Genetic diversity of KPC-2-producing Klebsiella pneumoniae complex from aquatic ecosystems

During the COVID-19 pandemic, the occurrence of carbapenem-resistant Klebsiella pneumoniae increased in human clinical settings worldwide. Impacted by this increase, international high-risk clones harboring carbapenemase-encoding genes have been circulating in different sources, including the environment. The blaKPC gene is the most commonly disseminated carbapenemase-encoding gene worldwide, whose transmission is carried out by different mobile genetic elements. In this study, blaKPC-2-positive Klebsiella pneumoniae complex strains were isolated from different anthropogenically affected aquatic ecosystems and characterized using phenotypic, molecular, and genomic methods. K. pneumoniae complex strains exhibited multidrug-resistant and extensively drug-resistant profiles, spotlighting the resistance to carbapenems, ceftazidime-avibactam, colistin, and tigecycline, which are recognized as last-line antimicrobial treatment options. Molecular analysis showed the presence of several antimicrobial resistance, virulence, and metal tolerance genes. In-depth analysis showed that the blaKPC-2 gene was associated with three different Tn4401 isoforms (i.e., Tn4401a, Tn4401b, and Tn4401i) and NTEKPC elements. Different plasmid replicons were detected and a conjugative IncN-pST15 plasmid harboring the blaKPC-2 gene associated with Tn4401i was highlighted. K. pneumoniae complex strains belonging to international high-risk (e.g., ST11 and ST340) and unusual clones (e.g., ST323, ST526, and ST4216) previously linked to clinical settings. In this context, some clones were reported for the first time in the environmental sector. Therefore, these findings evidence the occurrence of carbapenemase-producing K. pneumoniae complex strains in aquatic ecosystems and contribute to the monitoring of carbapenem resistance worldwide.

Rapid antibiotic susceptibility testing (RAST) of blood cultures in enterobacteria with inducible chromosomal AmpC-type β-lactamase

INTRODUCTION

Early and adequate treatment of bloodstream infections decreases patient morbidity and mortality. The objective is to develop a preliminary method for rapid antibiotic susceptibility testing (RAST) in enterobacteria with inducible chromosomal AmpC.

METHODS

RAST was performed directly on spiked blood cultures of 49 enterobacteria with inducible chromosomal AmpC. Results were read at 4, 6 and 8h of incubation. Commercial broth microdilution was considered the reference method. Disks of 10 antibiotics were evaluated.

RESULTS

The proportion of readable tests at 4h was 85%. All RAST could be read at 6 and 8h. For most antibiotics, the S or R result at 4, 6 and 8h was greater than 80% after tentative breakpoints were established and Area of Technical Uncertainty was defined.

CONCLUSIONS

This preliminary method seems to be of practical use, although it should be extended to adjust the breakpoints and differentiate them by species.

Genomic analysis of a cAmpC (CMY-41)-producing Citrobacter freundii ST64 isolated from patient

Antibiotic resistance in Citrobacter freundii is a public health concern. This study evaluated the closed genome of a C. freundii isolated from the stool of a hospitalized patient initially related to a Salmonella outbreak. Confirmation of the isolate was determined by whole-genome sequencing. Nanopore sequencing was performed using a MinION with a Flongle flow cell. Assembly using SPAdes and Unicycler yielded a closed genome annotated by National Center for Biotechnology Information Prokaryotic Genome Annotation Pipeline. Genomic analyses employed MLST 2.0, ResFinder4.1, PlasmidFinder2.1, and VFanalyzer. Phylogenetic comparison utilized the Center for Food Safety and Applied Nutrition (CFSAN)-single nucleotide polymorphism pipeline and Genetic Algorithm for Rapid Likelihood Inference. Antimicrobial susceptibility was tested by broth microdilution following Clinical and Laboratory Standards Institute criteria. Multi-locus sequence type in silico analysis assigned the C. freundii as sequence type 64 and the blaCMY-41 gene was detected in resistome investigation. The susceptibility to antibiotics, determined using Sensititre® plates, revealed resistance to aztreonam, colistin, cefoxitin, amoxicillin/clavulanic acid, sulfisoxazole, ampicillin, and streptomycin. The genetic relatedness of the C. freundii CFSAN077772 with publicly available C. freundii genomes revealed a close relationship to a C. freundii SRR1186659, isolated in 2009 from human stool in Tanzania. In addition, C. freundii CFSAN077772 is nested in the same cluster with C. freundii clinical strains isolated in Denmark, Mexico, Myanmar, and Canada, suggesting a successful intercontinental spread.

Pink colored breast milk! Serratia marcescens infection, series of 4 cases

BACKGROUND

Pink coloration of breast milk is uncommon and it´s associated with colonization by Serratia marcescens, which is most frequently isolated in intensive care settings. Misinterpretation of the pink coloration may lead to premature cessation of breastfeeding. The objective is to present four cases of pink discoloration.

METHODS

Two retrospective and two prospective cases of pink discoloration in breast milk are described, which were reported to the lead author.

RESULTS

Four healthy mother-infant pairs with documented pink discoloration are presented. S. marcescens was isolated from breast milk samples. All four infants were asymptomatic and underwent enterobacteria cultures. The mothers received outpatient antibiotic treatment, and two infants received treatment as well. Subsequent cultures yielded negative results, and the pink discoloration ceased. All mothers successfully resumed breastfeeding.

CONCLUSIONS

There are very few reported cases of pink breast milk in the global literature. Colonization by S. marcescens is not an indication for discontinuation of breastfeeding.

[Urinary tract infections including pyelonephritis]

Urinary tract infections (UTIs) are among the most common bacterial infections. The clinical phenotypes of UTIs are heterogeneous, ranging from rather benign uncomplicated infections to complicated UTIs and pyelonephritis to severe urosepsis. There has been a sharp increase in the incidence of severe UTIs, whilst the incidence of sepsis in general is declining. The classifications of UTIs partially differ between clinical and regulatory claims. Experience has also been gained over the last few years to define the appropriate endpoints that are used in clinical studies. Above all, patient-centered evaluation strategies of the endpoints were developed, in order to be able to identify the advantages of new antibiotics compared to traditional antibiotics. The development of new antibiotics for UTIs is essential, since multidrug-resistant enterobacteria, which belong to the typical bacterial spectrum of UTIs, are frequently associated with mortality from infections. In recent years, several new antibiotics/combinations that are particularly effective against multi-resistant gram-negative pathogens have been investigated for the treatment of UTIs.

Bats (Mammalia: Chiroptera) in urban-rural interfaces: community structure associated with pathogen screening in São Paulo-the largest metropolitan region in Brazil

Little is known about the influence of the urban environments on bat species 'ecology. The urbanization process potentially lead to critical ecological changes in bat communities' intra and interspecific pathogenic transmissions dynamics. To date, the monitoring of pathogens in bats in Brazil has only been done with bats found dead or alive in households, from rabies surveillance systems. The present work aimed to investigate how urbanization influenced bat richness, relative abundance and pathogen occurrence. Most captured bats were Phyllostomidae, especially Sturnira lilium, Artibeus lituratus, A. fimbriatus, Glossophaga soricina, and Platyrrhinus lineatus, among others. From preserved-rural towards urban areas the lesser the bat richness, the higher the relative abundance of the captured bats. Noise level, luminosity and relative humidity correlated with bat abundance. The proportion of genders, sexually active bats and their size (weight, right forearm length, and body condition index) were stable throughout the investigation. Still, the proportion of pregnant females was higher in Spring and the number of juveniles in Summer, evidencing the seasonality of reproduction. Several Enterobacteria were isolated, evidencing a significant role of bats in the circulation of pathogens of medical and veterinary interest. These results are crucial in the pursuit of a harmonious coexistence between humans, bats and domestic animals in areas with different levels of anthropization.

Resistance and Biofilm Production Profile of Potential Isolated from Kpètè-Kpètè Used to Produce Traditional Fermented Beer

This study aimed to characterize the pathogenicity of bacteria isolated from the starter of two traditional beers produced and consumed in Benin. After standard microbial identification, species were identified by specific biochemical tests such as catalase, coagulase, and API 20 E. Antibiotic sensitivity was tested according to the French Society of Microbiology Antibiogram Committee. The crystal violet microplate technique evaluated the biofilm production and conventional PCR was used to identify genes encoding virulence and macrolide resistance. According to our data, the traditional starter known as kpètè-kpètè that is used to produce beer is contaminated by Enterobacteriaceae and staphylococci species. Thus, 28.43% of the isolated bacteria were coagulase-negative staphylococci (CNS), and 10.93% coagulase-positive staphylococci (CPS). Six species such as Klebsiella terrigena (1.38%), Enterobacter aerogens (4.14%), Providencia rettgeri (5.51%), Chryseomonas luteola (6.89%), Serratia rubidae (15.16%), and Enterobacter cloacae (27.56%) were identified among Enterobacteriaceae. Those bacterial strains are multi-resistant to conventional antibiotics. The hight capability of produced biofilms was recorded with Enterobacter aerogens, Klebsiella terrigena (100%), Providencia rettgeri (75%), and Staphylococcus spp (60%). Enterobacter cloacae (4%) and coagulase-negative Staphylococcus (5.55%) harbor the macrolide resistance gene. For other strains, these genes were not detected. Foods contaminated with bacteria resistant to antibiotics and carrying a virulence gene could constitute a potential public health problem. There is a need to increase awareness campaigns on hygiene rules in preparing and selling these traditional beers.

Factors influencing somatic cell counts and bacterial contamination in unpasteurized milk obtained from water buffalo in Bangladesh

Little has been published on the factors influencing the safety and quality of milk derived from water buffalo in Bangladesh. This study aims to describe the milk hygiene parameters and milk chain characteristics of unpasteurized raw milk sold to consumers in order to improve milk hygiene. A quantitative study design evaluated somatic cell counts, total bacterial counts, and specific gram-negative (Enterobacteria) and gram-positive (staphylococci) pathogens in 377 aseptically collected milk samples. Samples were collected at multiple nodes along the buffalo milk value chain: 122 bulk tank milk samples were collected at the farm level, 109 milk samples at the middlemen level, and 111 milk samples at the milk collection centers. In addition, 35 samples were taken from various milk products at the retail level. It was found that progressively increasing somatic cell counts and bacterial counts, including potential pathogens, occurred along the milk chain. A seasonal increase in spring was found, varying based on the farming system (semi-intensive versus intensive). Other factors included water purity and cleanliness of containers, mixing buffalo and cow's milk, and the location of the water buffalo milk producer (coastal or river basin). This study demonstrated how improving udder health and milk hygiene along the water buffalo milk value chain would increase the safety and quality of water buffalo milk in the study area.

The relationship between unique gut microbiome-derived lipid metabolites and subsequent revascularization in patients who underwent percutaneous coronary intervention

BACKGROUND AND AIMS

Studies have recently revealed the linoleic acid metabolic pathway of Lactobacillus plantarum, the representative gut bacterium in human gastrointestinal tract, and the anti-inflammatory effects of metabolites in this pathway. However, no clinical trials have evaluated the association between these metabolites and revascularization in patients who underwent percutaneous coronary intervention (PCI).

METHODS

We retrospectively reviewed patients who underwent PCI with subsequent revascularization or coronary angiography (CAG) without revascularization. Patients with frozen blood samples at the index PCI and revascularization or follow-up CAG were enrolled.

RESULTS

Among 701 consecutive patients who underwent PCI, we enrolled 53 patients who underwent subsequent revascularization and 161 patients who underwent follow-up CAG without revascularization. Patients who underwent revascularization showed significantly lower plasma 10-oxo-octadecanoic acid (KetoB) levels (720.5 [551.6-876.5] vs. 818.4 [641.1-1103.6 pg/mL]; p = 0.01) at index PCI. Multivariate logistic regression analysis revealed that decreased plasma KetoB levels at the index PCI were independently associated with subsequent revascularization after PCI (odds ratio; 0.90 per 100 pg/mL increase, 95% confidence interval; 0.82-0.98). Additionally, in vitro experiments showed that the addition of purified KetoB suppressed the mRNA levels of IL-6 and IL-1β in macrophages and IL-1β mRNA in neutrophils.

CONCLUSIONS

Plasma KetoB level at index PCI was independently associated with subsequent revascularization after PCI, and KetoB could act as an anti-inflammatory lipid mediator in macrophages and neutrophils. The assessment of gut microbiome-derived metabolites may help predict revascularization after PCI.

Effect of Lactobacillus spp. cell-free supernatant against planktonic growth and biofilm formation of foodborne Escherichia coli isolates

The aim of this work was to evaluate the anti-Escherichia coli effect of cell-free supernatant (CFS) of Lactobacillus spp. against planktonic and biofilm forms of foodborne isolates. Escherichiacoli strains (P12, P25, P35 and P36), previously isolated from fresh filets of fish, were subjected to antimicrobial susceptibility determination by the disc-diffusion agar method. Subsequently, the antagonistic effect between probiotic and pathogenic strains was determined by spot overlay assay. Finally, the CFS activity against pre-established (12 h) biofilms was demonstrated through biomass quantification by crystal violet staining and scanning electron microscopy (SEM). All isolates presented some pattern of resistance, primarily to ampicillin and tetracycline. Probiotic strains presented high antagonistic effects against all E. coli strains, presenting inhibition zones (R) ranging from 15.60 to 20.67 mm. Additionally, the residual biomass of pre-established (12 h) biofilm was drastically reduced about 50% after CFS treatment (P < 0.01). What can be noted by SEM images, which show less surface-attached cells of CFS-treated biofilms of E. coli (P12). Thus, cell-free preparations produced from Lactobacillus spp. may represent a tool in the battle against planktonic cells and biofilm forms of antibiotic-resistant E. coli.

Bacteria spatial tracking in Urban Park soils with MALDI-TOF Mass Spectrometry and Specific PCR

Urban parks constitute one of the main leisure areas, especially for the most vulnerable people in our society, children, and the elderly. Contact with soils can pose a health risk. Microbiological testing is a key aspect in determining whether they are suitable for public use. The aim of this work is to map the spatial distribution of potential dangerous Enterobacteria but also bioremediation useful (lipase producers) isolates from soils in an urban park in the area of Valencia (Spain). To this end, our team has collected 25 samples of soil and isolated 500 microorganisms, using a mobile application to collect information of the soil samples (i.e. soil features, temperature, humidity, etc.) with geolocation. A combined protocol including matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) and 16S rDNA sequencing PCR has been established to characterize the isolates. The results have been processed using spatial statistical techniques (using Kriging method), taking into account the number of isolated strains, also proving the reactivity against standard pathogenic bacterial strains (Escherichia coli, Bacillus cereus, Salmonella, Pseudomonas and Staphylococcus aureus), and have increased the number of samples (to 896 samples) by interpolating spatially each parameter with this statistical method. The combined use of methods from biology and computer science allows the quality of the soil in urban parks to be predicted in an agile way, which can generate confidence in its use by citizens.

Fumarate, a central electron acceptor for Enterobacteriaceae beyond fumarate respiration and energy conservation

C4-dicarboxylates (C4-DCs) such as fumarate, l-malate and l-aspartate are key substrates for Enterobacteria such as Escherichia coli or Salmonella typhimurium during anaerobic growth. In general, C4-DCs are oxidants during biosynthesis, e.g., of pyrimidine or heme, acceptors for redox balancing, a high-quality nitrogen source (l-aspartate) and electron acceptor for fumarate respiration. Fumarate reduction is required for efficient colonization of the murine intestine, even though the colon contains only small amounts of C4-DCs. However, fumarate can be produced endogenously by central metabolism, allowing autonomous production of an electron acceptor for biosynthesis and redox balancing. Bacteria possess a complex set of transporters for the uptake (DctA), antiport (DcuA, DcuB, TtdT) and excretion (DcuC) of C4-DCs. DctA and DcuB exert regulatory functions and link transport to metabolic control through interaction with regulatory proteins. The sensor kinase DcuS of the C4-DC two-component system DcuS-DcuR forms complexes with DctA (aerobic) or DcuB (anaerobic), representing the functional state of the sensor. Moreover, EIIA^Glc from the glucose phospho-transferase system binds to DctA and presumably inhibits C4-DC uptake. Overall, the function of fumarate as an oxidant in biosynthesis and redox balancing explains the pivotal role of fumarate reductase for intestinal colonization, while the role of fumarate in energy conservation (fumarate respiration) is of minor importance.

Enhancing cell resistance for production of mixed microbiological reference materials with Salmonella and coliforms by freeze-drying

The reference material (RM) is a technical requirement for the quality assurance of analytical results and proficiency tests or interlaboratory comparisons. Microbiological RMs are most available in the dehydrated form, mainly by freeze-drying, and maintaining bacterial survival after preparation is a challenge. Thus, obtaining the most resistant cells is essential. Considering that bacteria present cross-response to dehydration after being submitted to an array of stress conditions, this study aimed to evaluate the influence of growth conditions on enterobacteria for the production of mixed microbiological RMs by freeze-drying in skim milk powder. Salmonella enterica serovar Enteritidis, Cronobacter sakazakii, Escherichia coli, and Citrobacter freundii were grown in a minimal medium with 0.5 M NaCl and 0 to 5.0 mM of manganese sulfate (MnSO4) until stationary phase. Salmonella Enteritidis presented an increased resistance to dehydration in the presence of Mn, while C. sakazakii was the most resistant to freeze-drying and further storage for 90 days. Mixed microbiological RMs were produced by freeze-drying and containing Salmonella Enteritidis and coliforms in skim milk powder with 100 mM of trehalose and the Salmonella survival rate was 91.2 to 93.6%. The mixed RM was stable after 30 days at -20 °C, and Salmonella and coliforms were detected by different methods being, the Rambach Agar the best for the bacterial differentiation. The results showed that the culture conditions applied in this study resulted in bacterial cells being more resistant to dehydration, freeze-drying, and stabilization for the production of mixed microbiological RMs more stable and homogeneous.

Identification and expression of bifunctional acid urea-degrading enzyme/urethanase from Enterobacter sp. R-SYB082 and its application in degradation of ethyl carbamate in Chinese rice wine (Huangjiu)

BACKGROUND

Ethyl carbamate (EC) is a potential carcinogen existing in fermented foods such as Chinese rice wine (Huangjiu). Since urea is an important precursor of EC, the degradation of urea could be an effective way to reduce EC in foods.

RESULTS

In this study, an Enterobacter sp. R-SYB082 with acid urea degradation characteristics was obtained through microbial screening. Further research isolated a new acid urea-degrading enzyme from R-SYB082 strain - ureidoglycolate amidohydrolase (UAH) - which could degrade EC directly. The cloning and expression of UAH in Escherichia coli BL21 (DE3) suggested that the activity of urea-degrading enzyme reached 3560 U L^-1 , while urethanase activity reached 2883 U L^-1 in the optimal fermentation condition. The enzyme had the dual ability of degrading substrate urea and product EC. The removal rate of EC in Chinese rice wine could reach 90.7%.

CONCLUSION

This study provided a new method for the integrated control of EC in Chinese rice wine and other fermented foods. © 2022 Society of Chemical Industry.

Greenhouse gas formation during the ensiling process of grass and lucerne silage

Silage is an essential global feedstuff and an emitter of greenhouse gases. However, few studies have examined the formation of carbon dioxide (CO₂), nitrous oxide (N₂O) and methane (CH₄) during the ensiling process. This study aimed to record the course of gas concentrations in forage during the ensiling process and determine the temporal variation in the (microbiological) formation processes. Grass and lucerne, each with two different dry matter (DM) concentrations (four variants, each n = 3), were ensiled in laboratory-scale barrels (120 L). Gas samples were taken from the headspace of the barrels and analysed using a gas chromatograph. The measurement period included the first 49 days of the ensiling process and the measurement interval was 0.5-48.0 h. For all variants, a rapid increase in CO₂ concentration and a one-time N₂O concentration peak was observed between ensiling hours 36 and 96. Lower DM concentration led to significantly faster CO₂ production (p < 0.05). Lucerne forage and higher DM concentrations led to significantly increased N₂O concentrations (p < 0.05). The extensive measurements demonstrated that butyric acid formation by clostridia contributes to CH₄ formation; thus, lucerne silage had a significantly higher concentration from ensiling day 13 (p < 0.05). Therefore, malfermentation actively contributes to the formation of greenhouse gases. The method described here provides further insights into greenhouse gas formation during the ensiling process and can thus help to improve ensiling research and management.

Characterization of a novel, biofilm dispersing, lytic bacteriophage against drug-resistant Enterobacter cloacae

AIM

To characterize a novel bacteriophage, En5822, isolated from the environment against Enterobacter cloacae and exploring its application as an alternate antimicrobial.

METHODS AND RESULTS

Bacteriophage was isolated from sewage sample by membrane-filtration immobilization technique. It was purified and studied for its various physical properties like microscopic structure, thermal and pH stability, latent period and burst time, antimicrobial and anti-biofilm activity as well as molecular aspects by genome sequencing and analysis. En5822 is a myovirus with relative pH and thermal stability. En5822 shows a notable reduction of host bacterial biofilm as well as planktonic cultures. Whole genome sequence analysis revealed that the En5822 genome does not contain undesirable temperate lifestyle genes, antibiotic resistance genes and toxin-encoding genes.

CONCLUSIONS

En5822 displays high lytic activity, specificity and biofilm reduction capability. It has a short latent period and high burst size that aid faster activity. Its genomic and physical attributes offer possibilities for its as an alternative antimicrobial for the treatment of drug-resistant E. cloacae infections.

SIGNIFICANCE AND IMPACT OF STUDY

The study describes a novel, naturally virulent bacteriophage from environment capable of lysing multi-drug resistant E. cloacae effectively. The phage could potentially serve as an alternative strategy for treating antibiotic-resistant infections.

[Gastric bacterial overgrowth: An unusual histological observation, not to be overlooked]

Gastric bacterial overgrowth is a rare situation, which may be associated with short- and long-term complications. It must be known from pathologists, since it might be detected incidentally at histological examination of gastric biopsies. We report here the case of a 74-year old woman, obese, without significant medical history, apart from a gastro-esophageal reflux treated by the long-term administration of proton pump inhibitors (PPI). In this patient, gastric bacterial overgrowth was detected at histological examination of gastric biopsies performed after colectomy for left colon adenocarcinoma. Large clusters of small, round, "coccoid" bacteria were present in the gastric mucus. Their characteristics were suggestive of enterobacteria. Bacterial proliferation was associated with severe and diffuse lesions of active gastritis. The course was rapidly unfavorable, and the patient rapidly deceased with multiple infections and multi-organ failure. In our observation, the pathogenesis of gastric bacterial overgrowth was probably multifactorial. It might have been facilitated by long-term PPI treatment and obesity, which are known risk factors, and promoted, in the post-operative setting, by multiple infections and immune failure. Our observation underlines that gastric bacterial overgrowth might be associated with severe gastritis, which might justify antibiotherapy. Other consequences of prolonged gastric dysbiosis cannot be excluded, such as the promotion of neoplastic lesions.

Effects of biostimulation by sugarcane bagasse and coffee grounds on sewage sludges, focusing agricultural use: Microbial characterization, respirometric assessment and toxicity reduction

Sewage sludge (SS) exhibits a relevant agronomic potential due to the high content of organic matter and nutrients. However, the presence of several toxic substances can prevent its agricultural application. This study evaluated if the incorporation of stimulating agents (coffee grounds and sugarcane bagasse) could contribute to an effective increase of the SS biodegradability in order to decrease its toxicity. The samples were prepared mixing aerobic or anaerobic sludge with soil, soil and bagasse, and soil and coffee grounds. Respirometric tests showed that stimulating agents enhanced the CO₂ production. However, in terms of biodegradation efficiency, more satisfactory results were verified for the anaerobic SS, especially when mixed with coffee grounds. The biodegradation also favored the SS sanitization, eliminating the Enterobacteria. For baseline toxicity (Microtox with Aliivibrio fischeri) and phytotoxicity (Lactuca sativa), all the initial samples showed higher effects. Nevertheless, after the biodegradation, this toxicity was significantly decreased and the best results were obtained for the mixtures containing only soil and sludge. For the AREc32 assay (NRF₂ mediated oxidative stress response), although a very weak response was observed, this effect was attenuated for the aerobic SS or completely eliminated for the anaerobic SS after the biodegradation. Thus, even though the use of biostimulation agents during the biodegradation led to an enhancement of microbial respiration, their incorporation to the samples do not seem to interfere in the decrease of the toxic potential of the studied SSs. However, the SS biodegradation in aerobiosis was crucial for toxicity reduction and to accelerate its maturity.

Prevalence of Diarrheagenic Escherichia coli (DEC) and Salmonella spp. with zoonotic potential in urban rats in Salvador, Brazil

Studies evaluating the occurrence of enteropathogenic bacteria in urban rats (Rattus spp.) are scarce worldwide, specifically in the urban environments of tropical countries. This study aims to estimate the prevalence of diarrhoeagenic Escherichia coli (DEC) and Salmonella spp. with zoonotic potential in urban slum environments. We trapped rats between April and June 2018 in Salvador, Brazil. We collected rectal swabs from Rattus spp., and cultured for E. coli and Salmonella spp., and screened E. coli isolates by polymerase chain reaction to identify pathotypes. E. coli were found in 70% of Rattus norvegicus and were found in four Rattus rattus. DEC were isolated in 31.3% of the 67 brown rats (R. norvegicus). The pathotypes detected more frequently were shiga toxin E. coli in 11.9%, followed by atypical enteropathogenic E. coli in 10.4% and enteroinvasive E. coli in 4.5%. From the five black rats (R. rattus), two presented DEC. Salmonella enterica was found in only one (1.4%) of 67 R. norvegicus. Our findings indicate that both R. norvegicus and R. rattus are host of DEC and, at lower prevalence, S. enterica, highlighting the importance of rodents as potential sources of pathogenic agents for humans.

Assessment of carbapenem-resistant Enterobacteriaceae-plate formula and quality control procedure

AIMS

To assess a cost-effective in-house selective plate formula for actively screening carbapenem-resistant Enterobacteriaceae (CRE).

METHODOLOGY AND RESULTS

The in-house formula included CHROMagar^TM Orientation, meropenem, and ingredients present in the Mac-Conkey formula, such as bile salts and crystal violet (pH 6.9-7.2). American Type Culture Collection strains and 200 clinical strains were used to validate the plate formula. The CRE plates had a sensitivity of 97.4% and a specificity of 98.8% with ATCC andor clinical strains used in the quality control procedure. A point prevalence survey among the 18 inpatients at Viet-Tiep hospital ICU using fecal swabs plated at the in-house agar plate showed a CRE prevalence of 44.4%.

CONCLUSION

The in-house plate had high sensitivity and specificity, particularly for Escherichia coli and the KESC group (Klebsiella spp., Enterobacter spp., Serratia marscescens, and Citrobacter spp.), and it may be widely applied as an alternative to other ready-to-use commercial plates.

SIGNIFICANCE AND IMPACT OF THE STUDY

The formula developed in the present study may facilitate the early detection and isolation of CRE and decrease transmission, particularly in low- and middle-income countries with a high rate of CRE colonization and limited access to ready-to-use commercial plates.

Creation of Golden Gate constructs for gene doctoring

Background

Gene doctoring is an efficient recombination-based genetic engineering approach to mutagenesis of the bacterial chromosome that combines the λ-Red recombination system with a suicide donor plasmid that is cleaved in vivo to generate linear DNA fragments suitable for recombination. The use of a suicide donor plasmid makes Gene Doctoring more efficient than other recombineering technologies. However, generation of donor plasmids typically requires multiple cloning and screening steps.

Results

We constructed a simplified acceptor plasmid, called pDOC-GG, for the assembly of multiple DNA fragments precisely and simultaneously to form a donor plasmid using Golden Gate assembly. Successful constructs can easily be identified through blue-white screening. We demonstrated proof of principle by inserting a gene for green fluorescent protein into the chromosome of Escherichia coli. We also provided related genetic parts to assist in the construction of mutagenesis cassettes with a tetracycline-selectable marker.

Conclusions

Our plasmid greatly simplifies the construction of Gene Doctoring donor plasmids and allows for the assembly of complex, multi-part insertion or deletion cassettes with a free choice of target sites and selection markers. The tools we developed are applicable to gene editing for a wide variety of purposes in Enterobacteriaceae and potentially in other diverse bacterial families.

Development of a combined immunochromatographic lateral flow assay for accurate and rapid Escherichia coli O157:H7 detection

Escherichia coli O157:H7 is an important pathogenic Bacterium that threatens human health. A convenient, sensitive and specific method for the E. coli O157:H7 detection is necessary. We developed two pairs of monoclonal antibodies through traditional hybridoma technology, one specifically against E. coli O157 antigen and the other specifically against E. coli H7 antigen. Using these two pairs of antibodies, we developed two rapid test kits to specifically detect E. coli O157 antigen and E. coli H7 antigen, respectively. The detection sensitivity for O157 positive E. coli is 1 × 10³ CFU per ml and for H7 positive E. coli is 1 × 10⁴ CFU per ml. Combining these two pairs of antibodies together, we developed a combo test strip that can specifically detect O157: H7, with a detection sensitivity of 1 × 10⁴ CFU per ml, when two detection lines are visible to the naked eye. This is currently the only rapid detection reagent that specifically detects O157: H7 by simultaneously detecting O157 antigen and H7 antigens of E. coli. Our product has advantages of simplicity and precision, and can be a very useful on-site inspection tool for accurate and rapid detection of E. coli O157:H7 infection.

Identification of enterobacteria in viscera of pigs afflicted with porcine reproductive and respiratory syndrome and other viral co-infections

In order to investigate enterobacteria presence involved in the secondary infections in Porcine Reproductive and Respiratory Syndrome (PRRS) pigs with different viral co-infections, we identified enterobacteria for guiding clinical treatment. Twenty-one diseased pigs were diagnosed with the PRRS virus (PRRSV) and other 7 virus primers by PCR/RT-PCR in the lung and spleen samples. Enterobacteria were isolated using MacConkey agar from 5 visceral samples of PRRS pigs, and identified by 16S rDNA sequencing. PRRSV was positive in 100% of the lung samples and 81.0% of the spleen samples. Seven diseased pigs were diagnosed with only PRRSV infection (33.3%), 7 pigs with PRRSV and 1 or 2 other viruses (33.3%) and 7 pigs with PRRSV and more than 2 types of other viruses (33.3%). PRRSV was more inclined to co-infect pigs with porcine group A rotavirus (PARV) with the co-infection rate of 52.4% (11/21). Approximately 13 types of bacteria were successfully isolated from lung, spleen, liver, kidney and lymph node samples of different PRRS pigs. Enterobacteria were isolated in 100% of lung, liver and lymph samples from pigs infected with PRRSV alone. However, the isolation rates were significantly decreased in the more than 3 viruses co-infection group. Escherichia coli was the most prevalent bacterium, followed by Morganella, Proteus, Shigella, Salmonella, Klebsiella and Aeromonas. Most of the isolated enterobacteria were opportunistic pathogens. Therefore, timely combination with antimicrobial agents is necessary for effective treatment of PRRS-infected pigs.

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PRRSV was more inclined to co-infect with PARV.

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Pigs co-infected with more virus, less enterobacteria were isolated from their viscera.

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Enterobacteria isolated from viscera of PRRS pigs were opportunistic pathogens.

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coli, Morganella and Proteus were the most prevalent enterobacteria.

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Secondary infection of enterobacteria should be considered in PRRS treatment.

Evaluation of the performance of Acuitas® Resistome Test and the Acuitas Lighthouse® software for the detection of β-lactamase-producing microorganisms

OBJECTIVES

Given the international spread of multidrug-resistant Gram-negative bacteria the need for prompt and precise characterization of underlying resistance traits has evolved into the cornerstone of infection control strategies. Novel commercial molecular tests enable rapid simultaneous testing for multiple resistance genes. We aimed to evaluate the performance of OpGen's Acuitas® Resistome Test and the Acuitas Lighthouse® software.

METHODS

The test is tailored towards detecting 46 β-lactamase genes (SHV and TEM variants associated with wild-type penicillin resistance, extended-spectrum β-lactamases [ESBLs], acquired AmpCs and carbapenemases) via a microfluidic polymerase chain reaction (PCR) array. In total 118 isolates part of the collection of the Bacteriology Laboratory of the Hellenic Pasteur Institute, specifically 96 enterobacterial isolates and 21 Acinetobacter baumannii, of divergent origins, with previously characterized β-lactamase content, were tested.

RESULTS

In the enterobacterial group all 69 carbapenemase genes of the KPC, VIM, NDM and OXA-48 types were correctly identified (sensitivity, specificity, positive predictive value [PPV] and negative predictive value [NPV] of 100%). Non-ESBL SHV enzymes, ESBLs (CTX-M, GES, VEB types) and acquired AmpC enzymes were also correctly characterized. Of the 35 SHV-ESBLs harboured, correct identification was possible in 32/35 isolates, with overall sensitivity, specificity, PPV and NPV for the Klebsiella pneumoniae group of 89.29%, 100%, 100% and 91.18%, respectively. For the A. baumannii group the test exhibited an overall sensitivity for carbapenemase detection of 96.55% and 100% PPV.

CONCLUSIONS

The OpGen Acuitas Resistome Test is an efficient molecular tool that can identify resistance threats in health care institutions with high diagnostic accuracy and be integrated into targeted surveillance protocols.

An improved cleaning system to reduce microbial contamination of poultry transport crates in the United Kingdom

AIM

Following previous research on improving the cleaning of crates used to transport broiler chickens from the farm to the abattoir, a demonstration project was undertaken to investigate improvements in crate washing on a commercial scale.

METHODS AND RESULTS

The soak tank of a conventional crate washing system was replaced with a high-performance washer fitted with high-volume, high-pressure nozzles. The wash water could be heated, and a greatly improved filtration system ensured that the nozzles did not lose performance or become blocked. Visual cleanliness scores and microbial counts were determined for naturally contaminated crates which had been randomly assigned to different cleaning protocols.

CONCLUSIONS

When a combination of mechanical energy, heat and chemicals (i.e. detergent and disinfectant) was used, the results showed significant improvements to crate cleaning. Reductions of up to 3·6 and 3·8 log₁₀ CFU per crate base were achieved for Campylobacter and Enterobacteriaceae, respectively, along with a marked improvement in visual cleanliness.

SIGNIFICANCE AND IMPACT OF THE STUDY

Broiler transport crates may become heavily contaminated with faeces and this may contribute to the spread of disease between farms. The results of this trial may be of use in reducing the spread of zoonotic pathogens in the poultry meat supply chain.

In vitro synergy between sodium deoxycholate and furazolidone against enterobacteria

Background

Antimicrobial combinations have been proven as a promising approach in the confrontation with multi-drug resistant bacterial pathogens. In the present study, we identify and characterize a synergistic interaction of broad-spectrum nitroreductase-activated prodrugs 5-nitrofurans, with a secondary bile salt, sodium deoxycholate (DOC) in growth inhibition and killing of enterobacteria.

Results

Using checkerboard assay, we show that combination of nitrofuran furazolidone (FZ) and DOC generates a profound synergistic effect on growth inhibition in several enterobacterial species including Escherichia coli, Salmonella enterica, Citrobacter gillenii and Klebsiella pneumoniae. The Fractional Inhibitory Concentration Index (FICI) for DOC-FZ synergy ranges from 0.125 to 0.35 that remains unchanged in an ampicillin-resistant E. coli strain containing a β-lactamase-producing plasmid. Findings from the time-kill assay further highlight the synergy with respect to bacterial killing in E. coli and Salmonella.

We further characterize the mechanism of synergy in E. coli K12, showing that disruption of the tolC or acrA genes that encode components of multidrug efflux pumps causes, respectively, a complete or partial loss, of the DOC-FZ synergy. This finding indicates the key role of TolC-associated efflux pumps in the DOC-FZ synergy. Overexpression of nitric oxide-detoxifying enzyme Hmp results in a three-fold increase in FICI for DOC-FZ interaction, suggesting a role of nitric oxide in the synergy. We further demonstrate that DOC-FZ synergy is largely independent of NfsA and NfsB, the two major activation enzymes of the nitrofuran prodrugs.

Conclusions

This study is to our knowledge the first report of nitrofuran-deoxycholate synergy against Gram-negative bacteria, offering potential applications in antimicrobial therapeutics. The mechanism of DOC-FZ synergy involves FZ-mediated inhibition of TolC-associated efflux pumps that normally remove DOC from bacterial cells. One possible route contributing to that effect is via FZ-mediated nitric oxide production.

Synovial Fluid Mediated Aggregation of Clinical Strains of Four Enterobacterial Species

Septic arthritis and prosthetic joint infection (PJI) are conditions commonly associated with Gram-positive cocci, however, a drastic increase in cases derived from enterobacterial species has been observed. Recently it has been reported by multiple groups that staphylococci rapidly form free-floating aggregates in the presence of synovial fluid. These aggregates are comparatively more resistant to antimicrobial challenge than their planktonic counterparts, and thus may play a role in the pathogenesis of joint infection. While staphylococcal aggregates have been the primary focus of interest in the field, it is unclear just how widespread synovial fluid mediated aggregation (SFMA) is in Gram negative enterobacteria (GNE). Through this work we have evaluated SFMA in clinical GNE isolated from PJIs. Two PJI clinical strains each of Enterobacter cloacae, Escherichia coli, Klebsiella pneumonia and Proteus mirabilis strains representing a range of antibiotic susceptibilities were exposed to 10% bovine synovial fluid supernatant (BSF) using a relatively simple, quick semi-quantitative method using an imaging plate reader. BSF stimulated aggregation within 0.5 h both strains of E. cloacae and P. mirabilis and one strain of E.coli. In one strain of P. mirabilis and E.coli, the size of the aggregates significantly increased from 0.5 to 2 h exposure. In contrast, neither K. pneumoniae strain aggregated in BSF. These preliminary findings show that aggregation can occur quickly in GNE, but the extent appears strain and species specific. Further work is required to assess the impact of SFMA on antibiotic tolerance, host innate immunity and the establishment of biofilms.

Evaluation of MASTDISCS combi Carba plus for the identification of metallo-β-lactamases, KPC and OXA-48 carbapenemase genes in Enterobacteriaceae clinical isolates

The increasing frequency of class A KPC enzymes, class B metallo-β-lactamases (MBLs) and class D OXA-48 enzymes in Enterobacteriaceae makes their early identification urgent. A simple commercial MASTDISCS combi Carba plus disc system (MAST-Carba plus) was designed for the identification of MBLs, KPC and OXA-48 carbapenemase genes in Enterobacteriaceae. To validate the MAST-Carba plus, a total of 77 isolates of carbapenemase-producing Enterobacteriaceae (CPE) and 84 isolates of noncarbapenemase-producing Enterobacteriaceae (non-CPE) were selected for differentiation of the genes of Enterobacteriaceae by MAST-Carba plus. Meanwhile, the carbapenemase genes such as bla_KPC , bla_IMP , bla_VIM , bla_NDM-1 and bla_OXA-48 were detected by PCR (polymerase chain reaction). Thus, when considered on the basis of PCR results, the sensitivity of MAST-Carba plus detection of KPC strains is 82·3%, the specificity is 100·0%, the positive predictive value is 100·0% and the negative predictive value is 92·4%. For MBLs strains, the sensitivity is 100·0%, the specificity is 97·1%, the positive predictive value is 84·6% and the negative predictive value is 100·0%. For OXA-48 strains, the sensitivity is 100·0%, the specificity is 99·4%, the positive predictive value is 80·0% and the negative predictive value is 100·0%. Our findings suggest that MAST-Carba plus is a rapid and promising method for identifying the MBLs, KPC and OXA-48 carbapenemase genes in Enterobacteriaceae, which could be exploited in basic microbiology laboratory to prevent the transmission of CPE. SIGNIFICANCE AND IMPACT OF THE STUDY: Not only detection of carbapenemases but also identification of their genes accurately and rapidly in Enterobacteriaceae is still a major challenge for clinical laboratories in order to prevent the transmission of carbapenemase-producing Enterobacteriaceae (CPE). Therefore, this study aimed to evaluate the performance of a new rapid method (MASTDISCS combi Carba plus) for the identification of metallo-β-lactamases (MBLs), KPC and OXA-48 carbapenemase genes in Enterobacteriaceae clinical isolates.

High clonal diversity of multidrug-resistant and extended spectrum beta-lactamase-producing Escherichia coli in a wastewater treatment plant

Increasing beta-lactam resistance has led to the exploration of different places, such as wastewater treatment plants (WWTPs) which have been considered to be reservoirs and sources of bacterial resistance. This work aims to determine the presence of beta-lactamase-producing-Enterobacteriaceae in different points of a WWTP in Colombia. Six samplings were carried out in 2017 in the raw influent, aeration tanks, recycled sludge and final effluent of a WWTP. The beta-lactamase-producing-Enterobacteriaceae were detected and identified using phenotypic and molecular methods. Of the 353 isolates included, 28.3% corresponded to enterobacteria. The most frequent microorganisms were Escherichia coli (83%), Citrobacter freundii (11%) and Enterobacter cloacae complex (4%). The 97% of enterobacteriaceae had at least one beta-lactamase, and the most prevalent were the bla_TEM (43.8%) and bla_CTX-M-1group (35.8%) which were detected specially in recycled sludge and final effluent sample points. High percentage of multidrug resistance (to beta-lactams and non-beta-lactam antibiotics) was detected in E. coli (63.2%). Additionally, the typing by PFGE and MLST showed high genotypic diversity and the presence of the successful ST131 clone, globally spread. This work highlights the strong role of E. coli as a vector for the dissemination of resistance and the beta-lactamases in aquatic environments.

Persistence of fecal indicator bacteria associated with zooplankton in a tropical estuary-west coast of India

In a study carried out during 2014, bacteria associated with zooplankton in the Zuari estuary were three to four orders of magnitude higher in abundance than in seawater. The live zooplankton carried much more bacterial load compared with the carcasses, and the fecal pellets harbored the highest density of bacteria, i.e., 8 × 10¹³ CFU cm^-3. The diversity of bacteria was higher in live zooplankton and also in seawater. But the activity of the zooplankton-associated bacteria was much higher compared with the free-living ones. Most of the associated bacteria belonged to the genus Enterobacter, Pseudomonas, Aeromonas, and Bacillus. In growth experiments, Aeromonas and Bacillus were found to have lower salinity optima than Enterobacter (20 psu) and Vibrio and Pseudomonas (normal seawater salinity). Better growth of bacteria was observed in the medium containing the diatom Chaetoceros sp. than Navicula sp. Bacterial isolates were also able to survive in oligotrophic conditions and produce optimum biomass in 2 days at salinity 5 psu, but in freshwater, the bacteria took a week's time to attain the optima. At salinities 0-35, the bacteria survived even for 3 months without nutrient addition, indicating resilience in these bacteria and mechanisms to persist in the estuaries even in adverse conditions.

Detection of extended-spectrum β-lactam, AmpC and carbapenem resistance in Enterobacteriaceae in beef cattle in Great Britain in 2015

AIMS

This study investigated the occurrence and genetic diversity of Enterobacteriaceae with extended-spectrum β-lactamase (ESBL)-, AmpC- and carbapenemase-mediated resistance in British beef cattle, and related risk factors.

METHODS AND RESULTS

Faecal samples (n = 776) were obtained from farms in England and Wales (n = 20) and Scotland (n = 20) in 2015. Isolates from selective agars were identified by MALDI ToF mass spectrometry. Selected isolates were characterized by multiplex PCR (bla_{CTX -M,} bla_{OXA ,} bla_SHV and bla_TEM genes), whole-genome sequencing (WGS), minimum inhibitory concentrations and pulsed-field gel electrophoresis. None of the faecal samples yielded carbapenem-resistant Escherichia coli. Ten (25%) of the farms tested positive for ESBL-producing CTX-M Enterobacteriaceae, 15 (37·5%) of the farms were positive for AmpC phenotype E. coli and none were positive for carbapenem-resistant E. coli. WGS showed a total of 30 different resistance genes associated with E. coli, Citrobacter and Serratia from ESBL agars, and colocation of resistance genes with bla_{CTX -M1} . Buying bulls and bringing in fattening cattle from another farm were identified as significant risk factors for positive samples harbouring CTX-M Enterobacteriaceae or AmpC phenotype E. coli respectively.

CONCLUSIONS

Beef cattle on a proportion of farms in GB carry ESBL-producing Enterobacteriaceae. Factors, such as operating as a closed herd, may have an important role in reducing introduction and transmission of resistant Enterobacteriaceae. The results indicate management factors may play an important role in impacting ESBL prevalence. In particular, further study would be valuable to understand the impact of maintaining a closed herd on reducing the introduction of resistant Enterobacteriaceae.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is the first study showing the presence of ESBL-producing Enterobacteriaceae in British beef cattle.

Degradation of various insecticides in cooked eggs during in vitro human digestion

The objective of this study was to determine the effects of cooking and in vitro human digestion on the changes of five insecticides-fipronil, bifenthrin, 1,1,1-trichloro-2,2-bis(p-chlorophenyl)ethane (DDT), 1,1-dichloro-2,2-bis(p-chlorophenyl)ethane (DDD), and 2,2-bis(p-chlorophenyl)-1,1-dichloroethylene (DDE)-in egg whites and yolks. Each insecticide was applied to egg whites and yolks at a concentration of 1000 μg/g. After cooking the egg whites and yolks, concentrations of bifenthrin, DDD, and DDE decreased (P < 0.05), whereas those of fipronil and DDT were unchanged (P > 0.05) in both egg whites and yolks. Next, an in vitro human digestion model that simulates all the steps of human digestion was employed. Until digestion in the small intestine, the concentrations of fipronil and DDT in the cooked egg whites and yolks were unchanged (P > 0.05), whereas those of bifenthrin, DDD, and DDE decreased (P < 0.05) at each digestion step. In the large intestinal digestion step with Escherichia coli and Lactobacillus sakei as enterobacteria, the concentrations of all the insecticides decreased (P < 0.05) in the cooked egg whites and yolks. Among the insecticides, bifenthrin showed the lowest concentration (P < 0.05). In conclusion, the use of bifenthrin as an insecticide would be comparatively less toxic than other insecticides in terms of environmental pollution and human health, because of its easy degradation.

Codon usage revisited: Lack of correlation between codon usage and the number of tRNA genes in enterobacteria

It is widely believed that if a high number of genes are found for any tRNA in a rapidly replicating bacteria, then the cytoplasmic levels of that tRNA will be high and an open reading frame containing a higher frequency of the complementary codon will be translated faster. This idea is based on correlations between the number of tRNA genes, tRNA concentration and the frequency of codon usage observed in a limited number of strains as well as from the fact that artificially changing the number of tRNA genes alters translation efficiency and consequently the amount of properly folded protein synthesized. tRNA gene number may greatly vary in a genome due to duplications, deletions and lateral transfer which in turn would alter the levels and functionality of many proteins. Such changes are potentially deleterious for fitness and as a result it is expected that changes in tRNA gene numbers should be accompanied by a modification of the frequency of codon usage. In contrast to this model, when comparing the number of tRNA genes and the frequency of codon usage of several Salmonella enterica and Escherichia coli strains we found that changes in the number of tRNA genes are not correlated to changes in codon usage. Furthermore, these changes are not correlated with a change in the efficiency of codon translation. These results suggest that once a genome gains or loses tRNA genes, it responds by modulating the concentrations of tRNAs rather than modifying its frequency of codon usage.

Modelling of factors influencing the effect of osmotic solution on reduction of selected microorganisms

AIMS

The goal of this research is to model the effects of two osmotic solutions factors on the reduction of selected microorganisms, and to assess the application in osmotic dehydration process of animal raw materials from the aspect of microbiological safety.

METHODS AND RESULTS

Sugar beet molasses and aquatic osmotic solution were prepared and inoculated with Escherichia coli, Listeria monocytogenes and Salmonella spp. Varied factors of osmotic solutions were: time, temperature and concentration of osmotic solutions. Samples of osmotic solutions were subjected to standard and modified microbiological ISO methods. The result showed that increase in factors had a positive effect on the reduction of microbiological load, while the time of the process was the most influential technological parameter. Number of L. monocytogenes was reduced to <10 CFU per g at the end of the process in the highest concentration of sugar beet molasses at all process temperatures.

CONCLUSIONS

Developed mathematical models of reduction ratios for tested microorganisms were statistically significant, allowing good prediction of reduction ratio values based on applied factors.

SIGNIFICANCE AND IMPACT OF THE STUDY

Obtained levels of reduction of all tested microorganisms present good base for the production of safe osmotically dehydrated products of animal origin.

Aerobic bacteria associated with chronic suppurative otitis media in Angola

Background

Chronic suppurative otitis media (CSOM) is an important cause of hearing loss in children and constitutes a serious health problem globally with a strong association to resource-limited living conditions. Topical antibiotics combined with aural toilet is the first-hand treatment for CSOM but antimicrobial resistance and limited availability to antibiotics are obstacles in some areas. The goal of this study was to define aerobic pathogens associated with CSOM in Angola with the overall aim to provide a background for local treatment recommendations.

Methods

Samples from ear discharge and the nasopharynx were collected and cultured from 152 patients with ear discharge and perforation of the tympanic membrane. Identification of bacterial species was performed with matrix-assisted laser desorption/ionization-time of flight mass spectrometry and pneumococci were serotyped using multiplex polymerase chain reactions. Antimicrobial susceptibility testing was done according to EUCAST.

Results

One hundred eighty-four samples from ear discharge and 151 nasopharyngeal swabs were collected and yielded 534 and 289 individual isolates, respectively. In all patients, correspondence rate of isolates from 2 ears in patients with bilateral disease was 27.3% and 9.3% comparing isolates from the nasopharynx and ear discharge, respectively. Proteus spp. (14.7%), Pseudomonas aeruginosa (13.2%) and Enterococcus spp. (8.8%) were dominating pathogens isolated from ear discharge. A large part of the remaining species belonged to Enterobacteriaceae (23.5%). Pneumococci and Staphylococcus aureus were detected in approximately 10% of nasopharyngeal samples. Resistance rates to quinolones exceeded 10% among Enterobacteriaceae and was 30.8% in S. aureus, whereas 6.3% of P. aeruginosa were resistant.

Conclusions

The infection of the middle ear in CSOM is highly polymicrobial, and isolates found in nasopharynx do not correspond well with those found in ear discharge. Pathogens associated with CSOM in Angola are dominated by gram-negatives including Enterobacteriaceae and P. aeruginosa, while gram-positive enterococci also are common. Based on the results of antimicrobial susceptibility testing topical quinolones would be the preferred antibiotic therapy of CSOM in Angola. Topical antiseptics such as aluminium acetate, acetic acid or boric acid, however, may be more feasible options due to a possibly emerging antimicrobial resistance.

Electronic supplementary material

The online version of this article (10.1186/s40249-018-0422-7) contains supplementary material, which is available to authorized users.

Development of diagnostic prediction tools for bacteraemia caused by third-generation cephalosporin-resistant enterobacteria in suspected bacterial infections: a nested case-control study

OBJECTIVES

Current guidelines for the empirical antibiotic treatment predict the presence of third-generation cephalosporin-resistant enterobacterial bacteraemia (3GCR-E-Bac) in case of infection only poorly, thereby increasing unnecessary carbapenem use. We aimed to develop diagnostic scoring systems which can better predict the presence of 3GCR-E-Bac.

METHODS

A retrospective nested case-control study was performed that included patients ≥18 years of age from eight Dutch hospitals in whom blood cultures were obtained and intravenous antibiotics were initiated. Each patient with 3GCR-E-Bac was matched to four control infection episodes within the same hospital, based on blood-culture date and onset location (community or hospital). Starting from 32 commonly described clinical risk factors at infection onset, selection strategies were used to derive scoring systems for the probability of community- and hospital-onset 3GCR-E-Bac.

RESULTS

3GCR-E-Bac occurred in 90 of 22 506 (0.4%) community-onset infections and in 82 of 8110 (1.0%) hospital-onset infections, and these cases were matched to 360 community-onset and 328 hospital-onset control episodes. The derived community-onset and hospital-onset scoring systems consisted of six and nine predictors, respectively. With selected score cut-offs, the models identified 3GCR-E-Bac with sensitivity equal to existing guidelines (community-onset: 54.3%; hospital-onset: 81.5%). However, they reduced the proportion of patients classified as at risk for 3GCR-E-Bac (i.e. eligible for empirical carbapenem therapy) with 40% (95%CI 21-56%) and 49% (95%CI 39-58%) in, respectively, community-onset and hospital-onset infections.

CONCLUSIONS

These prediction scores for 3GCR-E-Bac, specifically geared towards the initiation of empirical antibiotic treatment, may improve the balance between inappropriate antibiotics and carbapenem overuse.

Effect of In Vitro Human Digestion on Biogenic Amine (Tyramine) Formation in Various Fermented Sausages

Biogenic amines are formed in various fermented foods by microbial amino acid decarboxylation activities, and ingestion of these amines may cause human illness. However, the effect of digestion on the biogenic amines in fermented sausages has not been studied. This study was conducted to determine the effect of in vitro human digestion with the enterobacteria Escherichia coli and Lactobacillus casei on concentrations of the biogenic amine tyramine in six types of fermented sausages. Tyramine concentration was not significantly changed until simulated digestion in the small intestine. However, tyramine concentration for all sausage samples was increased after simulated digestion in the large intestine. Addition of E. coli and L. casei dramatically increased the tyramine concentrations ( P < 0.05). This result indicates that enterobacteria increase biogenic amine concentrations during human digestion.

Protocol for HeLa Cells Infection with Escherichia coli Strains Producing Colibactin and Quantification of the Induced DNA-damage

Strains of Escherichia coli bearing the pks genomic island synthesize the genotoxin colibactin. Exposure of eukaryotic cells to E. coli producing colibactin induces DNA damages, ultimately leading to cell cycle arrest, senescence and death. Here we describe a simple method to demonstrate the genotoxicity of bacteria producing colibactin following a short infection of cultured mammalian cells with pks ⁺ E. coli.

Re-classification within the serogroups O3 and O8 of Citrobacter strains

BACKGROUND

Citrobacter strains are opportunistic pathogens often responsible for serious enteric as well as extra-intestinal diseases, and therefore the O-antigenic scheme, still in use in diagnostic identification, should be set for proper serotyping. The structures of more than 30 different Citrobacter O-antigens (O-polysaccharide chains of the lipopolysaccharides) of 43 Citrobacter O-serogroups have been elucidated so far. However, relationships between strains in several heterogeneous serogroups still need to be clarified by immunochemical studies. These include complex serogroups O3 and O8, represented by 20 and 7 strains, respectively, which are the subject of the present work. Earlier, the O-polysaccharide structures have been determined for Citrobacter O3 strain Be35/57 (PCM 1508) and Citrobacter O8 strain Be64/57 (PCM 1536).

RESULTS

Serological studies (immunoblotting) carried out on Citrobacter lipopolysaccharides from different strains ascribed to serogroups O3 and O8 showed that each of these serogroups should be divided into non-cross-reacting subgroups. Based on the results of chemical analyses and ¹H and ¹³C NMR spectroscopy the structure of Citrobacter O-antigens from strains PCM 1504 (O6) and PCM 1573 (O2) have been established. Chemical data combined with serological analyses showed that several Citrobacter strains should be reclassified into other serogroups.

CONCLUSIONS

Immunochemical studies carried out on Citrobacter LPS, described in this paper, showed the expediency of reclassification of: 1) strains PCM 1504 and PCM 1573 from serogroups O6 and O2 to serogroups O3 and O8, respectively, 2) strains PCM 1503 and PCM 1505 from serogroups O3 and O8 to new serogroups O3a and O8a, respectively.

Screening of plants with antimicrobial activity against enterobacteria, Pseudomonas spp. and Staphylococcus spp

AIM

This study screened plants for antibacterial properties against bacteria of medical importance.

MATERIALS & METHODS

60 extracts were obtained from the leaves of ten plants (Jatropha weddelliana, Attalea phalerata, Buchenavia tomentosa, Croton doctoris, Mouriri elliptica, Mascagnia benthamiana, Senna aculeata, Unonopis guatterioides, Allagoptera leucocalyx and Bactris glaucescens) using different extraction methods: A) Ethanol 70°C/72 h; B) Water/5 min/100°C; C) Water/1 h/55°C; D) Water/72 h; E) Hexane/72 h and F) Ethanol 99°C/72 h. Enterobacteria/Pseudomonas and staphylococci reference strains and 201 clinical isolates were used. Primary screening was done using agar well-diffusion assay. MIC/minimum bactericidal concentration and chemical characterization were determined.

RESULTS

Extracts 5F and 3A showed the best MIC/minimum bactericidal concentration against clinical isolates and showed the presence of phenols.

CONCLUSION

The present study demonstrated that Mouriri elliptica and Buchenavia tomentosa were the most active plants against the studied bacteria.

'Nissabacter archeti' gen. nov., sp. nov., a new member of Enterobacteriaceae family, isolated from human sample at Archet 2 Hospital, Nice, France

We propose the main characteristics of a new bacterium species named Nissabacter archeti strain 2134 (CSURP3445 = LT631518), isolated from pustule scalp of a 29-year-old man at hospital Archet 2, Nice, south of France.

Formation of Biofilms by Foodborne Pathogens and Development of Laboratory In Vitro Model for the Study of Campylobacter Genus Bacteria Based on These Biofilms

We analyzed the formation of biofilms by 7 strains of Campylobacter genus bacteria and 18 strains of Enterobacteriaceae genus bacteria that were isolated from plant and animal raw materials, from finished products, and swabs from the equipment of the food industry. Biofilm formation on glass plates, slides and coverslips, microtubes made of polymeric materials and Petri dishes, and polystyrene plates of different profiles were analyzed. When studying the process of films formation, different effects on bacterial populations were simulated, including variation of growth factor composition of culture media, technique of creating of anaerobiosis, and biocide treatment (active chlorine solutions in a concentration of 100 mg/dm³). The formation of biofilms by the studied cultures was assessed by the formation of extracellular matrix stained with aniline dyes on glass and polystyrene surfaces after incubation; 0.1% crystal violet solution was used as the dye. The presence and density of biomatrix were assessed by staining intensity of the surfaces of contact with broth cultures or by optical density of the stained inoculum on a spectrophotometer. Biofilms were formed by 57% Campylobacter strains and 44% Enterobacteriaceae strains. The intensity of the film formation depended on culturing conditions and protocols, species and genus of studied isolates, and largely on adhesion properties of abiotic surfaces. In 30% of Enterobacteriaceae strains, the biofilm formation capacity tended to increase under the influence of chlorine-containing biocide solutions. Thus, we developed and tested under laboratory conditions a plate version of in vitro chromogenic model for evaluation of biofilm formation capacity of C. jejuni strains and studied stress responses to negative environmental factors.

Molecular epidemiology of carbapenemase-producing Enterobacteriaceae infection/colonisation in a hospital in Madrid

INTRODUCTION

A description is presented on the molecular epidemiology of carbapenemase-producing enterobacteriaceae infection in a tertiary hospital.

MATERIAL AND METHODS

A study was made on all the carbapenemase-producing enterobacteriaceae isolations obtained between February 2015 and March 2016 in the Hospital Universitario 12 de Octubre (Madrid). Phenotypic and molecular methods were used.

RESULTS

A total of 7 bacterial species were identified, with the majority being Klebsiella pneumoniae (K. pneumoniae) (78.9%) and Enterobacter cloacae (E. cloacae) (16.4%). The resistance of K. pneumoniae and E. cloacae for carbapenems was 88.7 and 88.6% for ertapenem, 21.4 and 54.3% for imipenem, and 20.8 and 34.3% for meropenem, respectively. The most frequent carbapenemase type was OXA-48 (91.1%) and VIM (71.4%) in E. cloacae. A total of 9K. pneumoniae clonal types were identified, including a majority pertaining to the sequence type ST11. In E. cloacae, 16 clonal types were identified.

CONCLUSIONS

The current increase in carbapenemase-producing enterobacteriaceae is mainly due to the spread of OXA-48-producing K. pneumoniae.

The pUltra plasmid series: A robust and flexible tool for fluorescent labeling of Enterobacteria

Fluorescent labeling has been an invaluable tool for the study of living organisms and bacterial species are no exception to this. Here we present and characterize the pUltra plasmids which express constitutively a fluorescent protein gene (GFP, RFP, YFP or CFP) from a strong synthetic promoter and are suitable for the fluorescent labeling of a broad range of Enterobacteria. The amount of expressed fluorophore from these genetic constructs is such, that the contours of the cells can be delineated on the basis of the fluorescent signal only. In addition, labeling through the pUltra plasmids can be used successfully for fluorescence and confocal microscopy while unambiguous distinction of cells labeled with different colors can be carried out efficiently by microscopy or flow cytometry. We compare the labeling provided by the pUltra plasmids with that of another plasmid series encoding fluorescent proteins and we show that the pUltra constructs are vastly superior in signal intensity and discrimination power without having any detectable growth rate effects for the bacterial population. We also use the pUltra plasmids to produce mixtures of differentially labeled pathogenic Escherichia, Shigella and Salmonella species which we test during infection of mammalian cells. We find that even inside the host cell, different strains can be distinguished effortlessly based on their fluorescence. We, therefore, conclude that the pUltra plasmids are a powerful labeling tool especially useful for complex biological experiments such as the visualization of ecosystems of different bacterial species or of enteric pathogens in contact with their hosts.

Occurrence of bacteria producing broad-spectrum beta-lactamases and qnr genes in hospital and urban wastewater samples

The aims were to investigate the level of antibiotic-resistant bacteria in hospital and urban wastewater and to determine the similarity of isolates obtained from wastewater and hospitalized patients. Wastewater samples were collected in September 2013 and 2014. After identification using MALDI-TOF MS, beta-lactamase production was determined by relevant phenotypic tests. Genes responsible for the production of single beta-lactamase groups and Qnr proteins were established. The epidemiological relationship of the isolates from wastewater and hospitalized patients was determined by PFGE. A total of 51 isolates of enterobacteria were obtained. Overall, 45.1% of them produced broad-spectrum beta-lactamases. Genes encoding TEM, SHV, CTX-M, CIT, DHA and EBC types of enzymes and Qnr proteins were detected. No broad-spectrum beta-lactamase production was confirmed in the urban wastewater treatment plant. The most important finding was the detection of two identical isolates of K. pneumoniae in 2013, one from a patient's urinary catheter and the other from a wastewater sample.

Enterobacteria and Vibrio from Macrobrachium amazonicum prawn farming in Fortaleza, Ceará, Brazil

OBJECTIVE

To investigate the isolation of enterobacteria associated with Macrobrachium amazonicum (M. amazonicum) farming and evaluate the in vitro antimicrobial susceptibility of Vibrio strains.

METHODS

Strains were isolated from female M. amazonicum prawns and environmental and hatchery water. Biochemical assays were used to identify bacterial genera and those belonging to the genus Vibrio were submitted to further analyses for species identification, through Vitek 2 automated system and serotyping. Susceptibility test was performed according to Clinical Laboratory Standards Institute.

RESULTS

The following genera of enterobacteria were recovered: Enterobacter (n = 11), Citrobacter (n = 10), Proteus (n = 2), Serratia (n = 2), Kluyvera (n = 2), Providencia (n = 2), Cedecea (n = 1), Escherichia (n = 1), Edwardsiella (n = 1) and Buttiauxella (n = 1). As for Vibrio, three species were identified: Vibrio cholerae non-O1/non-O139 (n = 4), Vibrio vulnificus (V. vulnificus) (n = 1) and Vibrio mimicus (n = 1). Vibrio spp. showed minimum inhibitory concentrations values within the susceptibility range established by Clinical Laboratory Standards Institute for almost all antibiotics, except for V. vulnificus, which presented intermediate profile to ampicillin.

CONCLUSIONS

Enterobacteria do not seem to be the most important pathogens associated with M. amazonicum farming, whereas the recovery of Vibrio spp. from larviculture, with emphasis on Vibrio cholerae and V. vulnificus, deserves special attention due to their role as potentially zoonotic aquaculture-associated pathogens. Furthermore, the intermediate susceptibility of V. vulnificus to ampicillin reflects the importance of monitoring drug use in prawn farming.

A Plasmid-Transposon Hybrid Mutagenesis System Effective in a Broad Range of Enterobacteria

Random transposon mutagenesis is a powerful technique used to generate libraries of genetic insertions in many different bacterial strains. Here we develop a system facilitating random transposon mutagenesis in a range of different Gram-negative bacterial strains, including Pectobacterium atrosepticum, Citrobacter rodentium, Serratia sp. ATCC39006, Serratia plymuthica, Dickeya dadantii, and many more. Transposon mutagenesis was optimized in each of these strains and three studies are presented to show the efficacy of this system. Firstly, the important agricultural pathogen D. dadantii was mutagenized. Two mutants that showed reduced protease production and one mutant producing the previously cryptic pigment, indigoidine, were identified and characterized. Secondly, the enterobacterium, Serratia sp. ATCC39006 was mutagenized and mutants incapable of producing gas vesicles, proteinaceous intracellular organelles, were identified. One of these contained a β-galactosidase transcriptional fusion within the gene gvpA1, essential for gas vesicle production. Finally, the system was used to mutate the biosynthetic gene clusters of the antifungal, anti-oomycete and anticancer polyketide, oocydin A, in the plant-associated enterobacterium, Dickeya solani MK10. The mutagenesis system was developed to allow easy identification of transposon insertion sites by sequencing, after facile generation of a replicon encompassing the transposon and adjacent DNA, post-excision. Furthermore, the system can also create transcriptional fusions with either β-galactosidase or β-glucuronidase as reporters, and exploits a variety of drug resistance markers so that multiple selectable fusions can be generated in a single strain. This system of various transposons has wide utility and can be combined in many different ways.

Advances in research of non-steroidal anti-inflammatory drugs induced small intestinal injury

Non-steroidal anti-inflammatory drugs (NSAIDs) have anti-inflammatory, anti-pyretic and analgesic properties and have been widely used in clinical practice; however, they can cause cytotoxicity in the gastrointestinal tract, especially in the intestine. The injurious effects of NSAIDs on the small intestine occur frequently and can lead to severe clinical outcomes. A multifactorial etiology is involved in the pathogenesis of these lesions. Current studies found that, in addition to the suppression of cyclooxygenase activity, several factors including enterobacterial invasion, neutrophil migration, enterohepatic cycling of NSAIDs, bile and mitochondrial injury have been implicated in the pathogenesis of these lesions. This article reviews the mechanisms and therapeutic strategies in NSAIDs induced intestinal injury.

β-lactamases produced by amoxicillin-clavulanate-resistant enterobacteria isolated in Buenos Aires, Argentina: a new blaTEM gene

Resistance to β-lactam/β-lactamase inhibitors in enterobacteria is a growing problem that has not been intensively studied in Argentina. In the present work, 54/843 enterobacteria collected in a teaching hospital of Buenos Aires city were ampicillin-sulbactam-resistant isolates remaining susceptible to second- and third-generation cephalosporins. The enzymatic mechanisms present in the isolates, which were also amoxicillin-clavulanic acid (AMC)-resistant (18/54) were herein analyzed. Sequencing revealed two different variants of blaTEM-1, being blaTEM-1b the most frequently detected allelle (10 Escherichia coli, 3 Klebsiella pneumoniae, 2 Proteus mirabilis and 1 Raoultella terrigena) followed by blaTEM-1a (1 K. pneumoniae). Amoxicillin-clavulanate resistance seems to be mainly associated with TEM-1 overproduction (mostly in E. coli) or co-expressed with OXA-2-like and/or SHV β-lactamases (K. pneumoniae and P. mirabilis). A new blaTEM variant (TEM-163) was described in an E. coli strain having an AMC MIC value of 16/8μg/ml. TEM-163 contains Arg275Gln and His289Leu amino acid substitutions. On the basis of the high specific activity and low IC50 for clavulanic acid observed, the resistance pattern seems to be due to overproduction of the new variant of broad spectrum β-lactamase rather than to an inhibitor-resistant TEM (IRT)-like behavior.

Characteristics of KPC-2-producing Klebsiella pneumoniae (ST258) clinical isolates from outbreaks in 2 Mexican medical centers

The KPC-producing Klebsiella pneumoniae sequence type 258 (ST258) is an important pathogen widely spread in nosocomial infections. In this study, we identified the KPC-2-producing K. pneumoniae clinical isolates of 2 unrelated outbreaks that corresponded to pandemic strain ST258. The isolates showed high resistance to cephalosporins, carbapenems, quinolones, and colistin. The KPC-2-producing K. pneumoniae isolates were compared to the previously studied KPC-3-producing K. pneumoniae isolates from an outbreak in Mexico; they showed an unrelated pulsed-field gel electrophoresis fingerprinting pattern and a different plasmid profile. The KPC-2 carbapenemase gene was identified in two 230- and 270-kb non-conjugative plasmids; however, 1 isolate transferred the KPC-2 gene onto an 80-kb plasmid. These findings endorse the need of carrying out a continuous molecular epidemiological surveillance of carbapenem-resistant isolates in hospitals in Mexico.