Emergence of Plasmid-Borne dfrA14 Trimethoprim Resistance Gene in Shigella sonnei

Genetics of resistance to trimethoprim in cotrimoxazole resistant uropathogenic Escherichia coli: integrons, transposons, and single gene cassettes

Cotrimoxazole, the combined formulation of sulfamethoxazole and trimethoprim, is one of the treatments of choice for several infectious diseases, particularly urinary tract infections. Both components of cotrimoxazole are synthetic antimicrobial drugs, and their combination was introduced into medical therapeutics about half a century ago. In Gram-negative bacteria, resistance to cotrimoxazole is widespread, being based on the acquisition of genes from the auxiliary genome that confer resistance to each of its antibacterial components. Starting from previous knowledge on the genotype of resistance to sulfamethoxazole in a collection of cotrimoxazole resistant uropathogenic Escherichia coli strains, this work focused on the identification of the genetic bases of the trimethoprim resistance of these same strains. Molecular techniques employed included PCR and Sanger sequencing of specific amplicons, conjugation experiments and NGS sequencing of the transferred plasmids. Mobile genetic elements conferring the trimethoprim resistance phenotype were identified and included integrons, transposons and single gene cassettes. Therefore, strains exhibited several ways to jointly resist both antibiotics, implying different levels of genetic linkage between genes conferring resistance to sulfamethoxazole (sul) and trimethoprim (dfrA). Two structures were particularly interesting because they represented a highly cohesive arrangements ensuring cotrimoxazole resistance. They both carried a single gene cassette, dfrA14 or dfrA1, integrated in two different points of a conserved cluster sul2-strA-strB, carried on transferable plasmids. The results suggest that the pressure exerted by cotrimoxazole on bacteria of our environment is still promoting the evolution toward increasingly compact gene arrangements, carried by mobile genetic elements that move them in the genome and also transfer them horizontally among bacteria.

Pesticides residues in leafy green vegetables and irrigation waters in Accra, Ghana

Pesticides are used in vegetable farming to control pests and diseases, reduce crop losses and improve yield. The study examined pesticide residues in irrigation waters and leafy green vegetables grown in some farming areas in Accra, Ghana. Three types of irrigation water sources (n = 23) and two exotic and four indigenous Ghanaian leafy vegetables (n = 34) from 10 farming areas in Accra, Ghana were collected and examined for 15 organochlorines, 13 organophosphorus and 9 synthetic pyrethroids pesticide residues using the modified QuEChERS procedure. Pesticide residues were detected on 50% (17/34) of the leafy vegetable and 52% (12/23) of the irrigation water samples analysed. Chlorpyrifos and deltamethrin were the most detected pesticide residues in the vegetables and irrigation water. About 26.5% of the vegetables contained pesticide residues exceeding the EU maximum residue limits, so vegetable farmers should be encouraged to comply with appropriate measures on pesticide use to enhance food safety.

Antibiotic-Resistance Profiles and Genetic Diversity of Shigella Isolates in China: Implications for Control Strategies

The urgent need for comprehensive and systematic analyses of Shigella as the key pathogen led us to meticulously explore the epidemiology and molecular attributes of Shigella isolates. Accordingly, we procured 24 isolates (10 from Xinjiang and 14 from Wuhan, China) and performed serotype identification and antimicrobial susceptibility testing. Resistance gene detection and homology analysis by polymerase chain reaction and pulsed-field gel electrophoresis (PFGE), respectively, were performed for genetic diversity analysis. All isolates were identified as Shigella flexneri, with 70% (35.4-91.9%) and 30% (8.1-64.6%) of the Xinjiang isolates and 85.7% (56.2-97.5%) and 14.3% (2/14, 2.5-43.9%) of the Wuhan isolates belonging to serotype 2a and serotype 2b, respectively. All isolates displayed resistance to at least two antibiotics and complete resistance to ampicillin. Multidrug resistance (MDR) was recorded in 70.8% (48.8-86.6%) of isolates, with Xinjiang isolates exhibiting relatively higher resistance to ampicillin-sulbactam, piperacillin, ceftriaxone, and aztreonam. Conversely, Wuhan isolates displayed higher MDR and resistance to tetracycline, ciprofloxacin, levofloxacin, and cefepime relative to Xinjiang isolates. Molecular scrutiny of antibiotic-resistance determinants revealed that blaTEM was the main mechanism of ampicillin resistance, blaCTX-M was the main gene for resistance to third- and fourth-generation cephalosporins, and tetB was the predominant gene associated with tetracycline resistance. Four Xinjiang and seven Wuhan isolates shared T1-clone types (>85%), and two Xinjiang and one Wuhan isolates were derived from the T6 clone with a high similarity of 87%. Six PFGE patterns (T1, T2, T5, T6-3, T8, and T10) of S. flexneri were associated with MDR. Thus, there is a critical need for robust surveillance and control strategies in managing Shigella infections, along with the development of targeted interventions and antimicrobial stewardship programs tailored to the distinct characteristics of Shigella isolates in different regions of China.

Genetic relatedness, antibiotic resistance, and virulence of Klebsiella pneumoniae isolated from health care and food sources in Wuhan, China

BACKGROUND

To investigate genetic relatedness and antibiotic resistance of Klebsiella pneumoniae from retail meat samples, clinical source samples, and hospital environmental samples in Wuhan, China.

METHODS

Hypermucoviscosity and biofilm formation of K. pneumoniae were assessed by string test and crystal violet staining. MICs of 18 antimicrobials were determined by broth microdilution. PCR detected 14 antibiotic resistance genes. Genetic relatedness and clonal dissemination were analyzed by PFGE.

RESULTS

Among 5,730 samples, 46 were tested positive for K pneumoniae, with higher rates observed in meat (23.4%) than in clinical samples (0.6%) and hospital environmental samples (8.0%). Meat-derived isolates showed high resistance to tetracycline (36.4%, 4/11), sulfonamide (27.3%, 3/11), and gentamicin (27.3%, 3/11), whereas clinical isolates exhibited significant resistance to ampicillin-sulbactam (32.3%, 10/31). Multidrug resistance was observed in 17.4% (8/46) of the isolates, particularly in hospital environmental samples (3/4). Biofilm production was observed in 88.1% (37/42) of K pneumoniae. Pulsed-field gel electrophoresis analysis revealed patient-to-patient K pneumoniae transmission, transmission between patients and hospital environment, as well as cross-contamination between markets.

CONCLUSIONS

The findings underscore the importance of comprehensive surveillance, infection control, and judicious antibiotic use in mitigating the impact of K pneumoniae on public health, especially in the food chain and health care settings.

Genomic characterization of a WHO critical priority isolate Enterobacter kobei ST2070 harboring OXA-10, KPC-2, and CTX-M-12 recovered from a water irrigation channel in Ecuador

The discharge of untreated or partially treated wastewater can have detrimental impacts on the quality of water bodies, posing a significant threat to public health and the environment. In Ecuador, previous research indicates a high prevalence of antimicrobial resistant (AMR) bacteria in surface waters affected by human activities, including irrigation channels. In this study, we analyzed sediment samples collected from an irrigation channel utilized for agricultural purposes in northern Ecuador, using microbiological techniques and whole-genome sequencing (WGS). Our investigation revealed the first documented occurrence of E. kobei in Ecuador and the initial report of environmental E. kobei ST2070. Furthermore, we identified the coexistence of OXA-10-type class D β-lactamase and KPC-2-type class A β-lactamase in the E. kobei isolate (UTA41), representing the first report of such a phenomenon in this species. Additionally, we detected various antibiotic resistance genes in the E. kobei UTA41 isolate, including blaCTX-M-12, fosA, aac(6')-lb, sul2, msr(E), and mph(A), as well as virulence genes such as bacterial efflux pump and siderophore biosynthesis genes. We also identified two intact prophage regions (Entero_186 and Klebsi_phiKO2) in the isolate. Our study presents the first evidence of E. kobei isolate containing two carbapenemase-encoding genes in environmental samples from Latin America. This finding indicates the potential spread of critical-priority bacteria in water samples originating from anthropogenic sources, such as urban wastewater discharges and livestock facilities.

Genetic insights of antibiotic resistance, pathogenicity (virulence) and phylogenetic relationship of Escherichia coli strains isolated from livestock, poultry and their handlers - a one health snapshot

BACKGROUND

Pathogenic and non-pathogenic strains of Escherichia coli harbouring antibiotic resistance genes (ARGs) from any source (clinical samples, animal settings, or environment) might be transmitted and contribute to the spread and increase of antibiotic resistance in the biosphere. The goal of this study was to investigate the genome to decipher the repertoire of ARGs, virulence genes carried by E. coli strains isolated from livestock, poultry, and their handlers (humans), and then unveil the genetic relatedness between the strains.

METHODS

Whole genome sequencing was done to investigate the genetic makeup of E. coli isolates (n = 20) [swine (n = 2), cattle (n = 2), sheep (n = 4), poultry (n = 7), and animal handlers (n = 5)] from southern India. The detection of resistome, virulome, biofilm forming genes, mobile genetic elements (MGE), followed by multilocus sequence typing (MLST) and phylogenetic analyses, were performed.

RESULTS

E. coli strains were found to be multi drug resistant, with a resistome encompassing > 20 ARGs, the virulome-17-22 genes, and > 20 key biofilm genes. MGE analysis showed four E. coli isolates (host: poultry, swine and cattle) harbouring composite transposons with ARGs/virulence genes (blaTEM, dfr, qnr/nleB, tir, eae,and esp) with the potential for horizontal transfer. MLST analyses revealed the presence of ST937 and ST3107 in both livestock/poultry and their handlers. Phylogenomic analyses with global E. coli isolates (human/livestock/poultry hosts) showed close relatedness with strains originating from different parts of the world (the United States, China, etc.).

CONCLUSION

The current study emphasizes the circulation of strains of pathogenic sequence types of clinical importance, carrying a diverse repertoire of genes associated with antibiotic resistance, biofilm formation and virulence properties in animal settings, necessitating immediate mitigation measures to reduce the risk of spread across the biosphere.

Microbiological Quality and Antimicrobial Resistance of Commercial Probiotic Products for Food-Producing Animals

Probiotics have been popularly used in livestock production as an alternative to antibiotics. This study aimed to investigate the microbiological quality and phenotypic and genotypic antimicrobial resistance of bacteria in probiotic products sold for food animals. A total of 45 probiotic products were examined for the number of viable cells, species, and antimicrobial susceptibility; the contamination of Escherichia coli and Salmonella; and the presence of 112 genes encoding resistance to clinically important antimicrobials and transferability of AMR determinants. The results showed that 29 of 45 products (64.4%) were incorrectly labeled in either number of viable cells or bacterial species. None of the tested products were contaminated with E. coli and Salmonella. A total of 33 out of 64 bacterial isolates (51.6%) exhibited resistance to at least one antimicrobial agent. Of the 45 products tested, 16 (35.5%) carried AMR genes. Almost all AMR genes detected in probiotic products were not correlated to the AMR phenotype of probiotic strains formulated in the products. Three streptomycin-resistant Lactobacillus isolates could horizontally transfer their AMR determinants. The findings demonstrated that the probiotic products could serve as reservoirs for the spread of AMR genes and may not yield benefits to animals as claimed. The need for the adequate quality control of probiotic products is highlighted.

Phytochemical constituents of Inula britannica as potential inhibitors of dihydrofolate reductase: A strategic approach against shigellosis

Shigella dysenteriae type 1 is considered as an epidemic in different developing countries, which is responsible for the most severe form of bacterial dysentery. It habitually can develop to the most severe form of dysentery with deadly complications. Development of drugs against this disease is still ongoing. Therefore, we used in silico studies to screen the Inula britannica phytocompounds that are used in traditional Chinese and Kampo Medicines and have activities against different diseases. Spinacetin, eupatin, chrysoeriol and diosmetin were successfully passed through the docking-based screening and absorption, distribution, metabolism, excretion and toxicity (ADMET) filtration. The estimated docking affinities of eupatin, diosmetin, chrysoeriol and spinacetin with Dihydrofolate reductase type 1 (DHFR-1), were -6.5, -6.5, -6.3 and -6.1 kcal/mol, respectively. Which were selected for further investigations based on their favorable ADME/Tox characteristics. Then, the 100 ns molecular dynamics (MD) simulations of apo DHFR, spinacetin-DHFR, eupatin-DHFR, chrysoeriol-DHFR and diosmetin-DHFR complexes were carried out. The RMSD fluctuations of the spinacetin, eupatin, chrysoeriol and diosmetin inside the binding site were explored. Subsequently, the effect of binding Spinacetin, eupatin, chrysoeriol and diosmetin upon the dynamic stability of protein was assessed. Additionally, Principal Component Analysis (PCA) and Hydrogen bond analysis was performed for the apo protein and the protein ligand complexes. The results revealed that chrysoeriol and eupatin has good inhibitory effects against DHFR-1 as treatment for Shigella dysenteriae type when compared to other compounds under study. Hence this study implies that eupatin and chrysoeriol are a significantly potential drug like molecule for the treatment of Shigellosis and must undergo validation through in vivo and in vitro experiments.Communicated by Ramaswamy H. Sarma.

Evidence for Complex Interplay between Quorum Sensing and Antibiotic Resistance in Pseudomonas aeruginosa

Quorum sensing (QS) is a cell-density-dependent, intercellular communication system mediated by small diffusible signaling molecules. QS regulates a range of bacterial behaviors, including biofilm formation, virulence, drug resistance mechanisms, and antibiotic tolerance. Enzymes capable of degrading signaling molecules can interfere in QS-a process termed as quorum quenching (QQ). Remarkably, previous work reported some cases where enzymatic interference in QS was synergistic to antibiotics against Pseudomonas aeruginosa. The premise of combination therapy is attractive to fight against multidrug-resistant bacteria, yet comprehensive studies are lacking. Here, we evaluate the effects of QS signal disruption on the antibiotic resistance profile of P. aeruginosa by testing 222 antibiotics and antibacterial compounds from 15 different classes. We found compelling evidence that QS signal disruption does indeed affect antibiotic resistance (40% of all tested compounds; 89/222), albeit not always synergistically (not synergistic for 19% of compounds; 43/222). For some tested antibiotics, such as sulfathiazole and trimethoprim, we were able to relate the changes in resistance caused by QS signal disruption to the modulation of the expression of key genes of the folate biosynthetic pathway. Moreover, using a P. aeruginosa-based Caenorhabditis elegans killing model, we confirmed that enzymatic QQ modulates the effects of antibiotics on P. aeruginosa's pathogenicity in vivo. Altogether, these results show that signal disruption has profound and complex effects on the antibiotic resistance profile of P. aeruginosa. This work suggests that combination therapy including QQ and antibiotics should be discussed not globally but, rather, in case-by-case studies. IMPORTANCE Quorum sensing (QS) is a cell-density-dependent communication system used by a wide range of bacteria to coordinate behaviors. Strategies pertaining to the interference in QS are appealing approaches to control microbial behaviors that depend on QS, including virulence and biofilms. Interference in QS was previously reported to be synergistic with antibiotics, yet no systematic assessment exists. Here, we evaluate the potential of combination treatments using the model opportunistic human pathogen Pseudomonas aeruginosa PA14. In this model, collected data demonstrate that QS largely modulates the antibiotic resistance profile of PA14 (for more than 40% of the tested drugs). However, the outcome of combination treatments is synergistic for only 19% of them. This research demonstrates the complex relationship between QS and antibiotic resistance and suggests that combination therapy including QS inhibitors and antibiotics should be discussed not globally but, rather, in case-by-case studies.

Antimicrobial Resistance Dynamics in Chilean Shigella sonnei Strains Within Two Decades: Role of Shigella Resistance Locus Pathogenicity Island and Class 1 and Class 2 Integrons

Shigellosis is an enteric infectious disease in which antibiotic treatment is effective, shortening the duration of symptoms and reducing the excretion of the pathogen into the environment. Shigella spp., the etiologic agent, are considered emerging pathogens with a high public health impact due to the increase and global spread of multidrug-resistant (MDR) strains. Since Shigella resistance phenotype varies worldwide, we present an overview of the resistance phenotypes and associated genetic determinants present in 349 Chilean S. sonnei strains isolated during the periods 1995–1997, 2002–2004, 2008–2009, and 2010–2013. We detected a great variability in antibiotic susceptibility patterns, finding 300 (86%) MDR strains. Mobile genetic elements (MGE), such as plasmids, integrons, and genomic islands, have been associated with the MDR phenotypes. The Shigella resistance locus pathogenicity island (SRL PAI), which encodes for ampicillin, streptomycin, chloramphenicol, and tetracycline resistance genes, was detected by PCR in 100% of the strains isolated in 2008–2009 but was less frequent in isolates from other periods. The presence or absence of SRL PAI was also differentiated by pulsed-field gel electrophoresis. An atypical class 1 integron which harbors the blaOXA–1-aadA1-IS1 organization was detected as part of SRL PAI. The dfrA14 gene conferring trimethoprim resistance was present in 98.8% of the 2008–2009 isolates, distinguishing them from the SRL-positive strains isolated before that. Thus, it seems an SRL-dfrA14 S. sonnei clone spread during the 2008–2009 period and declined thereafter. Besides these, SRL-negative strains harboring class 2 integrons with or without resistance to nalidixic acid were detected from 2011 onward, suggesting the circulation of another clone. Whole-genome sequencing of selected strains confirmed the results obtained by PCR and phenotypic analysis. It is highlighted that 70.8% of the MDR strains harbored one or more of the MGE evaluated, while 15.2% lacked both SRL PAI and integrons. These results underscore the temporal dynamics of antimicrobial resistance in S. sonnei strains circulating in Chile, mainly determined by the spread of MGE conferring MDR phenotypes. Since shigellosis is endemic in Chile, constant surveillance of antimicrobial resistance phenotypes and their genetic basis is a priority to contribute to public health policies.

Assessing the drug resistance profiles of oral probiotic lozenges

Background

Probiotic lozenges have been developed to harvest the benefits of probiotics for oral health, but their long-term consumption may encourage the transfer of resistance genes from probiotics to commensals, and eventually to disease-causing bacteria.

Aim

To screen commercial probiotic lozenges for resistance to antibiotics, characterize the resistance determinants, and examine their transferability in vitro.

Results

Probiotics of all lozenges were resistant to glycopeptide, sulfonamide, and penicillin antibiotics, while some were resistant to aminoglycosides and cephalosporins. High minimum inhibitory concentrations (MICs) were detected for streptomycin (>128 µg/mL) and chloramphenicol (> 512 µg/mL) for all probiotics but only one was resistant to piperacillin (MIC = 32 µg/mL). PCR analysis detected erythromycin (erm(T), ermB or mefA) and fluoroquinolone (parC or gyr(A)) resistance genes in some lozenges although there were no resistant phenotypes. The dfrD, cat-TC, vatE, aadE, vanX, and aph(3")-III or ant(2")-I genes conferring resistance to trimethoprim, chloramphenicol, quinupristin/dalfopristin, vancomycin, and streptomycin, respectively, were detected in resistant probiotics. The rifampicin resistance gene rpoB was also present. We found no conjugal transfer of streptomycin resistance genes in our co-incubation experiments.

Conclusion

Our study represents the first antibiotic resistance profiling of probiotics from oral lozenges, thus highlighting the health risk especially in the prevailing threat of drug resistance globally.

Antibiotic Resistance Profile of Salmonella enterica Isolated from Exotic and Indigenous Leafy Green Vegetables in Accra, Ghana

ABSTRACT

Fresh produce-borne enteric bacterial pathogens that are resistant to antibiotics have posed serious challenges to food safety and public health worldwide. This study was conducted to evaluate the antibiotic resistance profiles of Salmonella enterica isolates (n = 33) recovered from exotic and indigenous leafy green vegetable samples (n = 328) collected from 50 vegetable farms in 12 farming areas and 37 vegetable sellers in four market centers in Accra, Ghana, from March 2016 to March 2017 and to determine the distribution of integrons among antibiotic-resistant isolates. The susceptibility of the Salmonella isolates to 12 antibiotics was assayed with the standard disk diffusion assay. The MICs of the five most resisted antibiotics were determined with a twofold macrodilution method. A PCR assay was used to detect the presence of integrons in Salmonella isolates, and PCR products with the amplified integron gene cassette were purified and sequenced with the Sanger sequencing technology. The Salmonella isolates used in the study were resistant to at least one tested antibiotic, and 30.3% (10 of 33) of the isolates were multidrug resistant. Most isolates (81.8%) were resistant to sulfisoxazole. The MICs of tetracycline, cefoxitin, streptomycin, ampicillin, and sulfisoxazole were 16, 32, 64, 64, and >1,024 μg/mL, respectively. Five patterns of multidrug resistance were observed among the Salmonella isolates, and the most common patterns were AAuFox (30.3%) and AAuFoxSSu (18.1%). One (3.0%) of the 33 Salmonella isolates tested positive for the class 1 integron, with a gene cassette of about 800 bp. Nucleotide sequencing revealed that this class 1 integron carried a single gene, dfrA7. Further studies are needed to determine whether the consumption of contaminated leafy green vegetables is a route for acquiring antibiotic-resistant Salmonella in Accra, Ghana.

HIGHLIGHTS

Presence of β-Lactamase-producing Enterobacterales and Salmonella Isolates in Marine Mammals

Marine mammals have been described as sentinels of the health of marine ecosystems. Therefore, the aim of this study was to investigate (i) the presence of extended-spectrum β-lactamase (ESBL)- and AmpC-producing Enterobacterales, which comprise several bacterial families important to the healthcare sector, as well as (ii) the presence of Salmonella in these coastal animals. The antimicrobial resistance pheno- and genotypes, as well as biocide susceptibility of Enterobacterales isolated from stranded marine mammals, were determined prior to their rehabilitation. All E. coli isolates (n = 27) were screened for virulence genes via DNA-based microarray, and twelve selected E. coli isolates were analyzed by whole-genome sequencing. Seventy-one percent of the Enterobacterales isolates exhibited a multidrug-resistant (MDR) pheno- and genotype. The gene bla_CMY (n = 51) was the predominant β-lactamase gene. In addition, bla_TEM-1 (n = 38), bla_SHV-33 (n = 8), bla_CTX-M-15 (n = 7), bla_OXA-1 (n = 7), bla_SHV-11 (n = 3), and bla_DHA-1 (n = 2) were detected. The most prevalent non-β-lactamase genes were sul2 (n = 38), strA (n = 34), strB (n = 34), and tet(A) (n = 34). Escherichia coli isolates belonging to the pandemic sequence types (STs) ST38, ST167, and ST648 were identified. Among Salmonella isolates (n = 18), S. Havana was the most prevalent serotype. The present study revealed a high prevalence of MDR bacteria and the presence of pandemic high-risk clones, both of which are indicators of anthropogenic antimicrobial pollution, in marine mammals.

Proteomic analysis reveals differential responses of Listeria monocytogenes to free and nanoencapsulated nisin

The ability of Listeria monocytogenes grow on ready-to-eat food is a major concern in food safety. Natural antimicrobials, such as nisin, can be used to control this pathogen, but the increasing reports of nisin tolerance and resistance make necessary novel approaches to increase its effectiveness, such as encapsulation. The goal of this study was to investigate how L. monocytogenes ATCC7644 regulates and shapes its proteome in response to sublethal doses of nisin and nisin-loaded phosphatidylcholine liposomes (lipo-nisin), compared to untreated cells growing under optimal conditions. Total proteins were extracted from L. monocytogenes cells treated for 1 h with free and lipo-nisin. As result, of 803 proteins that were initially identified, 64 and 53 proteins were differentially upregulated and downregulated respectively, in the treatments with nisin and lipo-nisin. Changes of Listeria proteome in response to treatments containing nisin were mainly related to ATP-binding cassette (ABC) transporter systems, transmembrane proteins, RNA-binding proteins and diverse stress response proteins. Some of the proteins uniquely detected in samples treated with free nisin were the membrane proteins SecD, Lmo1539 and the YfhO enzyme, which are related to translocation of L. monocytogenes virulence factors, activation of the LiaR-mediated stress defense and glycosylation of wall teichoic acid, respectively. The L. monocytogenes treated with liposome encapsulated nisin showed no expression of some stress response factors as compared with the free nisin, suggesting a reduction of stress mediated response and production of nisin-resistance factors by exposure to encapsulated nisin.

Supershed Escherichia coli O157:H7 Has Potential for Increased Persistence on the Rectoanal Junction Squamous Epithelial Cells and Antibiotic Resistance

Supershedding cattle shed Escherichia coli O157:H7 (O157) at ≥ 104 colony-forming units/g feces. We recently demonstrated that a supershed O157 (SS-O157) strain, SS-17, hyperadheres to the rectoanal junction (RAJ) squamous epithelial (RSE) cells which may contribute to SS-O157 persistence at this site in greater numbers, thereby increasing the fecal O157 load characterizing the supershedding phenomenon. In order to verify if this would be the signature adherence profile of any SS-O157, we tested additional SS-O157 isolates (n = 101; each from a different animal) in the RSE cell adherence assay. Similar to SS-17, all 101 SS-O157 exhibited aggregative adherence on RSE cells, with 56% attaching strongly (>10 bacteria/cell; hyperadherent) and 44% attaching moderately (1-10 bacteria/cells). Strain typing using Polymorphic Amplified Typing Sequences (PATS) analysis assigned the 101 SS-O157 into 5 major clades but not to any predominant genotype. Interestingly, 69% of SS-O157 isolates were identical to human O157 outbreak strains based on pulsed field gel electrophoresis profiles (CDC PulseNet Database), grouped into two clades by PATS distinguishing them from remaining SS-O157, and were hyperadherent on RSE cells. A subset of SS-O157 isolates (n = 53) representing different PATS and RSE cell adherence profiles were analyzed for antibiotic resistance (AR). Several SS-O157 (30/53) showed resistance to sulfisoxazole, and one isolate was resistant to both sulfisoxazole and tetracycline. Minimum inhibitory concentration (MIC) tests confirmed some of the resistance observed using the Kirby-Bauer disk diffusion test. Each SS-O157 isolate carried at least 10 genes associated with AR. However, genes directly associated with AR were rarely amplified: aac (3)-IV in 2 isolates, sul2 in 3 isolates, and tetB in one isolate. The integrase gene, int, linked with integron-based AR acquisition/transmission, was identified in 92% of SS-O157 isolates. Our results indicate that SS-O157 isolates could potentially persist longer at the bovine RAJ but exhibit limited resistance towards clinical antibiotics.

Shigella: Antibiotic-Resistance Mechanisms And New Horizons For Treatment

Shigella spp. are a common cause of diarrheal disease and have remained an important pathogen responsible for increased rates of morbidity and mortality caused by dysentery each year around the globe. Antibiotic treatment of Shigella infections plays an essential role in reducing prevalence and death rates of the disease. However, treatment of these infections remains a challenge, due to the global rise in broad-spectrum resistance to many antibiotics. Drug resistance in Shigella spp. can result from many mechanisms, such as decrease in cellular permeability, extrusion of drugs by active efflux pumps, and overexpression of drug-modifying and -inactivating enzymes or target modification by mutation. Therefore, there is an increasing need for identification and evolution of alternative therapeutic strategies presenting innovative avenues against Shigella infections, as well as paying further attention to this infection. The current review focuses on various antibiotic-resistance mechanisms of Shigella spp. with a particular emphasis on epidemiology and new mechanisms of resistance and their acquisition, and also discusses the status of novel strategies for treatment of Shigella infection and vaccine candidates currently under evaluation in preclinical or clinical phases.

Use of whole genome sequencing in surveillance for antimicrobial-resistant Shigella sonnei infections acquired from domestic and international sources

Shigella species are a major cause of gastroenteritis worldwide, and Shigella sonnei is the most common species isolated within the United States. Previous surveillance work in Pennsylvania documented increased antimicrobial resistance (AMR) in S. sonnei associated with reported illnesses. The present study examined a subset of these isolates by whole genome sequencing (WGS) to determine the relationship between domestic and international isolates, to identify genes that may be useful for identifying specific Global Lineages of S. sonnei and to test the accuracy of WGS for predicting AMR phenotype. A collection of 22 antimicrobial-resistant isolates from patients infected within the United States or while travelling internationally between 2009 and 2014 was chosen for WGS. Phylogenetic analysis revealed both international and domestic isolates were one of two previously defined Global Lineages of S. sonnei, designated Lineage II and Lineage III. Twelve of 17 alleles tested distinguish these two lineages. Lastly, genome analysis was used to identify AMR determinants. Genotypic analysis was concordant with phenotypic resistance for six of eight antibiotic classes. For aminoglycosides and trimethoprim, resistance genes were identified in two and three phenotypically sensitive isolates, respectively. This article contains data hosted by Microreact.

Delineating the origins of the multidrug-resistant pathogens in ornamental fish farms by multilocus sequence typing and identification of a novel multidrug-resistant plasmid

To evaluate the overuse of antibiotics and to identify the origin of pathogens in the ornamental fish industry, we conducted a field investigation of three representative fish farms in Liaoning province, China. Drug-resistant pathogens in the fishponds and groundwater were isolated and subtyped by multilocus sequence typing (MLST). In total, 33 pathogenic strains, including Aeromonas veronii and five other pathogens, were isolated from diseased fish and from groundwater. MLST revealed that A. veronii obtained from diseased fish in three fish farms can be subtyped into four sequence types, which were also identified in the corresponding groundwater. All of the isolates obtained from diseased fish showed resistance to at least four antibiotics. Notably, Citrobacter freundii JY-17 exhibited resistance to the majority of the antibiotics and was a carrier of a megaplasmid with 15 drug resistance genes. PCR assays targeting β-lactam, kanamycin, macrolide, phenicol, sulfonamide, and trimethoprim resistance genes in the pathogens from the diseased fish and groundwater were also conducted. The results revealed strong correlations between antibiotic treatment and increased antimicrobial resistance in fish pathogens. The results suggested that groundwater is the origin of the pathogens in ornamental fish. Antibiotic treatment of ornamental fish promoted the emergence of resistant pathogens.

Closed Genome and Comparative Phylogenetic Analysis of the Clinical Multidrug Resistant Shigella sonnei Strain 866

Shigella sonnei is responsible for the majority of shigellosis infections in the US with over 500,000 cases reported annually. Here, we present the complete genome of the clinical multidrug resistant (MDR) strain 866, which is highly susceptible to bacteriophage infections. The strain has a circular chromosome of 4.85 Mb and carries a 113 kb MDR plasmid. This IncB/O/K/Z-type plasmid, termed p866, confers resistance to five different classes of antibiotics including ß-lactamase, sulfonamide, tetracycline, aminoglycoside, and trimethoprim. Comparative analysis of the plasmid architecture and gene inventory revealed that p866 shares its plasmid backbone with previously described IncB/O/K/Z-type Shigella spp. and Escherichia coli plasmids, but is differentiated by the insertion of antibiotic resistance cassettes, which we found associated with mobile genetic elements such as Tn3, Tn7, and Tn10. A whole genome-derived phylogenetic reconstruction showed the evolutionary relationships of S. sonnei strain 866 and the four established Shigella species, highlighting the clonal nature of S. sonnei.

An integrative, multi-omics approach towards the prioritization of Klebsiella pneumoniae drug targets

Klebsiella pneumoniae (Kp) is a globally disseminated opportunistic pathogen that can cause life-threatening infections. It has been found as the culprit of many infection outbreaks in hospital environments, being particularly aggressive towards newborns and adults under intensive care. Many Kp strains produce extended-spectrum β-lactamases, enzymes that promote resistance against antibiotics used to fight these infections. The presence of other resistance determinants leading to multidrug-resistance also limit therapeutic options, and the use of 'last-resort' drugs, such as polymyxins, is not uncommon. The global emergence and spread of resistant strains underline the need for novel antimicrobials against Kp and related bacterial pathogens. To tackle this great challenge, we generated multiple layers of 'omics' data related to Kp and prioritized proteins that could serve as attractive targets for antimicrobial development. Genomics, transcriptomics, structuromic and metabolic information were integrated in order to prioritize candidate targets, and this data compendium is freely available as a web server. Twenty-nine proteins with desirable characteristics from a drug development perspective were shortlisted, which participate in important processes such as lipid synthesis, cofactor production, and core metabolism. Collectively, our results point towards novel targets for the control of Kp and related bacterial pathogens.

Genomic epidemiology of Shigella in the United Kingdom shows transmission of pathogen sublineages and determinants of antimicrobial resistance

Shigella are globally important diarrhoeal pathogens that are endemic in low-to-middle income nations and also occur in high income nations, typically in travellers or community-based risk-groups. Shigella phylogenetics reveals population structures that are more reliable than those built with traditional typing methods, and has identified sublineages associated with specific geographical regions or patient groups. Genomic analyses reveal temporal increases in Shigella antimicrobial resistance (AMR) gene content, which is frequently encoded on mobile genetic elements. Here, we whole genome sequenced representative subsamples of S. flexneri 2a and S. sonnei (n = 366) from the United Kingdom from 2008 to 2014, and analysed these alongside publicly available data to make qualitative insights on the genomic epidemiology of shigellosis and its AMR within the broader global context. Combined phylogenetic, epidemiological and genomic anlayses revealed the presence of domestically-circulating sublineages in patient risk-groups and the importation of travel-related sublineages from both Africa and Asia, including ciprofloxacin-resistant sublineages of both species from Asia. Genomic analyses revealed common AMR determinants among travel-related and domestically-acquired isolates, and the evolution of mutations associated with reduced quinolone susceptibility in domestically-circulating sublineages. Collectively, this study provides unprecedented insights on the contribution and mobility of endemic and travel-imported sublineages and AMR determinants responsible for disease in a high-income nation.

Whole genome sequencing of Shigella sonnei through PulseNet Latin America and Caribbean: advancing global surveillance of foodborne illnesses

Objectives

Shigella sonnei is a globally important diarrhoeal pathogen tracked through the surveillance network PulseNet Latin America and Caribbean (PNLA&C), which participates in PulseNet International. PNLA&C laboratories use common molecular techniques to track pathogens causing foodborne illness. We aimed to demonstrate the possibility and advantages of transitioning to whole genome sequencing (WGS) for surveillance within existing networks across a continent where S. sonnei is endemic.

Methods

We applied WGS to representative archive isolates of S. sonnei (n = 323) from laboratories in nine PNLA&C countries to generate a regional phylogenomic reference for S. sonnei and put this in the global context. We used this reference to contextualise 16 S. sonnei from three Argentinian outbreaks, using locally generated sequence data. Assembled genome sequences were used to predict antimicrobial resistance (AMR) phenotypes and identify AMR determinants.

Results

S. sonnei isolates clustered in five Latin American sublineages in the global phylogeny, with many (46%, 149 of 323) belonging to previously undescribed sublineages. Predicted multidrug resistance was common (77%, 249 of 323), and clinically relevant differences in AMR were found among sublineages. The regional overview showed that Argentinian outbreak isolates belonged to distinct sublineages and had different epidemiologic origins.

Conclusions

Latin America contains novel genetic diversity of S. sonnei that is relevant on a global scale and commonly exhibits multidrug resistance. Retrospective passive surveillance with WGS has utility for informing treatment, identifying regionally epidemic sublineages and providing a framework for interpretation of prospective, locally sequenced outbreaks.

Socioeconomic Determinants of Cipro-floxacin-Resistant Shigella Infections in Bangladeshi Children

Background:

Shigella species (spp.) are a leading cause of moderate to severe diarrhea in children worldwide. The recent emergence of quinolone-resistant Shigella spp. gives cause for concern, and South Asia has been identified as a reservoir for global spread. The influence of socioeconomic status on antimicrobial resistance in developing countries, such as those in South Asia, remains unknown.

Methods:

We used data collected from 2009 to 2014 from a hospital specializing in the treatment of diarrhea in Dhaka, Bangladesh, to determine the relationship between ciprofloxacin-resistant Shigella spp. isolates and measures of socioeconomic status in Bangladeshi children less than 5 years of age.

Results:

We found 2.7% (230/8,672) of children who presented with diarrhea had Shigella spp. isolated from their stool, and 50% (115/230) had resistance to ciprofloxacin. Using multivariable logistic regression analysis, we found that children from families where the father's income was in the highest quintile had significantly higher odds of having ciprofloxacin-resistant Shigella spp. compared to children in the lowest quintile (OR = 6.1, CI 1.9-19). Factors protective against the development of resistance included access to improved sanitation (OR = 0.27, CI 0.11-0.7), and improved water sources (OR = 0.48, CI 0.25-0.92). We did not find a relationship between ciprofloxacin resistance and other proxies for socioeconomic status, including the presence of animals in the home, nutritional status, paternal education level, and the number of family members in the home.

Conclusions:

Although the associations between wealth and antimicrobial resistance are not fully understood, possible explanations include increased access and use of antibiotics, greater access to healthcare facilities and thus resistant pathogens, or greater consumption of commercially produced foods prepared with antibiotics.