Pathometagenomics reveals susceptibility to intestinal infection by Morganella to be mediated by the blood group-related B4galnt2 gene in wild mice

Infectious disease is widely considered to be a major driver of evolution. A preponderance of signatures of balancing selection at blood group-related genes is thought to be driven by inherent trade-offs in susceptibility to disease. B4galnt2 is subject to long-term balancing selection in house mice, where two divergent allele classes direct alternative tissue-specific expression of a glycosyltransferase in the intestine versus blood vessels. The blood vessel allele class leads to prolonged bleeding times similar to von Willebrand disease in humans, yet has been maintained for millions of years. Based on in vivo functional studies in inbred lab strains, it is hypothesized that the cost of prolonged bleeding times may be offset by an evolutionary trade-off involving susceptibility to a yet unknown pathogen(s). To identify candidate pathogens for which resistance could be mediated by B4galnt2 genotype, we here employed a novel "pathometagenomic" approach in a wild mouse population, which combines bacterial 16S rRNA gene-based community profiling with histopathology of gut tissue. Through subsequent isolation, genome sequencing and controlled experiments in lab mice, we show that the presence of the blood vessel allele is associated with resistance to a newly identified subspecies of Morganella morganii, a clinically important opportunistic pathogen. Given the increasing importance of zoonotic events, the approach outlined here may find useful application in the detection of emerging diseases in wild animal populations.

Microbiota profiling on itchy scalp with undetermined origin

Scalp pruritus is a common skin problem that remains therapeutic challenge. The relationships between the dysbiosis of microbiota and skin diseases have caught attention recently. However, there are few reports about microbiota on itchy scalp. This study investigated scalp microbial characteristics of subjects with mild scalp pruritus of undetermined origin and preliminarily screened physiological factors and bacteria potentially related to pruritus. The pruritus severity of 17 qualified females was evaluated by Visual Analogue Scale (VAS). Microbiota collection was done at both itchy (n = 20) and non-itchy sites (n = 27) at occiput and crown of the same subject and Illumina sequencing was performed at the V3-V4 hypervariable regions of 16S rRNA. The corresponding sebum content, hydration, pH, trans-epidermal water loss, erythema index and porphyrin numbers were also measured by skin tester. We identified 3044 amplicon sequence variants from 821 genera. The itchy and non-itchy sites had different microbiota structures (p = 0.045, by multivariate analysis of variance), while there were large inter- and intra-individual variations. Both sites had Staphylococcus, Cutibacterium and Lawsonella as predominant genera, which were not significantly related to pruritus. The use of three genera Lactobacillus, Morganella and Pseudomonas, could well distinguish non-itchy from itchy groups, whereas different composition patterns existed inside each group. Our investigation indicated that though the bacterial community structure on itchy scalp was individual specific, there was difference between itchy and non-itchy sites. The study provides new insights into microbiota profiling on itchy scalp, which will help microbiota-targeted therapeutic experiment or products design for scalp pruritus.

Alkaline Urine in the Emergency Department Predicts Nitrofurantoin Resistance

BACKGROUND

The Proteeae group (i.e., Proteus species, Morganella morganii, and Providencia species) frequently causes urinary tract infections (UTIs) and is generally resistant to nitrofurantoin. Proteeae species can produce urease, which can increase urine pH.

OBJECTIVE

Our aim was to determine whether higher urine pH in the emergency department is associated with nitrofurantoin resistance.

METHODS

A single health system database of emergency department patients aged 18 years and older who received urinalysis between April 18, 2014, and March 7, 2017, was examined using χ² test and multivariable regression analysis.

RESULTS

Of 67,271 urine samples analyzed, 13,456 samples grew a single bacterial species. Urine cultures growing the Proteeae group were associated with significantly more alkaline urine than other bacteriuria cultures (odds ratio [OR] 2.20, 95% confidence interval [CI] 2.06-2.36; p < 0.001). The Proteeae species represented 4.4% of urine samples at pH 5-7, 24.4% at pH 8-9, and 40.0% at pH 9. At urine pH 5-7, 80.4% of urine samples were sensitive to nitrofurantoin; however, this percentage decreased to 66.1% for urine pH 8-9 and 54.6% for urine pH 9. Nitrofurantoin had the highest OR (2.10, 95% CI 1.85-2.39) among cefazolin, ciprofloxacin, and trimethoprim/sulfamethoxazole for bacteriuria sensitive to those antibiotics at urine pH 5-7. At urine pH 8-9 and 9, nitrofurantoin had the lowest OR among the antibiotics: 0.48 (95% CI 0.42-0.54) and 0.31 (95% CI 0.24-0.40), respectively (p < 0.001 for both).

CONCLUSIONS

Urine pH of 8 or higher is associated with high rates of nitrofurantoin resistance.

A Genomic and Bioinformatics View of the Classification and Evolution of Morganella Species and Their Chromosomal Accessory Genetic Elements Harboring Antimicrobial Resistance Genes

In this study, draft-genome sequencing was conducted for 60 Chinese Morganella isolates, and furthermore, 12 of them were fully sequenced. Then, a total of 166 global sequenced Morganella isolates, including the above 60, were collected to perform average nucleotide identity-based genomic classification and core single nucleotide polymorphism-based phylogenomic analysis. A genome sequence-based species classification scheme for Morganella was established, and accordingly, the two conventional Morganella species were redefined as two complexes and further divided into four and two genospecies, respectively. At least 88 acquired antimicrobial resistance genes (ARGs) were disseminated in these 166 isolates and were prevalent mostly in the isolates from hospital settings. IS26/IS15DI, IS10 and IS1R, and Tn3-, Tn21-, and Tn7-subfamily unit transposons were frequently presented in these 166 isolates. Furthermore, a detailed sequence comparison was applied to 18 Morganella chromosomal accessory genetic elements (AGEs) from the fully sequenced 12 isolates, together with 5 prototype AGEs from GenBank. These 23 AGEs were divided into eight different groups belonging to composite/unit transposons, transposable prophages, integrative and mobilizable elements, and integrative and conjugative elements, and they harbored at least 52 ARGs involved in resistance to 15 categories of antimicrobials. Eleven of these 23 AGEs acquired large accessory modules, which exhibited complex mosaic structures and contained many antimicrobial resistance loci and associated ARGs. Integration of ARG-containing AGEs into Morganella chromosomes would contribute to the accumulation and dissemination of ARGs in Morganella and enhance the adaption and survival of Morganella under complex and diverse antimicrobial selection pressures. IMPORTANCE This study presents a comprehensive genomic epidemiology analysis on global sequenced Morganella isolates. First, a genome sequence-based species classification scheme for Morganella is established with a higher resolution and accuracy than those of the conventional scheme. Second, the prevalence of accessory genetic elements (AGEs) and associated antimicrobial resistance genes (ARGs) among Morganella isolates is disclosed based on genome sequences. Finally, a detailed sequence comparison of eight groups of 23 AGEs (including 19 Morganella chromosomal AGEs) reveals that Morganella chromosomes have evolved to acquire diverse AGEs harboring different profiles of ARGs and that some of these AGEs harbor large accessory modules that exhibit complex mosaic structures and contain a large number of ARGs. Data presented here provide a deeper understanding of the classification and evolution of Morganella species and also those of ARG-containing AGEs in Morganella at the genomic scale.

Impact of antibiotic susceptibility reporting on broad spectrum antibiotic use in serratia and morganella bacteremia

To minimize broad-spectrum antibiotic use, our microbiology laboratory changed antibiotic susceptibility reporting for AmpC-beta-lactamase producing Serratia marcescens and Morganella morganii in blood cultures to include results of narrow spectrum 3rd generation cephalosporins. We assessed the impact of this change on broad-spectrum antibiotic use and clinical outcomes. All adult patients with Serratia marcescens or Morganella morganii in blood culture 2 years pre- and post-change of susceptibility reporting were retrospectively reviewed. Exclusion: more than one pathogen isolated in their blood culture, did not receive antibiotics or died within 48 hours of positive blood culture. Outcomes: Rates of broad-spectrum antibiotic use, in-hospital mortality, clinical response and microbiologic success. There were 30 patients pre-change and 46 patients post-change of reporting. Cefepime use (broad-spectrum) decreased from 46.7% to 6.5% (p < 0.001) and 3^rd generation cephalosporin (narrow-spectrum) use increased (3.3% vs 34.8%, p = 0.0013) in the post-change cohort. This demonstrates the potential role of selective susceptibility reporting in antimicrobial stewardship.

Current antibiotic resistance patterns of rare uropathogens: survey from Central European Urology Department 2011-2019

BACKGROUND

While the resistance rates of commonly detected uropathogens are well described, those of less frequent Gram-negative uropathogenic bacteria have seldom been reported. The aim of this study was to examine the resistance rates of less frequent uropathogenic Gram-negatives in a population of patients treated in a Department of Urology of a tertiary referral centre in Central Europe over a period of 9 years.

METHODS

Data on all positive urine samples from urological in- and out-patients were extracted form the Department of Clinical Microbiology database from 2011 to 2019. Numbers of susceptible and resistant isolates per year were calculated for these uropathogens: Acinetobacter spp. (n = 74), Citrobacter spp. (n = 60), Enterobacter spp. (n = 250), Morganella morganii (n = 194), Providencia spp. (n = 53), Serratia spp. (n = 82) and Stenotrophomonas maltophilia (n = 27). Antimicrobial agents selected for the survey included: ampicillin, amoxicillin/clavulanic acid, piperacillin/tazobactam; cefuroxime, cefotaxime, ceftazidime and cefepime; ciprofloxacin and ofloxacin; gentamicin and amikacin; ertapenem, meropenem and imipenem; trimethoprim-sulfamethoxazole (co-trimoxazole), nitrofurantoin and colistin.

RESULTS

Penicillin derivatives have generally poor effect except piperacillin/tazobactam. Cefuroxime is not efficient unlike cefotaxime (except against Acinetobacter spp. and S. maltophilia). Susceptibility to fluoroquinolones is limited. Amikacin is somewhat more efficient than gentamicine but susceptibilities for both safely exceed 80%. Nitrofurantoin shows virtually no efficiency. Cotrimoxazole acts well against Citrobacter spp., Serratia spp. and it is the treatment of choice for S. maltophilia UTIs. Among carbapenems, ertapenem was less efficient than meropenem and imipenem except for S. maltophilia whose isolates were mostly not suceptible to any carbapenems.

CONCLUSIONS

Uropathogenic microorganisms covered in this report are noteworthy for their frequently multi-drug resistant phenotypes. Knowledge of resistance patterns helps clinicians choose the right empirical antibiotic treatment when the taxonomical assignment of the isolate is known but sensitivity results are pending.

Isolation of Morganella Morganii and Providencia Species from Clinical Samples in a Tertiary Care Hospital in North India

INTRODUCTION

The members of the tribe Proteeae, Morganella and Providencia are being increasingly recognized as important pathogens. The spectrum of disease caused by them is wide and in reported cases, the mortality is high. Previously both of these pathogens were considered to be rare pathogens as the potential to cause nosocomial transmission and infection was not much studied. But their phenomenal evolution and increase in multidrug-resistance (MDR) strains of these pathogens are posing a major threat toward public health throughout the world.

METHODS

This present study was carried out from July 2018 to December 2018 on all the pus and body fluid samples that were received in the Department of Microbiology. Samples were processed as per the standard Microbiological guidelines and also were analyzed for their antimicrobial susceptibility profile as per Clinical Laboratory Standards Institute.

RESULTS

Out of 8425 samples received, 2140 were culture positive, amongst which 19 samples (0.89%) were positive for Providencia species (9) and Morganella morganii(10). The male : female ratio of these 19 patients was 2.8 : 1 and maximum patients (13) belonged to 20-60 years. As far as risk factors are concerned, maximum patients were diabetics (7) followed by abnormal liver function tests (6), concomitant UTI (6), history of invasive procedure (5), prior exposure to antibiotics (5) and urinary catheterization (4). About 6 were polymicrobial infections. Antibiotic susceptibility patterns revealed that Providencia strains were sensitive to ampicillin- sulbactum (77.7%) and amikacin (77.7%), while all Morganella strains were 100% sensitive to tobramycin and piperacillintazobactam.

CONCLUSION

This study heralds in need for more research in this area as infections caused by these two pathogens are on the rise. Moreover, resistance to antimicrobials is also an increasingly common problem thus delaying the treatment and prognosis of the disease.

Antimicrobial susceptibility and distribution of extended-spectrum β-lactamases, AmpC β-lactamases and carbapenemases among Proteus, Providencia and Morganella isolated from global hospitalised patients with intra-abdominal and urinary tract infections: Results of the Study for Monitoring Antimicrobial Resistance Trends (SMART), 2008-2011

OBJECTIVES

The increasing trend of β-lactam resistance among Enterobacteriaceae is a worldwide problem. This study investigated isolates of the tribe Proteeae (Proteus, Providencia and Morganella) causing intra-abdominal and urinary tract infections from the worldwide Study for Monitoring Antimicrobial Resistance Trends (SMART) collected from 2008-2011.

METHODS

Antimicrobial susceptibility testing was performed on isolates with an ertapenem minimum inhibitory concentration >0.5mg/L or those phenotypically producing extended-spectrum β-lactamases (ESBLs). ESBLs, AmpC β-lactamases and carbapenemases were detected by multiplex PCR.

RESULTS

A total of 142 isolates, including Proteus mirabilis (n=121), Proteus vulgaris (n=3), Providencia stuartii (n=5), Providencia rettgeri (n=6) and Morganella morganii (n=7), were analysed. Proteus mirabilis was generally susceptible to ertapenem (∼90%) compared with imipenem (≤25%). The most common ESBLs were CTX-M types (n=64), followed by TEM (n=27) and SHV (n=7). CTX-M-1, CTX-M-2 and CTX-M-15 were the dominant CTX-M-type ESBLs in P. mirabilis isolates. CMY (n=14), which included CMY-2 (n=6), was the most common AmpC β-lactamase, followed by DHA (n=6) and FOX (n=4). NDM (n=7), which included NDM-1 (n=4), was the most common carbapenemase, followed by KPC (n=2). Isolates from hospital-associated infections had more complicated β-lactamase combinations than isolates from community-acquired infections.

CONCLUSION

The global emergence and spread of β-lactamase-producing Proteeae isolates are major issues in tackling antimicrobial resistance. Continuous monitoring of antimicrobial resistance trends and developing further resistance surveillance are necessary.

Comparative Epidemiology and Resistance Trends of Proteae in Urinary Tract Infections of Inpatients and Outpatients: A 10-Year Retrospective Study

Compared with infections caused by other bacterial pathogens, urinary tract infections (UTIs) caused by Proteae are often more severe and associated with a higher rate of recurrence, sequelae, and pyelonephritis. The aim of this retrospective study was to assess and compare the prevalence of UTIs caused by different species of the Proteae tribe (namely Proteus, Morganella and Providencia species) and the antibiotic resistance levels isolated from inpatients and outpatients in a primary- and tertiary-care teaching hospital in the Southern Great Plain of Hungary, during a 10-year study period. To evaluate the resistance trends of isolated strains, amoxicillin/clavulanic acid, ceftriaxone, meropenem, ertapenem, gentamicin, ciprofloxacin, and fosfomycin were chosen as indicator antibiotics, based on local antibiotic utilization data. Members of Proteae were more frequently isolated in the case of inpatients (7.20 ± 1.74% vs. 5.00 ± 0.88%; p = 0.0031), P. mirabilis was the most frequently isolated member of the group. The ratio of resistant strains to sulfamethoxazole/trimethoprim, ciprofloxacin, ceftriaxone, and fosfomycin was significantly higher in the inpatient group. In the case of amoxicillin/clavulanic acid, ceftriaxone, ciprofloxacin, and sulfamethoxazole/trimethoprim, the ratio of resistant isolates was markedly higher between 2013–2017 (p < 0.01). Resistance developments of Proteae, coupled with their intrinsic non-susceptibility to several antibiotics (tetracyclines, colistin, nitrofurantoin) severely limits the number of therapeutic alternatives, especially for outpatients.

Production of Biogenic Nanoparticles for the Reduction of 4-Nitrophenol and Oxidative Laccase-Like Reactions

Biogenic nanoparticles present a wide range of possibilities for use in industrial applications, their production is greener, they can be manufactured using impure feedstocks, and often have different catalytic abilities compared to their chemically made analogs. Nanoparticles of Ag, Pd, Pt, and the bi-elemental PdPt were produced by Morganella psychrotolerans and Desulfovibrio alaskensis and were shown to be able to reduce 4-nitrophenol, an industrial and toxic pollutant. Nanoparticles were recovered post-reaction and then reused, thus demonstrating continued activity. Biogenic PdNPs were shown to have enhanced specificity in a wide pH activity range in the oxidation of the three common substrates used 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) (ABTS), 2,6-Dimethoxyphenol and (2,6-DMP) and 3,3',5,5'-Tetramethylbenzidine (TMB) to determine oxidase-like activity. Overall Pd in a nanoparticle form exhibited higher oxidation activity than its ionic counterpart, highlighting the potential of biogenic nanoparticles over the use of ions or chemically made elemental forms.

Finer-Scale Phylosymbiosis: Insights from Insect Viromes

Viruses are the most abundant biological entity on the planet and interact with microbial communities with which they associate. The virome of animals is often dominated by bacterial viruses, known as bacteriophages or phages, which can (re)structure bacterial communities potentially vital to the animal host. Beta diversity relationships of animal-associated bacterial communities in laboratory and wild populations frequently parallel animal phylogenetic relationships, a pattern termed phylosymbiosis. However, little is known about whether viral communities also exhibit this eco-evolutionary pattern. Metagenomics of purified viruses from recently diverged species of Nasonia parasitoid wasps reared in the lab indicates for the first time that the community relationships of the virome can also exhibit complete phylosymbiosis. Therefore, viruses, particularly bacteriophages here, may also be influenced by animal evolutionary changes either directly or indirectly through the tripartite interactions among hosts, bacteria, and phage communities. Moreover, we report several new bacteriophage genomes from the common gut bacteria in Nasonia.

Phylosymbiosis was recently proposed to describe the eco-evolutionary pattern whereby the ecological relatedness (e.g., beta diversity relationships) of host-associated microbial communities parallels the phylogeny of the host species. Representing the most abundant biological entities on the planet and common members of the animal-associated microbiome, viruses can be influential members of host-associated microbial communities that may recapitulate, reinforce, or ablate phylosymbiosis. Here we sequence the metagenomes of purified viral communities from three different parasitic wasp Nasonia species, one cytonuclear introgression line of Nasonia, and the flour moth outgroup Ephestia kuehniella. Results demonstrate complete phylosymbiosis between the viral metagenome and insect phylogeny. Across all Nasonia contigs, 69% of the genes in the viral metagenomes are either new to the databases or uncharacterized, yet over 99% of the contigs have at least one gene with similarity to a known sequence. The core Nasonia virome spans 21% of the total contigs, and the majority of that core is likely derived from induced prophages residing in the genomes of common Nasonia-associated bacterial genera: Proteus, Providencia, and Morganella. We also assemble the first complete viral particle genomes from Nasonia-associated gut bacteria. Taken together, results reveal the first complete evidence for phylosymbiosis in viral metagenomes, new genome sequences of viral particles from Nasonia-associated gut bacteria, and a large set of novel or uncharacterized genes in the Nasonia virome. This work suggests that phylosymbiosis at the host-microbiome level will likely extend to the host-virome level in other systems as well.

IMPORTANCE Viruses are the most abundant biological entity on the planet and interact with microbial communities with which they associate. The virome of animals is often dominated by bacterial viruses, known as bacteriophages or phages, which can (re)structure bacterial communities potentially vital to the animal host. Beta diversity relationships of animal-associated bacterial communities in laboratory and wild populations frequently parallel animal phylogenetic relationships, a pattern termed phylosymbiosis. However, little is known about whether viral communities also exhibit this eco-evolutionary pattern. Metagenomics of purified viruses from recently diverged species of Nasonia parasitoid wasps reared in the lab indicates for the first time that the community relationships of the virome can also exhibit complete phylosymbiosis. Therefore, viruses, particularly bacteriophages here, may also be influenced by animal evolutionary changes either directly or indirectly through the tripartite interactions among hosts, bacteria, and phage communities. Moreover, we report several new bacteriophage genomes from the common gut bacteria in Nasonia.

A mutualism without honeydew: what benefits for Melissotarsus emeryi ants and armored scale insects (Diaspididae)?

Mutualisms between ants and sap-sucking insects generally involve clear benefits for both partners: the ants provide protection in exchange for honeydew. However, a single ant genus associates with armoured scale insects (Diaspididae) that do not excrete honeydew. We studied three colonies of Melissotarsus emeryi ants from two localities in Mozambique. Vast numbers of the diaspidid Morganella conspicua occupied galleries dug by the ants under the bark of living trees. Unlike free-living M. conspicua and other diaspidids, M. conspicua living with ants are known to lack shields, likely because they gain protection against enemies and desiccation. Nevertheless, we documented the occurrence of rare individuals with shields inside ant galleries, indicating that their glands continue to secrete wax and proteins as building material. This is likely to constitute a significant portion of the ants’ diet, in addition to diaspidid exuviae and excretions from the Malpighian tubules. Indeed, Melissotarsus workers cannot walk outside the galleries due to modified middle legs, forcing them to obtain all nourishment within the tree. Melissotarsus founding queens, however, must locate a suitable host tree while flying, and acquire diaspidid crawlers. This mutualism involves ants that are highly specialised to chew through living wood, and diaspidids that can also live freely outside the bark. It is extremely widespread in Africa and Madagascar, recorded from 20 tree families, and harmful effects on plant hosts require rapid study.

Infectious bacterial pathogens, parasites and pathological correlations of sewage pollution as an important threat to farmed fishes in Egypt

This paper is a part of a multi-disciplinary research "Application of Decentralized On-Site Water Treatment System in Egypt for Use in Agriculture and Producing Safe Fish and Animal Proteins". The project aimed to investigate the environmental impact of implementing sewage water before and after treatment using the effluent of the on-site decentralized Japanese' Johkasou system, in agriculture and producing fish protein. The aim is to establish such system in Egypt to strengthen the sanitary conditions of water resources. In the present study, the impact of the sewage pollution in some fish farms at El-Fayyum, Port Said and El-Dakahlia governorates in Egypt was carried out. Water and fish (Oreochromis niloticus and Mugil cephalus) samples were collected from private fish farms of such localities. Bacteriological and chemical examination of water samples revealed the existence of coliforms and many other bacterial species of significant human health hazards. The chemical parameters of water showed a marked deviation from normal levels while examination of fish flesh specimens indicated contamination with Streptococcus Sp., Staphylococcus Sp., and Salmonella in all examined localities. Other bacterial isolates of human health importance (Morganella morganii, Pseudomonas cepacia and Enterococcos durans) were identified. The parasitological examination revealed the presence of encysted metacercariae (EMC); Diplostomatidae, Prohemistomatidae and Heterphyidae. Moreover, two protozoan parasites (Mxyoboulus tilapiae and Ichthyophthirius multifilis) were also recorded. The histopathological examination revealed mild tissue reaction in case of bacterial infection and severe pathological lesions in different organs in case of EMC infection. Lamellar hyperplasia and mononuclear cell infiltration in branchial tissue was common findings. In skeletal muscles, atrophy of muscle fibres, myolysis and myophagia were detected.