Epidemiology and Pathogenesis of Providencia alcalifaciens Infections

Providencia alcalifaciens in a patient with a staghorn calculus: a novel presentation

A member of the Enterobacteriaceae family, Providencia alcalifaciens is typically recognized as a source of gastrointestinal illness. Although its pathogenicity is not well known, many studies have suggested its mechanism of action involves the invasion of the intestinal mucosal layer. Although P. alcalifaciens is a urease producing microorganism, it has not been associated with the formation of a staghorn calculus in the setting of a urinary tract infection. This organism is neither commonly pursued in research or investigation nor is it commonly tested for in the clinical setting. This is especially true when combined with other disease processes, such as calculus formation. The advancement of antibiotic resistance, such as carbapenemase-producing strains, should bring more attention and routine investigation to this organism in the acute stage of infection. In this case report we introduce a 43-year-old Cuban female, who presents with a left-sided staghorn calculi and urine culture positive for carbapenemase-producing P. alcalifaciens.

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.

Extended chloramination significantly enriched intracellular antibiotic resistance genes in drinking water treatment plants

Chloramination and chlorination are both strong barriers that prevent the transmission of potential pathogens to humans through drinking water. However, the comparative effects of chloramination and chlorination on the occurrence of antibiotic resistance genes (ARGs) in drinking water treatment plants (DWTPs) remain unknown. Herein, the antibiotic resistome in water before and after chloramination or chlorination was analyzed through metagenomic sequencing and then verified through quantitative real-time polymerase chain reaction (qPCR). After the treatment of 90 min, chloramination led to higher enrichment of the total relative abundance of intracellular ARGs (iARGs) in water than chlorination, whereas chlorination facilitated the release of more extracellular ARGs (eARGs) than chloramination. According to redundancy and Pearson's analyses, the total concentration of the observed iARGs in the finished water exhibited a strong positive correlation with ammonium nitrogen (NH₄⁺-N) concentration, presenting a linear upward trend with an increase in the NH₄⁺-N concentration. This indicated that NH₄⁺-N is a crucial driving factor for iARG accumulation during chloramination. iARG enrichment ceases if the duration of chloramination is shortened to 40 min, suggesting that shortening the duration would be a better strategy for controlling iARG enrichment in drinking water. These findings emphasized the potential risk of antibiotic resistance after extended chloramination, shedding light on the control of transmission of antibiotic-resistant bacteria through water by optimizing disinfection procedures in DWTPs.

Variations in gut microbiome and metabolites of dogs with acute diarrhea in poodles and Labrador retrievers

For different breeds of dogs with acute diarrhea, the gut microbiota and metabolome profiles are unclear. This prospective observational study analyzed the gut microbiomes of poodles with acute diarrhea and Labrador retrievers with acute diarrhea based on 16S amplicon sequencing, with respective healthy dogs as controls. Fecal non-target metabolomics and metagenomics were performed on poodles with acute diarrhea. This study found that the diversity and structure of the microbial community differed significantly between the two breeds in cohorts of healthy dogs. Two breeds of dogs with acute diarrhea demonstrated different changes in microbial communities and metabolic functions. The metabolism of starch and sucrose was significantly decreased in dogs with acute diarrhea, which may be attributed to the reduced activity of dextran dextrinase. Non-targeted metabolomics identified 21 abnormal metabolic pathways exhibited by dogs with acute diarrhea, including starch, amino acid, bile acid metabolism, etc., and were closely related to specific intestinal flora. This study provided new insights into breed specificity and the development of dietary treatment strategy in canine gastrointestinal disease.

Tumor microbiome - an integral part of the tumor microenvironment

The tumor microenvironment (TME) plays a significant role in tumor progression and cancer cell survival. Besides malignant cells and non-malignant components, including immune cells, elements of the extracellular matrix, stromal cells, and endothelial cells, the tumor microbiome is considered to be an integral part of the TME. Mounting evidence from preclinical and clinical studies evaluated the presence of tumor type-specific intratumoral bacteria. Differences in microbiome composition between cancerous tissues and benign controls suggest the importance of the microbiome-based approach. Complex host-microbiota crosstalk within the TME affects tumor cell biology via the regulation of oncogenic pathways, immune response modulation, and interaction with microbiota-derived metabolites. Significantly, the involvement of tumor-associated microbiota in cancer drug metabolism highlights the therapeutic implications. This review aims to summarize current knowledge about the emerging role of tumor microbiome in various types of solid malignancies. The clinical utility of tumor microbiome in cancer progression and treatment is also discussed. Moreover, we provide an overview of clinical trials evaluating the role of tumor microbiome in cancer patients. The research focusing on the communication between the gut and tumor microbiomes may bring new opportunities for targeting the microbiome to increase the efficacy of cancer treatment and improve patient outcomes.

Different oral and gut microbial profiles in those with Alzheimer's disease consuming anti-inflammatory diets

The number of people living with Alzheimer's disease (AD) is increasing alongside with aging of the population. Systemic chronic inflammation and microbial imbalance may play an important role in the pathogenesis of AD. Inflammatory diets regulate both the host microbiomes and inflammatory status. This study aimed to explore the impact of inflammatory diets on oral-gut microbes in patients with AD and the relationship between microbes and markers of systemic inflammation. The dietary inflammatory properties and the oral and gut microorganisms were analyzed using the dietary inflammatory index (DII) and 16S RNA in 60 patients with AD. The α-diversity was not related to the DII (p > 0.05), whereas the β-diversity was different in the oral microbiomes (R² = 0.061, p = 0.013). In the most anti-inflammatory diet group, Prevotella and Olsenella were more abundant in oral microbiomes and Alistipes, Ruminococcus, Odoribacter, and unclassified Firmicutes were in the gut microbiomes (p < 0.05). Specific oral and gut genera were associated with interleukin-6 (IL)-6, complement 3 (C3), high-sensitivity C-reactive protein (hs-CRP), IL-1β, IL-4, IL-10, IL-12, and tumor necrosis factor-α (TNF-α) (p < 0.05). In conclusion, anti-inflammatory diets seem to be associated with increased abundance of beneficial microbes, and specific oral and gut microbial composition was associated with inflammatory markers.

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.

Role of human gut bacteria in arsenic biosorption and biotransformation

There is growing evidence that human gut microbiota can metabolize arsenic (As); however, which bacteria play roles in this metabolism is unclear. In this study, we measured the abilities of 21 human gut bacteria strains from diverse clades to adsorb and transform As using in vitro method with the aim of determining which bacteria play a role in As metabolism. Seven strains showed high biosorption of As, ranging from 20.1 to 29.8%, which was attributed to functional groups on the bacterial surfaces, such as hydroxyl, amino, and carboxyl groups. Moreover, six of these seven strains were versatile, as they also had roles in reducing As(V) to As(III), which is mainly regulated by the arsC gene. Escherichia coli had the strongest tolerance to As and the highest reducing ability, with a value of 71.04-73.13 µM As/h. This study reveals that gut bacteria play essential roles in As biosorption and biotransformation, and provides a better understanding of which strains are involved, which has implications for the regulation of As toxicity-based gut bacteria and provides basic data for regulating arsenic to human health.

Synbiotics Alleviate Hepatic Damage, Intestinal Injury and Muscular Beclin-1 Elevation in Rats after Chronic Ethanol Administration

The purpose of this study was to investigate the beneficial effects of synbiotics on liver damage, intestinal health, and muscle loss, and their relevance in rats with chronic ethanol feeding. Thirty Wistar rats fed with a control liquid diet were divided into control and synbiotics groups, which were respectively provided with water or synbiotics solution (1.5 g/kg body weight/day) for 2 weeks. From the 3rd to 8th week, the control group was divided into a C group (control liquid diet + water) and an E group (ethanol liquid diet + water). The synbiotics group was separated in to three groups, SC, ASE, and PSE. The SC group was given a control liquid diet with synbiotics solution; the ASE group was given ethanol liquid diet with synbiotics solution, and the PSE group was given ethanol liquid diet and water. As the results, the E group exhibited liver damage, including increased AST and ALT activities, hepatic fatty changes, and higher CYP2E1 expression. Intestinal mRNA expressions of occludin and claudin-1 were significantly decreased and the plasma endotoxin level was significantly higher in the E group. In muscles, beclin-1 was significantly increased in the E group. Compared to the E group, the PSE and ASE groups had lower plasma ALT activities, hepatic fatty changes, and CYP2E1 expression. The PSE and ASE groups had significantly higher intestinal occludin and claudin-1 mRNA expressions and lower muscular beclin-1 expression when compared to the E group. In conclusion, synbiotics supplementation might reduce protein expression of muscle protein degradation biomarkers such as beclin-1 in rats with chronic ethanol feeding, which is speculated to be linked to the improvement of intestinal tight junction and the reduction of liver damage.

High burden of multidrug resistant bacteria detected in Little Akaki River

Spread of antimicrobial-resistant bacteria between humans and animals occurs when the environment is contaminated with animal and human wastes. A total of 30 samples were collected from the Akaki river to identify antimicrobial-resistant bacteria. Bacterial enumeration and characterization was done by spreading serially diluted water samples on MacConkey agar. Sixty four bacterial isolates were identified and susceptibility tested using VITEK 2. The most frequently identified bacteria were Providencia alcalifaciens 10 (15.6%), Kluyvera cryocrescens 9 (14.1%) and Citrobacter freundii 7(10.9%), respectively. Multiple drug resistant bacteria were identified, constituting 17 (28%) of the 64 identified isolates. Multiple antimicrobial resistance (MAR) index of the six sites laid in the range 0.13-0.27, being the highest score located downstream of all the sampling sites. Species MAR index varied from 0.12 to 0.40. Out of 64 isolates, 54 (84.4%) of them were resistant to Ampicillin. On the contrary, most of the isolates were sensitive to Amikacin and meropenem. In conclusion, our findings indicated E.coli count was above the WHO permissible levels. The predominant isolates were P. alcalifaciens, and C. freundii. The MAR index of major isolates was greater than two, implying the study sites were exposed to high-risk sources of human or animal contamination.

Genomic analysis of the nomenclatural type strain of the nematode-associated entomopathogenic bacterium Providencia vermicola

Background

Enterobacteria of the genus Providencia are mainly known as opportunistic human pathogens but have been isolated from highly diverse natural environments. The species Providencia vermicola comprises insect pathogenic bacteria carried by entomoparasitic nematodes and is investigated as a possible insect biocontrol agent. The recent publication of several genome sequences from bacteria assigned to this species has given rise to inconsistent preliminary results.

Results

The genome of the nematode-derived P. vermicola type strain DSM_17385 has been assembled into a 4.2 Mb sequence comprising 5 scaffolds and 13 contigs. A total of 3969 protein-encoding genes were identified. Multilocus sequence typing with different marker sets revealed that none of the previously published presumed P. vermicola genomes represents this taxonomic species. Comparative genomic analysis has confirmed a close phylogenetic relationship of P. vermicola to the P. rettgeri species complex. P. vermicola DSM_17385 carries a type III secretion system (T3SS-1) with probable function in host cell invasion or intracellular survival. Potentially antibiotic resistance-associated genes comprising numerous efflux pumps and point-mutated house-keeping genes, have been identified across the P. vermicola genome. A single small (3.7 kb) plasmid identified, pPVER1, structurally belongs to the qnrD-type family of fluoroquinolone resistance conferring plasmids that is prominent in Providencia and Proteus bacteria, but lacks the qnrD resistance gene.

Conclusions

The sequence reported represents the first well-supported published genome for the taxonomic species P. vermicola to be used as reference in further comparative genomics studies on Providencia bacteria. Due to a striking difference in the type of injectisome encoded by the respective genomes, P. vermicola might operate a fundamentally different mechanism of entomopathogenicity when compared to insect-pathogenic Providencia sneebia or Providencia burhodogranariea. The complete absence of antibiotic resistance gene carrying plasmids or mobile genetic elements as those causing multi drug resistance phenomena in clinical Providencia strains, is consistent with the invertebrate pathogen P. vermicola being in its natural environment efficiently excluded from the propagation routes of multidrug resistance (MDR) carrying genetic elements operating between human pathogens. Susceptibility to MDR plasmid acquisition will likely become a major criterion in the evaluation of P. vermicola for potential applications in biological pest control.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-08027-w.

Changes in the fecal microbiota in dogs with acute hemorrhagic diarrhea during an outbreak in Norway

Background

A severe form of acute hemorrhagic diarrhea syndrome (AHDS) occurred in dogs in the Oslo region of Norway during autumn 2019.

Objectives

To characterize the fecal microbiota of dogs with AHDS during the outbreak and compare it to that of healthy dogs from the same period and before the outbreak.

Animals

Dogs with AHDS (n = 50), dogs with nonhemorrhagic diarrhea (n = 3), and healthy dogs (n = 11) were sampled during the outbreak. In addition, 78 healthy dogs from the same region were sampled before the outbreak between 2017 and 2018.

Methods

Retrospective case‐control study. The fecal microbiotas were characterized using 16S rRNA gene amplicon sequencing.

Results

Dogs with AHDS had significantly different microbiota composition (R² = .07, P < .001) and decreased intestinal diversity relative to healthy dogs from the outbreak period (median, 2.7; range, 0.9‐3.5 vs median, 3.2; range, 2.6‐4.0; P < .001). The microbiota in dogs with AHDS was characterized by a decrease of Firmicutes and an outgrowth of Proteobacteria, with increased numbers of Clostridium perfringens and Providencia spp. Among the Providencia spp., 1 showed 100% sequence identity with a Providencia alcalifaciens strain that was cultivated and isolated from the same outbreak. No Providencia spp. was found in healthy dogs sampled before the outbreak.

Conclusions and Clinical Importance

Dogs with AHDS had marked changes in fecal microbiota including increased numbers of Providencia spp. and C. perfringens, which may have contributed to the severity of this illness.

A Survey of Bacterial Microcompartment Distribution in the Human Microbiome

Bacterial microcompartments (BMCs) are protein-based organelles that expand the metabolic potential of many bacteria by sequestering segments of enzymatic pathways in a selectively permeable protein shell. Sixty-eight different types/subtypes of BMCs have been bioinformatically identified based on the encapsulated enzymes and shell proteins encoded in genomic loci. BMCs are found across bacterial phyla. The organisms that contain them, rather than strictly correlating with specific lineages, tend to reflect the metabolic landscape of the environmental niches they occupy. From our recent comprehensive bioinformatic survey of BMCs found in genome sequence data, we find many in members of the human microbiome. Here we survey the distribution of BMCs in the different biotopes of the human body. Given their amenability to be horizontally transferred and bioengineered they hold promise as metabolic modules that could be used to probiotically alter microbiomes or treat dysbiosis.

The Changing Face of the Family Enterobacteriaceae (Order: "Enterobacterales"): New Members, Taxonomic Issues, Geographic Expansion, and New Diseases and Disease Syndromes

The family Enterobacteriaceae has undergone significant morphogenetic changes in its more than 85-year history, particularly during the past 2 decades (2000 to 2020). The development and introduction of new and novel molecular methods coupled with innovative laboratory techniques have led to many advances. We now know that the global range of enterobacteria is much more expansive than previously recognized, as they play important roles in the environment in vegetative processes and through widespread environmental distribution through insect vectors. In humans, many new species have been described, some associated with specific disease processes. Some established species are now observed in new infectious disease settings and syndromes. The results of molecular taxonomic and phylogenetics studies suggest that the current family Enterobacteriaceae should possibly be divided into seven or more separate families. The logarithmic explosion in the number of enterobacterial species described brings into question the relevancy, need, and mechanisms to potentially identify these taxa. This review covers the progression, transformation, and morphogenesis of the family from the seminal Centers for Disease Control and Prevention publication (J. J. Farmer III, B. R. Davis, F. W. Hickman-Brenner, A. McWhorter, et al., J Clin Microbiol 21:46-76, 1985, https://doi.org/10.1128/JCM.21.1.46-76.1985) to the present.

Sensitive and rapid detection of cytolethal distending toxin encoding genes in Providencia alcalifaciens

Cytolethal distending toxins (CDTs) produced by P. alcalifaciens are considered as potential virulence factors. A loop-mediated isothermal amplification (LAMP) method for the detection of cdtA, cdtB, and cdtC genes was established which showed high specificity and strong sensitivity. The LAMP assay showed a detection threshold was 3.13 pg/μl within 40 min.

Characterization of a novel AraC/XylS-regulated family of N-acyltransferases in pathogens of the order Enterobacterales

Enteroaggregative Escherichia coli (EAEC) is a diarrheagenic pathotype associated with traveler’s diarrhea, foodborne outbreaks and sporadic diarrhea in industrialized and developing countries. Regulation of virulence in EAEC is mediated by AggR and its negative regulator Aar. Together, they control the expression of at least 210 genes. On the other hand, we observed that about one third of Aar-regulated genes are related to metabolism and transport. In this study we show the AggR/Aar duo controls the metabolism of lipids. Accordingly, we show that AatD, encoded in the AggR-regulated aat operon (aatPABCD) is an N-acyltransferase structurally similar to the essential Apolipoprotein N-acyltransferase Lnt and is required for the acylation of Aap (anti-aggregation protein). Deletion of aatD impairs post-translational modification of Aap and causes its accumulation in the bacterial periplasm. trans-complementation of 042aatD mutant with the AatD homolog of ETEC or with the N-acyltransferase Lnt reestablished translocation of Aap. Site-directed mutagenesis of the E207 residue in the putative acyltransferase catalytic triad disrupted the activity of AatD and caused accumulation of Aap in the periplasm due to reduced translocation of Aap at the bacterial surface. Furthermore, Mass spectroscopy revealed that Aap is acylated in a putative lipobox at the N-terminal of the mature protein, implying that Aap is a lipoprotein. Lastly, deletion of aatD impairs bacterial colonization of the streptomycin-treated mouse model. Our findings unveiled a novel N-acyltransferase family associated with bacterial virulence, and that is tightly regulated by AraC/XylS regulators in the order Enterobacterales.

Although the regulatory scheme of AggR is well understood, the biological relevance of half of AggR-regulated proteins remains unknown. In this study we provide experimental evidence that the AggR-regulated AatD is a novel N-acyltransferase restricted to pathogens of the order Enterobacterales, including EAEC, ETEC, Yersinia sp., and C. rodentium. AatD is structurally similar to Lnt. However, unlike Lnt which is essential for cellular functions, AatD is a dedicated N-acyltransferase required for post-translational modification of virulence factors. Aap was identified as a lipoprotein acylated by AatD. Lipid modification in Aap provides an important post-translational mechanism to regulate the trafficking, stability and subcellular localization of Aap. In the absence of AatD, Aap is retained in the periplasmic space and cannot be translocated to the bacterial surface, presumably, restricting the biological function of the protein. Our data suggest that AggR and Aar virulence regulators, not only regulate the expression of Aap virulence factor at the transcriptional level, but also regulate translocation of Aap to the bacterial surface, which is required for full virulence of EAEC, unveiling an important mechanism of virulence regulation.