Classification, identification, and clinical significance of Proteus, Providencia, and Morganella

A novel PCR-based genotyping method for Proteus mirabilis - Intergenic region polymorphism analysis

Proteus mirabilis is a predominant species in cases of food poisoning associated with meat products and is also an opportunistic pathogen causing numerous infections in humans. This study aimed to differentiate P. mirabilis isolates using intergenic region polymorphism analysis (IRPA). The IRPA typing scheme was developed to amplify polymorphic fragments in intergenic regions (IGRs). The presence, absence, or size change of amplified products were identified and utilized as genetic markers for rapid differentiation of strains. A total of 75 P. mirabilis isolates were isolated from 63 fresh poultry and pork samples were subtyped using the IRPA and ERIC-PCR methods, and their antibiotic resistance profiles were tested. The majority of P. mirabilis isolates showed resistance to tetracycline (85.3%), doxycycline (93.3%), chloramphenicol (82.7%), streptomycin (92.0%), spectinomycin (80.0%), trimethoprim (97.3%); trimethoprim-sulfalleth (82.7%), and erythromycin (100.0%). In contrast, resistance rates to ceftriaxon, cefoxitin, cefepime, and cefotaxim were lower at only 17.3%, 5.3%, 6.7%, and 13.3%, respectively, among P. mirabilis isolates. Eleven loci were selected for analysis of the genetic diversity of 75 P. mirabilis isolates. A combination of 4 loci was determined as the optimal combination. The results compared to those obtained using ERIC-PCR for the same isolates. The Simpson's index of diversity was 0.999 for IRPA and 0.923 for ERIC-PCR, indicating that IRPA has a higher discriminatory power than ERIC-PCR. The concordance between IRPA and ERIC-PCR methods was low, primarily because IRPA classified isolates from the same ERIC cluster into separate clusters due to its high resolution. The IRPA method presented in this study offers a rapid, simple, reproducible, and economical approach for genotyping P. mirabilis.

Maternal vitamin D status during pregnancy and infant's gut microbiota: a prospective cohort study

Objectives

To prospectively explore the association of maternal serum 25(OH)D levels with the infant's gut microbiota in Chinese populations, and to evaluate its potential influence on the dynamic change patterns of offspring's gut microbiota from 1 to 6 months old.

Methods

Eighty-seven mother-infant dyads (vitamin D insufficient group vs. normal group = 59 vs. 28) were included in this longitudinal study. Two fecal samples were collected for the included infant at home by the parents at 1 month of age ("M1 phase") and 6 months of age ("M6 phase"). Gut microbiota were profiled by 16S rRNA gene sequencing. We performed mixed effects models on alpha diversity metrics, PERMANOVA tests on beta diversity distances, and linear discriminant analysis (LDA) to identify differently abundant taxa.

Results

We observed significantly lower Pielou's evenness and Shannon diversity in the vitamin D insufficient group in the M6 phase (p = 0.049 and 0.015, respectively), but not in the M1 phase (p > 0.05), and the dynamic changes in alpha diversity from 1 to 6 months old were significantly different according to maternal vitamin D status (p < 0.05). There were also significant differences in gut microbiota composition between the vitamin D insufficient group and normal group, both in the M1 and M6 phases (LDA score > 2.0, p < 0.05). Moreover, among the predicted metagenome functions, pathways related to amino acid biosynthesis, starch degradation, and purine nucleotides biosynthesis were enriched in the vitamin D insufficient group.

Conclusion

Our findings highlight that maternal vitamin D status plays a pivotal role in shaping the early-life gut microbiota of the next generation.

Enteropathogenic Providencia alcalifaciens: A Subgroup of P. alcalifaciens That Causes Diarrhea

Despite being considered a normal flora, Providencia alcalifaciens can cause diarrhea. In a previous study, strain 2939/90, obtained from a diarrheal patient, caused invasion and actin condensation in mammalian cells, and diarrhea in a rabbit model. Four TnphoA mutants of 2939/90 produced negligible invasion and actin condensation in mammalian cells. Now, the parent strain and the mutants have been sequenced to locate TnphoA insertion sites and determine the effect on virulence. A TnphoA insertion was detected in the type three secretion system (T3SS) locus on a large plasmid and not in a T3SS locus on the chromosome. In 52 genomes of P. alcalifaciens surveyed, the chromosomal T3SS locus was present in all strains, including both P. alcalifaciens genomic clades, which we classified as group A and group B. Plasmid T3SS was present in 21 of 52 genomes, mostly in group A genomes, which included isolates from an outbreak of hemorrhagic diarrhea in dogs. The TnphoA insertion only in the plasmid T3SS locus affected the invasion phenotype, suggested that this locus is critical for causation of diarrhea. We conclude that a subgroup of P. alcalifaciens that possesses this plasmid-mediated T3SS is an enteric pathogen that can cause diarrheal disease.

Pathogenic diversification of the gut commensal Providencia alcalifaciens via acquisition of a second type III secretion system

Providencia alcalifaciens is a Gram-negative bacterium found in a wide variety of water and land environments and organisms. It has been isolated as part of the gut microbiome of animals and insects, as well as from stool samples of patients with diarrhea. Specific P. alcalifaciens strains encode gene homologs of virulence factors found in other pathogenic members of the same Enterobacterales order, such as Salmonella enterica serovar Typhimurium and Shigella flexneri. Whether these genes are also pathogenic determinants in P. alcalifaciens is not known. Here we have used P. alcalifaciens 205/92, a clinical isolate, with in vitro and in vivo infection models to investigate P. alcalifaciens -host interactions at the cellular level. Our particular focus was the role of two type III secretion systems (T3SS) belonging to the Inv-Mxi/Spa family. T3SS 1b is widespread in Providencia spp. and encoded on the chromosome. T3SS 1a is encoded on a large plasmid that is present in a subset of P. alcalifaciens strains, which are primarily isolates from diarrheal patients. Using a combination of electron and fluorescence microscopy and gentamicin protection assays we show that P. alcalifaciens 205/92 is internalized into eukaryotic cells, rapidly lyses its internalization vacuole and proliferates in the cytosol. This triggers caspase-4 dependent inflammasome responses in gut epithelial cells. The requirement for the T3SS 1a in entry, vacuole lysis and cytosolic proliferation is host-cell type specific, playing a more prominent role in human intestinal epithelial cells as compared to macrophages. In a bovine ligated intestinal loop model, P. alcalifaciens colonizes the intestinal mucosa, inducing mild epithelial damage with negligible fluid accumulation. No overt role for T3SS 1a or T3SS 1b was seen in the calf infection model. However, T3SS 1b was required for the rapid killing of Drosophila melanogaster . We propose that the acquisition of two T3SS by horizontal gene transfer has allowed P. alcalifaciens to diversify its host range, from a highly virulent pathogen of insects to an opportunistic gastrointestinal pathogen of animals.

Proteus species bloodstream infections: Comparative epidemiology of three species

BACKGROUND

Although Proteus species are occasional causes of serious infections, their epidemiology has not been well defined. The objective was to describe the overall and species-specific occurrence and determinants of Proteus species bloodstream infection (BSI) in a large Australian population.

METHODS

All Queensland residents with Proteus species BSI identified within the publicly funded healthcare system between 2000 and 2019 were included.

RESULTS

A total of 2,143 incident episodes of Proteus species BSI were identified among 2,079 Queensland residents. The prevalence of comorbid illness differed with higher Charlson comorbidity scores observed with P. penneri and P. vulgaris, and higher prevalence of liver disease with P. penneri, higher comorbid cancer with P. vulgaris, and lower diabetes and renal disease prevalence with P. mirabilis BSIs.

CONCLUSION

This study provides novel information on the epidemiology of Proteus species BSI.

Spread of carbapenemase-producing Morganella spp from 2013 to 2021: a comparative genomic study

BACKGROUND

Morganella spp are opportunistic pathogens involved in various infections. Intrinsic resistance to multiple antibiotics (including colistin) combined with the emergence of carbapenemase producers reduces the number of active antimicrobials. The aim of this study was to characterise genetic features related to the spread of carbapenem-resistant Morganella spp.

METHODS

This comparative genomic study included extensively drug-resistant Morganella spp isolates collected between Jan 1, 2013, and March 1, 2021, by the French National Reference Center (NRC; n=68) and European antimicrobial resistance reference centres in seven European countries (n=104), as well as one isolate from Canada, two reference strains from the Pasteur Institute collection (Paris, France), and two colistin-susceptible isolates from Bicêtre Hospital (Kremlin-Bicêtre, France). The isolates were characterised by whole-genome sequencing, antimicrobial susceptibility testing, and biochemical tests. Complete genomes from GenBank (n=103) were also included for genomic analysis, including phylogeny and determination of core genomes and resistomes. Genetic distance between different species or subspecies was performed using average nucleotide identity (ANI). Intrinsic resistance mechanisms to polymyxins were investigated by combining genetic analysis with mass spectrometry on lipid A.

FINDINGS

Distance analysis by ANI of 275 isolates identified three groups: Morganella psychrotolerans, Morganella morganii subspecies sibonii, and M morganii subspecies morganii, and a core genome maximum likelihood phylogenetic tree showed that the M morganii isolates can be separated into four subpopulations. On the basis of these findings and of phenotypic divergences between isolates, we propose a modified taxonomy for the Morganella genus including four species, Morganella psychrotolerans, Morganella sibonii, Morganella morganii, and a new species represented by a unique environmental isolate. We propose that M morganii include two subspecies: M morganii subspecies morganii (the most prevalent) and M morganii subspecies intermedius. This modified taxonomy was supported by a difference in intrinsic resistance to tetracycline and conservation of metabolic pathways such as trehalose assimilation, both only present in M sibonii. Carbapenemase producers were mostly identified among five high-risk clones of M morganii subspecies morganii. The most prevalent carbapenemase corresponded to NDM-1, followed by KPC-2, and OXA-48. A cefepime-zidebactam combination was the most potent antimicrobial against the 172 extensively drug-resistant Morganella spp isolates in our collection from different European countries, which includes metallo-β-lactamase producers. Lipid A analysis showed that the intrinsic resistance to colistin was associated with the presence of L-ARA4N on lipid A.

INTERPRETATION

This global characterisation of, to our knowledge, the widest collection of extensively drug-resistant Morganella spp highlights the need to clarify the taxonomy and decipher intrinsic resistance mechanisms, and paves the way for further genomic comparisons.

FUNDING

None.

Composition of the Midgut Microbiota Structure of Haemaphysalis longicornis Tick Parasitizing Tiger and Deer

Haemaphysalis longicornis is a common tick species that carries several pathogens. There are few reports on the influence of different hosts on the structure of midgut microflora in H. longicornis. In this study, midgut contents of fully engorged female H. longicornis were collected from the surface of tiger (Panthera tigris) and deer (Dama dama). The bacterial genomic DNA of each sample was extracted, and the V3-V4 regions of the bacterial 16S rRNA were sequenced using the Illumina NovaSeq sequencing. The diversity of the bacterial community of the fully engorged female H. longicornis on the surface of tiger was higher than that of deer. In total, 8 phyla and 73 genera of bacteria annotations were detected in the two groups. At the phylum level, the bacterial phyla common to the two groups were Proteobacteria, Firmicutes, and Actinobacteriota. At the genus level, there were 20 common bacterial genera, among which the relative abundances of Coxiella, Morganella, Diplorickettsia, and Acinetobacter were high. The Morganella species was further identified to be Morganella morganii. The alpha diversity index indicated that the bacterial diversity of the tiger group was higher than that of the deer group. Bacteroidota, Patescibacteria, Desulfobacterota, Verrucomicrobiota, and Cyanobacteria were solely detected in the tiger group. A total of 52 bacterial genera were unique in the tiger group, while one bacterial genus was unique in the deer group. This study indicates that there are differences in the structure of the gut bacteria of the same tick species among different hosts. Further culture-based methods are needed to provide a more comprehensive understanding of the tick microbiota parasitizing different hosts.

Identification of Providencia spp. clinical isolates co-producing carbapenemases IMP-27, OXA-24, and OXA-58 in Mexico

Providencia rettgeri, belonging to the genus Providencia, had gained significant interest due to its increasing prevalence as a common pathogen responsible for healthcare-associated infections in hospitals. P. rettgeri isolates producing carbapenemases have been reported to reduce the efficiency of carbapenems in clinical antimicrobial therapy. However, coexistence with other resistance determinants is rarely reported. The goal of this study was the molecular characterization of carbapenemase-producing Providencia spp. clinical isolates. Among 23 Providencia spp. resistant to imipenem, 21 were positive to blaNDM-1; one positive to blaNDM-1 and blaOXA-58 like; and one isolate co-producing blaIMP-27, blaOXA-24/40 like, and blaOXA-58 like were identified. We observed a low clonal relationship, and the incompatibility groups Col3M and ColRNAI were identified in the plasmid harboring blaNDM-1. We report for the first time a P. rettgeri strain co-producing blaIMP-27, blaOXA-24-like, and blaOXA-58 like. The analysis of these resistance mechanisms in carbapenemase co-producing clinical isolates reflects the increased resistance.

Emergence and genomic chion of Proteus mirabilis harboring blaNDM-1 in Korean companion dogs

Proteus mirabilis is a commensal bacterium dwelling in the gastrointestinal (GI) tract of humans and animals. Although New Delhi metallo-β-lactamase 1 (NDM-1) producing P. mirabilis is emerging as a threat, its epidemiology in our society remains largely unknown. LHPm1, the first P. mirabilis isolate harboring NDM-1, was detected from a companion dog that resides with a human owner. The whole-genome study revealed 20 different antimicrobial resistance (AMR) genes against various classes of antimicrobial agents, which corresponded to the MIC results. Genomic regions, including MDR genes, were identified with multiple variations and visualized in a comparative manner. In the whole-genome epidemiological analysis, multiple phylogroups were identified, revealing the genetic relationship of LHPm1 with other P. mirabilis strains carrying various AMR genes. These genetic findings offer comprehensive insights into NDM-1-producing P. mirabilis, underscoring the need for urgent control measures and surveillance programs using a "one health approach".

Occurrence of coliforms and biofilm-forming bacteria in raw, treated, and distributed water from two waterwork systems in Osun State, Southwestern Nigeria

This study assessed the bacteriological quality of raw, treated, and distributed water from Ede-Erinle and Opa reservoirs in Osun State, Nigeria. This was to determine the potability of water from these waterwork stations. Eighteen sampling points were established across the two reservoir networks for this study. Samples were collected bi-monthly for two annual cycles. Serial dilution and pour plate methods were employed for the enumeration of bacterial load. Total heterotrophic bacteria count (THBC) and total coliform bacteria count (TCBC) were enumerated on nutrient and MacConkey agar at 37 °C, respectively. Bacterial isolates were characterized using biochemical identification methods with reference to Bergey's Manual of Determinative Bacteriology. Bacterial isolates and biofilm formation were further identified molecularly through the PCR method using specific universal primers. Mean values of THBC and TCBC in distributed water from Ede-Erinle (9.61 × 104 ± 1.50 × 104 CFU/mL; 69.56 ± 26.81 CFU/mL) and Opa waterworks (9.58 × 104 ± 2.55 × 104 CFU/mL; 142.94 ± 44.41 CFU/mL) exceeded permissible limits for drinking water. Paenibacillus lautus, Bacillus pseudomycoides, Pseudomonas aeruginosa, and Pseudomonas stutzeri showed biofilm-forming capacity. The study concluded that the presence of coliforms and biofilm-forming bacteria in distributed water implies that the water is unfit for consumption without further treatment.

Genomic revisitation and reclassification of the genus Providencia

Members of Providencia, although typically opportunistic, can cause severe infections in immunocompromised hosts. Recent advances in genome sequencing provide an opportunity for more precise study of this genus. In this study, we first identified and characterized a novel species named Providencia zhijiangensis sp. nov. It has ≤88.23% average nucleotide identity (ANI) and ≤31.8% in silico DNA-DNA hybridization (dDDH) values with all known Providencia species, which fall significantly below the species-defining thresholds. Interestingly, we found that Providencia stuartii and Providencia thailandensis actually fall under the same species, evidenced by an ANI of 98.59% and a dDDH value of 90.4%. By fusing ANI with phylogeny, we have reclassified 545 genomes within this genus into 20 species, including seven unnamed taxa (provisionally titled Taxon 1-7), which can be further subdivided into 23 lineages. Pangenomic analysis identified 1,550 genus-core genes in Providencia, with coenzymes being the predominant category at 10.56%, suggesting significant intermediate metabolism activity. Resistance analysis revealed that most lineages of the genus (82.61%, 19/23) carry a high number of antibiotic-resistance genes (ARGs) and display diverse resistance profiles. Notably, the majority of ARGs are located on plasmids, underscoring the significant role of plasmids in the resistance evolution within this genus. Three species or lineages (P. stuartii, Taxon 3, and Providencia hangzhouensis L12) that possess the highest number of carbapenem-resistance genes suggest their potential influence on clinical treatment. These findings underscore the need for continued surveillance and study of this genus, particularly due to their role in harboring antibiotic-resistance genes.

IMPORTANCE

The Providencia genus, known to harbor opportunistic pathogens, has been a subject of interest due to its potential to cause severe infections, particularly in vulnerable individuals. Our research offers groundbreaking insights into this genus, unveiling a novel species, Providencia zhijiangensis sp. nov., and highlighting the need for a re-evaluation of existing classifications. Our comprehensive genomic assessment offers a detailed classification of 545 genomes into distinct species and lineages, revealing the rich biodiversity and intricate species diversity within the genus. The substantial presence of antibiotic-resistance genes in the Providencia genus underscores potential challenges for public health and clinical treatments. Our study highlights the pressing need for increased surveillance and research, enriching our understanding of antibiotic resistance in this realm.

Phage P2-71 against multi-drug resistant Proteus mirabilis: isolation, characterization, and non-antibiotic antimicrobial potential

Proteus mirabilis, a prevalent urinary tract pathogen and formidable biofilm producer, especially in Catheter-Associated Urinary Tract Infection, has seen a worrying rise in multidrug-resistant (MDR) strains. This upsurge calls for innovative approaches in infection control, beyond traditional antibiotics. Our research introduces bacteriophage (phage) therapy as a novel non-antibiotic strategy to combat these drug-resistant infections. We isolated P2-71, a lytic phage derived from canine feces, demonstrating potent activity against MDR P. mirabilis strains. P2-71 showcases a notably brief 10-minute latent period and a significant burst size of 228 particles per infected bacterium, ensuring rapid bacterial clearance. The phage maintains stability over a broad temperature range of 30-50°C and within a pH spectrum of 4-11, highlighting its resilience in various environmental conditions. Our host range assessment solidifies its potential against diverse MDR P. mirabilis strains. Through killing curve analysis, P2-71's effectiveness was validated at various MOI levels against P. mirabilis 37, highlighting its versatility. We extended our research to examine P2-71's stability and bactericidal kinetics in artificial urine, affirming its potential for clinical application. A detailed genomic analysis reveals P2-71's complex genetic makeup, including genes essential for morphogenesis, lysis, and DNA modification, which are crucial for its therapeutic action. This study not only furthers the understanding of phage therapy as a promising non-antibiotic antimicrobial but also underscores its critical role in combating emerging MDR infections in both veterinary and public health contexts.

Impact of Larval Food Source on the Stability of the Bactrocera dorsalis Microbiome

Bacterial symbionts are crucial to the biology of Bactrocera dorsalis. With larval diet (fruit host) being a key factor that determines microbiome composition and with B. dorsalis using more than 400 fruits as hosts, it is unclear if certain bacterial symbionts are preserved and are passed on to B. dorsalis progenies despite changes in larval diet. Here, we conducted a fly rearing experiment to characterize diet-induced changes in the microbiome of female B. dorsalis. In order to explicitly investigate the impacts of larval diet on the microbiome, including potential stable bacterial constituents of B. dorsalis, we performed 16S rRNA sequencing on the gut tissues of teneral female flies reared from four different host fruits (guava, mango, papaya, and rose apple) infested using a single cohort of wild B. dorsalis that emerged from tropical almond (mother flies). Although B. dorsalis-associated microbiota were predominantly shaped by the larval diet, some major bacterial species from the mother flies were retained in progenies raised on different larval diets. With some variation, Klebsiella (ASV 1 and 2), Morganella (ASV 3), and Providencia (ASV 6) were the major bacterial symbionts that were stable and made up 0.1-80% of the gut and ovipositor microbiome of female teneral flies reared on different host fruits. Our results suggest that certain groups of bacteria are stably associated with female B. dorsalis across larval diets. These findings provide a basis for unexplored research on symbiotic bacterial function in B. dorsalis and may aid in the development of novel management techniques against this devastating pest of horticultural importance.

fosA11, a novel chromosomal-encoded fosfomycin resistance gene identified in Providencia rettgeri

This study investigated resistance genes corresponding to the fosfomycin resistance phenotype in clinical isolate Providencia rettgeri W986, as well as characterizing the enzymatic activity of FosA11 and the genetic environment. Antimicrobial susceptibility testing was performed using the agar microdilution method based on the Clinical and Laboratory Standards Institute guidelines. The whole genomic sequence of Providencia rettgeri W986 was obtained using Illumina sequencing and the PacBio platform. The fosA-11 gene was amplified by PCR and cloned into the pUCP20 vector. The recombinant strain pCold1-fosA11-BL21 was expressed to extract the target protein, and absorbance photometry was applied for enzymatic parameter determination. Minimal inhibitory concentration (MIC) tests showed that W986 conferred fosfomycin resistance and was inhibited by phosphonoformate, thereby indicating the presence of a FosA protein. A novel resistance gene designated as fosA11 was identified by whole-genome sequencing and bioinformatics analysis, and it shared 54.41%-64.23% amino acid identity with known FosA proteins. Cloning fosA11 into Escherichia coli obtained a significant increase (32-fold) in the MIC with fosfomycin. Determination of the enzyme kinetics showed that FosA11 had a high catalytic effect on fosfomycin, with Km = 18 ± 4 and Kcat = 56.1 ± 3.2. We also found that fosA11 was located on the chromosome, but the difference in the GC content between the chromosome and fosA11 was dubious, and thus further investigation is required. In this study, we identified and characterized a novel fosfomycin inactivation enzyme called FosA11. The origin and prevalence of the fosA11 gene in other bacteria require further investigation.IMPORTANCEFosfomycin is an effective antimicrobial agent against Enterobacterales strains. However, the resistance rate of fosfomycin is increasing year by year. Therefore, it is necessary to study the deep molecular mechanism of bacterial resistance to fosfomycin. We identified a novel chromosomal fosfomycin glutathione S-transferase, FosA11 from Providencia rettgeri, which shares a very low identity (54.41%-64.23%) with the previously known FosA and exhibits highly efficient catalytic ability against fosfomycin. Analysis of the genetic context and origin of fosA11 displays that the gene and its surrounding environments are widely conserved in Providencia and no mobile elements are discovered, implying that FosA11 may be broadly important in the natural resistance to fosfomycin of Providencia species.

The Microbial Diversity on the Surface of Smear-Ripened Cheeses and Its Impact on Cheese Quality and Safety

Smear-ripened cheeses are characterized by a viscous, red-orange surface smear on their rind. It is the complex surface microbiota on the cheese rind that is responsible for the characteristic appearance of this cheese type, but also for the wide range of flavors and textures of the many varieties of smear-ripened cheeses. The surface smear microbiota also represents an important line of defense against the colonization with undesirable microorganisms through various types of interaction, such as competitive exclusion or production of antimicrobial substances. Predominant members of the surface smear microbiota are salt-tolerant yeast and bacteria of the phyla Actinobacteria, Firmicutes, and Proteobacteria. In the past, classical culture-based approaches already shed light on the composition and succession of microorganisms and their individual contribution to the typicity of this cheese type. However, during the last decade, the introduction and application of novel molecular approaches with high-resolution power provided further in-depth analysis and, thus, a much more detailed view of the composition, structure, and diversity of the cheese smear microbiota. This led to abundant novel knowledge, such as the identification of so far unknown community members. Hence, this review is summarizing the current knowledge of the diversity of the surface smear microbiota and its contribution to the quality and safety of smear-ripened cheese. If the succession or composition of the surface-smear microbiota is disturbed, cheese smear defects might occur, which may promote food safety issues. Hence, the discussion of cheese smear defects in the context of an increased understanding of the intricate surface smear ecosystem in this review may not only help in troubleshooting and quality control but also paves the way for innovations that can lead to safer, more consistent, and higher-quality smear-ripened cheeses.

Genomic epidemiology and heterogeneity of Providencia and their blaNDM-1-carrying plasmids

Providencia as an opportunistic pathogen can cause serious infection, and moreover the emergence of multi-drug-resistant Providencia strains poses a potentially life-threatening risk to public health. However, a comprehensive genomic study to reveal the population structure and dissemination of Providencia is still lacking. In this study, we conducted a genomic epidemiology analysis on the 580 global sequenced Providencia isolates, including 257 ones sequenced in this study (42 ones were fully sequenced). We established a genome sequence-based species classification scheme for Providencia, redefining the conventional 11 Providencia species into seven genocomplexes that were further divided into 18 genospecies, providing an extensively updated reference for Providencia species discrimination based on the largest Providencia genome dataset to date. We then dissected the profile of antimicrobial resistance genes and the prevalence of multi-drug-resistant Providencia strains among these genocomplexes/genospecies, disclosing the presence of diverse and abundant antimicrobial resistance genes and high resistance ratios against multiple classes of drugs in Providencia. We further dissected the genetic basis for the spread of blaNDM-1 in Providencia. blaNDM-1 genes were mainly carried by five incompatible (Inc) groups of plasmids: IncC, IncW, IncpPROV114-NR, IncpCHS4.1-3, and IncpPrY2001, and the last three were newly designated in this study. By tracking the spread of blaNDM-1-carrying plasmids, IncC, IncpPROV114-NR, IncpCHS4.1-3, and IncpPrY2001 plasmids were found to be highly involved in parallel horizontal transfer or vertical clonal expansion of blaNDM-1 among Providencia. Overall, our study provided a comprehensive genomic view of species differentiation, antimicrobial resistance prevalence, and plasmid-mediated blaNDM-1 dissemination in Providencia.

Organ agar serves as physiologically relevant alternative for in vivo bacterial colonization

Animal models for host-microbial interactions have proven valuable, yielding physiologically relevant data that may be otherwise difficult to obtain. Unfortunately, such models are lacking or nonexistent for many microbes. Here, we introduce organ agar, a straightforward method to enable the screening of large mutant libraries while avoiding physiological bottlenecks. We demonstrate that growth defects on organ agar were translatable to bacterial colonization deficiencies in a murine model. Specifically, we present a urinary tract infection agar model to interrogate an ordered library of Proteus mirabilis transposon mutants, with accurate prediction of bacterial genes critical for host colonization. Thus, we demonstrate the ability of ex vivo organ agar to reproduce in vivo deficiencies. Organ agar was also useful for identifying previously unknown links between biosynthetic genes and swarming motility. This work provides a readily adoptable technique that is economical and uses substantially fewer animals. We anticipate this method will be useful for a wide variety of microorganisms, both pathogenic and commensal, in a diverse range of model host species.

Occurrence of mcr genes and alterations in mgrB gene in intrinsic colistin- resistant Enterobacterales isolated from chicken meat samples

BACKGROUND

Tolerance of gram negative pathogens toward last resort colistin is mediated by mcr genes and alterations in chromosomal mgrB via modification of lipopolysaccharide through the PmrAB and PhoPQ component system. Proteus sp., Morganella sp., Neisseria sp., Burkholderia sp. and Providencia sp. are intrinsic resistant to colistin drug. Recent reports have shown that colistin intrinsic resistant organisms harbor and act as reservoirs for mcr genes.

AIM

To evaluate the presence of mcr-1 to mcr-5 genes and alterations in mgrB gene in intrinsic colistin-resistant gram negative bacteria isolated from chicken meat samples in Coimbatore district, Tamil Nadu, India.

METHODS

One hundred chicken meat samples were collected during 2019-20. Samples were enriched and plated on MacConkey agar supplemented with colistin (2 μg/ml). The bacterial isolates were then identified using biochemical tests. DNA were extracted from isolates using the thermal lysis method. mcr-1 to mcr-5 and mgrB genes was detected using conventional PCR and agarose gel electrophoresis methods.

RESULT AND CONCLUSION

The presence of mcr-1 to mcr-5 genes was found to be 23 % (23/100). mcr-1 and mcr-5 genes were not detected in sample isolates. 17/23 samples positive for mcr genes were also found to be carrying alterations in mgrB gene. Phenotypic characterization of these isolates revealed that these bacteria were belonging to colistin intrinsic resistant gram negative bacteria such as Proteus sp., Providencia sp., and Morganella sp. Intrinsic resistant bacteria could act as a potential reservoir and disseminate mcr genes to the colistin sensitive non-intrinsic pathogens of clinical importance in the environment.

Microbiome of Zoophytophagous Biological Control Agent Nesidiocoris tenuis

Many insects are associated with endosymbionts that influence the feeding, reproduction, and distribution of their hosts. Although the small green mirid, Nesidiocoris tenuis (Reuter) (Hemiptera: Miridae), a zoophytophagous predator that feeds on plants as well as arthropods, is a globally important biological control agent, its microbiome has not been sufficiently studied. In the present study, we assessed the microbiome variation in 96 N. tenuis individuals from 14 locations throughout Japan, based on amplicon sequencing of the 16S ribosomal RNA gene. Nine major bacteria associated with N. tenuis were identified: Rickettsia, two strains of Wolbachia, Spiroplasma, Providencia, Serratia, Pseudochrobactrum, Lactococcus, and Stenotrophomonas. Additionally, a diagnostic PCR analysis for three typical insect reproductive manipulators, Rickettsia, Wolbachia, and Spiroplasma, was performed on a larger sample size (n = 360) of N. tenuis individuals; the most prevalent symbiont was Rickettsia (69.7%), followed by Wolbachia (39.2%) and Spiroplasma (6.1%). Although some symbionts were co-infected, their prevalence did not exhibit any specific tendency, such as a high frequency in specific infection combinations. The infection frequency of Rickettsia was significantly correlated with latitude and temperature, while that of Wolbachia and Spiroplasma was significantly correlated with host plants. The predominance of these bacteria and the absence of obligate symbionts suggested that the N. tenuis microbiome is typical for predatory arthropods rather than sap-feeding insects. Rickettsia and Wolbachia were vertically transmitted rather than horizontally transmitted from the prey. The functional validation of each symbiont would be warranted to develop N. tenuis as a biological control agent.

Whole-Genome Sequence and Pathogenicity Analysis of Providencia Heimbachae Causing Diarrhea in Weaned Piglets

Providencia heimbachae was previously identified in piglets with post-weaned diarrhea and associated with hindlimb paralysis. However, the pathogenic mechanisms and virulence factors of P. heimbachae are not fully known. Whole-genome sequence analysis will be helpful to extend our understanding of the characterization of P. heimbachae at a genomic level. In this study, we sequenced the whole genome of P. heimbachae for the first time using PacBio RS II sequencers and assembled de novo through hierarchical genome assembly process (HGAP). Furthermore, we performed further genome annotation. The genome of P. heimbachae 99101 consists of a circular chromosome (4,262,828 bp) and a circular plasmid (231,957 bp) with G + C contents of 40.43 and 47.16%, respectively. Genome-wide sequence analysis yielded a total of 286 predicted virulence factors, 178 resistance genes, 17 chaperone protein manipulators of fimbriae, 47 genes involved in the encoding of flagellin, 12 cell membrane-associated virulence genes, 18 Enterobacteriaceae common antigens, etc. Based on genome analysis, we preliminarily confirmed through animal experiments that the capsule was the virulence factor of P. heimbachae causing hindlimb paralysis in animals. Our study provides a genetic basis for further elucidation of the characteristics and functional mechanisms of P. heimbachae as a conditionally pathogenic bacterium, as well as a direction for research into the mechanism of action of P. heimbachae infecting humans, extending knowledge of P. heimbachae as an important zoonotic pathogen.

Antimicrobial Susceptibility Trends of Proteeae Isolates From a Tertiary-Care Hospital in Western Saudi Arabia

BACKGROUND

The tribe Proteeae comprises Proteus, Providencia, and Morganella species. TheseGram-negative rods are of concern in that they are involved in diverse human infections, particularly in hospital settings. In the last two decades, there has been a sharp increase in infections by multidrug-resistant (MDR) Proteeae. Therefore, the objectives of this study were to: (i) assess the prevalence of infections caused by tribe Proteeae, (ii)determine the antimicrobial susceptibility profile of the test isolates, and (iii) identify the underlying risk factors for acquisition of infection by MDR strains.

METHODS

During the period from January 2019 to December 2020, we conducted a retrospective review of the electronic medical and laboratory records of adult patients who received care at our institution. In addition, we analyzed the risk factors associated with acquisition of infections by members of the tribe Proteeae using univariate and multivariate regression models.

RESULTS

Overall 403 adult patients (average age 59.69 ± 20.33 years) were enrolled into this study (196 males; 48.6%, and 207 females; 51.4%). Proteus mirabilis was the leading pathogen (70.7%; n=285), followed by Morganella morganii (20.1%; n=81), and Providencia species (9.2%; n=37). Most of the isolates were recovered from urine (59.3%; n=239), followed by wound swabs (23.1%; n=93), with the least from blood samples (1.7%; n=7). Out of 403 Proteeae isolates, 27.3% (n=110) were found to be extended-spectrum β-lactamase (ESBL)-producers, whereas 18.4% (n=74) were MDR. Patient's age, concomitant diabetes mellitus (DM), and long hospital stays were independently associated with infection by MDR strains.

CONCLUSION

Infections by MDR Proteeae are leading causes for morbidity in our tertiary-care facility. Strict adherence to infection control precautions, as well as effective implementation of antimicrobial stewardship programs, are crucial to overcome these superbugs.

Exploring Proteus mirabilis Methionine tRNA Synthetase Active Site: Homology Model Construction, Molecular Dynamics, Pharmacophore and Docking Validation

Currently, the treatment of Proteus mirabilis infections is considered to be complicated as the organism has become resistant to numerous antibiotic classes. Therefore, new inhibitors should be developed, targeting bacterial molecular functions. Methionine tRNA synthetase (MetRS), a member of the aminoacyl-tRNA synthetase family, is essential for protein biosynthesis offering a promising target for novel antibiotics discovery. In the context of computer-aided drug design (CADD), the current research presents the construction and analysis of a comparative homology model for P. mirabilis MetRS, enabling development of novel inhibitors with greater selectivity. Molecular Operating Environment (MOE) software was used to build a homology model for P. mirabilis MetRS using Escherichia coli MetRS as a template. The model was evaluated, and the active site of the target protein predicted from its sequence using conservation analysis. Molecular dynamic simulations were performed to evaluate the stability of the modeled protein structure. In order to evaluate the predicted active site interactions, methionine (the natural substrate of MetRS) and several inhibitors of bacterial MetRS were docked into the constructed model using MOE. After validation of the model, pharmacophore-based virtual screening for a systemically prepared dataset of compounds was performed to prove the feasibility of the proposed model, identifying possible parent compounds for further development of MetRS inhibitors against P. mirabilis.

Evolution of an Alternative Genetic Code in the Providencia Symbiont of the Hematophagous Leech Haementeria acuecueyetzin

Strict blood-feeding animals are confronted with a strong B-vitamin deficiency. Blood-feeding leeches from the Glossiphoniidae family, similarly to hematophagous insects, have evolved specialized organs called bacteriomes to harbor symbiotic bacteria. Leeches of the Haementeria genus have two pairs of globular bacteriomes attached to the esophagus which house intracellular "Candidatus Providencia siddallii" bacteria. Previous work analyzing a draft genome of the Providencia symbiont of the Mexican leech Haementeria officinalis showed that, in this species, the bacteria hold a reduced genome capable of synthesizing B vitamins. In this work, we aimed to expand our knowledge on the diversity and evolution of Providencia symbionts of Haementeria. For this purpose, we sequenced the symbiont genomes of three selected leech species. We found that all genomes are highly syntenic and have kept a stable genetic repertoire, mirroring ancient insect endosymbionts. Additionally, we found B-vitamin pathways to be conserved among these symbionts, pointing to a conserved symbiotic role. Lastly and most notably, we found that the symbiont of H. acuecueyetzin has evolved an alternative genetic code, affecting a portion of its proteome and showing evidence of a lineage-specific and likely intermediate stage of genetic code reassignment.

A correlation study between virulence factors and multidrug resistance among clinical isolates of Proteus mirabilis

Treatment of Proteus mirabilis infections is a challenge due to the high abundance of virulence factors and the high intrinsic resistance to antimicrobials. Multidrug resistance (MDR) and extensive drug resistance (XDR) further challenge the control of P. mirabilis infection. This study aimed to investigate the correlation between virulence determinants and multidrug resistance in 100 clinical isolates of P. mirabilis collected in Alexandria from December 2019 to June 2021. Susceptibility to antimicrobials was tested by the Kirby Bauer method. Detection of swarming, urease, protease, hemolysin, and biofilm formation was performed phenotypically and by PCR amplification of zapA, flaA, ureC, mrpA, atfA, ucaA, hpmA, and luxS. MDR and XDR were detected in 34% and 5%, respectively. All isolates were positive for motility, swarming, urease, and protease production. Ninety percent were positive for hemolysin production, while 73% formed biofilm. All isolates possessed the ureC and zapA genes. The luxS, flaA, ucaA, hpmA, mrpA, and atfA genes were detected in 99%, 98%, 96% 90%, 89%, and 84%, respectively. The presence of a single biofilm-related gene was statistically correlated with non-biofilm production (P= 0.018). It was concluded that P. mirabilis isolates from catheterized-urine samples were significantly associated with biofilm formation. MDR and virulence were not statistically correlated. A significant positive correlation was detected between some virulence genes in P. mirabilis. Non-MDR isolates of P. mirabilis had a high abundance of virulence factors with no statistically significant difference from MDR. Most of the MDR and all XDR isolates could produce biofilm.

Proteus mirabilis: A rare cause of pneumonia, radiologically mimicking malignancy of the lung

Key clinical message

Lesions that are suspected for malignancy need be managed by a multidisciplinary team. Utilization of radiological as well as pathological diagnostic modalities ensures correct diagnosis and thus timely intervention.

Abstract

Introduction

Proteus mirabilis is a Gram-negative rod. It is a highly motile bacterium that belongs to the Enterobacteriaceae. Lung infection and pneumonia caused by p. mirabilis is extremely rare and occurs in patients with chronic debilitation or chronic lung disease.

Case Presentation

A 65-year-Old Woman presented with dry cough, dyspnoea on exertion, and chest pain of 4 months' duration. She received multiple medications including antibiotics but without any resolution of her symptoms. Computed Tomography scan of the chest was performed reported a tumor in the upper lobe of the left lung with multiple associated pulmonary nodules. The impression was that of metastatic lung disease with superimposed acute infection. Accordingly, the patient was reevaluated and a diagnostic bronchoscopy with multiple endobronchial biopsies and broncho-alveolar lavage was done. The gram stain showed Gram-Negative Bacilli and the bacteria identified P. mirabilis.

Conclusion

Mass lesions suspected for malignancy should be managed with involvement of multiple medical disciplines, to ensure correct and timely diagnosis. This is to avoid miss-management.

Population-based study of Morganella-Proteus-Providencia group bloodstream infections

Background

There is a paucity of studies investigating the population-based epidemiology of Morganella-Proteus-Providencia (MPP) group infections. Our objective was to determine the incidence, risk factors, and outcome of MPP group bloodstream infections (BSI), and explore species-specific differences.

Methods

Population-based surveillance was conducted in the western interior of British Columbia, Canada, between April 1, 2010 and March 30, 2020.

Results

Sixty-two incident MPP group BSI occurred for an annual incidence of 3.4 per 100,000 residents; rates for Morganella morganii, Proteus mirabilis, and Providencia species were 0.5, 2.6, and 0.3 per 100,000 population, respectively. The median year of age was 72.5 and was different (p = 0.03) among the groups. Most (92%) MPP group BSIs were of community-onset. Significant differences were observed in the distribution of clinical focus of infection, with most notably 81% of P. mirabilis BSI due to genitourinary focus as compared to 60% and 22% for Providencia species and M. morganii, respectively. Comorbid illnesses that increased the risk for development of MPP group BSI (incidence rate ratio; 95% CI) were HIV infection (37.0; 4.4-139.6), dementia (11.5; 6.1-20.7), cancer (6.4; 3.2-11.9), stroke 6.5 (2.8-13.3), and diabetes 2.7 (1.3-5.0). Thirteen, one, and none of the cases with P. mirabilis, M. morganii, and Providencia species BSI died within 30 days of index culture for respective all cause case-fatalities of 27%, 11%, and 0% (p = 0.1).

Conclusions

Although collectively responsible for a substantial burden of illness, the epidemiology of MPP group BSI varies significantly by species.

Gut bacterial communities in Atlantic bottlenose dolphins (Tursiops truncatus) throughout a disease-driven (Morbillivirus) unusual mortality event

Gut microbiomes are important determinants of animal health. In sentinel marine mammals where animal and ocean health are connected, microbiome impacts can scale to ecosystem-level importance. Mass mortality events affect cetacean populations worldwide, yet little is known about the contributory role of their gut bacterial communities to disease susceptibility and progression. Here, we characterized bacterial communities from fecal samples of common bottlenose dolphins, Tursiops truncatus, across an unusual mortality event (UME) caused by dolphin Morbillivirus (DMV). 16S rRNA gene sequence analysis revealed similar diversity and structure of bacterial communities in individuals stranding before, during, and after the 2013-2015 Mid-Atlantic Bottlenose Dolphin UME and these trends held in a subset of dolphins tested by PCR for DMV infection. Fine-scale shifts related to the UME were not common (10 of 968 bacterial taxa) though potential biomarkers for health monitoring were identified within the complex bacterial communities. Accordingly, acute DMV infection was not associated with a distinct gut bacterial community signature in T. truncatus. However, temporal stratification of DMV-positive dolphins did reveal changes in bacterial community composition between early and late outbreak periods, suggesting that gut community disruptions may be amplified by the indirect effects of accumulating health burdens associated with chronic morbidity.

Sequencing and Characterization of M. morganii Strain UM869: A Comprehensive Comparative Genomic Analysis of Virulence, Antibiotic Resistance, and Functional Pathways

Morganella morganii is a Gram-negative opportunistic Enterobacteriaceae pathogen inherently resistant to colistin. This species causes various clinical and community-acquired infections. This study investigated the virulence factors, resistance mechanisms, functional pathways, and comparative genomic analysis of M. morganii strain UM869 with 79 publicly available genomes. The multidrug resistance strain UM869 harbored 65 genes associated with 30 virulence factors, including efflux pump, hemolysin, urease, adherence, toxin, and endotoxin. Additionally, this strain contained 11 genes related to target alteration, antibiotic inactivation, and efflux resistance mechanisms. Further, the comparative genomic study revealed a high genetic relatedness (98.37%) among the genomes, possibly due to the dissemination of genes between adjoining countries. The core proteome of 79 genomes contains the 2692 core, including 2447 single-copy orthologues. Among them, six were associated with resistance to major antibiotic classes manifested through antibiotic target alteration (PBP3, gyrB) and antibiotic efflux (kpnH, rsmA, qacG; rsmA; CRP). Similarly, 47 core orthologues were annotated to 27 virulence factors. Moreover, mostly core orthologues were mapped to transporters (n = 576), two-component systems (n = 148), transcription factors (n = 117), ribosomes (n = 114), and quorum sensing (n = 77). The presence of diversity in serotypes (type 2, 3, 6, 8, and 11) and variation in gene content adds to the pathogenicity, making them more difficult to treat. This study highlights the genetic similarity among the genomes of M. morganii and their restricted emergence, mostly in Asian countries, in addition to their growing pathogenicity and resistance. However, steps must be taken to undertake large-scale molecular surveillance and to direct suitable therapeutic interventions.

Total Synthesis of the Repeating Units of Proteus penneri 26 and Proteus vulgaris TG155 via a Common Disaccharide

Herein, we report the first total synthesis of the trisaccharide and tetrasaccharide repeating units of P. penneri 26 and P. vulgaris TG155, respectively, having a common disaccharide unit, 3-α-l-QuipNAc-(1 → 3)-α-d-GlcpNAc-(1 →. Striking features of the targets are the presence of rare sugar units, l-quinovosamine and l-rhamnosamine, all joined through α-glycosidic linkages. Major challenges in the formation of 1,2-cis glycosidic linkages in the case of d-glucosamine, l-quinovosamine, and d-galactosamine have been addressed.

Organ agar serves as physiologically relevant alternative for in vivo colonization

Animal models for host-microbial interactions have proven valuable, yielding physiologically relevant data that may be otherwise difficult to obtain. Unfortunately, such models are lacking or nonexistent for many microbes. Here, we introduce organ agar, a straightforward method to enable the screening of large mutant libraries while avoiding physiological bottlenecks. We demonstrate that growth defects on organ agar were translatable to colonization deficiencies in a murine model. Specifically, we present a urinary tract infection agar model to interrogate an ordered library of Proteus mirabilis transposon mutants, with accurate prediction of bacterial genes critical for host colonization. Thus, we demonstrate the ability of ex vivo organ agar to reproduce in vivo deficiencies. This work provides a readily adoptable technique that is economical and uses substantially fewer animals. We anticipate this method will be useful for a wide variety of microorganisms, both pathogenic and commensal, in a diverse range of model host species.

Complicated pyelonephritis caused by Proteus alimentorum in a woman with peritoneal cancer: a case report

BACKGROUND

Proteus spp. are widespread in the environment and comprise a part of the normal flora of the human gastrointestinal tract. Only six species in this genus, including Proteus mirabilis, Proteus vulgaris, Proteus terrae, Proteus penneri, Proteus hauseri, and Proteus faecis, have been isolated from human clinical specimens. However, there are no reports of Proteus alimentorum isolated from humans, and the clinical characteristics of P. alimentorum infection are unknown.

CASE PRESENTATION

An 85-year-old female patient with peritoneal cancer was hospitalized for complicated pyelonephritis and bacteremia caused by P. alimentorum. The patient received antimicrobial therapy and was discharged on day 7 of hospitalization. No recurrence was observed 14 days after the treatment. Various methods were used to identify the Proteus sp. Furthermore, the VITEK-2 GN ID card resulted in low discrimination between P. hauseri and P. penneri. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry showed P. hauseri with a spectral score of 2.22 as the best match. Nevertheless, the pathogen was identified as P. alimentorum based on genetic investigation using 16 S rRNA gene sequencing and biochemical tests.

CONCLUSION

Proteus alimentorum is a human pathogen, and its infection has an excellent therapeutic response to antimicrobials based on antimicrobial susceptibility. Genomic methods may be helpful for the precise identification of P. alimentorum.

Structure and Assembly of the Proteus mirabilis Flagellar Motor by Cryo-Electron Tomography

Proteus mirabilis is a Gram-negative Gammaproteobacterium and a major causative agent of urinary tract infections in humans. It is characterized by its ability to switch between swimming motility in liquid media and swarming on solid surfaces. Here, we used cryo-electron tomography and subtomogram averaging to reveal the structure of the flagellar motor of P. mirabilis at nanometer resolution in intact cells. We found that P. mirabilis has a motor that is structurally similar to those of Escherichia coli and Salmonella enterica, lacking the periplasmic elaborations that characterize other more specialized gammaproteobacterial motors. In addition, no density corresponding to stators was present in the subtomogram average suggesting that the stators are dynamic. Finally, several assembly intermediates of the motor were seen that support the inside-out assembly pathway.

Role of Bacterial Surface Components in the Pathogenicity of Proteus mirabilis in a Murine Model of Catheter-Associated Urinary Tract Infection

Proteus mirabilis (PM) is a Gram-negative, rod-shaped bacterium that causes catheter-associated urinary tract infections (CAUTIs). The specific roles of bacterial surface components (BSCs) in PM pathogenicity and CAUTIs remain unknown. To address this knowledge gap, we utilized relevant in vitro adhesion/invasion models and a well-established murine model of CAUTI to assess the ability of wildtype (WT) and seven mutant strains (MSs) of PM with deficiencies in various genes encoding BSCs to undergo the infectious process (including adhesion to catheters) in both model systems. Overall, MSs adhesion to catheters and the different cell types tested was significantly reduced compared to WT, while no invasion of cells was evident at 24 h. In vivo, WT showed a greater number of planktonic (urine) bacteria, bacteria adherent to catheters, and bacteria adherent to/invading bladder tissue when compared to the MSs. Bacterial counts in urine for PMI3191 and waaE mutants were lower than that for WT and other MSs. The complementation of mutated BSC genes resulting in the biggest defects restored the invasion phenotype both in vitro and in vivo. BSCs play a critical role at various steps in the pathogenicity of PM including adhesion to indwelling medical devices and adhesion/invasion of urinary tissue in vivo.

Epidemic characteristics of the SXT/R391 integrated conjugative elements in multidrug-resistant Proteus mirabilis isolated from chicken farm

This study was designed to depict prevalence and antimicrobial resistance characteristics of Proteus mirabilis (P. mirabilis) strains in 4 chicken farms and to probe the transfer mechanism of resistance genes. A total of 187 P. mirabilis isolates were isolated from 4 chicken farms. The susceptibility testing of these isolates to 14 antimicrobials showed that the multidrug resistance (MDR) rate was as high as 100%. The β-lactamase resistance genes bla_OXA-1, bla_CTX-M-1G, bla_CTX-M-9G and colistin resistance gene mcr-1 were highly carried in the P. mirabilis isolates. An MDR strain W47 was selected for whole genome sequencing (WGS) and conjugation experiment. The results showed that W47 carried 23 resistance genes and 64 virulence genes, and an SXT/R391 integrated conjugative elements (ICEs) named ICEPmiChn5 carrying 17 genes was identified in chromosome. ICEPmiChn5 was able to be excised from the chromosome of W47 forming a circular intermediate, but repeated conjugation experiments were unsuccessful. Among 187 P. mirabilis isolates, 144 (77.01%, 144/187) isolates carried ICEPmiChn5-like ICEs, suggesting that ICEs may be the major vector for the transmission of resistance genes among MDR chicken P. mirabilis strains in this study. The findings were conducive to insight into the resistance mechanism of chicken P. mirabilis strains and provide a theoretical basis for the use of antibiotics for the treatment of MDR P. mirabilis infections in veterinary clinic.

Structural and Serological Characterization of the O Antigen of Proteus mirabilis Clinical Isolates Classified into a New Proteus Serogroup, O84

Two closely related Proteus mirabilis smooth strains, Kr1 and Ks20, were isolated from wound and skin samples, respectively, of two infected patients in central Poland. Serological tests, using the rabbit Kr1-specific antiserum, revealed that both strains presented the same O serotype. Their O antigens are unique among the Proteus O serotypes, which had been described earlier, as they were not recognized in an enzyme-linked immunosorbent assay (ELISA) by a set of Proteus O1-O83 antisera. Additionally, the Kr1 antiserum did not react with O1-O83 lipopolysaccharides (LPSs). The O-specific polysaccharide (OPS, O antigen) of P. mirabilis Kr1 was obtained via the mild acid degradation of the LPSs, and its structure was established via a chemical analysis and one- and two-dimensional ¹H and ¹³C nuclear magnetic resonance (NMR) spectroscopy applied to both initial and O-deacetylated polysaccharides, where most β-2-acetamido-2-deoxyglucose (N-acetylglucosamine) (GlcNAc) residues are non-stoichiometrically O-acetylated at positions 3, 4, and 6 or 3 and 6, and a minority of α-GlcNAc residues are 6-O-acetylated. Based on the serological features and chemical data, P. mirabilis Kr1 and Ks20 were proposed as candidates to a new successive O-serogroup in the genus Proteus, O84, which is another example of new Proteus O serotypes identified lately among serologically differentiated Proteus bacilli infecting patients in central Poland.

Determination of the Bacterial Community of Mustard Pickle Products and Their Microbial and Chemical Qualities

We assessed the microbial and chemical qualities and microbiomes of 14 mustard pickle products coded sequentially from A to N and sold in traditional Taiwanese markets. The results showed that the aerobic plate count and lactic acid bacteria count of commercially available mustard pickle products were 2.18-4.01 and <1.0-3.77 log CFU/g, respectively. Moreover, no coliform bacteria, Escherichia coli, Staphylococcus aureus, Salmonella spp., or Listeria monocytogenes were detected in any of the samples. Analysis of the chemical quality showed that the sulfite content of all samples exceeded 30 ppm, which is the food additive limit in Taiwan. Furthermore, the mean contents of eight biogenic amines in the mustard pickle product samples were below 48.0 mg/kg. The results of high-throughput sequencing showed that the dominant bacterial genera in sample A were Proteus spp. (25%), Vibrio (25%), and Psychrobacter (10%), in sample C they were Weissella (62%) and Lactobacillus (15%), in sample E it was Lactobacillus (97%), and in sample J it was Companilactobacillus (57%). Mustard pickle product samples from different sources contained different microbiomes. The dominant bacterial family was Lactobacillaceae in all samples except for sample A. In contrast, the microbiome of sample A mainly consisted of Morganellaceae and Vibrionaceae, which may have resulted from environmental contamination during storage and sales. The result of this work suggests it may be necessary to monitor sulfite levels and potential sources of bacterial contamination in mustard pickle products, and to take appropriate measures to rule out any public health risks.

Identification of an indole biodegradation gene cluster from Providencia rettgeri and its contribution in selectively biosynthesizing Tyrian purple

Tyrian purple, mainly composed of 6, 6'-dibromoindigo, is a precious dye extracted from sea snails. In this study, we found Tyrian purple can be selectively produced by a bacterial strain GS-2 when fed with 6-bromotryptophan in the presence of tryptophan. This GS-2 strain was then identified as Providencia rettgeri based on bacterial genome sequencing analysis. An indole degradation gene cluster for indole metabolism was identified from this GS-2 strain. The heterologous expression of the indole degradation gene cluster in Escherichia coli BL21 (DE3) and in vitro enzymatic reaction demonstrated that the indole biodegradation gene cluster may contribute to selectively biosynthesizing Tyrian purple. To further explore the underlying mechanism of the selectivity, we explored the intermediates in this indole biodegradation pathway using liquid chromatography electrospray ionization quadrupole time-of-flight mass spectrometry (LC-ESI-QTOF-MS/MS), which indicated that the indole biodegradation pathway in Providencia rettgeri is the catechol pathway. Interestingly, the monooxygenase GS-C co-expressed with its corresponding reductase GS-D in the cluster has better activity for the biosynthesis of Tyrian purple compared with the previously reported monooxygenase from Methylophaga aminisulfidivorans (MaFMO) or Streptomyces cattleya cytochrome P450 enzyme (CYP102G4). This is the first study to show the existence of an indole biodegradation pathway in Providencia rettgeri, and the indole biodegradation gene cluster can contribute to the selective production of Tyrian purple.

Construction of an Ordered Transposon Library for Uropathogenic Proteus mirabilis HI4320

Ordered transposon libraries are a valuable resource for many bacterial species, especially those with difficult methods for generating targeted genetic mutations. Here, we present the construction of an ordered transposon library for the bacterial urinary tract pathogen Proteus mirabilis strain HI4320. This library will facilitate future studies into P. mirabilis biology. For large experimental screens, it may be used to overcome bottleneck constraints and avoid biased outcomes resulting from gene length. For smaller studies, the library allows sidestepping the laborious construction of single targeted mutants. This library, containing 18,432 wells, was condensed into a smaller library containing 1,728 mutants. Each selected mutant had a single transposon insertion in an open reading frame, covering 45% of predicted genes encoded by P. mirabilis HI4320. This coverage was lower than expected and was due both to library wells with no mapped insertions and a surprisingly high proportion of mixed clones and multiple transposon insertion events. We offer recommendations for improving future library construction and suggestions for how to use this P. mirabilis library resource. IMPORTANCE Ordered libraries facilitate large genetic screens by guaranteeing high genomic coverage with a minimal number of mutants, and they can save time and effort by reducing the need to construct targeted mutations. This resource is now available for P. mirabilis, a common and complicating agent of catheter-associated urinary tract infection. We also present obstacles encountered during library construction with the goal to aid others who would like to construct ordered transposon libraries in other species.

AadA36, a novel chromosomal aminoglycoside nucleotidyltransferase from a clinical isolate of Providencia stuartii

In this study, we characterized a novel chromosome-encoded aminoglycoside nucleotidyltransferase (ANT), AadA36, from the Providencia stuartii strain P14 isolated from the sputum specimen of a burn patient at a hospital in Wenzhou, China. Among the functionally characterized ANTs, AadA36 shared the highest amino acid sequence identity of 51.91% with AadA14. The whole genome of P. stuartii P14 consisted of one chromosome and two plasmids (designated pP14-166 and pP14-114). A total of 19 genes with ≥80% similarity with functionally characterized antimicrobial resistance genes (ARGs) were identified in the whole genome, including aminoglycosides [aac(2')-Ia, aph(6)-Id, aph(3″)-Ib, aac(6')-Ib, ant(3″)-IIa, aph(3')-Ia], β-lactams (bla _CMY-2 and bla _OXA-10) and so on. Antimicrobial susceptibility testing showed that the aadA36 gene conferred specific resistance to spectinomycin and streptomycin, and the minimum inhibitory concentration (MIC) of these antimicrobials increased 128- and 64-fold compared with the control strain. The kinetic parameters of AadA36 were consistent with the MIC data of spectinomycin and streptomycin, with k_cat /K_m ratios of (1.07 ± 2.23) × 10⁴ M^-1 s^-1 and (8.96 ± 1.01) × 10³ M^-1 s^-1, respectively. The identification of a novel aminoglycoside resistance gene will help us further understand the complexity of the resistance mechanisms and provide deep insights into the dissemination of resistance genes in the microbial population.

Proteus mirabilis and Klebsiella pneumoniae as pathogens capable of causing co-infections and exhibiting similarities in their virulence factors

The genera Klebsiella and Proteus were independently described in 1885. These Gram-negative rods colonize the human intestinal tract regarded as the main reservoir of these opportunistic pathogens. In favorable conditions they cause infections, often hospital-acquired ones. The activity of K. pneumoniae and P. mirabilis, the leading pathogens within each genus, results in infections of the urinary (UTIs) and respiratory tracts, wounds, bacteremia, affecting mainly immunocompromised patients. P. mirabilis and K. pneumoniae cause polymicrobial UTIs, which are often persistent due to the catheter biofilm formation or increasing resistance of the bacteria to antibiotics. In this situation a need arises to find the antigens with features common to both species. Among many virulence factors produced by both pathogens urease shows some structural similarities but the biggest similarities have been observed in lipids A and the core regions of lipopolysaccharides (LPSs). Both species produce capsular polysaccharides (CPSs) but only in K. pneumoniae these antigens play a crucial role in the serological classification scheme, which in Proteus spp. is based on the structural and serological diversity of LPS O-polysaccharides (OPSs). Structural and serological similarities observed for Klebsiella spp. and Proteus spp. polysaccharides are important in the search for the cross-reacting vaccine antigens.

Prevalence, antibiotic profile, virulence determinants, ESBLs, and non-β-lactam encoding genes of MDR Proteus spp. isolated from infected dogs

This study investigated the prevalence, antibiogram, virulence, extended-spectrum β-lactamases (ESBLs), and non-β-lactam encoding genes of Proteus species isolated from infected dogs in Ismailia province, Egypt. The study was conducted on 70 fecal swabs collected from dogs with diarrhea for bacteriological identification of Proteus spp. The positive isolates were evaluated for antibiotic susceptibility, molecular tests of virulence, ESBLs, and non-β-lactam encoding genes. Prevalence of Proteus spp. was 35.7% (25/70), including Proteus mirabilis (n = 23) and Proteus vulgaris (n = 2). The Proteus spp. prevalence revealed diversity, higher in males than females, in ages &lt; 12 weeks. Investigation of antimicrobial resistance was found against penicillin and amoxicillin (100%), amoxicillin–clavulanic acid (32%), cephalosporins: cefotaxime and ceftazidime (36%), and monobactam: aztreonam (28%) as ESBLs, in addition to tetracycline (32%) and trimethoprim sulfamethoxazole (100%). The strains retrieved by PCR revealed ureC, zapA, and rsbA virulence genes with variant prevalence as 92%, 60%, and 52%, respectively. In addition, the recovered strains contained ESBL genes with a dramatic variable prevalence of 100%, 92%, 36%, and 32%, to blaTEM, blaSHV, blaCTX-M, and blaOXA-1, respectively, and non β-lactam encoding genes with a prevalence of 100%, 48%, 44%, 20%, and 12%, to sul1, tetA, intI1, qnrA, and aadA1. Moreover, 28% (7/25) of recovering strains were MDR (multidrug-resistant) up to four classes of antimicrobials, and 48% (12/25) of the examined strains were MDR up to three antimicrobial classes. In conclusion, to the best of our knowledge, our study could be the first report recording MDR Proteus spp. in dogs in Egypt.

Lipopolysaccharide -mediated resistance to host antimicrobial peptides and hemocyte-derived reactive-oxygen species are the major Providencia alcalifaciens virulence factors in Drosophila melanogaster

Bacteria from the genus Providencia are ubiquitous Gram-negative opportunistic pathogens, causing “travelers’ diarrhea”, urinary tract, and other nosocomial infections in humans. Some Providencia strains have also been isolated as natural pathogens of Drosophila melanogaster. Despite clinical relevance and extensive use in Drosophila immunity research, little is known about Providencia virulence mechanisms and the corresponding insect host defenses. To close this knowledge gap, we investigated the virulence factors of a representative Providencia species—P. alcalifaciens which is highly virulent to fruit flies and amenable to genetic manipulations. We generated a P. alcalifaciens transposon mutant library and performed an unbiased forward genetics screen in vivo for attenuated mutants. Our screen uncovered 23 mutants with reduced virulence. The vast majority of them had disrupted genes linked to lipopolysaccharide (LPS) synthesis or modifications. These LPS mutants were sensitive to cationic antimicrobial peptides (AMPs) in vitro and their virulence was restored in Drosophila mutants lacking most AMPs. Thus, LPS-mediated resistance to host AMPs is one of the virulence strategies of P. alcalifaciens. Another subset of P. alcalifaciens attenuated mutants exhibited increased susceptibility to reactive oxygen species (ROS) in vitro and their virulence was rescued by chemical scavenging of ROS in flies prior to infection. Using genetic analysis, we found that the enzyme Duox specifically in hemocytes is the source of bactericidal ROS targeting P. alcalifaciens. Consistently, the virulence of ROS-sensitive P. alcalifaciens mutants was rescued in flies with Duox knockdown in hemocytes. Therefore, these genes function as virulence factors by helping bacteria to counteract the ROS immune response. Our reciprocal analysis of host-pathogen interactions between D. melanogaster and P. alcalifaciens identified that AMPs and hemocyte-derived ROS are the major defense mechanisms against P. alcalifaciens, while the ability of the pathogen to resist these host immune responses is its major virulence mechanism. Thus, our work revealed a host-pathogen conflict mediated by ROS and AMPs.

Pathogens express special molecules or structures called virulence factors to successfully infect a host. By identifying these factors, we can learn how hosts fight and how pathogens cause infections. Here, we identified virulence factors of the human and fruit fly pathogen Providencia alcalifaciens, by infecting flies with a series of mutants of this pathogen. In this way, we detected 23 mutants that were less virulent. Some of these less virulent mutants were hypersensitive to fruit fly immune defense molecules called antimicrobial peptides (AMPs), while others were sensitive to reactive oxygen species (ROS) produced by the immune cells. Notably, AMPs-sensitive mutants remained virulent in a Drosophila mutant that lacks AMPs, while pathogens sensitive to oxidative stress retained their virulence in a fruit fly mutant devoid of oxidative species. These results suggest that the ability of P. alcalifaciens to resist two major host immune molecules, namely AMPs and ROS, is the major virulence mechanism. Overall, our systematic analysis of P. alcalifaciens virulence factors has identified the major defense mechanisms of the fruit fly against this pathogen and the bacterial mechanisms to combat these immune responses.

Genomic characteristics of clinical multidrug-resistant Proteus isolates from a tertiary care hospital in southwest China

Multidrug-resistant (MDR) Proteus, especially those strains producing extended-spectrum β-lactamases (ESBL) and carbapenemases, represents a major public health concern. In the present work, we characterized 27 MDR Proteus clinical isolates, including 23 Proteus mirabilis, three Proteus terrae, and one Proteus faecis, by whole-genome analysis. Among the 27 isolates analyzed, SXT/R391 ICEs were detected in 14 strains, and the complete sequences of nine ICEs were obtained. These ICEs share a common backbone structure but also have different gene contents in hotspots and variable regions. Among them, ICEPmiChn2826, ICEPmiChn2833, ICEPmiChn3105, and ICEPmiChn3725 contain abundant antibiotic resistance genes, including the ESBL gene bla_CTX-M-65. The core gene phylogenetic analysis of ICEs showed their genetic diversity, and revealed the cryptic dissemination of them in Proteus strains from food animals and humans on a China-wide scale. One of the isolates, FZP3105, acquired an NDM-1-producing MDR plasmid, designated pNDM_FZP3105, which is a self-transmissible type 1/2 hybrid IncC plasmid. Analysis of the genetic organization showed that pNDM_FZP3105 has two novel antibiotic resistance islands bearing abundant antibiotic resistance genes, among which bla_NDM-1 is located in a 9.0 kb ΔTn125 bracketed by two copies of IS26 in the same direction. In isolates FZP2936 and FZP3115, bla_KPC-2 was detected on an IncN plasmid, which is identical to the previously reported pT211 in Zhejiang province of China. Besides, a MDR genomic island PmGRI1, a variant of PmGRI1-YN9 from chicken in China, was identified on their chromosome. In conclusion, this study demonstrates abundant genetic diversity of mobile genetic elements carrying antibiotic resistance genes, especially ESBL and carbapenemase genes, in clinical Proteus isolates, and highlights that the continuous monitoring on their transmission and further evolution is needed.

Can Urinalysis and Past Medical History of Kidney Stones Predict Urine Antibiotic Resistance?

Introduction

Urinary tract infections (UTI) are one of the most common infections encountered in the emergency department (ED) with an estimated 2–3 million annual visits. Commonly prescribed antibiotics for UTIs have shown growing rates of resistance. Previous studies lack direction on improving UTI treatment based on the labs available to the bedside clinician.

Methods

We sought to determine if antibiotic resistance in UTIs was related to demographics, urinalysis, and history of renal failure or kidney stones. We conducted an analysis of 892 women ≥18 years of age discharged from the ED with a UTI diagnosis. We assessed predictors of nitrofurantoin resistance, cefazolin resistance, ciprofloxacin resistance, and trimethoprim-sulfamethoxazole resistance using unadjusted and multivariable logistic regression models.

Results

Antibiotic resistance was 13.6% for nitrofurantoin, 11.9% for cefazolin, 12.8% for ciprofloxacin, and 17.1% for trimethoprim-sulfamethoxazole. In multivariable analysis, significant independent associations with an increased likelihood of resistance to nitrofurantoin were observed for less urine blood (OR [per 1 category increase of score] 0.81; P = 0.02); greater mucous (OR [per 1 category increase of score] 1.22; P = 0.02); less specific gravity urine (OR [per 1 category increase] 0.87; P = 0.04), and presence of any history of kidney stones (OR 3.24; P = 0.01). There were no significant predictors for cefazolin resistance (all P ≥0.06); age was the only significant predictor of ciprofloxacin resistance (OR per 10 year increase] 1.10, P = 0.05), and lower specific gravity urine was significantly associated with an increased risk of resistance to trimethoprim- sulfamethoxazole (OR [per 1 category increase] 0.88, P = 0.04).

Conclusion

Women with any history of kidney stones may have bacteriuria resistant to nitrofurantoin, suggesting that providers might consider alternative antibiotic therapies in this scenario.

Bacterial Prevalence in Skin, Urine, Diarrheal Stool, and Respiratory Samples from Dogs

The emergence of bacterial infections in companion animals is a growing concern as humans can also be infected through the transmission of pathogenic bacteria. Because there have been few studies conducted on companion animals, the extent and significance of prevalence in veterinary practices remain unknown. This is the first nationwide surveillance report aimed at elucidating the prevalence pattern and associated infections of isolated bacteria from dogs in Korea. Bacterial isolates were collected from seven different laboratories participating in the Korean Veterinary Antimicrobial Resistance Monitoring System from 2018 to 2019. The samples were obtained from the diarrheal stool, skin/ear, urine, and respiratory samples of veterinary hospital-visited dogs. Isolation and identification of bacterial species was carried out using a bacterial culture approach and then confirmed with matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF) and polymerase chain reaction (PCR). Out of 3135 isolates in dogs, 1085, 1761, 171, and 118 were extracted from diarrheal stool, skin/ear, urine, and respiratory samples, respectively. The overall prevalence of bacteria was higher among two age groups (1-5 and 6-10 years) with a 66.5 percent prevalence. This study showed that Escherichia coli was the most prevalent species among isolated bacterial species of diarrheal and urine origin, whereas Staphylococcus pseudintermedius was the most prevalent among skin and respiratory sample isolates. The data on the prevalence of bacteria for each dog specimen could provide basic information to estimate the extent of bacterial infection and antimicrobial resistance development and to guide veterinarians in therapeutic decisions in clinical practices throughout Korea.

Pectin supplementation ameliorates intestinal epithelial barrier function damage by modulating intestinal microbiota in lipopolysaccharide-challenged piglets

During weaning, infants and young animals are susceptible to severe enteric infections, thus inducing intestinal microbiota dysbiosis, intestinal inflammation, and impaired intestinal barrier function. Pectin (PEC), a prebiotic polysaccharide, enhances intestinal health with the potential for therapeutic effect on intestinal diseases. One 21-days study was conducted to investigate the protective effect of pectin against intestinal injury induced by intraperitoneal injection of Escherichia coli lipopolysaccharide (LPS) in a piglet model. A total of 24 piglets (6.77±0.92 kg BW; Duroc × Landrace × Large White; barrows; 21 d of age) were randomly assigned into three groups: control group, LPS-challenged group, and PEC + LPS group. Piglets were administrated with LPS or saline on d14 and d21 of the experiment. All piglets were slaughtered and intestinal samples were collected after 3 h administration on d21. Pectin supplementation ameliorated the LPS-induced inflammation response and damage to the ileal morphology. Meanwhile, pectin also improved intestinal mucin barrier function, increased the mRNA expression of MUC2, and improved intestinal mucus glycosylation. LPS challenge reduced the diversity of intestinal microbiota and enriched the relative abundance of Helicobacter. Pectin restored alpha diversity improved the structure of the gut microbiota by enriching anti-inflammatory bacteria and short-chain fatty acid (SCFA)-producing bacteria, and increased the concentrations of acetate. In addition, Spearman rank correlation analysis also revealed the potential relationship between intestinal microbiota and intestinal morphology, intestinal inflammation, and intestinal glycosylation in piglets. Taken together, these results indicate that pectin enhances intestinal integrity and barrier function by altering intestinal microbiota composition and their metabolites, which subsequently alleviates intestinal injury and finally improves the growth performance of piglets.

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.

Gut Microbial Profile in Asymptomatic Gallstones

There are few studies on the changes of gut microbiota in patients with gallstones, especially in patients with asymptomatic gallstones, and there are some deficiencies in these studies, for instance, the effects of metabolic factors on gut microbiota are not considered. Here, we selected 30 asymptomatic gallstone patients from the survey population, and 30 controls according to the age and BMI index matching principle. The 16SrDNA technology was used to detect and compare the structural differences in the gut microbiota between the two groups. Compared with healthy controls, the abundance of gut microbiota in patients with gallstones increased significantly, while the microbiota diversity decreased. At the level of phylum, both groups were dominated by Firmicutes, Bacteroides, Proteobacteria, and Actinobacteria. At the genus level, there were 15 species with significant differences in abundance between the two groups. Further subgroup analysis found that only unclassified Lactobacillales showed differences in the intestines of gallstones patients with hypertension, non-alcoholic fatty liver disease, or patients with elevated BMI (≧24). The structure of gut microbiota in patients with gallstones changed significantly, and this might be related to the occurrence of gallstones, rather than metabolic factors such as hypertension, non-alcoholic fatty liver disease, and obesity.