Infections caused by Kluyvera species in humans

Genomic insights into the evolution, pathogenicity, and extensively drug-resistance of emerging pathogens Kluyvera and Phytobacter

Introduction

Kluyvera is a Gram-negative, flagellated, motile bacillus within the Enterobacteriaceae. The case reports of clinical infections shed light on the importance of this organism as an emerging opportunistic pathogen. The genus Phytobacter, which often be misidentified with Kluyvera, is also an important clinically relevant member of the Enterobacteriaceae. However, the identification of Kluyvera and Phytobacter is problematic, and their phylogenetic relationship remains unclear.

Methods

Here, 81 strains of Kluyvera and 16 strains of Phytobacter were collected. A series of comparative genomics approaches were applied to the phylogenetic relationship reconstruction, virulence related genes profiles description, and antibiotic resistance genes prediction.

Results

Using average nucleotide identity (ANI) and in silico DNA-DNA hybridization (isDDH), we offered reliable species designations of 97 strains, in which 40 (41.24%) strains were incorrectly labeled. A new Phytobacter genomospecies-1 were defined. Phytobacter and Kluyvera show great genome plasticity and inclusiveness, which may be related to their diverse ecological niches. An intergenomic distances threshold of 0.15875 was used for taxonomy reassignments at the phylogenomic-group level. Further principal coordinates analysis (PCoA) revealed 11 core genes of Kluyvera (pelX, mdtL, bglC, pcak-1, uhpB, ddpA-2, pdxY, oppD-1, cptA, yidZ, csbX) that could be served as potential identification targets. Meanwhile, the Phytobacter specific virulence genes clbS, csgA-C, fliS, hsiB1_vipA and hsiC1_vipB, were found to differentiate from Kluyvera. We concluded that the evolution rate of Kluyvera was 5.25E-6, approximately three times higher than that of Phytobacter. Additionally, the co-existence of ESBLs and carbapenem resistance genes were present in approximately 40% strains, suggesting the potential development of extensively drug-resistant or even fully drug-resistant strains.

Discussion

This work provided a better understanding of the differences between closely related species Kluyvera and Phytobacter. Their genomes exhibited great genome plasticity and inclusiveness. They not only possess a potential pathogenicity threat, but also a risk of multi-drug resistance. The emerging pathogens Kluyvera and Phytobacter warrant close attention.

Kluyvera ascorbata: An Unusual Cause of Septic Shock in a Patient With Urothelial Cancer

Kluyvera ascorbata is a gram-negative bacillus which is a rare cause of clinically significant infections in humans. We report a rare case of K. ascorbata infection causing septic shock in a patient with a history of urothelial cancer. After the antimicrobial susceptibility testing, the patient was successfully treated with ceftriaxone. Recognition of the disease-producing potential of this rare pathogen with prompt initiation of effective antimicrobial coverage is paramount for appropriate management in the adult immunocompromised population. To our knowledge, this is the first case report of septic shock secondary to K. ascorbata urinary tract infection.

Genomic Characteristion of Opportunistic Pathogen Kluyvera Reveals a Novel CTX-M Subgroup

A rising incidence of clinical infections has been caused by Kluyvera, a significant opportunistic pathogen. Meanwhile, Kluyvera acts as an important reservoir of blaCTX-Ms, which are the dominant genes of class A extended-spectrum β-lactamases (ESBLs). In this work, 60 strains of Kluyvera were subjected to phylogenetic relationship reconstruction, antimicrobial susceptibility testing, and antibiotic resistance genes prediction. All mature blaCTX-Ms were gathered to perform subgroup reclassification. The findings demonstrate that Kluyvera has a large gene pool with significant genetic flexibility. Notably, 25% of strains showed simultaneous detection of ESBLs and carbapenem resistance genes. The genotypes of fourteen novel blaCTX-Ms were identified. A new subgroup classification approach for blaCTX-Ms was defined by using 20 amino acid site variants, which could split blaCTX-Ms into 10 subgroups. The results of the subgroup division were consistent with the phylogenetic clustering. More significantly, we proposed a novel blaCTX-M subgroup, KLUS, that is chromosomally encoded in K. sichuanensis and the new species put forward in this study, showing amino acid differences from the currently known sequences. Cloning and transformation tests demonstrated that the recipient bacteria had a robust phenotype of cefotaxime resistance. Closely related Kluyvera species had blaCTX-Ms in the same subgroup. Our research lays the groundwork for a deeper comprehension of Kluyvera and emphasizes how important a blaCTX-M reservoir it is. We provide an update on blaCTX-M subgroups reclassification from the aspects of phylogenetic relationship, amino acid differences, and the new subgroup KLUS, which needs to be strengthen monitored due to its strong resistance phenotype to cefotaxime.

Effects of cadmium and diethylhexyl phthalate on skin microbiota of Rana chinensis tadpoles

Skin microbiotas play a crucial role in the health, homeostasis, and immune function of amphibians. The contaminants in water could affect the structure and composition of microbial communities. The effects of coexisting pollutants on frogs cannot be adequately explained by a single exposure due to the coexistence of Cd and DEHP in the environment. Following exposure to Cd and/or DEHP, we examined the histological characteristics of Rana chensinensis tadpoles. We also used the 16S rRNA gene sequencing technique to assess the relative abundance of skin microbial communities among tadpoles from each treatment group. Our findings indicate that R. chensinensis' skin experienced some degree of injury due to exposure to Cd and DEHP, which led to the imbalance of their skin microbial community homeostasis and thus interfered with the normal trial status of the host. That may eventually lead to the decline of the amphibian population.

Kluyvera intermedia bacteremia with septic shock: A case report

Background

Kluyvera intermedia is a bacterium indigenous to humans. But Kluyvera intermedia bacteremia has been not reported thus far. We report a case of Kluyvera intermedia bacteremia with septic shock due to left obstructive pyelonephritis as a result of urolithiasis.

Case presentation

A 66-year-old woman with septic shock due to left obstructive pyelonephritis was transferred to our hospital. Tazobactam/Piperacillin 4.5 g was administered every 8 h for 5 days. The patient's condition improved, and she was transferred back to the previous hospital. Kluyvera intermedia was obtained by blood cultures. The patient was successfully treated with a two-week course of antibiotics.

Conclusions

We describe the first case of bacteremia with septic shock caused by Kluyvera intermedia. Kluyvera intermedia can be a causative pathogen of septic shock. Since this bacterium has not been reported in the past, we expect further reports and the accumulation of cases in the future.

Integrated metagenomic and metatranscriptomic analysis reveals actively expressed antibiotic resistomes in the plastisphere

The plastisphere is viewed as a reservoir for the antibiotic resistome in water environments and may pose health concerns. However, the expression profiles of the resistome in the plastisphere are largely unknown. Here, we profiled the occurrence, abundance, and transcriptional level of antibiotic resistance genes (ARGs), plasmid associated ARGs, microbial composition and ARG bacterial hosts in the plastisphere and urban river water using 16S rRNA gene sequencing, metagenomic sequencing, and metatranscriptomic sequencing methods. A total of 173 ARGs conferring resistance to 24 major classes of antibiotics commonly prescribed to humans and animals were detected in the plastisphere. Of these, 75 genes were observed with transcriptional activity, indicating that the antibiotic resistome in the plastisphere was not only present, but also actively expressed. Human pathogens belonging to family Enterobacteriaceae were identified as bacterial hosts of ARGs in the plastisphere. The opportunistic and multidrug resistant human pathogen Enterobacter cloacae was found to actively express tetG and confer tetracycline resistance to the plastisphere. Furthermore, 39 genes were identified as "plasmid associated ARGs" in the plastisphere, displaying a higher proportion of transcript abundance compared with water. The above results suggest that the plastisphere is a hotspot for antibiotic resistome acquisition, expression, and dissemination.

Complete Genome Sequence of Kluyvera sp. CRP, a Cellulolytic Strain Isolated from Red Panda Feces (Ailurus fulgens)

The enterobacterium genus Kluyvera is widely distributed in the environment and a rare source of infection in humans. Kluyvera sp. strain CRP was isolated from feces of a healthy, captive Chinese red panda (Ailurus fulgens), and its complete genome (5,157,963 bp, 54.80% GC content) was established through hybrid assembly.

Surveillance and prevalence of antimicrobial resistant bacteria from public settings within urban built environments: Challenges and opportunities for hygiene and infection control

Antimicrobial resistant (AMR) bacteria present one of the biggest threats to public health; this must not be forgotten while global attention is focussed on the COVID-19 pandemic. Resistant bacteria have been demonstrated to be transmittable to humans in many different environments, including public settings in urban built environments where high-density human activity can be found, including public transport, sports arenas and schools. However, in comparison to healthcare settings and agriculture, there is very little surveillance of AMR in the built environment outside of healthcare settings and wastewater. In this review, we analyse the existing literature to aid our understanding of what surveillance has been conducted within different public settings and identify what this tells us about the prevalence of AMR. We highlight the challenges that have been reported; and make recommendations for future studies that will help to fill knowledge gaps present in the literature.

Soul of the Jukskei River: The Extent of Bacterial Contamination in the Jukskei River in Gauteng Province, South Africa

River water quality is an important health issue as the water is utilised for drinking, domestic and agricultural use in developing countries. This study aimed to investigate the effect water from a major city has on the water quality of the Jukskei River that daylights in Johannesburg, South Africa. The river water samples were analysed for physio-chemical properties, microbiology, antibiotic resistance of bacterial isolates, genetic markers, and potentially toxic metals. Data analysis revealed increased electrical conductivity, total dissolved solids, and turbidity since 2010. Total Coliform and Escherichia coli detected were above the South African water quality guidelines for domestic, recreational, and irrigation purposes. Additionally, sodium, zinc, nickel, lithium, and lead exceeded the guidelines in domestic, recreational, and irrigation water. Pathogenic strains of E. coli (aEPEC, EHEC, EIEC, and EAEC) were isolated from the water. Various other potentially pathogenic organisms that have been implicated as causes of gastro-intestinal, and a wide range of other diseases, were also detected and demonstrated multiple levels of resistance to antibiotics tested. The results show that the river water is a potential health threat to downstream users. These results will feed into the environmental management action plan for Water for the Future (NGO group).

A Novel Salmonella Periplasmic Protein Controlling Cell Wall Homeostasis and Virulence

Horizontal gene transfer has shaped the evolution of Salmonella enterica as pathogen. Some functions acquired by this mechanism include enzymes involved in peptidoglycan (PG) synthesis and remodeling. Here, we report a novel serovar Typhimurium protein that is absent in non-pathogenic bacteria and bears a LprI functional domain, first reported in a Mycobacterium tuberculosis lipoprotein conferring lysozyme resistance. Based on the presence of such domain, we hypothesized a role of this S. Typhimurium protein in PG metabolism. This protein, which we named ScwA for Salmonellacell wall-related regulator-A, controls positively the levels of the murein lytic transglycosylase MltD. In addition, the levels of other enzymes that cleave bonds in the PG lattice were affected in a mutant lacking ScwA, including a soluble lytic tranglycosylase (Slt), the amidase AmiC, and a few endo- and carboxypeptidases (NlpC, PBP4, and AmpH). The scwA gene has lower G+C content than the genomic average (43.1 vs. 52.2%), supporting acquisition by horizontal transfer. ScwA is located in the periplasm, stabilized by two disulfide bridges, produced preferentially in stationary phase and down-regulated following entry of the pathogen into eukaryotic cells. ScwA deficiency, however, results in a hypervirulent phenotype in the murine typhoid model. Based on these findings, we conclude that ScwA may be exploited by S. Typhimurium to ensure cell envelope homeostasis along the infection and to prevent host overt damage. This role could be accomplished by controlling the production or stability of a reduced number of peptidoglycan hydrolases whose activities result in the release of PG fragments.

Selection of plant growth promoting rhizobacteria sharing suitable features to be commercially developed as biostimulant products

Plant biostimulants (PBs) are an eco-friendly alternative to chemical fertilisers because of their minimal or null impact on human health and environment, while ensuring optimal nutrient uptake and increase of crop yield, quality and tolerance to abiotic stress. Although there is an increasing interest on microbial biostimulants, the optimal procedure to select and develop them as commercial products is still not well defined. This work proposes and validates a procedure to select the best plant growth promoting rhizobacteria (PGPR) as potential active ingredients of commercial PBs. The stepwise screening strategy was designed based on literature analysis and consists of six steps: (i) determination of the target crop and commercial strategy, (ii) selection of growth media for the isolation of microbial candidates, (iii) screening for traits giving major agronomical advantages, (iv) screening for traits related to product development, (v) characterisation of the mode of action of PGPR and (vi) assessment of plant growth efficacy. The strategy was validated using a case study: PGPR combined with humic acids to be applied on tomato plants. Among 200 bacterial strains isolated from tomato rhizosphere, 39 % were able to grow in presence of humic acids and shared the ability to solubilise phosphate. After the screening for traits related to product development, only 6 % of initial bacterial strains were sharing traits suitable for the further development as potential PBs. In fact, the selected bacterial strains were able to produce high cell mass and tolerated drought, aspects important for the mass production and formulation. These bacterial strains were not able to produce antibiotics, establish pathogenic interaction with plants and did not belong to bacterial species associated to human, animal and plant diseases. Most importantly, five of the selected bacterial strains were able to promote tomato seedling vigour in experiments carried out in vitro. These bacterial strains were furtherly characterised for their ability to colonize effectively tomato plant roots, produce phytohormones and solubilise soil minerals. This characterisation led to the selection of two candidates that showed the ability to promote tomato plant growth in experiments carried out in greenhouse conditions. Overall, this work provides a flow diagram for the selection of PGPR candidates to be successfully developed and commercialized as PBs. The validation of the flow diagram led to the selection of two bacterial strains belonging to Pantoea and Pseudomonas genera, potential active ingredients of new commercial PBs.

Maize (Zea mays L. Sp.) varieties significantly influence bacterial and fungal community in bulk soil, rhizosphere soil and phyllosphere

The plant-microbe interaction can affect ecosystem function, and many studies have demonstrated that plant species influence relevant microorganisms. In this study, microbial communities in bulk soil, rhizosphere soil and phyllosphere from different maize varieties were investigated using high-throughput sequencing method. Results demonstrated that cultivar Gaoneng 1 (G1) showed higher bacterial diversity in soil (both bulk and rhizosphere soils) and lower bacterial diversity in the phyllosphere, while cultivar Gaoneng 2 (G2) had lower fungal diversity in both the soil and phyllosphere compare to the other cultivars. The bacterial community structure of soils among the three varieties was significantly different; however, no significant differences were found in the soil fungal community and phyllosphere bacterial and fungal community. The soil networks from cultivar G1 and phyllosphere networks from cultivar Zhengdan (ZD) have the highest complexity in contrast to the other two cultivars. In conclusion, the bacterial community structure in bulk soil of different cultivars was significantly different, so do the co-occurrence ecological networks of phyllosphere bacterial community. This study comprehensively analyzed the microbial community among different maize cultivars and could be useful for guiding practices, such as evaluation of new plant cultivars and quality predictions of these varieties at the microbial level.

Precise Species Identification and Taxonomy Update for the Genus Kluyvera With Reporting Kluyvera sichuanensis sp. nov

Kluyvera is a genus within the family Enterobacteriaceae and can cause various human infections but remains poorly studied. A carbapenem-resistant bla_NDM–1-carrying Kluyvera strain 090646^T was isolated from a hospital sink in Chengdu, Sichuan province, China. Whole genome sequencing of the strain revealed that it had 28.2 to 42.3% in silico DNA-DNA hybridization (isDDH) scores and 84.15 to 90.10% average nucleotide identity (ANI) values with other Kluyvera species. Both values are well below the ≥ 70.0% isDDH and ≥ 95–96% ANI cutoffs to define bacterial species, suggesting that the strain represents a novel species of the genus Kluyvera, for which the name Kluyvera sichuanensis. nov. is proposed. Type strain of K. sichuanensis is 090646^T (=GDMCC 1.1872^T =KCTC 82166^T). Strain 090646^T can be differentiated from other Kluyvera species by its ability to utilize D-sorbitol but not β-galactosidase (ONPG), D-mannose, glycerin, raffinose, nor sucrose. There were 47 genome sequences labeled as Kluyvera in GenBank, which were curated for precise species identification. Only 33 of the 47 genomes were indeed of Kluyvera and four novel Kluyvera genomospecies were identified, highlighting that the species assignation of bacterial genomes in GenBank need to be curated. Genome sequencing for more strains is required to understand the genus Kluyvera.

Reducing food waste in residential complexes using a pilot-scale on-site system

A pilot-scale on-site system combining biological treatment and a drying stage was applied to achieve mass reduction of food waste (FW) at an urban residential complex. The effectiveness of biodegrading the organic portion of FW via microorganisms existing in FW improved by 38.80% by controlling rates of FW loading and air-flow. In one stage of the on-site biological treatment, the major bacterial community was identified to be mesophilic and facultative; Lactobacillus was the most dominant genus, accounting for 78.1% of bacterial community. Total mass reduction of FW approached 90.15% by increasing removal of both moisture and the organic portion of FW. In addition, the solids and liquids of the final by-products have the potential to be recycled into resources such as fertilizer, a bio-solid refuse fuel or external carbon sources for wastewater treatment plants. The proposed decentralized system offers practical and environmental approaches for FW management in residential complexes.

Polymicrobial infection with Kluyvera species secondary to pressure necrosis of the hand, a case report

Kluyvera is a rare infection in the upper extremity. Originally identified as an opportunistic pathogen, the virulence of Kluyvera has been debated. An elderly male presented with multiple pressure sores after being found down for an unknown time period. A hand abscess bacterial culture grew Kluyvera species as part of a polymicrobial infection. Despite multiple debridements, antibiotics and wound care, his clinical course ultimately was unsatisfactory and eventually fatal.

The role of urbanization in soil and groundwater contamination by heavy metals and pathogenic bacteria: A case study from Oman

This study assessed the perception of urban residents of A'Seeb city, Oman, about the impact of their activities on environment. A sociological survey using questionnaire was used to know the residents' perceptions about urban gardening, municipal-waste disposal, and soil and water contamination. Viable pathogenic bacteria, water soluble metals, basic cations, salinity, and texture were quantified and identified in soil and groundwater in proximity of urban gardens and municipal-waste disposal sites. The majority of surveyed residents are not paying attention to the negative consequences of their activities on soil and environment. Although the measured heavy metals concentrations in some of the contaminated sites were significant but still below the international standards. Fecal contaminants reported in in some samples from gardens, garbage-disposal sites and groundwater. Human pathogens belonging to risk group-2 including Klebsiella pneumonia, Shigella spp and E. Coil were identified. More socio-environmental studies required to correlate the behavior of urban residents and pollution and to delineate the sources of the detected pathogenic bacteria. Our results set a foundation for future studies on urban soils and associated residence behaviors and practices in Oman and the neighboring Gulf countries.

Prevalence and diversity of blaTEM, blaSHV and blaCTX-M variants among multidrug resistant Klebsiella spp. from an urban riverine environment in India

In the present study, we have investigated prevalence and diversity of ESBL genes among Klebsiella isolates obtained from highly polluted stretch of river Yamuna, India. Phenotypic screenings of 116 Klebsiella isolates revealed ~30% were positive for ESBL production. Antibiotic profiling showed multidrug resistance phenotype among 90% isolates. Prevalence of blaTEM, blaSHV and blaCTX-M genes were found to be 57, 54 and 48% respectively. Furthermore, we identified eight variants of blaSHV (SHV-1, SHV-11, SHV-27, SHV-28, SHV-38, SHV-61, SHV-144, SHV-148), three each of blaTEM (TEM-1, TEM-116, TEM-206) and blaCTX-M (CTX-M-15, CTX-M-55, CTX-M-188) among Klebsiella spp. Co-occurrence of blaTEM, blaSHV and blaCTX-M (any two or all three) was observed among 45% Klebsiella isolates. Occurrence of blaCTX-M-188 and blaTEM-206 in environmental isolates of K. pneumoniae has not been reported earlier. Identification of blaTEM-206, blaSHV-27 and blaSHV-144 from Klebsiella spp. and blaTEM-116 from K. quasipneumoniae and K. variicola is the first report from India.

Origin of the plasmid-mediated fosfomycin resistance gene fosA3

Background

fosA3 is the most commonly reported plasmid-mediated fosfomycin resistance gene among Enterobacteriaceae.

Objectives

To identify the origin of fosA3.

Methods

The chromosome of Kluyvera georgiana clinical strain YDC799 was fully sequenced with single-molecule real-time sequencing. Comparative genetic analysis was performed for K. georgiana YDC799, K. georgiana type strain ATCC 51603 and representative fosA3-carrying plasmids. fosA genes were cloned in Escherichia coli to confirm function.

Results

K. georgiana YDC799 harboured fosA (designated fosAKG) and blaCTX-M-8 on the chromosome. The genetic environments surrounding fosA3 and bounded by IS26 were nearly identical with the corresponding regions of K. georgiana YDC799 and ATCC 51603. The amino acid sequence of FosAKG from YDC799 and K. georgiana ATCC 51603 shared 99% and 94% identity with FosA3, respectively. Cloned FosAKG conferred fosfomycin resistance with an MIC of >1024 mg/L for E. coli.

Conclusions

The plasmid-mediated fosA3 gene was likely mobilized from the chromosome of K. georgiana by an IS26-mediated event.

The Microbiomes of Pancreatic and Duodenum Tissue Overlap and Are Highly Subject Specific but Differ between Pancreatic Cancer and Noncancer Subjects

BACKGROUND

In mice, bacteria from the mouth can translocate to the pancreas and impact pancreatic cancer progression. In humans, oral bacteria associated with periodontal disease have been linked to pancreatic cancer risk. It is not known if DNA bacterial profiles in the pancreas and duodenum are similar within individuals.

METHODS

Tissue samples were obtained from 50 subjects with pancreatic cancer or other conditions requiring foregut surgery at the Rhode Island Hospital (RIH), and from 34 organs obtained from the National Disease Research Interchange. 16S rRNA gene sequencing was performed on 189 tissue samples (pancreatic duct, duodenum, pancreas), 57 swabs (bile duct, jejunum, stomach), and 12 stool samples.

RESULTS

Pancreatic tissue samples from both sources (RIH and National Disease Research Interchange) had diverse bacterial DNA, including taxa typically identified in the oral cavity. Bacterial DNA across different sites in the pancreas and duodenum were highly subject specific in both cancer and noncancer subjects. Presence of genus Lactobacillus was significantly higher in noncancer subjects compared with cancer subjects and the relative abundance of Fusobacterium spp., previously associated with colorectal cancer, was higher in cancer subjects compared with noncancer subjects.

CONCLUSIONS

Bacterial DNA profiles in the pancreas were similar to those in the duodenum tissue of the same subjects, regardless of disease state, suggesting that bacteria may be migrating from the gut into the pancreas. Whether bacteria play a causal role in human pancreatic cancer needs to be further examined.

IMPACT

Identifying bacterial taxa that differ in cancer patients can provide new leads on etiologically relevant bacteria.

The first case of third-generation cephalosporins resistant Kluyvera ascorbata biliary tract infection in Japan: A case report and review of the literature

Introduction

Kluyvera ascorbata is a gram-negative, catalase-positive, oxidase-negative, aerobic fermentative bacterium with flagella. This organism colonizes in the human body and its pathogenicity is extremely low; few clinical cases of K. ascorbata infection have been reported.

Presentation of case

We report on a patient who experienced severe sepsis and acute cholangitis due to K. ascorbata bacteremia and was treated with levofloxacin following antibiotic susceptibility testing. To our knowledge, this is the first case report of third-generation cephalosporins resistant K. ascorbata infection in Japan.

Discussion

Although this pathogen produces innate CTX-M type β-lactamases and is generally resistant to first- and second-generation penicillins and cephalosporins, multi-drug resistant K. ascorbata infection, including ceftriaxone resistant infection has seldom been reported.

Conclusion

The increase of drug-resistant pathogens is of concern; in such cases, rapid microbial identification and appropriate antibiotic selection are crucial for successful treatment.

First Report of an OXA-48- and CTX-M-213-Producing Kluyvera Species Clone Recovered from Patients Admitted in a University Hospital in Madrid, Spain

Enterobacterales species other than Klebsiella pneumoniae also contribute to OXA-48 carbapenemase endemicity. We studied the emergence of an OXA-48-producing Kluyvera species clone, which expresses the novel CTX-M-213 enzyme, colonizing patients in our hospital. Rectal swabs from patients admitted in four wards (March 2014 to March 2016; R-GNOSIS project) were seeded onto Chromo ID-ESBL) and Chrom-CARB/OXA-48 chromogenic agar plates. Carbapenemases and extended-spectrum β-lactamases (ESBLs) were characterized (PCR, sequencing, cloning, and site-directed mutagenesis), and antibiotic susceptibility was determined. Clonal relatedness was established (XbaI pulsed-field gel electrophoresis [XbaI-PFGE]), and plasmid content was studied (transformation, S1 nuclease digestion-PFGE, SB-hybridization, restriction fragment length polymorphism [RFLP] analysis [DraI and HpaI], and PCR [incompatibility group and repA, traU, and parA genes]). Whole-genome sequencing (WGS) (Illumina HiSeq-2500) and further bioinformatics analysis of plasmids (PLACNET and plasmidSPAdes) were performed. Patients' charts were reviewed. Six unrelated patients (median age, 75 years [range, 59 to 81 years]; 4/6 male patients) colonized with OXA-48-producing Kluyvera species isolates (>95% similarity of the PFGE pattern) were identified. Nosocomial acquisition was demonstrated. In two patients, OXA-48-producing Kluyvera species isolates coexisted with OXA-48-producing Raoultella ornithinolytica, K. pneumoniae, and Escherichia coli The bla _OXA-48 gene was located on an ∼60-kb IncL plasmid related to IncL/M-pOXA-48a and the novel bla _CTX-M-213 gene in a conserved chromosomal region of Kluyvera species isolates. CTX-M-213, different from CTX-M-13 (K56E) but conferring a similar β-lactam resistance profile, was identified. Genomic analysis also revealed a 177-kb IncF plasmid (class I integron harboring sul1 and aadA2) and an 8-kb IncQ plasmid (IS4-bla _FOX-8). We describe the first bla _OXA-48 plasmid in Kluyvera spp. and the novel chromosomal CTX-M-213 enzyme and highlight further nosocomial dissemination of bla _OXA-48 through clonal lineages or plasmids related to IncL/M-pOXA-48a.

Horizontal transfer of antibiotic resistance genes in clinical environments

A global medical crisis is unfolding as antibiotics lose effectiveness against a growing number of bacterial pathogens. Horizontal gene transfer (HGT) contributes significantly to the rapid spread of resistance, yet the transmission dynamics of genes that confer antibiotic resistance are poorly understood. Multiple mechanisms of HGT liberate genes from normal vertical inheritance. Conjugation by plasmids, transduction by bacteriophages, and natural transformation by extracellular DNA each allow genetic material to jump between strains and species. Thus, HGT adds an important dimension to infectious disease whereby an antibiotic resistance gene (ARG) can be the agent of an outbreak by transferring resistance to multiple unrelated pathogens. Here, we review the small number of cases where HGT has been detected in clinical environments. We discuss differences and synergies between the spread of plasmid-borne and chromosomal ARGs, with a special consideration of the difficulties of detecting transduction and transformation by routine genetic diagnostics. We highlight how 11 of the top 12 priority antibiotic-resistant pathogens are known or predicted to be naturally transformable, raising the possibility that this mechanism of HGT makes significant contributions to the spread of ARGs. HGT drives the evolution of untreatable "superbugs" by concentrating ARGs together in the same cell, thus HGT must be included in strategies to prevent the emergence of resistant organisms in hospitals and other clinical settings.

Complete Genome Sequence of Kluyvera intestini sp. nov., Isolated from the Stomach of a Patient with Gastric Cancer

We report here an update to the draft genome sequence of Kluyvera intestini sp. nov. strain GT-16, generated using MinION long-read sequencing technology. The complete genome sequence of the human-derived strain GT-16 measured 5,768,848 bp. An improved high-quality complete genome sequence provides insights into the mobility potential of resistance genes in this species.

A Case of Urinary Tract Infection and Severe Sepsis Caused by Kluyvera ascorbata in a 73-Year-Old Female with a Brief Literature Review

Infections that are caused by Kluyvera bacteria have been previously reported in the medical literature; however, they seem to be less common. Herein, we report a case of urinary tract infection and severe sepsis caused by Kluyvera ascorbata in a 73-year-old female. We also did a brief literature review of infections caused by this organism in adults.

Draft Genome Sequence of Kluyvera intestini Strain GT-16 Isolated from the Stomach of a Patient with Gastric Cancer

Here, we report the complete genome sequence of the novel, non-spore-forming Kluyvera intestini strain GT-16, isolated from the stomach of a patient with gastric cancer. The genome is 5,868,299 bp in length with a G+C content of 53.0%. It possesses 5,350 predicted protein-coding genes encoding virulence factors and antibiotic resistance proteins.

Structural and Biochemical Characterization of Rm3, a Subclass B3 Metallo-β-Lactamase Identified from a Functional Metagenomic Study

β-Lactamase production increasingly threatens the effectiveness of β-lactams, which remain a mainstay of antimicrobial chemotherapy. New activities emerge through both mutation of previously known β-lactamases and mobilization from environmental reservoirs. The spread of metallo-β-lactamases (MBLs) represents a particular challenge because of their typically broad-spectrum activities encompassing carbapenems, in addition to other β-lactam classes. Increasingly, genomic and metagenomic studies have revealed the distribution of putative MBLs in the environment, but in most cases their activity against clinically relevant β-lactams and, hence, the extent to which they can be considered a resistance reservoir remain uncharacterized. Here we characterize the product of one such gene, blaRm3, identified through functional metagenomic sampling of an environment with high levels of biocide exposure. blaRm3 encodes a subclass B3 MBL that, when expressed in a recombinant Escherichia coli strain, is exported to the bacterial periplasm and hydrolyzes clinically used penicillins, cephalosporins, and carbapenems with an efficiency limited by high Km values. An Rm3 crystal structure reveals the MBL superfamily αβ/βα fold, which more closely resembles that in mobilized B3 MBLs (AIM-1 and SMB-1) than other chromosomal enzymes (L1 or FEZ-1). A binuclear zinc site sits in a deep channel that is in part defined by a relatively extended N terminus. Structural comparisons suggest that the steric constraints imposed by the N terminus may limit its affinity for β-lactams. Sequence comparisons identify Rm3-like MBLs in numerous other environmental samples and species. Our data suggest that Rm3-like enzymes represent a distinct group of B3 MBLs with a wide distribution and can be considered an environmental reservoir of determinants of β-lactam resistance.

Prevalence and Antibiotic Resistance Profiles of Extended-Spectrum β-Lactamase-Producing Escherichia coli Isolated from Healthy Broilers in Shandong Province, China

Food-producing animals carrying extended-spectrum β-lactamase-producing Escherichia coli (ESBL-EC) have posed a potential threat to human and animal health. However, information regarding ESBL-EC in the intensive broiler breeding areas of Shandong Province, People's Republic of China, is very limited. The goal of our study was to investigate the prevalence and drug resistance characteristics of ESBL-EC in healthy broilers from Shandong Province. A total of 142 ESBL-EC isolates were collected from four prefectures in Shandong Province from October 2014 to February 2015. ESBL-EC isolates were frequently detected (142 of 160 samples, 88.8%) in healthy broilers. Antibiotic susceptibility testing showed that all 142 ESBL-EC isolates were resistant to ampicillin, piperacillin, and cefazolin but were sensitive to imipenem and meropenem. All ESBL-EC isolates carried one or more of the bla genes, in which blaCTX-M, blaTEM-1, and blaSHV-5 genes were identified in 142, 106, and 5 isolates, respectively. The blaCTX-M gene includes blaCTX-M-15 (56), blaCTX-M-65 (42), blaCTX-M-55 (36), blaCTX-M-14 (21), blaCTX-M-79 (1), blaCTX-M-3 (1), blaCTX-M-123 (1), and blaCTX-M-132 (1). In addition, 17 ESBL-EC isolates cocarried the genes of the CTX-M-1 and CTX-M-9 groups. Our findings indicate that healthy broiler flocks in Shandong Province in China are an important reservoir for ESBL-EC, with blaCTX-M and blaTEM-1 being the prevalent resistance genes identified.

bla CTX-M-152, a Novel Variant of CTX-M-group-25, Identified in a Study Performed on the Prevalence of Multidrug Resistance among Natural Inhabitants of River Yamuna, India

Natural environment influenced by anthropogenic activities creates selective pressure for acquisition and spread of resistance genes. In this study, we determined the prevalence of Extended Spectrum β-Lactamases producing gram negative bacteria from the River Yamuna, India, and report the identification and characterization of a novel CTX-M gene variant bla_CTX-M-152. Of the total 230 non-duplicate isolates obtained from collected water samples, 40 isolates were found positive for ESBL production through Inhibitor-Potentiation Disc Diffusion test. Based on their resistance profile, 3% were found exhibiting pandrug resistance (PDR), 47% extensively drug resistance (XDR), and remaining 50% showing multidrug resistant (MDR). Following screening and antimicrobial profiling, characterization of ESBLs (bla_TEMand bla_CTX-M), and mercury tolerance determinants (merP, merT, and merB) were performed. In addition to abundance of bla_TEM-116 (57.5%) and bla_CTX-M-15 (37.5%), bacteria were also found to harbor other variants of ESBLs like bla_CTX-M-71 (5%), bla_CTX-M-3 (7.5%), bla_CTX-M-32 (2.5%), bla_CTX-M-152 (7.5%), bla_CTX-M-55 (2.5%), along with some non-ESBLs; bla_TEM-1 (25%) and bla_OXY (5%). Additionally, co-occurrence of mercury tolerance genes were observed among 40% of isolates. In silico studies of the new variant, bla_CTX-M-152were conducted through modeling for the generation of structure followed by docking to determine its catalytic profile. CTX-M-152 was found to be an out-member of CTX-M-group-25 due to Q26H, T154A, G89D, P99S, and D146G substitutions. Five residues Ser70, Asn132, Ser237, Gly238, and Arg273 were found responsible for positioning of cefotaxime into the active site through seven H-bonds with binding energy of -7.6 Kcal/mol. Despite small active site, co-operative interactions of Ser237 and Arg276 were found actively contributing to its high catalytic efficiency. To the best of our knowledge, this is the first report of bla_CTX-M-152 of CTX-M-group-25 from Indian subcontinent. Taking a note of bacteria harboring such high proportion of multidrug and mercury resistance determinants, their presence in natural water resources employed for human consumption increases the chances of potential risk to human health. Hence, deeper insights into mechanisms pertaining to resistance development are required to frame out strategies to tackle the situation and prevent acquisition and dissemination of resistance determinants so as to combat the escalating burden of infectious diseases.

Identification of potential drug targets by subtractive genome analysis of Escherichia coli O157:H7: an in silico approach

Bacterial enteric infections resulting in diarrhea, dysentery, or enteric fever constitute a huge public health problem, with more than a billion episodes of disease annually in developing and developed countries. In this study, the deadly agent of hemorrhagic diarrhea and hemolytic uremic syndrome, Escherichia coli O157:H7 was investigated with extensive computational approaches aimed at identifying novel and broad-spectrum antibiotic targets. A systematic in silico workflow consisting of comparative genomics, metabolic pathways analysis, and additional drug prioritizing parameters was used to identify novel drug targets that were essential for the pathogen’s survival but absent in its human host. Comparative genomic analysis of Kyoto Encyclopedia of Genes and Genomes annotated metabolic pathways identified 350 putative target proteins in E. coli O157:H7 which showed no similarity to human proteins. Further bio-informatic approaches including prediction of subcellular localization, calculation of molecular weight, and web-based investigation of 3D structural characteristics greatly aided in filtering the potential drug targets from 350 to 120. Ultimately, 44 non-homologous essential proteins of E. coli O157:H7 were prioritized and proved to have the eligibility to become novel broad-spectrum antibiotic targets and DNA polymerase III alpha (dnaE) was the top-ranked among these targets. Moreover, druggability of each of the identified drug targets was evaluated by the DrugBank database. In addition, 3D structure of the dnaE was modeled and explored further for in silico docking with ligands having potential druggability. Finally, we confirmed that the compounds N-coeleneterazine and N-(1,4-dihydro-5H-tetrazol-5-ylidene)-9-oxo-9H-xanthene-2-sulfon-amide were the most suitable ligands of dnaE and hence proposed as the potential inhibitors of this target protein. The results of this study could facilitate the discovery and release of new and effective drugs against E. coli O157:H7 and other deadly human bacterial pathogens.

Kluyvera ascorbata infections in children: a case series

Kluyvera is a relatively newly described member of the Enterobacteriaceae family that rarely causes infections in humans. In the pediatric population, it is described in association with clinically significant infections ranging from urinary tract infections to sepsis with multiorgan failure. Our aim is to determine the clinical significance of K. ascorbata infections in the pediatric population at our institution. We retrospectively analyzed clinical microbiology data as from 2006 and identified four clinically significant isolates in this period. The isolates were from four cases who presented with sepsis, bacteremia associated with central venous catheter, pyelonephritis and intraabdominal collection. The ages of these patients ranged between seven months to 17 years. All patients received prompt antimicrobial treatment on the basis of susceptibility testing and good clinical response was obtained in all patients. Successful treatment options include third-generation cephalosporins, aminoglycosides, betalactams with beta-lactamase inhibitors and carbapenems. Clinicians should be aware of the spectrum of disease and increasing clinical importance associated with this pathogen.

Enterobacterial colonization in captive red-eared sliders (Trachemys scripta elegans)

The handling of turtles and other reptiles can be associated with risk of pathogenic enterobacteria transmission, mainly Salmonella spp. The aim of this study was to identify the enterobacteria in cloacal swabs of 39 red-eared sliders (Trachemys scripta elegans). Cloacal swabs from 39 captive individuals were analyzed. After sample enrichment in brain-heart infusion broth and 1% peptone water, bacterial isolation was performed through cultivation in blood, MacConkey and xylose lysine desoxycholate agar. Bacterial identification was achieved through conventional tests and automated turbidity analysis. The results indicated the growth of Kluyvera ascorbata (38/39), Leclercia adecarboxylata (37/39), Raoultella planticola (30/39), Citrobacter freundii (20/39), Proteus spp. (15/39), and Escherichia coli (5/39). Salmonella spp. were not detected. The intestinal enterobacteria identified inthis study differed from that reported in the literature for other reptiles.

The carriage of antibiotic resistance by enteric bacteria from imported tokay geckos (Gekko gecko) destined for the pet trade

The emergence of antibiotic-resistant bacteria is a growing public health concern and has serious implications for both human and veterinary medicine. The nature of the global economy encourages the movement of humans, livestock, produce, and wildlife, as well as their potentially antibiotic-resistant bacteria, across international borders. Humans and livestock can be reservoirs for antibiotic-resistant bacteria; however, little is known about the prevalence of antibiotic-resistant bacteria harbored by wildlife and, to our knowledge, limited data has been reported for wild-caught reptiles that were specifically collected for the pet trade. In the current study, we examined the antibiotic resistance of lactose-positive Enterobacteriaceae isolates from wild-caught Tokay geckos (Gekko gecko) imported from Indonesia for use in the pet trade. In addition, we proposed that the conditions under which wild animals are captured, transported, and handled might affect the shedding or fecal prevalence of antibiotic resistance. In particular we were interested in the effects of density; to address this, we experimentally modified densities of geckos after import and documented changes in antibiotic resistance patterns. The commensal enteric bacteria from Tokay geckos (G. gecko) imported for the pet trade displayed resistance against some antibiotics including: ampicillin, amoxicillin/clavulanic acid, cefoxitin, chloramphenicol, kanamycin and tetracycline. There was no significant difference in the prevalence of antibiotic-resistant bacteria after experimentally mimicking potentially stressful transportation conditions reptiles experience prior to purchase. There were, however, some interesting trends observed when comparing Tokay geckos housed individually and those housed in groups. Understanding the prevalence of antibiotic resistant commensal enteric flora from common pet reptiles is paramount because of the potential for humans exposed to these animals to acquire antibiotic-resistant bacteria and the potential for released pets to disseminate these bacteria to native wildlife.

Evaluation of microbial load in oropharyngeal mucosa from tannery workers

Background

Animal skin provides an ideal medium for the propagation of microorganisms and it is used like raw material in the tannery and footware industry. The aim of this study was to evaluate and identify the microbial load in oropharyngeal mucosa of tannery employees.

Methods

The health risk was estimated based on the identification of microorganisms found in the oropharyngeal mucosa samples. The study was conducted in a tanners group and a control group. Samples were taken from oropharyngeal mucosa and inoculated on plates with selective medium. In the samples, bacteria were identified by 16S ribosomal DNA analysis and the yeasts through a presumptive method. In addition, the sensitivity of these microorganisms to antibiotics/antifungals was evaluated.

Results

The identified bacteria belonged to the families Enterobacteriaceae, Pseudomonadaceae, Neisseriaceae, Alcaligenaceae, Moraxellaceae, and Xanthomonadaceae, of which some species are considered as pathogenic or opportunistic microorganisms; these bacteria were not present in the control group. Forty-two percent of bacteria identified in the tanners group are correlated with respiratory diseases. Yeasts were also identified, including the following species: Candida glabrata, Candida tropicalis, Candida albicans, and Candida krusei. Regarding the sensitivity test of bacteria identified in the tanners group, 90% showed sensitivity to piperacillin/tazobactam, 87% showed sensitivity to ticarcillin/clavulanic acid, 74% showed sensitivity to ampicillin/sulbactam, and 58% showed sensitivity to amoxicillin/clavulanic acid.

Conclusion

Several of the bacteria and yeast identified in the oropharyngeal mucosa of tanners have been correlated with infections in humans and have already been reported as airborne microorganisms in this working environment, representing a health risk for workers.

Epidemiology of Enterobacteriaceae producing CTX-M type extended spectrum β-lactamase (ESBL)

Over the past 20 years, some Enterobacteriaceae mainly Escherichia coli, Klebsiella pneumoniae, and Proteus mirabilis have demonstrated acquisition of plasmids secreting ESBL. CTX-M type ESBL have been isolated worldwide and their incidence has increased dramatically and is still increasing leading to a major therapeutic issue. Currently more than 150 allelic variants of CTX-M have been identified. These enzymes are classified in five major phylogenetic groups based on their gene sequences: CTX-M -1, CTX-M-2, CTX-M-8, CTX-M-9, CTX-M-25; two additional groups have been reported recently: CTX-M-74 and CTX-M-75. The important dissemination of these enzymes has led to an increased use of carbapenems. Their global community and nosocomial dissemination is often associated with a virulent E. coli clone ST131 producing CTX-M-15.

Antimicrobial resistance and antimicrobial resistance genes in marine bacteria from salmon aquaculture and non-aquaculture sites

Antimicrobial resistance (AR) detected by disc diffusion and antimicrobial resistance genes detected by DNA hybridization and polymerase chain reaction with amplicon sequencing were studied in 124 marine bacterial isolates from a Chilean salmon aquaculture site and 76 from a site without aquaculture 8 km distant. Resistance to one or more antimicrobials was present in 81% of the isolates regardless of site. Resistance to tetracycline was most commonly encoded by tetA and tetG; to trimethoprim, by dfrA1, dfrA5 and dfrA12; to sulfamethizole, by sul1 and sul2; to amoxicillin, by blaTEM ; and to streptomycin, by strA-strB. Integron integrase intl1 was detected in 14 sul1-positive isolates, associated with aad9 gene cassettes in two from the aquaculture site. intl2 Integrase was only detected in three dfrA1-positive isolates from the aquaculture site and was not associated with gene cassettes in any. Of nine isolates tested for conjugation, two from the aquaculture site transferred AR determinants to Escherichia coli. High levels of AR in marine sediments from aquaculture and non-aquaculture sites suggest that dispersion of the large amounts of antimicrobials used in Chilean salmon aquaculture has created selective pressure in areas of the marine environment far removed from the initial site of use of these agents.

Cephalosporin resistance among animal-associatedEnterobacteria: a current perspective

Beta-lactam antimicrobials are an important class of drugs used for the treatment of infection. Resistance can arise by several mechanisms, including the acquisition of genes encoding beta-lactamases from other bacteria, alterations in cell membrane permeability and over expression of endogenous beta-lactamases. The acquisition of beta-lactamase resistance genes by both Salmonella and Escherichia coli appears to be on the rise, which may pose potential problems for the treatment of infections in both human and animal medicine. The prudent use of clinically important antimicrobials is therefore critical to maintain their effectiveness. Where possible, the use of newer generation cephalosporins should be limited in veterinary medicine.

Resistance and inactivation kinetics of bacterial strains isolated from the non-chlorinated and chlorinated effluents of a WWTP

The microbiological quality of water from a wastewater treatment plant that uses sodium hypochlorite as a disinfectant was assessed. Mesophilic aerobic bacteria were not removed efficiently. This fact allowed for the isolation of several bacterial strains from the effluents. Molecular identification indicated that the strains were related to Aeromonas hydrophila, Escherichia coli (three strains), Enterobacter cloacae, Kluyvera cryocrescens (three strains), Kluyvera intermedia, Citrobacter freundii (two strains), Bacillus sp. and Enterobacter sp. The first five strains, which were isolated from the non-chlorinated effluent, were used to test resistance to chlorine disinfection using three sets of variables: disinfectant concentration (8, 20 and 30 mg·L(-1)), contact time (0, 15 and 30 min) and water temperature (20, 25 and 30 °C). The results demonstrated that the strains have independent responses to experimental conditions and that the most efficient treatment was an 8 mg·L(-1) dose of disinfectant at a temperature of 20 °C for 30 min. The other eight strains, which were isolated from the chlorinated effluent, were used to analyze inactivation kinetics using the disinfectant at a dose of 15 mg·L(-1) with various retention times (0, 10, 20, 30, 60 and 90 min). The results indicated that during the inactivation process, there was no relationship between removal percentage and retention time and that the strains have no common response to the treatments.

The scourge of antibiotic resistance: the important role of the environment

Antibiotic resistance and associated genes are ubiquitous and ancient, with most genes that encode resistance in human pathogens having originated in bacteria from the natural environment (eg, β-lactamases and fluoroquinolones resistance genes, such as qnr). The rapid evolution and spread of "new" antibiotic resistance genes has been enhanced by modern human activity and its influence on the environmental resistome. This highlights the importance of including the role of the environmental vectors, such as bacterial genetic diversity within soil and water, in resistance risk management. We need to take more steps to decrease the spread of resistance genes in environmental bacteria into human pathogens, to decrease the spread of resistant bacteria to people and animals via foodstuffs, wastes and water, and to minimize the levels of antibiotics and antibiotic-resistant bacteria introduced into the environment. Reducing this risk must include improved management of waste containing antibiotic residues and antibiotic-resistant microorganisms.

Antimicrobial use in aquaculture re-examined: its relevance to antimicrobial resistance and to animal and human health

The worldwide growth of aquaculture has been accompanied by a rapid increase in therapeutic and prophylactic usage of antimicrobials including those important in human therapeutics. Approximately 80% of antimicrobials used in aquaculture enter the environment with their activity intact where they select for bacteria whose resistance arises from mutations or more importantly, from mobile genetic elements containing multiple resistance determinants transmissible to other bacteria. Such selection alters biodiversity in aquatic environments and the normal flora of fish and shellfish. The commonality of the mobilome (the total of all mobile genetic elements in a genome) between aquatic and terrestrial bacteria together with the presence of residual antimicrobials, biofilms, and high concentrations of bacteriophages where the aquatic environment may also be contaminated with pathogens of human and animal origin can stimulate exchange of genetic information between aquatic and terrestrial bacteria. Several recently found genetic elements and resistance determinants for quinolones, tetracyclines, and β-lactamases are shared between aquatic bacteria, fish pathogens, and human pathogens, and appear to have originated in aquatic bacteria. Excessive use of antimicrobials in aquaculture can thus potentially negatively impact animal and human health as well as the aquatic environment and should be better assessed and regulated.

A novel adenovirus species associated with an acute respiratory outbreak in a baboon colony and evidence of coincident human infection

Adenoviruses (AdVs) are DNA viruses that infect many vertebrate hosts, including humans and nonhuman primates. Here we identify a novel AdV species, provisionally named “simian adenovirus C (SAdV-C),” associated with a 1997 outbreak of acute respiratory illness in captive baboons (4 of 9) at a primate research facility in Texas. None of the six AdVs recovered from baboons (BaAdVs) during the outbreak, including the two baboons who died from pneumonia, were typeable. Since clinical samples from the two fatal cases were not available, whole-genome sequencing of nasal isolates from one sick baboon and three asymptomatic baboons during the outbreak was performed. Three AdVs were members of species SAdV-C (BaAdV-2 and BaAdV-4 were genetically identical, and BaAdV-3), while one (BaAdV-1) was a member of the recently described SAdV-B species. BaAdV-3 was the only AdV among the 4 isolated from a sick baboon, and thus was deemed to be the cause of the outbreak. Significant divergence (<58% amino acid identity) was found in one of the fiber proteins of BaAdV-3 relative to BaAdV-2 and -4, suggesting that BaAdV-3 may be a rare SAdV-C recombinant. Neutralizing antibodies to the other 3 AdVs, but not BaAdV-3, were detected in healthy baboons from 1996 to 2003 and staff personnel from 1997. These results implicate a novel adenovirus species (SAdV-C) in an acute respiratory outbreak in a baboon colony and underscore the potential for cross-species transmission of AdVs between humans and nonhuman primates.

Adenoviruses (AdVs) are DNA viruses that infect many animals, including humans and monkeys. In 1997, an outbreak of acute respiratory illness from AdVs occurred in a baboon colony in Texas. Here we use whole-genome sequencing and antibody testing to investigate new AdVs in baboons (BaAdVs) during the outbreak, one of which, BaAdV-3, came from a sick animal. By sequence analysis, BaAdV-3 may be a recombinant strain that arose from a related BaAdV found in baboons nearby in the colony (who were not sick) and yet another unknown AdV. We also found antibodies to these new BaAdVs in baboons and staff personnel at the facility. Taken together, our findings of a new AdV species as the cause of an acute respiratory outbreak in a baboon colony underscore the ongoing threat from emerging viruses that may carry the potential for cross-species transmission between monkeys and humans.

CTX-M-type β-lactamases: a successful story of antibiotic resistance

Production of extended-spectrum β-lactamases (ESBLs) is the principal mechanism of resistance to oxyimino-cephalosporins evolved by members of the family Enterobacteriaceae. Among the several ESBLs emerged among clinical pathogens, the CTX-M-type enzymes have proved the most successful in terms of promiscuity and diffusion in different epidemiological settings, where they have largely replaced and outnumbered other types of ESBLs. Originated by the capture and mobilization of chromosomal β-lactamase genes of strains of Kluyvera species, the blaCTX-M genes have become associated with a variety of mobile genetic elements that have mediated rapid and efficient inter-replicon and cell-to-cell dissemination involving highly successful enterobacterial lineages (e.g. Escherichia coli ST131 and ST405, or Klebsiella pneumoniae CC11 and ST147) to yield high-risk multiresistant clones that have spread on a global scale. The CTX-Mβ-lactamase lineage exhibits a striking plasticity, with a large number of allelic variants belonging in several sublineages, which can be associated with functional heterogeneity of clinical relevance. This review article provides an update on CTX-M-type ESBLs, with focus on structural and functional diversity, epidemiology and clinical significance.

Epidemiology and genetics of CTX-M extended-spectrum β-lactamases in Gram-negative bacteria

CTX-M enzymes, the plasmid-mediated cefotaximases, constitute a rapidly growing family of extended-spectrum β-lactamases (ESBLs) with significant clinical impact. CTX-Ms are found in at least 26 bacterial species, particularly in Escherichia coli, Klebsiella pneumoniae and Proteus mirabilis. At least 109 members in CTX-M family are identified and can be divided into seven clusters based on their phylogeny. CTX-M-15 and CTX-M-14 are the most dominant variants. Chromosome-encoded intrinsic cefotaximases in Kluyvera spp. are proposed to be the progenitors of CTX-Ms, while ISEcp1, ISCR1 and plasmid are closely associated with their mobilization and dissemination.