of Tetracycline and Sulfonamide Resistance Genes in Salmonella spp.: Literature Review

Tetracyclines and sulfonamides are broad-spectrum antibacterial agents which have been used to treat bacterial infections for over half a century. The widespread use of tetracyclines and sulfonamides led to the emergence of resistance in a diverse group of bacteria. This resistance can be studied by searching for resistance genes present in the bacteria responsible for different resistance mechanisms. Salmonella is one of the leading bacteria causing foodborne diseases worldwide, and its resistance to tetracyclines and sulfonamides has been widely reported. The literature review searched the Virtual Health Library for articles with specific data in the studied samples: the resistance genes found, the primers used in PCR, and the thermocycler conditions. The results revealed that Salmonella presented high rates of resistance to tetracycline and sulfonamide, and the most frequent samples used to isolate Salmonella were poultry and pork. The tetracycline resistance genes most frequently detected from Salmonella spp. were tetA followed by tetB. The gene sul1 followed by sul2 were the most frequently sulfonamide resistance genes present in Salmonella. These genes are associated with plasmids, transposons, or both, and are often conjugative, highlighting the transference potential of these genes to other bacteria, environments, animals, and humans.

Genotypic and Phenotypic Characterization of Antimicrobial Resistance Profiles in Non-typhoidal Salmonella enterica Strains Isolated From Cambodian Informal Markets

Non-typhoidal Salmonella enterica is a pathogen of global importance, particularly in low and middle-income countries (LMICs). The presence of antimicrobial resistant (AMR) strains in market environments poses a serious health threat to consumers. In this study we identified and characterized the genotypic and phenotypic AMR profiles of 81 environmental S. enterica strains isolated from samples from informal markets in Cambodia in 2018–2019. AMR genotypes were retrieved from the NCBI Pathogen Detection website (https://www.ncbi.nlm.nih.gov/pathogens/) and using ResFinder (https://cge.cbs.dtu.dk/services/) Salmonella pathogenicity islands (SPIs) were identified with SPIFinder (https://cge.cbs.dtu.dk/services/). Susceptibility testing was performed by broth microdilution according to the Clinical and Laboratory Standards Institute (CLSI) standard guidelines M100-S22 using the National Antimicrobial Resistance Monitoring System (NARMS) Sensititre Gram Negative plate. A total of 17 unique AMR genes were detected in 53% (43/81) of the isolates, including those encoding tetracycline, beta-lactam, sulfonamide, quinolone, aminoglycoside, phenicol, and trimethoprim resistance. A total of 10 SPIs (SPI-1, 3–5, 8, 9, 12–14, and centisome 63 [C63PI]) were detected in 59 isolates. C63PI, an iron transport system in SPI-1, was observed in 56% of the isolates (n = 46). SPI-1, SPI-4, and SPI-9 were present in 13, 2, and 5% of the isolates, respectively. The most common phenotypic resistances were observed to tetracycline (47%; n = 38), ampicillin (37%; n = 30), streptomycin (20%; n = 16), chloramphenicol (17%; n = 14), and trimethoprim-sulfamethoxazole (16%; n = 13). This study contributes to understanding the AMR genes present in S. enterica isolates from informal markets in Cambodia, as well as support domestic epidemiological investigations of multidrug resistance (MDR) profiles.

Effect of ciprofloxacin and in vitro gut conditions on biofilm of Escherichia coli isolated from clinical and environmental sources

AIM

This study aimed at characterizing the biofilm-forming ability of drug-resistant and sensitive Escherichia coli under in vitro gut conditions and in the presence of ciprofloxacin.

METHODS AND RESULTS

153 E. coli isolates comprising 80 from clinical and 73 from environment source were studied for their ability to form biofilm under control and in vitro simulated gut conditions. The integrity of preformed biofilm on exposure to ciprofloxacin was assessed. Expression of biofilm-associated genes was analysed using qPCR. A high degree of resistance was observed in clinical isolates with a concomitant prevalence of bla_TEM . Bile, pH and low temperature enabled the E. coli biofilm to resist the effect of ciprofloxacin. Clinical isolates of E. coli formed strong biofilms in in vitro gut conditions following exposure to high concentration of ciprofloxacin. The expression of biofilm genes varied between different gut conditions viz., presence of bile, pH and low temperature, included in this study.

CONCLUSIONS

This study demonstrates the importance of papC and csgA for maintaining the biofilm integrity upon antibiotic exposure. Escherichia coli form biofilm as a survival strategy to adapt to the conditions in their environment irrespective of their drug resistance status.

SIGNIFICANCE AND IMPACT OF THE STUDY

The study provides an understanding of the effect of different parameters of the gut conditions during infection and the effect of antibiotic on survival and biofilm-forming ability of clinical and environmental E. coli isolates. It further suggests that bacteria resort to biofilm formation as one of the mechanisms to adjust to alterations in gut conditions and once the biofilm is formed, it requires high concentration of ciprofloxacin to eradicate it.

Evaluation of loop-mediated isothermal amplification assay along with conventional and real-time PCR assay for sensitive detection of pathogenic Vibrio parahaemolyticus from seafood sample without enrichment

The primary reason for foodborne illness is improper seafood safety testing, and hence, an appropriate tool for testing is the key to control the outbreaks. The current study aimed to develop a loop-mediated isothermal amplification (LAMP) assay to detect pathogenic Vibrio parahaemolyticus, important foodborne pathogen, targeting tdh, and trh genes. The specificity of the LAMP assay was good without any false-positive and false-negative results. The assay was highly sensitive and could detect the pathogenic V. parahaemolyticus as low as 1 CFU/reaction in spiked seafood samples and 1 pg of extracted DNA. Out of 62 seafood samples from India’s southwest coastal region tested with LAMP assay, eight (12.9%) were positive for trh, and seven (11.29%) samples were positive tdh gene. LAMP-based on tdh and trh was found to be significantly more sensitive (p < 0.05) than conventional PCR and nearly equal sensitive as real-time PCR (RT-PCR) for the detection of pathogenic V. parahaemolyticus. Our study shows that LAMP assay can be a better approach as a point-of-care (POC) diagnostic tool and could detect pathogenic V. parahaemolyticus on seafood samples directly without enrichment and isolation. The high sensitivity and simplicity make LAMP assay a better alternative method than the conventional method and RT-PCR for the detection of pathogens. LAMP assay can be considered as a good alternative to PCR for the routine detection of pathogenic V. parahaemolyticus in seafood.

Occurrence of antibiotic resistance among Gram negative bacteria isolated from effluents of fish processing plants in and around Mangalore

The presence of antibiotic-resistant bacteria in seafood not only poses a serious health risk for the consumers but also contributes to the spread of these antibiotic-resistant bacteria in the natural environments through the effluents discharged from the fish processing plants. The aims of this study were to isolate Gram-negative bacteria from the effluents of fish processing plants in and around Mangalore, India and to profile their antibiotic resistance pattern. Maximum resistance was seen for ampicillin (40.78%) followed by tetracycline (40.22%) and nitrofurantoin (29.05%). Further, the detection of genes that contribute to antibiotic resistance revealed the presence of sulfonamide resistance genes (sul1 and sul2) and extended spectrum β-lactamase genes (bla _CTX-M, bla _TEM) in a few isolates. The presence of such bacteria in fish processing effluents is a matter of great concern because they can contribute significantly to the antibiotic resistance in the natural environment. It is imperative that seafood processing plants follow the safe disposal of effluents in order to reduce or eliminate the antibiotic resistance menace.

Effect of bile on growth and biofilm formation of non-typhoidal salmonella serovars isolated from seafood and poultry

Bacterial cells adopt various strategies to adapt themselves in diverse environmental conditions. Salmonella is one such bacteria with diverse mechanisms to survive, replicate and infect in wide host range. This study aims at investigating the biofilm-forming ability of multidrug-resistant and sensitive Salmonella serovars on exposure to bile. Antibiogram of all the isolates was determined by disk diffusion method and their biofilm-forming ability in the presence or absence of bile was assessed by microtiter plate assay. Biofilm results were validated by calcofluor, Congo red plate and test tube method. Few isolates were selected for further study of their expression of biofilm related genes on exposure to bile using real time PCR. Among the 59 isolates of Salmonella isolated from seafood and poultry, 30 isolates were multi-drug resistant (MDR). Under control conditions, 57% (n = 25) of the serovars were able to form biofilm. While, 86% (n = 51) of the serovars produced biofilm in the presence of bile. The relative gene expression study of the selected serovars for 8 different genes showed a striking difference in the expression levels, supporting the hypothesis that the presence of bile triggers biofilm formation in food associated strains of non-typhoidal Salmonella by upregulation of genes involved in biofilm production.

Rapid visual detection of Vibrio parahaemolyticus in seafood samples by loop-mediated isothermal amplification with hydroxynaphthol blue dye

The detection and monitoring of Vibrio parahaemolyticus pathogen in aquatic foods have become essential for preventing outbreaks. In this study, loop-mediated isothermal amplification (LAMP) assay with the azo dye, hydroxynaphthol blue (HNB) was developed targeting species-specific tlh gene. The assay was carried out on 62 seafood samples that included clam and shrimp and compared with conventional LAMP assay performed with the commonly used fluorescent dye, conventional PCR, and real-time PCR (RT-PCR). Of 62 samples studied for tlh gene, 32 (51.61%) gave positive by HNB-LAMP, which comprised 22 (70.96%) clam samples and 10 (32.25%) shrimp samples. The HNB-LAMP assay was found to be highly sensitive, specific, and superior to conventional PCR (p > 0.05). RT-PCR presented higher sensitivity than HNB-LAMP; however, it has the limitation of being cost-intensive and requiring technical expertise to perform. HNB-LAMP is affordable, rapid, simple, and easy to perform, allowing naked eye visualization.

High Prevalence of Multiple Antibiotic-Resistant, Extended-Spectrum β-Lactamase (ESBL)-Producing Escherichia coli in Fresh Seafood Sold in Retail Markets of Mumbai, India

In this study, fresh seafood in retail markets was investigated for the antibiotic susceptibility patterns of the faecal indicator Escherichia coli and distribution of important β-lactamase encoding genes. E. coli were isolated from 50 (37 fish and 13 shellfish) fresh seafood samples and studied with respect to the phenotypic and genotypic characters of antibiotic resistance. Of 475 E. coli isolates from fresh seafood, 71.58% exhibited extended-spectrum β-lactamase (ESBL)-positive phenotypes. A high percentage of isolates were resistant to indicator cephalosporins cefotaxime (95%), cefpodoxime (90.88%) and ceftazidime (90.29%). Relatively higher susceptibilities were recorded against imipenem (74.41%), cefoxitin (66.76%) and meropenem (51.18%). The multiple antibiotic resistance (MAR) index of 97.35% of the isolates was above 0.18. The ESBL genes bla_CTX-M, bla_SHV and bla_TEM were detected in 62.37%, 23.35% and 2.6% of E. coli isolates, respectively. The ESBL-producing isolates also harboured the metallo-β-lactamase-encoding genes bla_OXA (7.06%), bla_NDM (4.42%) and bla_VIM (0.88%). This study highlights the risk of dissemination of multidrug resistant E. coli in seafood consumer communities and also the need to improve the hygiene of the coastal waters, landing centres and the retail markets.

Draft genome sequences of Salmonella Oslo isolated from seafood and its laboratory generated auxotrophic mutant

In recent years, the concept of bacteria-mediated cancer therapy has gained significant attention as an alternative to conventional therapy. The focus has been on non-typhoidal Salmonella (NTS), particularly S. Typhimurium, for its anti-cancer properties, however, other NTS serovars such as Salmonella Oslo, which are associated with foodborne illnesses could potentially be effective anti-cancer agents. Here, we report the draft genome sequence of Salmonella Oslo isolated from seafood and its laboratory generated auxotrophic mutant.

Plasmid-mediated fluoroquinolone resistance associated with extra-intestinal Escherichia coli isolates from hospital samples

Background & objectives

Infection from fluoroquinolone-resistant extra-intestinal Escherichia coli is a global concern. In this study, isolation and characterization of fluoroquinolone-resistant extra-intestinal E. coli isolates obtained from hospital samples were undertaken to detect plasmid-mediated quinolone resistance (PMQR) genes.

Methods

Forty three isolates of E. coli obtained from patients with extra-intestinal infections were subjected to antibiogram to detect fluoroquinolone resistance. The mechanism of fluoroquinolone resistance was determined by the detection of PMQR genes and mutations in quinolone resistance determining region (QRDR).

Results

Of the 43 isolates, 36 were resistant to nalidixic acid (83.72%) and 28 to ciprofloxacin (65.11%). Eight E. coli isolates showed total resistance to both the antimicrobials without any minimum inhibitory concentration. The detection of PMQR genes with qnr primers showed the presence of qnrA in two, qnrB in six and qnrS in 21 isolates. The gene coding for quinolone efflux pump (qepA) was not detected in any of the isolates tested. The presence of some unexpressed PMQR genes in fluoroquinolone sensitive isolates was also observed.

Interpretation & conclusions

The detection of silent PMQR genes as observed in the present study presents a risk of the transfer of the silent resistance genes to other microorganisms if present in conjugative plasmids, thus posing a therapeutic challenge to the physicians. Hence, frequent monitoring is to be done for all resistance determinants.

Phenotypic & genotypic study of antimicrobial profile of bacteria isolates from environmental samples

Background & objectives

The resistance to antibiotics in pathogenic bacteria has increased at an alarming rate in recent years due to the indiscriminate use of antibiotics in healthcare, livestock and aquaculture. In this context, it is necessary to monitor the antibiotic resistance patterns of bacteria isolated from the environmental samples. This study was conducted to determine the phenotypic and genotypic profile of antimicrobial resistance in Gram-negative bacteria isolated from environmental samples.

Methods

Two hundred and fifty samples were collected from different sources, viz. fish and fishery products (99), livestock wastes (81) and aquaculture systems (70), in and around Mangaluru, India. Isolation, identification and antimicrobial profiling were carried out as per standard protocols. The isolates were screened for the presence of resistance genes using PCR.

Results

A total of 519 Gram-negative bacteria comprising Escherichia coli (116), Salmonella spp. (14), Vibrio spp. (258), Pseudomonas spp. (56), Citrobacter spp. (26) and Proteus spp. (49) were isolated and characterized from 250 samples obtained from different sources. A total of 12 antibiotics were checked for their effectiveness against the isolates. While 31.6 per cent of the isolates were sensitive to all the antibiotics used, 68.4 per cent of the isolates showed resistance to at least one of the antibiotics used. One-third of the isolates showed multidrug resistance. Maximum resistance was observed for ampicillin (43.4%), followed by nitrofurantoin (20.8%). Least resistance was seen for carbapenems and chloramphenicol. PCR profiling of the resistant isolates confirmed the presence of resistance genes corresponding to their antibiotic profile.

Interpretation & conclusions

This study results showed high rate of occurrence of antimicrobial resistance and their determinants in Gram-negative bacteria isolated from different environmental sources.

Prevalence of Antimicrobial Resistance and Virulence Gene Elements of Salmonella Serovars From Ready-to-Eat (RTE) Shrimps

Gastrointestinal illnesses continue to be a global public health risk. Exposure to foodborne Salmonella directly or indirectly through consumption of ready-to-eat seafood can be an important route of infection to humans. This study was designed to estimate the population cell density, prevalence, virulence gene signatures, and antibiotic resistance of Salmonella serovars from ready-to-eat shrimps. Ready-to-eat (RTE) shrimp samples were obtained from different open markets in Delta and Edo States, Nigeria from November 2016 to October 2017. We employed classical and polymerase chain reaction (PCR) approaches. The mean Salmonella species enumerated from the RTE shrimps ranged from -0.301 to 5.434 log₁₀ cfu/g with 210/1440 (14.58%) of the RTE shrimp samples harbored Salmonella species. After biochemical and PCR approach, the identified isolates were Salmonella Enteritidis 11(24.4%), Salmonella Typhimurium 14 (31.1%) and other Salmonella spp. 20 (44.4%). All Salmonella species recovered were resistant to penicillin and erythromycin with 100% sensitivity to cefotaxime, cephalothin, colistin, and polymyxin B. Findings on the multidrug-resistant (MDR) profile showed that a total of 9/14 (64.3%) of Salmonella Enteritidis were resistant to 5 antibiotics which belongs to 3 different groups of antimicrobials with a multiple antibiotic-resistant (MAR) index of 0.21; while 3/11 (27.3%) of Salmonella Typhimurium were resistant to 11 antibiotics which belongs to 7 different groups of antimicrobials with a MAR index of 0.46. Virulence genes (spiA, sipB, invA, sif A, fljB, and sefA) and resistance genes (class 1 and II integrase, sul2, catB3, flor, tmp, bla _TEM, strB, dfr1, and tetC) were also detected in some of the Salmonella species with variable percentage. This study indicates that ready-to-eat shrimps are probable reservoirs harboring Salmonella strains. The identified Salmonella isolates which exhibited virulence determinants and antibiotic-resistant coupled with high MAR index constitute a consumer health risk to the communities.

Core genome sequence analysis to characterize Salmonella enterica serovar Rissen ST469 from a swine production chain

Salmonella enterica subsp. enterica serotype Rissen is the predominant serotype found in Thai pork production and can be transmitted to humans through contamination of the food chain. This study was conducted to investigate the genetic relationships between serovar Rissen isolates from all levels of the pork production chain and evaluate the ability of the in silico antimicrobial resistance (AMR) genotypes to predict the phenotype of serovar Rissen. A total of 38 serovar Rissen isolates were tested against eight antibiotic agents by a disk diffusion method and the whole genomes of all isolates were sequenced to detect AMR genetic elements using the ResFinder database.A total of 86.84% of the isolates were resistant to tetracycline, followed by ampicillin (78.96%) and sulfonamide-trimethoprim (71.05%). Resistance to more than one antimicrobial agent was observed in 78.95% of the isolates, with the most common pattern showing resistance to ampicillin, chloramphenicol, streptomycin, sulfonamide-trimethoprim, and tetracycline. The results of genotypic AMR indicated that 89.47% of the isolates carried tet(A), 84.22% carried bla_TEM-1B, 78.95% carried sul3, and 78.95% carried dfrA12. The genotypic prediction of phenotypic resistance resulted in a mean sensitivity of 97.45% and specificity of 75.48%. Analysis by core genome multilocus sequence typing (cgMLST) demonstrated that the Salmonella isolates from various sources and different locations shared many of the same core genome loci. This implies that serovar Rissen has infected every stage of the pork production process and that contamination can occur in every part of the production chain.

Multiple Food-Animal-Borne Route in Transmission of Antibiotic-Resistant Salmonella Newport to Humans

Characterization of transmission routes of Salmonella among various food-animal reservoirs and their antibiogram is crucial for appropriate intervention and medical treatment. Here, we analyzed 3728 Salmonella enterica serovar Newport (S. Newport) isolates collected from various food-animals, retail meats and humans in the United States between 1996 and 2015, based on their minimum inhibitory concentration (MIC) toward 27 antibiotics. Random Forest and Hierarchical Clustering statistic was used to group the isolates according to their MICs. Classification and Regression Tree (CART) analysis was used to identify the appropriate antibiotic and its cut-off value between human- and animal-population. Two distinct populations were revealed based on the MICs of individual strain by both methods, with the animal population having significantly higher MICs which correlates to antibiotic-resistance (AR) phenotype. Only ∼9.7% (267/2763) human isolates could be attributed to food-animal origins. Furthermore, the isolates of animal origin had less diverse antibiogram than human isolates (P < 0.001), suggesting multiple sources involved in human infections. CART identified trimethoprim-sulfamethoxazole to be the best classifier for differentiating the animal and human isolates. Additionally, two typical AR patterns, MDR-Amp and Tet-SDR dominant in bovine- or turkey-population, were identified, indicating that distinct food-animal sources could be involved in human infections. The AR analysis suggested fluoroquinolones (i.e., ciprofloxacin), but not extended-spectrum cephalosporins (i.e., ceftriaxone, cefoxitin), is the adaptive choice for empirical therapy. Antibiotic-resistant S. Newport from humans has multiple origins, with distinct food-animal-borne route contributing to a significant proportion of heterogeneous isolates.

Spread of mcr-1-carrying Enterobacteriaceae in sewage water from Spain

Objectives

The mobile colistin resistance gene mcr-1 has been identified worldwide in human and animal sources, while its occurrence in the environment is still largely unknown. The aim of this study was to investigate the presence of mcr-1 -harbouring Enterobacteriaceae in water samples obtained from rivers and waste water treatment plants in the area of Barcelona, Spain.

Methods

The presence of mcr-1 was detected by PCR. Bacterial identification was performed via MALDI-TOF MS. Resistance to colistin was determined by a broth dilution method. The epidemiological relationship between the positive isolates was assessed with PFGE and ST was determined by MLST. Plasmid characterization was performed by transformation experiments, antimicrobial susceptibility testing and incompatibility group PCR.

Results

Thirty MDR isolates bearing mcr-1 , 29 Escherichia coli (ST632 and ST479) and 1 Klebsiella pneumoniae (ST526), were identified in sewage from two different waste water treatment plants, whereas the gene was not found in river water. All isolates, including the K. pneumoniae , harboured bla CTX-M-55 and bla TEM-1 . mcr-1 was in all cases associated with an IncI2 plasmid, which only conferred resistance to colistin. mcr-1 was harboured by two predominant E. coli clones that were found in both waste water treatment plants.

Conclusions

This study showed a high occurrence of mcr-1 in the sewage of Barcelona, mainly due to the dissemination of two E. coli pulsotypes that are circulating in the population. The presence of mcr-1 in the environment is a cause for concern, and suggests high prevalence of mcr-1 in the community.

Antimicrobial Resistance Percentages of Salmonella and Shigella in Seafood Imported to Jordan: Higher Percentages and More Diverse Profiles in Shigella

This study determined the prevalence and antimicrobial resistance of human-specific ( Shigella spp.) and zoonotic ( Salmonella enterica ) foodborne pathogens in internationally traded seafood. Sixty-four Salmonella and 61 Shigella isolates were obtained from 330 imported fresh fish samples from Egypt, Yemen, and India. The pathogens were isolated on selective media, confirmed by PCR, and tested for antimicrobial resistance. Approximately 79 and 98% of the Salmonella and Shigella isolates, respectively, exhibited resistance to at least one antimicrobial, and 8 and 49% exhibited multidrug resistance (resistance to three or more antimicrobial classes). Generally, Salmonella exhibited high resistance to amoxicillin-clavulanic acid, cephalothin, streptomycin, and ampicillin; very low resistance to kanamycin, tetracycline, gentamicin, chloramphenicol, nalidixic acid, sulfamethoxazole-trimethoprim, and ciprofloxacin; and no resistance to ceftriaxone. Meanwhile, Shigella spp. exhibited high resistance to tetracycline, amoxicillin-clavulanic acid, cephalothin, streptomycin, and ampicillin; low resistance to kanamycin, nalidixic acid, sulfamethoxazole-trimethoprim, and ceftriaxone; and very low resistance to gentamicin and ciprofloxacin. Salmonella isolates exhibited 14 resistance profiles, Shigella isolates 42. This study is novel in showing that a human-specific pathogen has higher antimicrobial resistance percentages and more diverse profiles than a zoonotic pathogen. Thus, the impact of antimicrobial use in humans is as significant as, if not more significant than, it is in animals in spreading antibiotic resistance through food. This study also demonstrates that locally derived antimicrobial resistance can spread and pose a public health risk worldwide through seafood trade and that high resistance would make a possible outbreak difficult to control. So, capacity building and monitoring harvest water areas are encouraged in fish producing countries.

Differential expression of virulence genes and role of gyrA mutations in quinolone resistant and susceptible strains of Salmonella Weltevreden and Newport isolated from seafood

AIMS

To investigate the differential expression of virulence genes and role of gyrA mutations in quinolone resistant and susceptible strains of Salmonella isolated from seafood.

METHODS AND RESULTS

Forty Salmonella isolates from seafood were tested for antibiotic sensitivity. Minimal inhibitory concentration (MIC) was determined and two nalidixic acid-resistant isolates, viz Salmonella Weltevreden (SW9) and Salmonella Newport (SN36) were selected for identifying the mechanism of resistance. SW9 showed mutation in the gyrA gene at codon 83 (Ser to Tyr) while SN36 presented at codon 87 (Asp to Asn). Experimental induction of resistance to a sensitive Salm. Newport (SN71) showed point mutation at codon 87 (Asp to Gly) in the gyrA gene, and was designated SN71R. All the isolates resistant to nalidixic acid had a single mutation at different positions in the gyrA gene. However, induction of resistance to a sensitive Salm. Weltevreden (SW30) was exceptional in that it did not show any mutation in the gyrA region. Use of Phe-Arg-β-naphthylamide (PAβN) also could not reduce MIC below the Clinical and Laboratory Standards Institute guidelines revealing the absence of efflux mediated resistance. Thus, the resistance mechanism in SW30R is unknown. The growth rate of quinolone resistant isolates was slower than the susceptible ones. The resistant isolates showed decreased epithelial cell invasion and intracellular replication. The mRNA expression levels of some of the genes were significantly (P < 0·005) reduced in SN71R compared to the sensitive strain (SN71).

CONCLUSIONS

Nalidixic acid-resistant Salmonella strains are associated with lower virulence and pathogenicity than the sensitive strains.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study provided valuable information on the difference in the growth, cytotoxicity, infectivity and expression of virulence genes in resistant and susceptible strains. Furthermore, the gyrA mutation was shown to be the main mechanism of quinolone resistance in Salmonella other than the overexpression of efflux pumps or the presence of plasmid mediated quinolone resistance genes.

Monitoring and evaluation of antibiotic resistance genes in four municipal wastewater treatment plants in Harbin, Northeast China

The development and proliferation of antibiotic resistance in pathogenic and environmental microorganisms is of great concern for public health. In this study, the distribution and removal efficiency of intI1 and eight subtypes of antibiotic resistance genes (ARGs) for tetracycline, sulfonamides, beta-lactams resistance in four municipal wastewater treatment plants (WWTPs) in Harbin, which locates in Songhua River basin in cold areas of China, were monitored by real-time fluorescent quantitative PCR. The results showed that intI1 and 6 ARGs except for blaTEM and blaSHV were detected in wastewater and sludge samples and 0.3-2.7 orders of magnitude of ARGs removal efficiency in the four WWTPs were observed. The investigation on the removal of ARGs of different treatment units in one WWTP showed that the biological treatment unit played the most important role in ARGs removal (1.2-1.8 orders of magnitude), followed by UV disinfection, while primary physical treatment units can hardly remove any ARGs. Although all the WWTPs can remove ARGs effectively, ARGs concentrations are still relatively high in the effluent, their further attenuation should be investigated.

Metagenomic Assembly Reveals Hosts of Antibiotic Resistance Genes and the Shared Resistome in Pig, Chicken, and Human Feces

The risk associated with antibiotic resistance disseminating from animal and human feces is an urgent public issue. In the present study, we sought to establish a pipeline for annotating antibiotic resistance genes (ARGs) based on metagenomic assembly to investigate ARGs and their co-occurrence with associated genetic elements. Genetic elements found on the assembled genomic fragments include mobile genetic elements (MGEs) and metal resistance genes (MRGs). We then explored the hosts of these resistance genes and the shared resistome of pig, chicken and human fecal samples. High levels of tetracycline, multidrug, erythromycin, and aminoglycoside resistance genes were discovered in these fecal samples. In particular, significantly high level of ARGs (7762 ×/Gb) was detected in adult chicken feces, indicating higher ARG contamination level than other fecal samples. Many ARGs arrangements (e.g., macA-macB and tetA-tetR) were discovered shared by chicken, pig and human feces. In addition, MGEs such as the aadA5-dfrA17-carrying class 1 integron were identified on an assembled scaffold of chicken feces, and are carried by human pathogens. Differential coverage binning analysis revealed significant ARG enrichment in adult chicken feces. A draft genome, annotated as multidrug resistant Escherichia coli, was retrieved from chicken feces metagenomes and was determined to carry diverse ARGs (multidrug, acriflavine, and macrolide). The present study demonstrates the determination of ARG hosts and the shared resistome from metagenomic data sets and successfully establishes the relationship between ARGs, hosts, and environments. This ARG annotation pipeline based on metagenomic assembly will help to bridge the knowledge gaps regarding ARG-associated genes and ARG hosts with metagenomic data sets. Moreover, this pipeline will facilitate the evaluation of environmental risks in the genetic context of ARGs.

Draft Genome Sequence of Multidrug Resistant Salmonella enterica serovar Weltevreden Isolated from Seafood

Salmonella enterica subsp. enterica serovar Weltevereden is the most frequent serovar isolated from Asia. Here, we report a draft genome sequence of multidrug resistant Salmonella Weltevreden 9 isolated from seafood. Whole-genome of this isolate and annotation will help enhance the understanding of this pathogenic multidrug-resistant serovar.

Reconnaissance of 47 antibiotics and associated microbial risks in seafood sold in the United States

Aquaculture production has nearly tripled in the last two decades, bringing with it a significant increase in the use of antibiotics. Using liquid chromatography/tandem mass spectrometry (LC-MS/MS), the presence of 47 antibiotics was investigated in U.S. purchased shrimp, salmon, catfish, trout, tilapia, and swai originating from 11 different countries. All samples (n=27) complied with U.S. FDA regulations and five antibiotics were detected above the limits of detection: oxytetracycline (in wild shrimp, 7.7ng/g of fresh weight; farmed tilapia, 2.7; farmed salmon, 8.6; farmed trout with spinal deformities, 3.9), 4-epioxytetracycline (farmed salmon, 4.1), sulfadimethoxine (farmed shrimp, 0.3), ormetoprim (farmed salmon, 0.5), and virginiamycin (farmed salmon marketed as antibiotic-free, 5.2). A literature review showed that sub-regulatory levels of antibiotics, as found here, can promote resistance development; publications linking aquaculture to this have increased more than 8-fold from 1991 to 2013. Although this study was limited in size and employed sample pooling, it represents the largest reconnaissance of antibiotics in U.S. seafood to date, providing data on previously unmonitored antibiotics and on farmed trout with spinal deformities. Results indicate low levels of antibiotic residues and general compliance with U.S. regulations. The potential for development of microbial drug resistance was identified as a key concern and research priority.

Antimicrobial-resistant genes associated with Salmonella spp. isolated from human, poultry, and seafood sources

Antimicrobial-resistant salmonellosis is a significant public health concern globally. A study was conducted to screen for Salmonella species from a total of 120 samples, of which 50 were retail meat samples purchased from five randomly selected sales outlets in the city of Mangalore, India. Twenty poultry fecal materials freshly voided before slaughter were obtained with sterile spatula and placed in sterile sealable polythene envelopes, and 20 clams were purchased from the estuaries of Nethravathi and Kankarnady market. In addition, 30 clinical isolates from Nigeria suspected to be Salmonella by only cultural characterization were also included in the study. In all, 30 samples-6 poultry, 8 seafood, and 16 Salmonella isolates from clinical samples-were confirmed positive by PCR and used in this study. The disk-diffusion test was performed to determine the zone of inhibition, and detection of resistance genes was tested by PCR targeting various antimicrobial genes. Resistance to tetracycline (TET), cotrimoxazole, nalidixic acid, nitrofurantion, and piperacillin/tazobactin was found in 66.7%, 60%, 53.3%, 50% and 50% of the isolates, respectively. About 60-100% of MDR isolates possessed antibiotic-resistant genes, of the tetracyclines resistant isolates, 20 (100%) 6 (30%), 7 (35%), and 10 (50%) carried tetA, tetB, tetC, and tetG genes, respectively. Of 18 cotrimoxazole-resistant strains, 18 (100%), 14 (77.7%), and 4 (22.2%) had sul1, sul2, and sul3 genes, respectively. Of the 14 multidrug-resistant isolates tested, 8 (61%) and 9 (69%) were positive for cmlA and cmlB genes, respectively, 10 (1.4%) tested positive for aph(3)11a genes, 8 (57%) tested positive for aac(3)lla, while none was positive for the aac6 gene. The results show the presence of antibiotic-resistant Salmonella spp. in food samples from India and in human samples from Nigeria.

Antimicrobial resistance in Salmonella enterica serovar typhi and paratyphi in South Asia-current status, issues and prospects

The human race owes a debt of gratitude to antimicrobial agents, penicillin and its successors that have saved people from tremendous pain and suffering in the last several decades. Unfortunately, this consideration is no more true, as millions of people are prone to the challenging threat of emergence of antimicrobial resistance worldwide and the menace is more distressing in developing countries. Comparable with other bacterial species, Salmonella enterica serovar Typhi (S. typhi) and Paratyphi (S. paratyphi) have been evolving multidrug resistance (MDR) against a wide array of antibiotics, including chloramphenicol, ampicillin and co-trimoxazole, and globally affecting 21 million people with 220,000 deaths each year. S. typhi and S. paratyphi infections are also endemic in South Asia and a series of antibiotics used to treat these infections, have been losing efficacy against enteric fever. Currently, quinolones are regarded as a choice to treat MDR Salmonella in these regions. Travel-related cases of enteric fever, especially from South Asian countries are the harbinger of the magnitude of MDR Salmonella in that region. Conclusively, the MDR will continue to grow and the available antimicrobial agents would become obsolete. Therefore, a radical and aggressive approach in terms of rational use of antibiotics during treating infections is essentially needed.

Emergence and dissemination of antibiotic resistance: a global problem

Antibiotic resistance is a major problem in clinical health settings. Interestingly the origin of many of antibiotic resistance mechanisms can be traced back to non-pathogenic environmental organisms. Important factors leading to the emergence and spread of antibiotic resistance include absence of regulation in the use of antibiotics, improper waste disposal and associated transmission of antibiotic resistance genes in the community through commensals. In this review, we discussed the impact of globalisation on the transmission of antibiotic resistance genes in bacteria through immigration and export/import of foodstuff. The significance of surveillance to define appropriate use of antibiotics in the clinic has been included as an important preventive measure.

Simultaneous detection of Salmonella pathogenicity island 2 and its antibiotic resistance genes from seafood

Salmonella enterica serovars are virulent pathogens of humans and animals with many strains possessing multiple drug resistance traits. They have been found to carry resistance to ampicillin, chloramphenicol, florfenicol, streptomycin, sulfonamides, and tetracycline (ACSSuT-resistant). A rapid and sensitive multiplex PCR (mPCR)-based assay was developed for the detection of Salmonella serovars from seafood. Six sets of primers which are one primer pair targeting Salmonella specific gene invA (284 bp), two Salmonella pathogenicity island 2 (SPI-2) genes ssaT (780 bp) and sseF (888 bp) and three antibiotic resistance genes floR (198 bp), sul1 (425 bp), tetG (550 bp) were used for the study. The specificity and sensitivity of the assay were tested by spiking shrimp/fish/clam homogenate with viable cells of Salmonella. This assay allows for the cost effective and reliable detection of pathogenic Salmonella enterica from seafood. The mPCR developed in the present study proved to be a potent analytical tool for the rapid identification of multidrug-resistant Salmonella serovars from seafood.