Antimicrobial Resistance Traits Research Articles

Determination of Antibiotic Resistance Profile and Virulence Genes in Escherichia coli Isolates from Palestinian Patients

Introduction: Escherichia coli (E. coli) is considered one of the most frequent intestinal and extraintestinal pathogen.
 Methods: A total of 49 isolates of E. coli were collected from different clinical samples, from different hospitals in Northern West Bank-Palestine, during January-March 2019.
 Aims: To detect the distribution of Type III secretion system (T3SS) genes, class 1, 2 and 3 integrons, virulence factors (fyuA, papGIII, iutA and sfa⁄foc) using multiplex PCR and antibiotic resistance using disc diffusion method.
 Results: In this study, E. coli isolates showed high resistance rate against different types of antibiotics and 71.4% of the isolates were multidrug resistant (MDR). Only class 1 integron was detected in these isolates with prevalence 57%, and 65.7% of MDR isolates carried integron genes. The prevalence of T3SS genes was 0.0%. In addition, results of this study showed that the prevalence of virulence genes papGIII, sfa⁄foc, fyuA and iutA was 4.1%, 40%, 64%, and 79.6%, respectively.
 Conclusions: The isolates of E. coli showed high resistance rate against different types of antibiotics. The co-occurrence of class 1 integrons and antimicrobial resistance genes in these isolates is an additional threat for spread of the antimicrobial resistance traits which may further complicate future strategies for treatment the infections caused by this pathogen. In addition, E. coli isolated from Palestinian patients showed one or more virulence factors that could increase their pathogenic potential.

Phenotypic and Genotypic Antimicrobial Resistance Traits of Vibrio cholerae Non-O1/Non-O139 Isolated From a Large Austrian Lake Frequently Associated With Cases of Human Infection.

Vibrio cholerae belonging to serogroups other than O1 and O139 are opportunistic pathogens which cause infections with a variety of clinical symptoms. Due to the increasing number of V. cholerae non-O1/non-O139 infections in association with recreational waters in the past two decades, they have received increasing attention in recent literature and by public health authorities. Since the treatment of choice is the administration of antibiotics, we investigated the distribution of antimicrobial resistance properties in a V. cholerae non-O1/non-O139 population in a large Austrian lake intensively used for recreation and in epidemiologically linked clinical isolates. In total, 82 environmental isolates - selected on the basis of comprehensive phylogenetic information - and nine clinical isolates were analyzed for their phenotypic antimicrobial susceptibility. The genomes of 46 environmental and eight clinical strains were screened for known genetic antimicrobial resistance traits in CARD and ResFinder databases. In general, antimicrobial susceptibility of the investigated V. cholerae population was high. The environmental strains were susceptible against most of the 16 tested antibiotics, except sulfonamides (97.5% resistant strains), streptomycin (39% resistant) and ampicillin (20.7% resistant). Clinical isolates partly showed additional resistance to amoxicillin-clavulanic acid. Genome analysis showed that crp, a regulator of multidrug efflux genes, and the bicyclomycin/multidrug efflux system of V. cholerae were present in all isolates. Nine isolates additionally carried variants of blaCARB–7 and blaCARB–9, determinants of beta-lactam resistance and six isolates carried catB9, a determinant of phenicol resistance. Three isolates had both blaCARB–7 and catB9. In 27 isolates, five out of six subfamilies of the MATE-family were present. For all isolates no genes conferring resistance to aminoglycosides, macrolides and sulfonamides were detected. The apparent lack of either known antimicrobial resistance traits or mobile genetic elements indicates that in cholera non-epidemic regions of the world, V. cholerae non-O1/non-O139 play a minor role as a reservoir of resistance in the environment. The discrepancies between the phenotypic and genome-based antimicrobial resistance assessment show that for V. cholerae non-O1/non-O139, resistance databases are currently inappropriate for an assessment of antimicrobial resistance. Continuous collection of both data over time may solve such discrepancies between genotype and phenotype in the future.

Antimicrobial Resistance and Resistance Determinant Insights into Multi-Drug Resistant Gram-Negative Bacteria Isolates from Paediatric Patients in China.

IntroductionThe emergence of multi-drug-resistant Gram-negative bacteria (GNB) is a concern in China and globally. This study investigated antimicrobial resistance traits and resistance determinant detection in GNB isolates from paediatric patients in China.MethodsIn the present study, a total of 170 isolates of GNB including the most prevalent Escherichia coli, Klebsiella pneumoniae and Acinetobacter baumannii were collected from Shenzhen Children’s Hospital, China. ESBLs production was confirmed by using the combination disc diffusion method, and carbapenemase production was confirmed by using a carbapenem inactivation method followed by antimicrobial susceptibility. In addition, β-lactamase-encoding genes and co-existence of plasmid-borne colistin resistance mcr-1 gene were determined by PCR and sequencing.ResultsOverall, 170 etiological agents (GNB) were recovered from 158 paediatric patients. The most prevalent species was E. coli 40% (n=68), followed by K. pneumoniae 17.64% (n=30), and Enterobacter cloacae 14.11% (n=24). Of 170 GNB, 71.76% (n=122) were multi-drug-resistant, 12.35% (n=21) extreme-drug resistant, and 7.64% (n=13) single-drug-resistant, while 8.23% (n=14) were sensitive to all of the studied antibiotics. The prevalence of ESBLs and carbapenemase producers were 60% and 17%, respectively. blaCTX-M was the most prevalent resistance gene (59.42%), followed by blaTEM (41.17%), blaSHV (34.270%), blaKPC (34.11%), blaOXA-48 (18.82%) and blaNDM-1 (17.64%).ConclusionThe present study provides insights into the linkage between the resistance patterns of GNB to commonly used antibiotics and their uses in China. The findings are useful for understanding the genetics of resistance traits and difficulty in tackling of GNB in paediatric patients.

Prevalence and characterization of methicillin-resistant Staphylococcus pseudintermedius from symptomatic companion animals in Northern Italy: Clonal diversity and novel sequence types

The aim of this study was to assess the prevalence, the genotypic diversity, the antimicrobial resistance traits of canine and feline clinical methicillin-resistant Staphylococcus pseudintermedius (MRSP) isolates in a diagnostic laboratory in Italy during 2015-2016.All isolates were characterized by multilocus sequence typing (MLST), staphylococcal cassette chromosome (SCC)-mec typing and staphylococcal protein A (spa)-typing. The resistance profiles were assessed by antimicrobial susceptibility testing and confirmed genotypically by the detection of mecA gene and by microarray analyses.The prevalence of MRSP isolates was high (31.6%). All the strains were multidrug resistant and the most frequent clone was ST71-SCCmec type II-III. These results confirm a high prevalence of MRSP amongst clinical samples from pets in Italy. These isolates show multidrug resistance features that are of concern both in veterinary and human medicine for clinical and epidemiological reasons.

β-lactam resistance genes in bacteriophage and bacterial DNA from wastewater, river water, and irrigation water in Washington State

Our objective was to determine whether β-lactamase genes are carried within bacteriophage capsids, as a first step towards exploring the possible role of bacteriophages as vehicles for dispersal of antimicrobial resistance genes through an agricultural region of Washington State. Water samples (n = 178) from municipal wastewater treatment plants, river and irrigation canals were collected over a period of eight months. The occurrence of four β-lactam resistance gene groups (blaTEM, blaCTX-M, blaPSE and blaCMY-2) and three carbapenem resistance genes (blaKPC, blaOXA-48-like, and blaNDM) in bacterial and phage fractions of water samples was evaluated by PCR. All of the seven targeted resistance genes were detected both in wastewater and river water samples. Relatively high proportions of samples (7.3%–64.9%) positive for resistance genes were found in bacteriophage fractions of water samples compared to the bacterial fractions (5.4%–36.8%). blaOXA-48-like (57.3%) and blaTEM (64.0%) were the most prevalent antimicrobial resistance genes detected at all the sampling points. Resistance genes are commonly present in treated wastewater flowing through municipal and agricultural environments, indicating a plausible role for this water in the dissemination of antimicrobial resistance traits, including blaCTX-M.

Virulence gene profiles, antimicrobial resistance and phylogenetic groups of fecal Escherichia coli strains isolated from broiler chickens in Algeria.

The objective of the study was to determine the virulence and antimicrobial resistance traits of 100 fecal E. coli strains isolated from clinically healthy chickens in Algeria. Most of isolates belonged to phylogroups A (45%) and B1 (37%) and showed a great diversity in DNA profiles. The genes fimH, tsh, entB, iutA, irp2, fyuA, iroN, sitA, etsA, etsB, eitA, iss, traT, ompT, hlyF, vat, ibeA, cvaA, cvaB5', cvaB3', cvaC, cma and cbi were detected. Combinations of virulence genes defined 67 virulence profiles. High resistance rates (62‑97%) were noted for amoxicillin, amoxicillin‑clavulanic acid, cefazolin, fluoroquinolones, tetracycline, trimethoprim, sulfonamides and sulfamethoxazole/ trimethoprim, and 93% of strains were multidrug‑resistant. Combinations of resistance phenotypes defined 59 resistance patterns. The genes blaTEM, blaSHV, blaCTX‑M‑1, tetA, tetB, qnrB, qnrS1, sul1, sul2, sul3, dfrA1, dfrA7, dfrA12 and dfrA14 were identified and class 1 integrons were detected in 49% of isolates. A rate of 37% of strains was resistant to mercury, with the presence of merA gene. The study reports the presence in the avian strains isolated from fecal swabs of virulence genes of plasmid origin characteristic of ExPEC strains associated with high resistance to first‑line antibiotics and class 1 integrons, this augurs a risk for human and animal health.

Competence for Natural Transformation Is Common among Clinical Strains of Resistant Acinetobacter spp.

Horizontal gene transfer events provide the basis for extensive dissemination of antimicrobial resistance traits between bacterial populations. Conjugation is considered to be the most frequent mechanism behind new resistance acquisitions in clinical pathogens but does not fully explain the resistance patterns seen in some bacterial genera. Gene transfer by natural transformation has been described for numerous clinical isolates, including some Acinetobacter species. The main aim of this study was to determine to what extent clinical, resistant Acinetobacter spp. isolates, express competence for natural transformation. Twenty-two clinical Acinetobacter spp. isolates collected over a 16-year time period, from five different geographical separated and/or distinct Portuguese Hospitals were tested for natural transformability. Fourteen isolates, including 11 A. baumannii, 2 A. nosocomialis and 1 Acinetobacter sp., were identified as competent on semisolid media facilitating surface-motility. Competent Acinetobacter isolates were found in all the hospitals tested. Furthermore, osmolarity was shown to influence the uptake of exogenous DNA by competent A. baumannii A118. Our study demonstrates that natural competence is common among clinical isolates of Acinetobacter spp., and hence likely an important trait for resistance acquisition.

Genomically Informed Strain-Specific Recovery of Shiga Toxin–Producing Escherichia coli during Foodborne Illness Outbreak Investigations

Next-generation sequencing plays an important role in the characterization of clinical bacterial isolates for source attribution purposes during investigations of foodborne illness outbreaks. Once an illness cluster and a suspect food vehicle have been identified, food testing is initiated for confirmation and to determine the scope of a contamination event so that the implicated lots may be removed from the marketplace. For biochemically diverse families of pathogens such as Shiga toxin-producing Escherichia coli (STEC), the ability to detect specific strains may be hampered by the lack of a universal selective enrichment approach for their recovery against high levels of background microbiota. The availability of whole genome sequence data for a given outbreak STEC strain prior to commencement of food testing may provide food microbiologists an opportunity to customize selective enrichment techniques favoring the recovery of the outbreak strain. Here we demonstrate the advantages of using the publicly available ResFinder tool in the analysis of STEC model strains belonging to serotypes O111 and O157 to determine antimicrobial resistance traits that can be used in formulating strain-specific enrichment media to enhance recovery of these strains from microbiologically complex food samples. The improved recovery from ground beef of model STEC strains with various antimicrobial resistance profiles was demonstrated using three classes of antibiotics as selective agents, suggesting the universal applicability of this new approach in supporting foodborne illness investigations.

Salmonella enterica recovery from river waters of the Maryland Eastern Shore reveals high serotype diversity and some multidrug resistance

The Delmarva Peninsula, a major agricultural and recreational region for the U.S. states of Delaware, Maryland and Virginia, experiences recurrent salmonellosis disease. Previous studies point to water environments as a potential persistent environmental reservoir of Salmonella enterica. To evaluate this hypothesis, water from the four main rivers of the Maryland Eastern Shore on the Delmarva Peninsula was tested for the presence of S. enterica, and recovered isolates were characterized for antimicrobial resistance. Sampling was performed in autumn and spring to evaluate temporal persistence at twenty four sites along the Choptank, Nanticoke, Pocomoke and Wicomico Rivers. Water (10 L) was filtered through sterile modified Moore swabs in situ. Swabs were selectively enriched for S. enterica and presumptive salmonellae were confirmed by PCR amplification of the Salmonella-specific invA and hilA genes. The serogroup of 402 isolates was determined, followed by serotype characterization for 157 isolates selected to represent all the identified serogroups across all samples. S. enterica was isolated from all the rivers in both seasons and was detected in 35/46 (65%) of surface water samples, with equivalent recovery in spring (70%) and fall (61%). The likelihood of isolating S. enterica was higher for the Nanticoke and Pocomoke Rivers, χ2 (3, N = 46) = 12.75, p < 0.01. In total, 18 serotypes of S. enterica were identified, and serotype diversity differed between the fall and spring samplings. Newport was the most frequently isolated serotype, both overall and in the fall, identified in 8/46 samples (17%). Typhimurium was the predominant serotype in spring. Some temporal and biogeographic patterns were observed in S. enterica recovery, but 6/18 serotypes were identified in both seasons. The majority (84%) of isolates were pan-susceptible, including all those tested from the Wicomico River (N = 19). Twenty five isolates (16%) from 9 samples were resistant to at least one antimicrobial, including serotypes Typhimurium, Newport, Litchfield, III 17:z10: e,n,x,z15, III 60:I and IV_40:z4: z32: -. Of the isolates that were resistant to a single antimicrobial (N = 12), resistance was to streptomycin or sulfisoxazole. Thirteen isolates were multidrug resistant, nine exhibiting resistance to ampicillin, sulfisoxazole, tetracycline, amoxicillin/clavulanic acid, cefoxitin and ceftriaxone, and four to sulfisoxazole and tetracycline. The widespread presence and diversity of S. enterica in Delmarva rivers are concerning given the frequent use of rivers and tributaries as a source of irrigation and for recreation. Future research should seek to determine specific point sources of S. enterica for surface river waters, and risks associated with acquisition of antimicrobial resistance traits.

Molecular Insights into Antimicrobial Resistance Traits of Commensal Human Gut Microbiota.

Antimicrobial resistance (AMR) among bacterial species that resides in complex ecosystems is a natural phenomenon. Indiscriminate use of antimicrobials in healthcare, livestock, and agriculture provides an evolutionary advantage to the resistant variants to dominate the ecosystem. Ascendency of resistant variants threatens the efficacy of most, if not all, of the antimicrobial drugs commonly used to prevent and/or cure microbial infections. Resistant phenotype is very common in enteric bacteria. The most common mechanisms of AMR are enzymatic modifications to the antimicrobials or their target molecules. In enteric bacteria, most of the resistance traits are acquired by horizontal gene transfer from closely or distantly related bacterial population. AMR traits are generally linked with mobile genetic elements (MGEs) and could rapidly disseminate to the bacterial species through horizontal gene transfer (HGT) from a pool of resistance genes. Although prevalence of AMR genes among pathogenic bacteria is widely studied in the interest of infectious disease management, the resistance profile and the genetic traits that encode resistance to the commensal microbiota residing in the gut of healthy humans are not well-studied. In the present study, we have characterized AMR phenotypes and genotypes of five dominant commensal enteric bacteria isolated from the gut of healthy Indians. Our study revealed that like pathogenic bacteria, enteric commensals are also multidrug-resistant. The genes encoding antibiotic resistance are physically linked with MGEs and could disseminate vertically to the progeny and laterally to the distantly related microbial species. Consequently, the AMR genes present in the chromosome of commensal gut bacteria could be a potential source of resistance functions for other enteric pathogens.

Antimicrobial Resistance and Virulence-Associated Traits of Campylobacter jejuni Isolated From Poultry Food Chain and Humans With Diarrhea.

The objective of this study was to test the prevalence of virulence-associated markers and antimicrobial resistance in 624 C. jejuni isolated from poultry food chain, i. e., chicken feces (n = 160), poultry carcasses (n = 157), poultry meat (n = 152) and from humans (n = 155). All human strains were positive for 9 out of 13 putative virulence genes responsible for expression of pathogenic factors involved in different stages of the infection. The presence of all markers was also high in strains from chicken feces, carcasses and meat although not all of them were identified in 100% of the isolates. On the other hand, the virB11, wlaN, and iam putative pathogenic genes were detected in only 1.9, 15.2, and 20.5% of strains, respectively. C. jejuni isolates, irrespective of the origin, were highly resistant to ciprofloxacin (92.5% isolates), followed by nalidixic acid (88.9%) and tetracycline (68.4%). In case of ciprofloxacin, significantly more isolates from poultry feces, carcasses and meat were resistant than those obtained from humans and the same relationship was observed for tetracycline where the isolates from chicken feces were more often resistant than C. jejuni of carcasses and meat origin. A low number of strains was resistant to streptomycin (18.4% isolates) and only 5 strains (0.8%) displayed resistance to erythromycin. A relationship between resistance to fluoroquinolones and presence of selected pathogenic markers was observed, e.g., from 83.3% strains with the virB11 to 93.4% with the docA genes were resistant to ciprofloxacin. The isolates that did not possess any of the pathogenic traits were also mainly resistant to this antimicrobial, although the number of such strains was usually low, except virB11 (612 isolates), wlaN (529 strains), and iam (496 isolates). Furthermore, resistance to tetracycline was somehow associated with the presence of the virulence associated genes wlaN and virB11 (56.8 and 75.0% isolates, respectively). The present study shows a high antimicrobial resistance to quinolones and tetracycline of C. jejuni isolated along poultry food chain and from patients with diarrhea, which was closely correlated with the presence of several virulence genes playing a role in the pathogenesis of Campylobacter infection.

Impact of systemic antimicrobial therapy on mucosal staphylococci in a population of dogs in Northwest England.

Antimicrobial-resistant bacteria are increasingly isolated from veterinary patients. To determine risk factors for antimicrobial resistance (AMR) among canine mucosal staphylococci following routine antimicrobial treatment with cefalexin (CFX), clavulanate-amoxicillin (AC), cefovecin (CVN), clindamycin (CD) or a fluoroquinolone (FQ). Mucosal swab samples (n = 463) were collected from 127 dogs pre-treatment, immediately, and at one- and three-months post-treatment. Staphylococci were identified phenotypically and biochemically as coagulase negative (CoNS) or coagulase positive (CoPS); CoPS were speciated by nuc gene PCR. Antimicrobial susceptibility was determined using disc diffusion and mecA gene carriage by PCR. Multilevel, multivariable models examined associations between risk factors and presence/absence of CoPS, meticillin resistance (MR), multidrug-resistance (MDR) and fluoroquinolone resistance (FQR). The percentage of samples with CoNS increased and with CoPS (including S. pseudintermedius) decreased immediately post-treatment with CFX, CVN and CD (P ≤ 0.001) and one month post-treatment with CD (P = 0.003). By three months post-treatment, there was no significant difference compared to pre-treatment samples. Immediately post-treatment with FQs there was significantly increased risk of isolating MRS (P = 0.002), MDR (P = 0.002) or FQR (P = 0.013) staphylococci and of MDR following CFX treatment (P = 0.019). The percentage of samples with AMR staphylococci declined from immediately to three months post-treatment and there was no significant difference between resistance prevalence at one or three months post-treatment for most AMR traits and treatment groups. Exceptions include increased MDR following FQ (P = 0.048) or CFX (P = 0.021), at one and three months post-treatment, respectively. Systemic antimicrobials impact on mucosal staphylococci. Immediately after therapy, the mucosa may be a reservoir for AMR staphylococci that are a source of mobile genetic elements carrying AMR genes.

Aeromonas hydrophila from marketed mullet (Mugil cephalus) in Egypt: PCR characterization of β-lactam resistance and virulence genes.

Aeromonas hydrophila has been isolated from various fish species in Egypt and is known to carry virulence and antimicrobial resistance genes, which pose a risk for public health. The aim of the present study is to report, for the first time, the infection of mullet (Mugil cephalus) with A. hydrophila and to clarify the potential association between antimicrobial resistance and virulence traits encoded in A. hydrophila. In this study, the occurrence of A. hydrophila in marketed mullet and the antimicrobial resistance phenotypes of these isolates were determined. Aeromonas hydrophila isolates were screened for the presence of virulence and β-lactam resistance genes; the correlation between both gene groups was also investigated. The infection rate of examined mullet with A. hydrophila was 37% (50/135). The highest antimicrobial resistance was detected to cefoxitin (100%), followed by ampicillin (84%), ceftazidime (56%) and cefotaxime (40%). Only 4% of the isolates were resistant to erythromycin; 6% were resistant to both gentamicin and kanamycin with no resistance to ciprofloxacin. Variable frequencies of virulence and β-lactam resistance genes were evident from PCR, where aerA and blaTEM predominated. The study also indicated a general weak positive correlation (R=0·3) between both virulence and β-lactam resistance genes. Some of the studied virulence genes (e.g. aerA:hlyA and hlyA:ast) were found to correlate positively. The presence of virulence and resistance genes in A. hydrophila from food sources poses a serious threat to public health. To our knowledge, this is the first report describing the occurrence of A. hydrophila in mullet and highlighting the coexistence of virulence and β-lactam resistance genes encoded by these bacteria. These data provide insights into the potential association of antimicrobial resistance and virulence genes in A. hydrophila from marketed mullet in Egypt, which could pose threats to humans even if a weak positive correlation exists between both genes.

Nasal carriage and antimicrobial susceptibility of Coagulase–Negative Staphylococci (CoNS) among healthy veterinary students in Greece

During last decades CoNS and especially the methicillin-resistant (MRCoNS) ones have become important pathogens and their infections are usually associated with healthcare settings. CoNS are considered as source of antimicrobial resistance traits for other bacteria and thus the evaluation of their prevalence in the community contributes significantly to the risk assessment in relation to public health. The aim of the present study was the investigationof the nasal carriage and antimicrobial susceptibly of CoNS among healthy veterinary students. From 81 healthy students of the School of Veterinary Medicine, Aristotle University of Thessaloniki, Greece, 24 strains were isolated from 22 (27.16%) students. Of them 54% were identified as Staphylococcus haemolyticus, 45.8% as Staphylococcus warneri, 16.6% as Staphylococcus epidermidis, 4.2% as Staphylococcus pasteuri and 4.2% as Staphylococcus capitis. All isolates were resistant to penicillin, 33.3% were resistant to amoxicillin/clavulanic acid, 29.2% to erythromycin, 4.2% to oxacillin, 4.2% to gentamycin and 4.2% to trimethoprim/sulfamethoxazole. The resistant to oxacillin isolate belonged to the S. epidermidis species and proved to carry the mecA gene. This study showed that the rate of nasal carriage of CoNS among veterinary students in Greece was low. The analysis of the standardised questionnaire, that was completed for each participating student during sampling, showed that pet owners tested positive for the coagulase-negative staphylococci were at a significantly lower rate (p-value=0.007) compared to non-pet owners. Moreover, among the participants who had visited a hospital over the last six months, the percentage of positive results in coagulase-negative staphylococci was significantly lower compared to that of the other participants (p-value=0.048). Although only one student found to carry methicillin-resistant S. epidermidis, its presence is evidence that this pathogen may circulate among veterinarians and the personnel of veterinary health establishments. Surveillance programs should also be performed in veterinary units because the emergence resistant bacteria in this environment may represent a risk to public health.

Staphylococcus edaphicus sp. nov., Isolated in Antarctica, Harbors the mecC Gene and Genomic Islands with a Suspected Role in Adaptation to Extreme Environments.

Two Gram-stain-positive, coagulase-negative staphylococcal strains were isolated from abiotic sources comprising stone fragments and sandy soil in James Ross Island, Antarctica. Here, we describe properties of a novel species of the genus Staphylococcus that has a 16S rRNA gene sequence nearly identical to that of Staphylococcus saprophyticus However, compared to S. saprophyticus and the next closest relatives, the new species demonstrates considerable phylogenetic distance at the whole-genome level, with an average nucleotide identity of <85% and inferred DNA-DNA hybridization of <30%. It forms a separate branch in the S. saprophyticus phylogenetic clade as confirmed by multilocus sequence analysis of six housekeeping genes, rpoB, hsp60, tuf, dnaJ, gap, and sod Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and key biochemical characteristics allowed these bacteria to be distinguished from their nearest phylogenetic neighbors. In contrast to S. saprophyticus subsp. saprophyticus, the novel strains are pyrrolidonyl arylamidase and β-glucuronidase positive and β-galactosidase negative, nitrate is reduced, and acid produced aerobically from d-mannose. Whole-genome sequencing of the 2.69-Mb large chromosome revealed the presence of a number of mobile genetic elements, including the 27-kb pseudo-staphylococcus cassette chromosome mec of strain P5085T (ψSCCmecP5085), harboring the mecC gene, two composite phage-inducible chromosomal islands probably essential to adaptation to extreme environments, and one complete and one defective prophage. Both strains are resistant to penicillin G, ampicillin, ceftazidime, methicillin, cefoxitin, and fosfomycin. We hypothesize that antibiotic resistance might represent an evolutionary advantage against beta-lactam producers, which are common in a polar environment. Based on these results, a novel species of the genus Staphylococcus is described and named Staphylococcus edaphicus sp. nov. The type strain is P5085T (= CCM 8730T = DSM 104441T).IMPORTANCE The description of Staphylococcus edaphicus sp. nov. enables the comparison of multidrug-resistant staphylococci from human and veterinary sources evolved in the globalized world to their geographically distant relative from the extreme Antarctic environment. Although this new species was not exposed to the pressure of antibiotic treatment in human or veterinary practice, mobile genetic elements carrying antimicrobial resistance genes were found in the genome. The genomic characteristics presented here elucidate the evolutionary relationships in the Staphylococcus genus with a special focus on antimicrobial resistance, pathogenicity, and survival traits. Genes encoded on mobile genetic elements were arranged in unique combinations but retained conserved locations for the integration of mobile genetic elements. These findings point to enormous plasticity of the staphylococcal pangenome, shaped by horizontal gene transfer. Thus, S. edaphicus can act not only as a reservoir of antibiotic resistance in a natural environment but also as a mediator for the spread and evolution of resistance genes.

Molecular Insights into Antimicrobial Resistance Traits of Multidrug Resistant Enteric Pathogens isolated from India

Emergence of antimicrobial resistant Gram-negative bacteria has created a serious global health crisis and threatens the effectiveness of most, if not all, antibiotics commonly used to prevent and treat bacterial infections. There is a dearth of detailed studies on the prevalence of antimicrobial resistance (AMR) patterns in India. Here, we have isolated and examined AMR patterns of 654 enteric pathogens and investigated complete genome sequences of isolates from six representative genera, which in aggregate encode resistance against 22 antibiotics representing nine distinct drug classes. This study revealed that ~97% isolates are resistant against ≥2 antibiotics, ~24% isolates are resistant against ≥10 antibiotics and ~3% isolates are resistant against ≥15 antibiotics. Analyses of whole genome sequences of six extensive drug resistant enteric pathogens revealed presence of multiple mobile genetic elements, which are physically linked with resistance traits. These elements are therefore appearing to be responsible for disseminating drug resistance among bacteria through horizontal gene transfer. The present study provides insights into the linkages between the resistance patterns to certain antibiotics and their usage in India. The findings would be useful to understand the genetics of resistance traits and severity of and difficulty in tackling AMR enteric pathogens.

Distribution of species and antimicrobial resistance among enterococci isolated from the fecal microbiota of captive blue-fronted parrot (Amazona aestiva) in Rio de Janeiro, Brazil

Enterococcal strains recovered from fecal samples of captive blue-fronted parrots (Amazona aestiva) assisted at two wild animal screening centers in Rio de Janeiro, Brazil, were identified as Enterococcus hirae (the predominant species; 75.3%), followed by Enterococcus faecalis (17.3%), Enterococcus casseliflavus (4.8%), Enterococcus gallinarum (1.7%), and Enterococcus hermanniensis (0.9%). All strains were susceptible to linezolid and teicoplanin. Rates of nonsusceptibility (including resistant and intermediate categories) to other 16 antimicrobials tested varied from 69.3% to 0.4%, A considerable proportion (48.0%) of the strains was multidrug-resistant and diverse genetic determinants associated with antimicrobial resistance were identified. Tetracycline-resistant strains carried the tet(M) and/or tet(L) genes. Macrolides resistance was associated with the erm(B), erm(A) and mefA genes, while 43.2% of the isolates were negative for the investigated genes. High-level resistance to gentamicin associated with the aac(6′)-le-aph(2″)-la gene was detected in one E. faecalis strain. The two strains presenting high-level resistance to streptomycin were negative for the ant(6′)-Ia, ant(3′)-Ia, ant(9′)-Ia and ant(9′)-Ib genes. The vat(D) gene was found in all the 47 quinupristin/dalfopristin resistant strains identified as non-E. faecalis. Analysis of PFGE profiles of E. hirae strains after restriction with SmaI demonstrated the occurrence of five clonal groups. The predominant E. hirae clone was distributed among birds in the two institutions, suggesting that this clone was well adapted to the host and environments investigated. The four clonal groups identified among E. faecalis were composed by small numbers of strains and, generally, restricted to birds in the same sector. The occurrence of enterococcal strains exhibiting antimicrobial resistance traits and carrying genetic determinants that represent potential threats to the health of both humans and animals, in the intestinal microbiota of A. aestiva, highlights the need for additional monitoring studies to elucidate the population structure and the dynamics of transmission of these microorganisms among animals, humans and the environment.

Prevalence and Characterization of Campylobacter jejuni Isolated from Retail Chicken in Tianjin, China

Campylobacter jejuni is an important foodborne pathogen worldwide; however, there is a lack of information on the prevalence and antibiotic-resistant profile of C. jejuni in the People's Republic of China. We determined the prevalence and characteristics of C. jejuni on the retail level in Tianjin, one of the five national central cities in China. A total of 227 samples of chicken wings, legs, and breasts were collected from supermarkets and wet markets; 42 of these samples were confirmed to be positive for Campylobacter contamination. The contamination rates of C. jejuni and other Campylobacter species were 13.7% (31 of 227 samples) and 5.7% (13 of 227 samples), respectively. A group of 31 C. jejuni isolates was subjected to antimicrobial susceptibility testing. All (100%) the selected isolates were resistant to ciprofloxacin and nalidixic acid; 77.4% were resistant to tetracycline, 67.7% to doxycycline, 35.5% to gentamicin, 25.8% to clindamycin and florfenicol, 19.4% to chloramphenicol, and 12.9% to erythromycin and azithromycin. A remarkably high proportion (41.9%) of multidrug-resistant isolates was identified. Multilocus sequence typing was conducted to study the population structure of the C. jejuni strains and their relationship to human isolates. The correlation between antimicrobial resistance traits and certain sequence types (STs) or clonal complexes was determined as well. A great genetic diversity of poultry isolates was identified, with 11 STs belonging to 6 clonal complexes and 11 singleton STs. The novel STs accounted for 40.9% (n = 9) of the 22 STs. ST-21, ST-353, ST-354, ST-443, ST-607, and ST-828 complexes had been previously identified from human isolates. This study revealed an extensive level of antimicrobial resistance and genetic diversity in C. jejuni isolated from chicken products in Tianjin, highlighting the necessity of performing enforced interventions to reduce Campylobacter prevalence in China.

Antimicrobial Resistance of Salmonella Serovars and Campylobacter spp. Isolated from an Opportunistic Gull Species, Yellow-legged Gull ( Larus michahellis ).

Wildlife is a natural reservoir of Salmonella and Campylobacter, the most important human foodborne pathogens worldwide. Free-living birds have the potential to transport, over large distances, such zoonotic bacteria that may harbor antimicrobial resistance traits. On the northeastern Iberian coast, we assessed the role of Yellow-legged Gulls ( Larus michahellis ) as reservoirs of antimicrobial resistance in Salmonella and thermophilic Campylobacter isolates recovered from gulls at three colonies, with varying degrees of dependence on refuse dumps as food sources. Of the 39 Salmonella isolates we tested, 17 were multiresistant (resistance to three antimicrobial families), with eight being Salmonella enterica serovar Typhimurium. Other clinically relevant Salmonella serovars showing multiresistance included Hadar, Bredeney, and Virchow. Relevant Campylobacter antimicrobial resistances were detected among three Campylobacter jejuni isolates, of which all three showed resistance to nalidixic acid, two were resistant to ciprofloxacin, one was resistant to enrofloxacin, and one was resistant to tetracycline. Our results highlight the importance of free-living gulls with opportunistic feeding habits in the dissemination of enteric pathogens resistant to multiple antimicrobial agents of public health concern.

Biofilm-forming and antimicrobial resistance traits of staphylococci isolated from goat dairy plants.

Biofilm-associated antimicrobial resistance is of increasing importance to the maintenance and spread of foodborne pathogens in the food industry. This study aimed to investigate the ability to form biofilm and the antimicrobial resistance of staphylococci contaminating small-scale goat milk dairy plants. Sixty isolates were tested for antimicrobial resistance against 20 drugs by the microdilution method. Biofilm-forming traits were assessed by the microtiter plate method (MtP), Congo red agar method (CRA), and icaD gene detection by polymerase chain reaction (PCR). High antimicrobial resistance to ampicillin (60/60; 100%), penicillin G (21/60; 35%), and erythromycin (15/60; 25%) was observed, but all isolates were susceptible to amoxicillin/K-clavulanate, ceftriaxone, ciprofloxacin, gentamicin, levofloxacin, linezolid, and moxifloxacin. No resistance to oxacillin or vancomycin was seen among Staphylococcus aureus. Twenty-seven isolates (27/60; 45%) were considered to form biofilm according to MtP, and similar biofilm-producing frequencies were observed in coagulase-negative staphylococci (CoNS) (20/44; 45.4%) and S. aureus (7/16; 43.7%). The icaD gene was observed only in S. aureus isolates. There was no association between biofilm production and antimicrobial resistance. A higher frequency of biofilm-producing staphylococci was found in isolates from bulk tank milk and hand swabs. On the other hand, isolates from pasteurized milk showed lower frequency of biofilm formation. Staphylococci contaminating goat dairy plants are potential biofilm producers. The results suggest no association between the ability to form biofilm and antimicrobial resistance.