Molecular detection of zoonotic pathogens causing gastroenteritis in humans: Salmonella spp., Shigella spp. and Escherichia coli isolated from Rattus species inhabiting chicken farms in North West Province, South Africa.

Rodents are key carriers and reservoirs of various pathogens of public health importance to both human and animal diseases. This research was carried out in order to identify the selected pathogens, namely, Shigella spp., Salmonella spp. and Escherichia coli from rats that inhabit the poultry houses. A total of 154 samples from captured rats were examined for the zoonotic bacterial pathogens, of which 3.3%, 29.9% and 20.7% were harbouring Shigella spp., Salmonella spp., and E. coli, respectively. A total of 14 Shigella isolates expressed presence of ipaH gene, of which eight and five were positive for S. sonnei and S. boydii, respectively. For Salmonella, 68 isolates were positive for invA and other genes including spy with 26 (38%), sdfI 2 (18%), spvC 14 (20%), hilA 28 (41%), misL 43 (63%), orfL 31 (46%) and spiC 38 (56%). For E. coli, the aggR gene was the most prevalent (62 [42%]), followed by the eae gene, which was only detected in 21 (14%) isolates, while stx gene was not detected in any of the samples. This study shows that zoonotic pathogens with virulence genes are circulating in rodents from selected chicken farms in the North West Province of South Africa. Rodents must therefore be regarded as important carriers of zoonotic pathogens that can potentially infect both humans and animals.

Rodentibacter haemolyticus sp. nov. isolated from laboratory rodents.

Nine strains of a Rodentibacter-related bacterium were isolated over a period of 38 years from a laboratory mouse (Mus musculus), seven laboratory rats (Rattus norvegicus) and a Syrian hamster (Mesocricetus auratus) in Düsseldorf and Heidelberg, Germany. The isolates are genotypically and phenotypically distinct from all previously described Rodentibacter species. Sequence analysis of 16S rRNA and rpoB gene sequences placed the isolates as a novel lineage within the genus Rodentibacter. In addition to the single-gene analysis, the whole genome sequence of the strain 1625/19T revealed distinct genome-to-genome distance values to the other Rodentibacter species. The genomic DNA G+C content of strain 1625/19T was 40.8 mol% within the range of Rodentibacter. At least six phenotypic characteristics separate the new isolates from the other Rodentibacter species, with Rodentibacter heylii being the most closely related. In contrast to the latter, the new strains display ß-haemolysis and are ß-glucuronidase, d-mannitol and sorbitol positive, but fail to produce lysine decarboxylase and trehalose. The genotypic and phenotypic differences between the novel strains and the other closely related strains of the genus Rodentibacter indicate that they represent a novel species within the genus Rodentibacter, family Pasteurellaceae, for which the name Rodentibacter haemolyticus sp. nov. is proposed. The type strain 1625/19T, (=DSM 111151T=CCM 9081T), was isolated in 2019 from the nose of a laboratory mouse (Mus musculus) in Düsseldorf, Germany.

Is Carriage of Leptospira interrogans by Rats Influenced by the Urban Environment or Population Density?

Leptospira interrogans is one of the most important zoonotic pathogens globally. In urban settings, Norway rats (Rattus norvegicus) are important reservoirs of L. interrogans, but it is unclear how this bacterium is transmitted among rats. Both environmental features and rat population density may determine the prevalence of this pathogen in rat populations as well as the spillover risk to people. While these factors could play an important role in transmission between rats, it is unknown whether such factors influence prevalence among rats at a fine scale. Our objective was to determine if carriage of L. interrogans by rats could be explained by variation in the environment or in rat population density. Rats were live-trapped in a single neighborhood of Vancouver, Canada during two study periods (2011-12; 2016-17) and were tested for L. interrogans. The physical environment of each city block was recorded using a comprehensive, in-person environmental survey. Using generalized linear mixed modelling, we found no evidence of an association between carriage of L. interrogans and environmental features or rat population density, suggesting that these were not the primary drivers of its distribution among rats within this neighborhood. Understanding factors that promote L. interrogans transmission can be used to inform management approaches to minimize public health risks.

Detection and characterization of Enterobacteriaceae family members carried by commensal Rattus norvegicus from Tehran, Iran.

Wild rats are known to carry different microorganisms and are considered a reservoir of zoonotic pathogens worldwide. The urban rats were collected from five districts of Tehran and Gram-negative bacteria (GNB) were isolated from fecal samples and were identified using classical biochemical tests. The antibiotic susceptibility patterns of isolated bacteria were determined by Kirby-Bauer disk diffusion method, the results of which were interpreted in line with CLSI guideline. The frequency of antibiotic-resistant genes was identified using multiplex-PCR. Moreover, PCR method was used to identify the frequency of Escherichia coli O157:H7 and main categories of diarrheagenic E. coli including EPEC, ETEC, EIEC, EAEC, and STEC pathotypes. A total of 100 Rattus norvegicus were trapped and fecal samples were collected. Overall, 72 fecal samples were positive for GNB. E. coli (n = 46/72) had the highest frequency among the isolated GNB. Among E. coli isolates, the highest and lowest resistance rates belonged to ampicillin (56.5%) and ceftriaxone (0%), respectively. Klebsiella spp. was 100% resistant to imipenem, and streptomycin (0%) was the most effective antimicrobial agent on Klebsiella spp. Among surveyed genes, blaTEM (95.8%) and blaaadA-1 (58.3%) had the highest frequency, while blaKPC, and blaCMY-2 were not detected among Enterobacteriaceae. Herein, O157: H7 serotype was not detected and aEPEC (87%) was the most common pathotype detected. Results suggested that rodents might be a reservoir of antimicrobial-resistant pathogens and rodent control along with implementation of surveillance programs should be considered as a critical priority for urban health.

Composition of gut and oropharynx bacterial communities in Rattus norvegicus and Suncus murinus in China.

BACKGROUND: Rattus norvegicus and Suncus murinus are important reservoirs of zoonotic bacterial diseases. An understanding of the composition of gut and oropharynx bacteria in these animals is important for monitoring and preventing such diseases. We therefore examined gut and oropharynx bacterial composition in these animals in China. RESULTS: Proteobacteria, Firmicutes and Bacteroidetes were the most abundant phyla in faecal and throat swab samples of both animals. However, the composition of the bacterial community differed significantly between sample types and animal species. Firmicutes exhibited the highest relative abundance in throat swab samples of R. norvegicus, followed by Proteobacteria and Bacteroidetes. In throat swab specimens of S. murinus, Proteobacteria was the predominant phylum, followed by Firmicutes and Bacteroidetes. Firmicutes showed the highest relative abundance in faecal specimens of R. norvegicus, followed by Bacteroidetes and Proteobacteria. Firmicutes and Proteobacteria had almost equal abundance in faecal specimens of S. murinus, with Bacteroidetes accounting for only 3.07%. The family Streptococcaceae was most common in throat swab samples of R. norvegicus, while Prevotellaceae was most common in its faecal samples. Pseudomonadaceae was the predominant family in throat swab samples of S. murinus, while Enterobacteriaceae was most common in faecal samples. We annotated 33.28% sequences from faecal samples of S. murinus as potential human pathogenic bacteria, approximately 3.06-fold those in R. norvegicus. Potential pathogenic bacteria annotated in throat swab samples of S. murinus were 1.35-fold those in R. norvegicus. CONCLUSIONS: Bacterial composition of throat swabs and faecal samples from R. norvegicus differed from those of S. murinus. Both species carried various pathogenic bacteria, therefore both should be closely monitored in the future, especially for S. murinus.

Rats as potential reservoirs for neglected zoonotic Bartonella species in Flanders, Belgium.

BACKGROUND: Bartonella spp. are vector-borne pathogens transmitted to humans via blood-sucking arthropods. Rodents such as the black rat (Rattus rattus) and Norway rat (R. norvegicus) are thought to be the main reservoirs. An infection with rodent-associated Bartonella spp. may cause severe symptoms in humans such as endocarditis and neuroretinitis. The current knowledge of Bartonella prevalence in rats from western Europe is scarce. METHODS: Rats and a few other rodent by-catches were trapped in the context of a rodenticide resistance study at different sites in Flanders, Belgium. During dissection, biometric data were collected, and spleen tissues were taken. DNA was extracted from spleen samples and tested for Bartonella spp. by conventional generic polymerase chain reaction (PCR). To determine the Bartonella species, a selected number of amplicons were sequenced and compared with GenBank entries. RESULTS: In total, 1123 rodents were trapped. The predominate species was R. norvegicus (99.64%). Other rodents trapped included: two water voles (Arvicola amphibius, 0.18%); one colour rat (R. norvegicus forma domestica, 0.09%); and one muskrat (Ondatra zibethicus, 0.09%). PCR analysis of 1097 rodents resulted in 410 (37.37%, 95% CI: 34.50-40.31%) Bartonella spp. DNA-positive samples. Bartonella tribocorum (94.68%, 95% CI: 88.02-98.25%) was the most frequently detected Bartonella species, followed by B. grahamii (3.19%, 95% CI: 0.66-9.04%) and B. doshiae (1.06%, 95% CI: 0.03-5.79%). An uncultured Bartonella species occurred in one water vole (1.06%, 95% CI: 0.03-5.79%). There was a significantly higher Bartonella prevalence in older rats compared to juveniles and a significant difference in Bartonella prevalence concerning the localisation of trapping sites. In contrast, there was no statistically significant difference in Bartonella prevalence regarding sex, degree of urbanisation and season. CONCLUSIONS: Based on the high prevalence found, we conclude that the Norway rat seems to be a key reservoir host for zoonotic B. tribocorum in Belgium.

Modulation of gut microbiota in rats fed whole egg diets by processing duck egg to preserved egg.

Pidan, as the preserved duck egg, is a traditional alkaline-pickled food in China. Previous studies have suggested preserved egg white has an anti-inflammatory effect, though the mechanism of action was unclear. In this work, the difference of peptides distribution in the digestive products was identified from those of duck egg. The effects of preserved egg diet on the modulation of gut microbiota as well as the alteration in fecal metabolites were further investigated. Minor variations of gut microbiota in phylum level were observed between preserved and fresh duck egg diet groups, even though, preserved egg diet intake attributed to increases in the relative abundance of Prevotella and Phascolarctobacterium (p < 0.05), while Ruminococcaceae and Allobaculum were quantitatively decreased (p < 0.05). In terms of metabolites, the contents of acetic acid (p < 0.01) and propionic acid (p < 0.05) were significantly increased in the preserved egg diet group. It was speculated that the preserved egg diet might alter the proportion of short-chain fatty acids (SCFAs) in the gut of rats by modulating specific intestinal bacteria, and subsequently play an active role in anti-inflammatory effects. Compared to the fresh egg group, the bacterial produced SCFAs of preserved egg group were increased in abundance (p < 0.05), which may have potential anti-obesity and anti-inflammatory effects. The results provide a novel insight into the relationship between preserved egg intake, gut microbiota and potential positive effects on host health.

Antibiotic-resistant Escherichia coli isolated from urban rodents in Hanoi, Vietnam.

Antimicrobial resistance (AMR) is a global public health concern for both clinical and veterinary medicine. Rodent feces are one of the major infectious sources of zoonotic pathogens including AMR bacteria. So far, there are limited studies reported focused on Escherichia coli isolated in rodent feces from rural and suburban areas in Vietnam. In this study, we investigated the prevalence of antimicrobial resistance in E. coli isolated from feces samples of 144 urban rodents caught in Hanoi, Vietnam. A total of 59 AMR E. coli was isolated from urban rodents of which 42 were multidrug-resistant (MDR) isolates (resistance to at least three classes of antimicrobial agents), four were extended-spectrum ß-lactamase (ESBL) producing isolates and five were colistin-resistant isolates. The highest prevalence of the resistance was against ampicillin (79.7%: 47/59), followed by tetracycline (78.0%: 46/59), nalidixic acid (67.8%: 40/59), sulfamethoxazole-trimethoprim (59.3%: 35/59), chloramphenicol (45.8%: 27/59), ciprofloxacin (44.1%: 26/59), cefotaxime (30.5%: 18/59), cefodizime (23.7%: 14/59), amoxicillin-clavulanate (22.0%: 13/59), and gentamicin (22.0%: 13/59). With regard to the virulence genes associated with diarrheagenic E. coli (DEC), only aaiC gene found in one AMR isolate. In general, the use of antimicrobials does not aim to treat rodents except for companion animals. However, our findings show the carriage of AMR and MDR E. coli in urban rodents and highlight the potential risk of rodents in Hanoi acting as a reservoir of transferable MDR E. coli, including ESBL-producing, colistin-resistant E. coli, and virulence-associated with DEC.

Bartonella kosoyi sp. nov. and Bartonella krasnovii sp. nov., two novel species closely related to the zoonotic Bartonella elizabethae, isolated from black rats and wild desert rodent-fleas.

The genus Bartonella (Family: Bartonellaceae; Order: Rhizobiales; Class: Alphaproteobacteria) comprises facultative intracellular Gram-negative, haemotropic, slow-growing, vector-borne bacteria. Wild rodents and their fleas harbor a great diversity of species and strains of the genus Bartonella, including several zoonotic ones. This genetic diversity coupled with a fastidious nature of the organism results in a taxonomic challenge that has led to a massive collection of uncharacterized strains. Here, we report the genomic and phenotypic characterization of two strains, members of the genus Bartonella (namely Tel Aviv and OE 1-1), isolated from Rattus rattus rats and Synosternus cleopatrae fleas, respectively. Scanning electron microscopy revealed rod-shaped bacteria with polar pili, lengths ranging from 1.0 to 2.0 µm and widths ranging from 0.3 to 0.6 µm. OE 1-1 and Tel Aviv strains contained one single chromosome of 2.16 and 2.23 Mbp and one plasmid of 29.0 and 41.5 Kbp, with average DNA G+C contents of 38.16 and 38.47 mol%, respectively. These strains presented an average nucleotide identity (ANI) of 89.9 %. Bartonella elizabethae was found to be the closest phylogenetic relative of both strains (ANI=90.9-93.6 %). The major fatty acids identified in both strains were C18:1ω7c, C18 : 0 and C16 : 0. They differ from B. elizabethae in their C17 : 0 and C15 : 0 compositions. Both strains are strictly capnophilic and their biochemical profiles resembled those of species of the genus Bartonella with validly published names, whereas differences in arylamidase activities partially assisted in their speciation. Genomic and phenotypic differences demonstrate that OE 1-1 and Tel Aviv strains represent novel individual species, closely related to B. elizabethae, for which we propose the names Bartonella kosoyi sp. nov. and Bartonella krasnovii sp. nov.

Detection of Bartonella sp. in ticks and their small mammal hosts in mangrove forests of Peninsular Malaysia.

Bacteria of the genus Bartonella have been known as emerging zoonotic pathogens for several human diseases including cat scratch disease, Carrion's disease and trench fever. Numerous species of small mammals have been reported to play a role as a suitable reservoir to many pathogenic Bartonella. These infections are thought to be transmitted through blood-feeding arthropod vectors such as ticks, fleas and lice. The purpose of this study is to detect the presence of Bartonella species from tick samples collected from small mammals in mangrove forests of Peninsular Malaysia. Herein, 38 individual ticks and their small mammals host were evaluated for the presence of Bartonella DNA by conventional PCR targeting the 16S rRNA intergenic spacer region (ITS) and partial sequencing of 460 bp from this locususing Bartonella genus-specific primers. Two tick individuals from Dermacentor auratus and Haemaphysalis hystricis collected from Rattus tiomanicus (host), were PCR-positive for Bartonella DNA amplification. No Bartonella amplification was possible in other tick species (Amblyomma sp.). Phylogenetic analysis of ITS fragments demonstrated that the sequences from ticks were closely related to Bartonella phoceensis, a species that has been reported from black rats (Rattus rattus) in Australia. This is the first report of a Bartonella bacteria detected in ticks from small mammals in Malaysia. Further research should be warranted to investigate the transmission of Bartonella and the potential impact of this zoonotic pathogen in animals and humans as this mangrove ecosystem is significant for local economy and tourism.

Talaromyces atroroseus in HIV and non-HIV patient: A first report from Indonesia.

We performed morphology, molecular study and antifungal susceptibility test on 10 Talaromyces sp. isolates: eight clinical isolates (human immunodeficiency virus (HIV) and non-HIV-patient) and two isolates from rats. All strains produced red soluble pigment and microscopically showed Penicillium-like structure in room temperature and yeast-like structure in 37°C. Based on molecular analysis, nine isolates were identified as Talaromyces atroroseus (including the isolates from rats) and one as T. marneffei. Our susceptibility result of T. marneffei supports the use of amphotericin B, itraconazole for talaromycosis marneffei management. Talaromyces atroroseus showed variable MIC to echinocandin, azole derivatives, 5-flucytosine and amphotericin B.

Leptospira infection in rats: A literature review of global prevalence and distribution.

BACKGROUND: The role of rodents in Leptospira epidemiology and transmission is well known worldwide. Rats are known to carry different pathogenic serovars of Leptospira spp. capable of causing disease in humans and animals. Wild rats (Rattus spp.), especially the Norway/brown rat (Rattus norvegicus) and the black rat (R. rattus), are the most important sources of Leptospira infection, as they are abundant in urban and peridomestic environments. In this study, we compiled and summarized available data in the literature on global prevalence of Leptospira exposure and infection in rats, as well as compared the global distribution of Leptospira spp. in rats with respect to prevalence, geographic location, method of detection, diversity of serogroups/serovars, and species of rat. METHODS: We conducted a thorough literature search using PubMed without restrictions on publication date as well as Google Scholar to manually search for other relevant articles. Abstracts were included if they described data pertaining to Leptospira spp. in rats (Rattus spp.) from any geographic region around the world, including reviews. The data extracted from the articles selected included the author(s), year of publication, geographic location, method(s) of detection used, species of rat(s), sample size, prevalence of Leptospira spp. (overall and within each rat species), and information on species, serogroups, and/or serovars of Leptospira spp. detected. FINDINGS: A thorough search on PubMed retrieved 303 titles. After screening the articles for duplicates and inclusion/exclusion criteria, as well as manual inclusion of relevant articles, 145 articles were included in this review. Leptospira prevalence in rats varied considerably based on geographic location, with some reporting zero prevalence in countries such as Madagascar, Tanzania, and the Faroe Islands, and others reporting as high as >80% prevalence in studies done in Brazil, India, and the Philippines. The top five countries that were reported based on number of articles include India (n = 13), Malaysia (n = 9), Brazil (n = 8), Thailand (n = 7), and France (n = 6). Methods of detecting or isolating Leptospira spp. also varied among studies. Studies among different Rattus species reported a higher Leptospira prevalence in R. norvegicus. The serovar Icterohaemorrhagiae was the most prevalent serovar reported in Rattus spp. worldwide. Additionally, this literature review provided evidence for Leptospira infection in laboratory rodent colonies within controlled environments, implicating the zoonotic potential to laboratory animal caretakers. CONCLUSIONS: Reports on global distribution of Leptospira infection in rats varies widely, with considerably high prevalence reported in many countries. This literature review emphasizes the need for enhanced surveillance programs using standardized methods for assessing Leptospira exposure or infection in rats. This review also demonstrated several weaknesses to the current methods of reporting the prevalence of Leptospira spp. in rats worldwide. As such, this necessitates a call for standardized protocols for the testing and reporting of such studies, especially pertaining to the diagnostic methods used. A deeper understanding of the ecology and epidemiology of Leptospira spp. in rats in urban environments is warranted. It is also pertinent for rat control programs to be proposed in conjunction with increased efforts for public awareness and education regarding leptospirosis transmission and prevention.

Potential use of high-throughput sequencing of bacterial communities for postmortem submersion interval estimation.

Microorganisms play vital roles in the natural decomposition of carcasses in aquatic systems. Using high-throughput sequencing techniques, we evaluated the composition and succession of microbial communities throughout the decomposition of rat carcasses in freshwater. A total of 4,428,781 high-quality 16S rRNA gene sequences and 2144 operational taxonomic units were obtained. Further analysis revealed that the microbial composition differed significantly between the epinecrotic (rat skins) and the epilithic (rocks) samples. During the carcass decomposition process, Proteobacteria became the dominant phylum in the epinecrotic, epilithic, and environmental (water) samples, followed by Firmicutes in the epinecrotic samples and Bacteroidetes in the epilithic and water samples. Microbial communities were influenced by numerous environmental factors, such as dissolved oxygen content and conductivity. Our study provides new insight about postmortem submersion interval (PMSI) estimation in aquatic environments.

Bacterial species to be considered in quality assurance of mice and rats.

Bacteria are relevant in rodent quality assurance programmes if (a) the animals are at risk and (b) presence in the animals makes a difference for animal research or welfare, for example because the agent regulates clinical disease progression or impacts its host in other ways. Furthermore, zoonoses are relevant. Some bacterial species internationally recommended for the health monitoring of rats and mice, that is, Citrobacter rodentium, Corynebacterium kutscheri, Salmonella spp. and Streptococcus pneumonia, are no longer found in either laboratory or pet shop rats or mice, while there is still a real risk of impact on animal research and welfare from Filobacterium rodentium, Clostridium piliforme, Mycoplasma spp., Helicobacter spp. and Rodentibacter spp., while Streptobacillus moniliformis may be considered a serious zoonotic agent in spite of a very low risk. Modern molecular techniques have revealed that there may, depending on the research type, be equally good reasons for knowing the colony status of some commensal bacteria that are essential for the induction of specific rodent models, such as Alistipes spp., Akkermansia muciniphila, Bifidobacterium spp., Bacteroides fragilis, Bacteroides vulgatus, Faecalibacterium prausnitzii, Prevotella copri and segmented filamentous bacteria. In future, research groups should therefore consider the presence or absence of a short list of defined bacterial species relevant for their models. This list can be tested by cost-effective sequencing or even a simple multiple polymerase chain reaction approach, which is likely to be cost-neutral compared to more traditional screening methods.

Prevention and control of leptospirosis in people and surveillance of the pathogenic Leptospira in rats and in surface water found at villages.

BACKGROUND: Leptospirosis is a major public health problem in Thailand. This disease is caused by a Leptospira infection. Leptospira is found in rats and other animals that can contaminate soil and water resources. This research aimed to (1) study the perceptions and preventive measures taken to control leptospirosis among local populations and (2) to detect Leptospira in rats and natural surface water. METHODS: This cross-sectional study was performed in both villages with and without case histories of leptospirosis. The research procedures were divided into 2 parts. First, the perceptions and preventive measures for leptospirosis used data from 108 sampled subjects that were recruited in May 2015. Second, the rats and surface water samples were collected. DNA was extracted from collected samples and then specific genes specific to Leptospira were detected using PCR technique. RESULTS: The awareness of leptospirosis of samples in two villages was at high level with the same percentage being at 91.6%. However, the preventive behaviors to leptospirosis of participants from both villages were found to be at only the moderate level. Leptospira detection in rats and surface water used a PCR technique. There was no Leptospira found in any of the 270 rat samples and 100 surface water samples taken from both villages. CONCLUSION: Regardless, perception and preventive behaviors for dealing with leptospirosis should be continuously encouraged even when its presence is not detected. Clearly, people have to practice good behaviors for the prevention of this pathogen to be safe.

The rise of pneumonic plague in Madagascar: current plague outbreak breaks usual seasonal mould.

Madagascar has just emerged from the grip of an acute urban pneumonic plague outbreak, which began in August 2017, before the usual plague season of October-April and outside the traditional plague foci in the northern and central highlands. The World Health Organization reported a total of 2417 confirmed, probable and suspected cases, including 209 deaths between 1 August and 26 November 2017. The severity and scope of this outbreak, which has affected those in higher socioeconomic groups as well as those living in poverty, along with factors including the potential for use of multi-drug-resistant strains of plague in bioterrorism, highlights the ongoing threat posed by this ancient disease. Factors likely to have contributed to transmission include human behaviour, including burial practices and movement of people, poor urban planning leading to overcrowding and ready transmission by airborne droplets, climatic factors and genomic subtypes. The outbreak demonstrates the importance of identifying targeted pneumonic plague therapies and of developing vaccines that can be administered in planned programmes in developing countries such as Madagascar where plague is endemic. The dominance of pneumonic plague in this outbreak suggests that we need to focus more urgently on the danger of person-to-person transmission, as well as the problem of transmission of plague from zoonotic sources.

Effects of Probiotic Lactobacillus acidophilus Strain INMIA 9602 Er 317/402 and Putative Probiotic Lactobacilli on DNA Damages in the Small Intestine of Wistar Rats In Vivo.

Double-strand breaks in the DNA of the small intestine in male Wistar rats were studied using a neutral comet assay after 7 days of feeding with a single strain probiotic formulation Narine (Vitamax-E, Armenia), containing Lactobacillus acidophilus strain Er-2317/402 Narine, and putative probiotics L. rhamnosus Vahe and L. delbrueckii IAHAHI. Type 0 (undamaged DNA), type 1 (head diameter 13.18-17.08 µm), and type 2 (14.15-µm head diameter) damaged DNA comets were studied in control and lactobacilli-fed rats using the neutral comet assay. Lactobacilli-fed rats were shown to carry only type 0 (undamaged) DNA.Thus, the effects of probiotic Lactobacillus acidophilus strain INMIA 9602 Er 317/402 and putative probiotic lactobacilli on DNA damage in the small intestine of Wistar rats in vivo was shown, and the neutral comet assay is suggested as a potential tool for the in vivo selection of putative probiotics with DNA-protective activity.

Rat as an overlooked reservoir for Coxiella burnetii: A public health implication.

Q fever is a zoonosis with a mounting public health concern throughout the world. Rodents have been assumed to be a potential reservoir for Coxiella burnetii, a bacterium which causes Q fever. The current study was carried out to investigate the possible role of rats in the epidemiology of such disease. For this purpose, fecal samples were collected from 75 rats (55 Rattus norvegicus and 20 Rattus rattus) trapped from Giza governorate, Egypt. DNAs were extracted and samples were examined for the presence of C. burnetii using nested PCR technique. Out of examined rats, 5 yielded C. burnetii in their feces with an overall prevalence 6.7%, whereas the prevalence rates among R. norvegicus and R. rattus were (2/55) 3.6% and (3/20) 15% respectively. In addition, the phylogenetic analysis of three selected amplicons (2 R. rattus and one R. norvegicus) revealed that these sequences were highly related to each others and to those detected among humans. In conclusion, the results of the current study point out the role of rats as a potential reservoir for C. burnetii.

The spleen microbiota of small wild mammals reveals distinct patterns with tick-borne bacteria.

BACKGROUND: Wild mammals serve as reservoirs for a variety of microbes and play an important role in the enzootic cycles of these microbes. Some of them are vector-borne bacteria in the genera Anaplasma, Ehrlichia and Rickettsia of the order Rickettsiales, which can cause febrile illnesses in human beings as well as animals. Anaplasma spp., Ehrlichia spp. and many spotted fever group (SFG) Rickettsia spp. are transmitted to mammalian hosts by tick vectors during blood meals. As a powerful sequencing method, the next generation sequencing can reveal the complexity of bacterial communities in humans and animals. Compared with limited studies on blood microbiota, however, much fewer studies have been carried out on spleen microbiota, which is very scarce in wild mammals. Chongming Island is the third biggest island in China. It was unclear whether there were any vector-borne bacteria in Chongming Island. In the present study, we explored the bacterial microbiota in the spleens of wild mice and shrews from the rural areas of Chongming Island and investigated the prevalence of vector-borne bacteria. METHODOLOGY/PRINCIPAL FINDINGS: Genomic DNAs were extracted from the spleen samples of 35 mice and shrews. The 16S rDNA V3-V4 regions of the DNA extracts were amplified by PCR and subjected to the 16S rDNA-targeted metagenomic sequencing on an Illumina MiSeq platform. All the 35 spleen samples obtained data with sufficient coverage (99.7-99.9%) for analysis. More than 1,300,000 sequences were obtained after quality control and classified into a total of 1,967 operational taxonomic units (OTUs) clustered at 97% similarity. The two most abundant bacterial phyla were Firmicutes and Proteobacteria according to the analysis of rarefied sequences. Among the bacterial communities detected in this study, Anaplasma, Rickettsia and Coxiella were adjacently clustered by hierarchical analysis. Significant differences in many bacterial features between Anaplasma-positive and Anaplasma-negative samples were identified by LEfSe analysis and Wilcoxon rank-sum test, suggesting that the Anaplasma-infection of small wild mammals was associated with a specific pattern of spleen microbiota. CONCLUSIONS/SIGNIFICANCE: Our study has comprehensively characterized the complex bacterial profiles in the spleens of wild mice and shrews from Chongming Island, Shanghai city. This work has revealed distinct spleen bacterial communities associated with tick-borne bacteria in wild animals. The detection of tick-borne bacteria highlights the risk of contracting pathogens with public health importance upon tick-exposure in the studied areas.

Bifidobacterium pseudolongum in the Ceca of Rats Fed Hi-Maize Starch Has Characteristics of a Keystone Species in Bifidobacterial Blooms.

Starches resistant to mammalian digestion are present in foods and pass to the large bowel, where they may be degraded and fermented by the microbiota. Increases in relative abundances of bifidobacteria (blooms) have been reported in rats whose diet was supplemented with Hi-Maize resistant starch. We determined that the bifidobacterial species present in the rat cecum under these circumstances mostly belonged to Bifidobacterium animalis However, cultures of B. animalis isolated from the rats failed to degrade Hi-Maize starch to any extent. In contrast, Bifidobacterium pseudolongum also detected in the rat microbiota had high starch-degrading ability. Transcriptional comparisons showed increased expression of a type 1 pullulanase, alpha-amylase, and glycogen debranching enzyme by B. pseudolongum when cultured in medium containing Hi-Maize starch. Maltose was released into the culture medium, and B. animalis cultures had shorter doubling times in maltose medium than did B. pseudolongum Thus, B. pseudolongum, which was present at a consistently low abundance in the microbiota, but which has extensive enzymatic capacity to degrade resistant starch, showed the attributes of a keystone species associated with the bifidobacterial bloom.IMPORTANCE This study addresses the microbiology and function of a natural ecosystem (the rat gut) using DNA-based observations and in vitro experimentation. The microbial community of the large bowel of animals, including humans, has been studied extensively through the use of high-throughput DNA sequencing methods and advanced bioinformatics analysis. These studies reveal the compositions and genetic capacities of microbiotas but not the intricacies of how microbial communities function. Our work, combining DNA sequence analysis and laboratory experiments with cultured strains of bacteria, revealed that the increased abundance of bifidobacteria in the rat gut, induced by feeding indigestible starch, involved a species that cannot itself degrade the starch (Bifidobacterium animalis) but cohabits with a species that can (Bifidobacterium pseudolongum). B. pseudolongum has the characteristics of a keystone species in the community because it had low abundance but high ability to perform a critical function, the hydrolysis of resistant starch.