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Background: Rat models are valuable tools to study the lung microbiota in diseases. Yet the impacts of different lung parts, young and mature adult stages, and the different batches of the same conditions on the healthy rat lung microbiome have not been investigated., Methods: The rat lung microbiome was analyzed to clarify the lung part-dependent and age-dependent differences and to evaluate the effects of several 'batch environmental factors' on normal rats, after eliminating potential contamination., Results: The results showed that the contamination could be identified and excluded. The lung microbiome from left and right lung parts was very similar so one representative part could be used in the microbiome study. There were significantly different lung microbial communities between the young and mature adult groups, and also between the different feeding batches groups of the same repetitive feeding conditions, but a common lung microbiota characterized by Firmicutes , Bacteroidetes , Proteobacteria , and Actinobacteria as the most dominant phyla were present in all adult rats. It indicated that the experiment under the same condition of the same rats batch was needed to compare the difference in the lung microbiota and repeated experiments were necessary to confirm the results., Conclusion: These data represented that the lung bacterial communities were dynamic and rapidly susceptible to environmental influence, clustered strongly by age or different feeding batches but similar in the different lung tissue parts. This study improved the basic understanding of the potential effects on the lung microbiome of healthy rats.

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 ipa H gene, of which eight and five were positive for S. sonnei and S. boydii , respectively. For Salmonella , 68 isolates were positive for inv A and other genes including spy with 26 (38%), sdf I 2 (18%), spv C 14 (20%), hil A 28 (41%), mis L 43 (63%), orf L 31 (46%) and spi C 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.

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 1625/19 T revealed distinct genome-to-genome distance values to the other Rodentibacter species. The genomic DNA G+C content of strain 1625/19 T 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 β-haemolysis and are β-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 1625/19 T , (=DSM 111151 T =CCM 9081 T ), was isolated in 2019 from the nose of a laboratory mouse ( Mus musculus ) in Düsseldorf, Germany.

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, bla TEM (95.8%) and bla aadA-1 (58.3%) had the highest frequency, while bla KPC , and bla CMY-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.

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., (© Wildlife Disease Association 2021.)

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.

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.

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., (Copyright © 2020 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.)

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., (© The Author(s) 2019. Published by Oxford University Press on behalf of The International Society for Human and Animal Mycology.)

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 β-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.

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.

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 C 18:1 ω7 c , C 18 : 0 and C 16 : 0 . They differ from B. elizabethae in their C 17 : 0 and C 15 : 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.

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.

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.

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., (Copyright © 2019 The Authors. Published by Elsevier Ltd.. All rights reserved.)

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., Competing Interests: The authors have declared that no competing interests exist.

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.

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.

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., (Copyright © 2018 Elsevier Ltd. All rights reserved.)

Rat bite fever due to Streptobacillus moniliformis induces typical but not pathognomonic clinical signs, such as local purulent wound infection followed by maculopapular exanthema, myalgia as well as purulent joint infections. Severe complications, such as osteomyelitis and endocarditis are possible. it seems that this infection is rarely diagnosed but this infection could be much more common because the final diagnostic proof is difficult to achieve. Firstly, the culture of these bacteria is critical because the bacteria are fastidious and secondly the exact differentiation of the isolates is hardly possible by standard laboratory methods. Modern techniques such as mass spectroscopy (MALDI-TOF) and molecular biology allow a precise clarification. Surgical cleansing of infection sites in combination with a rational antibiotic therapy, for example with beta-lactam antibiotics, are generally able to cure the infection if treatment is started early enough. In addition, vaccinations, for example against tetanus and rabies have to be considered in this situation as for all other bite wound infections.

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., (Copyright © 2018 American Society for Microbiology.)

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., Competing Interests: The authors have declared that no competing interests exist.

Analysis of whole genome sequencing data uncovered a previously undetected outbreak of Salmonella Enteritidis that had been on-going for four years. Cases were resident in all countries of the United Kingdom and 40% of the cases were aged less than 11 years old. Initial investigations revealed that 30% of cases reported exposure to pet snakes. A case-control study was designed to test the hypothesis that exposure to reptiles or their feed were risk factors. A robust case-definition, based on the single nucleotide polymorphism (SNP) profile, increased the power of the analytical study. Following univariable and multivariable analysis, exposure to snakes was the only variable independently associated with infection (Odds ratio 810 95% CI (85-7715) p < 0.001). Isolates of S. Enteritidis belonging to the outbreak profile were recovered from reptile feeder mice sampled at the retail and wholesale level. Control measures included improved public health messaging at point of sale, press releases and engagement with public health and veterinary counterparts across Europe. Mice destined to be fed to reptiles are not regarded as pet food and are not routinely tested for pathogenic bacteria. Routine microbiological testing to ensure feeder mice are free from Salmonella is recommended., (Crown Copyright © 2017. Published by Elsevier Ltd. All rights reserved.)

This study investigated the host response to a polymicrobial pulpal infection consisting of Streptococcus anginosus and Enterococcus faecalis , bacteria commonly implicated in dental abscesses and endodontic failure, using a validated ex vivo rat tooth model. Tooth slices were inoculated with planktonic cultures of S. anginosus or E. faecalis alone or in coculture at S. anginosus / E. faecalis ratios of 50:50 and 90:10. Attachment was semiquantified by measuring the area covered by fluorescently labeled bacteria. Host response was established by viable histological cell counts, and inflammatory response was measured using reverse transcription-quantitative PCR (RT-qPCR) and immunohistochemistry. A significant reduction in cell viability was observed for single and polymicrobial infections, with no significant differences between infection types (∼2,000 cells/mm 2 for infected pulps compared to ∼4,000 cells/mm 2 for uninfected pulps). E. faecalis demonstrated significantly higher levels of attachment (6.5%) than S. anginosus alone (2.3%) and mixed-species infections (3.4% for 50:50 and 2.3% for 90:10), with a remarkable affinity for the pulpal vasculature. Infections with E. faecalis demonstrated the greatest increase in tumor necrosis factor alpha (TNF-α) (47.1-fold for E. faecalis , 14.6-fold for S. anginosus , 60.1-fold for 50:50, and 25.0-fold for 90:10) and interleukin 1β (IL-1β) expression (54.8-fold for E. faecalis , 8.8-fold for S. anginosus , 54.5-fold for 50:50, and 39.9-fold for 90:10) compared to uninfected samples. Immunohistochemistry confirmed this, with the majority of inflammation localized to the pulpal vasculature and odontoblast regions. Interestingly, E. faecalis supernatant and heat-killed E. faecalis treatments were unable to induce the same inflammatory response, suggesting E. faecalis pathogenicity in pulpitis is linked to its greater ability to attach to the pulpal vasculature., (Copyright © 2018 American Society for Microbiology.)

Weaning is an essential and important event for infants and rodent animals, and the dietary supplementation plays a crucial role in regulating the composition and function of gut microbiota in the initial period after weaning. In this study, we investigated the potential effects of two probiotics along with three polysaccharides (PP) in weaned rats. Male SD rats, 21 days of age, were divided into two groups: one group was administered with PP for four weeks and the other was not. Body weight, food intake, gut epithelial barrier function, digestive enzyme activities, and the composition and function of gut microbiota were analyzed. The dietary PP increased the body weight and food intake, promoted gut epithelial barrier integrity, and elevated the activities of digestive enzymes. Moreover, the microbial community structure was different between the two groups. At the genus level, Bifidobacterium, Lactobacillus, and Allobaculum were significantly increased, whereas Anaerostipes, Enterococcus, and Parabacteroides were observably reduced. Furthermore, PP significantly increased amino acid metabolism, energy metabolism, and SCFA-related metabolism. This study shows that synbiotics containing probiotics (L. acidophilus NCFM and B. lactis Bi-07) in combination with polysaccharides (LBP, PCPs, and Lentinan) can modulate the composition of gut microbiota, stimulate the maturation of gut microbiota biological function, and promote the growth performance in weaned rats.

Introduction: Leptospirosis remains a major public health threat in Cambodia. In this study, we aimed at facilitating the development of preventive strategies against leptospirosis in Cambodia by conducting molecular epidemiological surveys of Leptospira infection among wild rodents., Materials and Methods: One hundred sixty-three wild rodents were captured in the capital Phnom Penh and surrounding areas, and their kidneys and bladders were collected for analysis. Identification of wild rodent species was determined by using the cytochrome c oxidase I gene. TaqMan PCR of the flagellin B gene (flaB) was performed to detect Leptospira, and species of the isolates were identified by flaB sequencing analysis., Results: The species and respective number of rodents collected were as follows: Rattus norvegicus, 80 (49.1%); Rattus argentiventer, 53 (32.5%); Rattus exulans, 6 (3.7%); Rattus indica, 15 (9.2%); Maxomys surifer, 3 (1.8%); and Rattus sp., 6 (3.7%). Leptospira was detected in 20 out of the 163 rodents (12.3%) and was categorized as either Leptospira interrogans or Leptospira noguchii. R. norvegicus had the highest prevalence of Leptospira (17.5%), and R. argentiventer and Rattus sp. showed infection rates of 9.4% and 16.7%, respectively., Conclusions: Based on these results, wild rodents living in urban areas of Cambodia were found to be important reservoirs of highly virulent Leptospira. The flaB sequence results of our study provided information regarding the prevalence of Leptospira species, which was dependent on the rodent species. This study is the first study on leptospirosis in wild rodents in the urban areas of Cambodia, where there is limited information on leptospirosis.

Three strains, CLM-U50 T , CLM-R50 and IVIC-Bov1, belonging to the genus Leptospira, were isolated in Venezuela from a patient with leptospirosis, a domestic rat (Rattus norvegicus) and a cow (Bos taurus), respectively. The initial characterisation of these strains based on the rrs gene (16S rRNA) suggested their designation as a novel species within the 'intermediates' group of the genus Leptospira. Further phylogenomic characterisation based on single copy core genes was consistent with their separation into a novel species. The average nucleotide identity between these three strains was >99 %, but below 89 % with respect to any previously described leptospiral species, also supporting their designation as a novel species. Given this evidence, these three isolates were considered to represent a novel species, for which the name Leptospiravenezuelensis sp. nov. is proposed, with CLM-U50 T (=CIP 111407 T =DSM 105752 T ) as the type strain.

Plague, primarily a disease of rodents, is most frequently transmitted by fleas and causes potentially fatal infections in humans. In Uganda, plague is endemic to the West Nile region. Primary prevention for plague includes control of rodent hosts or flea vectors, but targeting these efforts is difficult given the sporadic nature of plague epizootics in the region and limited resource availability. Here, we present a community-based strategy to detect and report rodent deaths (rat fall), an early sign of epizootics. Laboratory testing of rodent carcasses is used to trigger primary and secondary prevention measures: indoor residual spraying (IRS) and community-based plague education, respectively. During the first 3 years of the program, individuals from 142 villages reported 580 small mammal deaths; 24 of these tested presumptive positive for Yersinia pestis by fluorescence microscopy. In response, for each of the 17 affected communities, village-wide IRS was conducted to control rodent-associated fleas within homes, and community sensitization was conducted to raise awareness of plague signs and prevention strategies. No additional presumptive Y. pestis -positive carcasses were detected in these villages within the 2-month expected duration of residual activity for the insecticide used in IRS. Despite comparatively high historic case counts, no human plague cases were reported from villages participating in the surveillance program; five cases were reported from elsewhere in the districts. We evaluate community participation and timeliness of response, report the frequency of human plague cases in participating and surrounding villages, and evaluate whether a program such as this could provide a sustainable model for plague prevention in endemic areas.

Global reports of emergent pathogens in humans have intensified efforts to identify wildlife reservoirs. Subterranean mammals, such as bathyergid mole rats, are largely overlooked, despite their high-level exposure to soil-dwelling microbes. Initial assessment of bathyergid reservoir potential was determined using a broad-range 16S rRNA PCR approach, which revealed an 83% PCR-positivity for the 234 bathyergid lung samples evaluated. The presence of the Bacillus cereus complex, a ubiquitous bacterial assemblage, containing pathogenic and zoonotic species, was confirmed through nucleotide sequencing, prior to group- and species-specific PCR sequencing. The latter allowed for enhanced placement and prevalence estimations of Bacillus in four bathyergid species sampled across a range of transformed landscapes in the Western Cape Province, South Africa. Two novel Bacillus strains (1 and 2) identified on the basis of the concatenated 16S rRNA-groEL-yeaC data set (2066 nucleotides in length), clustered with B. mycoides (ATCC 6462) and B. weihenstephanensis (WSBC 10204), within a well-supported monophyletic lineage. The levels of co-infection, evaluated with a groEL strain-specific assay, developed specifically for this purpose, were high (71%). The overall Bacillus presence of 17.95% (ranging from 0% for Georychus capensis to 45.35% for Bathyergus suillus) differed significantly between host species (χ 2  = 69.643; df = 3; P < 0.05), being significantly higher in bathyergids sampled near an urban informal settlement (χ 2  = 70.245; df = 3; P < 0.05). The results highlight the sentinel potential of soil-dwelling mammals for monitoring anthropogenically introduced, opportunistic pathogens and the threats they pose to vulnerable communities, particularly in the developing world.

Kocuria marina has recently emerged as a cause for catheter-related bloodstream infections in patients with underlying health complications. One K. marina strain was recently isolated from the lung tissues of a wild urban rat (Rattus rattus diardii) caught during rodent surveillance. Here, we present the draft genome of the first K. marina animal isolate, K. marina TRE150902.

Changes in host-parasite ecological interactions during biological invasion events may affect both the outcome of invasions and the dynamics of exotic and/or endemic infections. We tested these hypotheses, by investigating ongoing house mouse (Mus musculus domesticus) and black rat (Rattus rattus) invasions in Senegal (West Africa). We used a 16S gene rRNA amplicon sequencing approach to study potentially zoonotic bacterial communities in invasive and native rodents sampled along two well-defined independent invasion routes. We found that individual host factors (body mass and sex) were important drivers of these bacterial infections in rodents. We observed that the bacterial communities varied along invasion routes and differed between invasive and native rodents, with native rodents displaying higher overall bacterial diversity than invasive rodents. Differences in prevalence levels for some bacterial Operational Taxonomic Units (OTUs) provided support for ecological processes connecting parasitism and invasion success. Finally, our results indicated that rodent invasions may lead to the introduction of exotic bacterial genera and/or to changes in the prevalence of endemic ones. This study illustrates the difficulty of predicting the relationship between biodiversity and disease risks, and advocate for public health prevention strategies based on global pathogen surveillance followed by accurate characterization of potential zoonotic agents.

This study was undertaken to investigate drug resistance in Escherichia coli (E. coli) strains isolated from bamboo rats in Zhejiang province of China. One hundred and fifty-four E. coli strains were isolated from dead bamboo rats. Polymerase chain reaction (PCR) was used to detect the representative genes encoding resistance to commonly used β-lactam antibiotics. Highest resistance was observed for cefradine (24.03%), followed by penicillin (20.78%) and ceftazidime (20.13%). The isolation rates of β-lactam resistance genes were 53.25, 48.70, 15.58 and 14.29% for bla TEM , bla CTX-M , bla OXA and bla SHV , respectively, while 62 (40.26%) E. coli isolates harbored multiple β-lactam resistance genes. These results also suggested that long term use of these antibiotics leads to antibimicrobial resistance. We believe that this study will provide a guideline for veterinarians and a research basis for examining resistance-encoding genes in other food animals like bamboo rats.

Knowledge of pathogen ecology, including the impacts of environmental factors on pathogen and host dynamics, is essential for determining the risk that zoonotic pathogens pose to people. This review synthesizes the scientific literature on environmental factors that influence the ecology and epidemiology of zoonotic microparasites (bacteria, viruses and protozoa) in globally invasive urban exploiter wildlife species (i.e., rock doves [Columba livia domestica], European starlings [Sturnus vulgaris], house sparrows [Passer domesticus], Norway rats [Rattus norvegicus], black rats [R. rattus] and house mice [Mus musculus]). Pathogen ecology, including prevalence and pathogen characteristics, is influenced by geographical location, habitat, season and weather. The prevalence of zoonotic pathogens in mice and rats varies markedly over short geographical distances, but tends to be highest in ports, disadvantaged (e.g., low income) and residential areas. Future research should use epidemiological approaches, including random sampling and robust statistical analyses, to evaluate a range of biotic and abiotic environmental factors at spatial scales suitable for host home range sizes. Moving beyond descriptive studies to uncover the causal factors contributing to uneven pathogen distribution among wildlife hosts in urban environments may lead to targeted surveillance and intervention strategies. Application of this knowledge to urban maintenance and planning may reduce the potential impacts of urban wildlife-associated zoonotic diseases on people.

Cryptosporidium spp. is an important causative agent of intestinal parasitoses-induced diarrhoea in humans and animals worldwide. Rodents (small mammals), the main reservoir of infections, are globally expanded and overpopulated, which increases the risk of transfer of human and zoonotic pathogens from the genus Cryptosporidium. In this study, Cryptosporidium was detected in wild immunocompetent asymptomatic small mammals. Altogether 262 fecal samples were collected from five areas in Eastern Slovakia from four different rodent species (Myodes glareolus, Apodemus agrarius, Apodemus flavicollis, Rattus norvegicus), eight samples originated from two insectivore species (Sorex araneus, Crocidura suaveolens), and two sample from a carnivore Mustela nivalis. The samples were examined using a method modified in our laboratory, based on the use of specific primers on a small subunit rRNA (18S rRNA) gene for species identification, and amplification of GP60 gene coding 60-kDa glycoprotein for genotype determination. The following species were identified: Cryptosporidium parvum (n=15), genotypes IIaA18G3R1 (n=11; KU311673), IIaA10G1R1 (n=1; KU311670), IIcA5G3a (n=1; KU311669), IIiA10 (n=2; KU311672); Cryptosporidium suis (n=4; KU311671); Cryptosporidium scrofarum (n=28); Cryptosporidium environment sp. (n=12; KU311677); Cryptosporidium muskrat genotype I (n=3; KU311675); Cryptosporidium muskrat genotype II (n=3; KU311676). From one of the rodent, the species Cryptosporidium hominis genotype IbA10G2 (KU311668) was identified for the first time. The results of this study indicate low host specificity of the detected Cryptosporidium species and imply the importance of free-living small mammals in urban and suburban habitats as a potential source of human cryptosporidiosis., (Copyright © 2017. Published by Elsevier B.V.)

Background: A study was conducted to confirm the status of rats as the carrier of pathogenic leptospira in Kuala Lumpur, Malaysia., Method: A total of 140 urine samples were collected from trapped rats. These samples were cultured in EMJH enriched media and 18 of these samples (12.9%) were found to be positive when observed under x40 by dark field microscope. Genomic DNA was extracted from all the 18 native isolates for PCR., Result: All the 18 isolates generated the expected 786 base pair band when the set of primers known to amplify LipL32 gene were utilized. These results showed that the primers were suitable to be used for the identification of pathogenic leptospira from the 18 rat samples., Conclusion: The sequencing of the PCR products and BLAST analysis performed on each representative isolates confirmed the pathogenic status of all these native isolates as the LipL32 gene was detected in all the Leptospira isolates. This indicates that the rats are carriers of the pathogenic leptospira in the study area, and therefore are of public health importance.

We examined 33 rodents captured in an urban area of Osaka City, Japan for IgG antibodies against Seoul virus, severe fever with thrombocytopenia syndrome virus, hepatitis E virus, Leptospira interrogans, Yersinia pestis, spotted fever, typhus and scrub typhus group rickettsiae. We found that 3 (9.1%) and 1 (3.0%) of the 33 rodents had antibodies against L. interrogans and spotted fever group rickettsiae, respectively. DNAs of leptospires were detected from 2 of the 3 seropositive rodents, but DNA of rickettsia was not detected. Phylogenetic analysis and multiple locus sequence typing revealed that the 2 leptospires were L. interrogans belonging to a novel sequence type. There is a potential risk for acquiring rodent-borne zoonotic pathogens even in cities in developed countries.

Different species of rodents are potential transmitters of multiple zoonotic agents such as Leptospira spp., a spirochete that causes leptospirosis. This is an infectious disease that has a negative impact on pig production because it generates large productive, reproductive and economic losses. In swine farms, the most common rodent species are house mice (Mus musculus), brown rats (Rattus norvegicus) and black rats (Rattus rattus), which act as maintenance hosts for different serovars of Leptospira, contaminating the environment, food and water through urine, and putting human and animal health at risk. For this reason, the objective of this article is to describe the role of rodents in the transmission of Leptospira in swine farms. For this purpose, a bibliographic search was carried out in different databases such as Science Direct, Scopus, Redalyc, PubMed and SciELO. The results of the literature review show that there are few studies that report the importance of rodents in the transmission of Leptospira in swine farms. The onset of the disease depends to a large extent on the presence, contact and control of rodents in farms, although environmental factors, agent survival and hygiene, among others, must also be considered.

Background: Rickettsiae are obligate intracellular bacteria responsible for many febrile syndromes around the world, including in sub-Saharan Africa. Vectors of these pathogens include ticks, lice, mites and fleas. In order to assess exposure to flea-associated Rickettsia species in Madagascar, human and small mammal samples from an urban and a rural area, and their associated fleas were tested., Results: Anti-typhus group (TGR)- and anti-spotted fever group rickettsiae (SFGR)-specific IgG were detected in 24 (39%) and 21 (34%) of 62 human serum samples, respectively, using indirect ELISAs, with six individuals seropositive for both. Only two (2%) Rattus rattus out of 86 small mammals presented antibodies against TGR. Out of 117 fleas collected from small mammals, Rickettsia typhi, a TGR, was detected in 26 Xenopsylla cheopis (24%) collected from rodents of an urban area (n = 107), while two of these urban X. cheopis (2%) were positive for Rickettsia felis, a SFGR. R. felis DNA was also detected in eight (31%) out of 26 Pulex irritans fleas., Conclusions: The general population in Madagascar are exposed to rickettsiae, and two flea-associated Rickettsia pathogens, R. typhi and R. felis, are present near or in homes. Although our results are from a single district, they demonstrate that rickettsiae should be considered as potential agents of undifferentiated fever in Madagascar.

Leptospirosis is mainly considered an occupational disease, prevalent among agriculture, sewage works, forestry, and animal slaughtering populations. However, putative risk to miners and their inclusion in the high-risk leptospirosis group remain in need of rigorous analysis. Therefore, a study was conducted with the objective to assess the leptospirosis seroprevalence among miners of two districts of Tamil Nadu, India. A total of 244 sera samples from Pudukkottai miners (124) and Karur miners (120) were analyzed by microscopic agglutination test. Antibodies to leptospires were detected in 94 samples giving an overall seroprevalence of 38.5%. The seroprevalence was higher among Pudukkottai miners (65.3%) when compared with Karur miners (10.8%). Seroprevalence among control population (13%) was significantly less than that of the Pudukkottai miners marking a possible high-risk population group distinction. Subject sera most commonly reacted with organisms of the serogroup Autumnalis, and the pattern was similar in carrier animals of the study areas. Two leptospires were isolated from kidney samples of rats. The prevalence of Autumnalis among rodents and humans source tracked human leptospirosis among the miners. The study also determined that Pudukkottai miners are subjected to high-risk challenges such as exposure to water bodies on the way to the mines (odds ratio [OR] = 10.6), wet mine areas (OR = 10.6), rat infestation (OR = 4.6), and cattle rearing (OR = 10.4) and are thus frequently exposed to leptospirosis compared with Karur miners. Hence, control strategies targeting these populations will likely to prove to be effective remediation strategies benefiting Pudukkottai miners and workers in similar environments across occupations., (© The American Society of Tropical Medicine and Hygiene.)

An indole-, oxidase- and catalase-negative, non-motile bacterium, strain OGS16T, was isolated from an oral swab of a feral black rat (Rattus rattus) in 2007 in Japan. It stained Gram-negative and had pleomorphic, rod-shaped, non-spore-forming cells. Based on 16S rRNA gene sequence analyses, strain OGS16T was assigned to the genus Streptobacillus, with 16S rRNA gene sequence similarities of 99.3, 99.0, 98.6 and 95.5% to the type strains of Streptobacillus moniliformis, Streptobacillus notomytis, Streptobacillus felis and Streptobacillus hongkongensis, respectively. Strain OGS16T could also be differentiated clearly from other species of the genus Streptobacillus by rpoB, groEL and recA nucleotide and deduced amino acid sequence analysis. DNA-DNA relatedness as obtained by average nucleotide identity was 89.10% between strain OGS16T and Streptobacillus moniliformis DSM 12112T. Chemotaxonomic and physiological data for strain OGS16T were congruent with results for other closely related members of the family Leptotrichiaceae, represented by highly similar enzyme profiles and fatty acid patterns. MALDI-TOF MS analysis also proved suitable in discriminating strain OGS16T unequivocally from all currently described taxa of the genus Streptobacillus. On the basis of these data, we propose the novel species Streptobacillus ratti sp. nov., with the type strain OGS16T (=JCM 31098T=DSM 101843T). The G+C content of the DNA of the type strain is 25.9 mol% and the genome size is 1.50 Mbp.

Bacteria of the genus Bartonella have been described in multiple mammalian hosts with many species capable of causing disease in humans. Cats and various species of rats have been reported to play a role as vertebrate hosts to a number of Bartonella spp. This study aimed to identify Bartonella spp. in Western Australia, Dirk Hartog Island (DHI), and Christmas Island (CI) and to investigate the presence of potential arthropod vectors. Feral cats were collected from CI (n = 35), DHI (n = 23) and southwest Western Australia (swWA; n = 58), and black rats were collected from CI (n = 48). Individuals were necropsied, ectoparasites were collected by external examination of carcasses, and splenic tissue was collected for polymerase chain reaction analysis to detect Bartonella DNA. Bartonella henselae DNA was detected from two cats and Bartonella koehlerae DNA from one cat in southwest WA, but Bartonella DNA was not identified in cats on DHI or CI. Bartonella phoceensis (28/48 = 58.3%) and a novel Bartonella genotype (8/48 = 16.7%) based on the internal transcribed space region were detected in the spleens of black rats on CI. Detection of Bartonella spp. in each location corresponded to the presence of ectoparasites. Cats from southwest WA harbored four species of fleas, including Ctenocephalides felis, and black rats on CI were infested with multiple species of ectoparasites, including mites, fleas, and lice. Conversely, cats on Dirk Hartog and CI were free of ectoparasites. This study has identified the DNA of Bartonella species from island and mainland swWA with some (B. henselae and B. koehlerae) of known zoonotic importance. This study further extends the geographical range for the pathogenic B. koehlerae. The association of Bartonella with ectoparasites is unsurprising, but little is known about the specific vector competence of the ectoparasites identified in this study.

We report herein the investigation of a leptospirosis outbreak occurring in triathlon competitors on Réunion Island, Indian Ocean. All participants were contacted by phone or email and answered a questionnaire. Detection and molecular characterization of pathogenic Leptospira was conducted in inpatients and in rodents trapped at the vicinity of the event. Of the 160 athletes competing, 101 (63·1%) agreed to participate in the study. Leptospirosis was biologically confirmed for 9/10 suspected cases either by real-time PCR or serological tests (MAT or ELISA). The total attack rate, children's attack rate, swimmers' attack rate, and the attack rate in adult swimmers were respectively estimated at 8·1% [95% confidence interval (CI) 4·3-14·7], 0%, 12·7% (95% CI 6·8-22·4) and 23·1% (95% CI 12·6-33·8). Leptospirosis cases reported significantly more wounds [risk ratio (RR) 4·5, 95% CI 1·6-13], wore complete neoprene suits less often (RR 4·3, 95% CI 1·3-14·5) and were most frequently unlicensed (RR 6·6, 95% CI 2·9-14·8). The epidemiological investigation supported that some measures such as the use of neoprene suits proved efficient in protecting swimmers against infection. PCR detection in rats revealed high Leptospira infection rates. Partial sequencing of the 16S gene and serology on both human and animal samples strongly suggests that rats were the main contaminators and were likely at the origin of the infection in humans.

Background: Urban leptospirosis has increasingly been reported in both developing and developed countries. The control of the disease is limited because our understanding of basic aspects of the epidemiology, including the transmission routes of leptospires among rat populations, remains incomplete. Through the ability to distinguish among Leptospira strains in rats, multispacer sequence typing (MST) could provide a modern understanding of Leptospira epidemiology; however, to our knowledge, the distribution of Leptospira strains among urban rat colonies has not been investigated using MST., Aims and Methodology: The objective of this study was to identify the Leptospira strains present in rats (Rattus norvegicus) in Lyon (France) using MST and to characterize their spatial distribution. Kidneys and urine were collected from rats trapped live in seven locations in the city and in one suburban location. Each location was considered to represent a rat colony. Bacterial cultures and quantitative polymerase chain reaction (qPCR) assays were performed, and the L. interrogans DNA identified was then genotyped using MST. The distributions of Leptospira strains were spatially described., Key Results: Among 84 wild rats, MST profiles were obtained in 35 of 37 rats that had a positive result for L. interrogans by bacterial culture and/or qPCR analyses. All of the MST profiles were related to reference strains previously isolated from human patients that belong to the serogroup Icterohaemorrhagiae and the serovars [strain(s)] Copenhageni [Wijinberg or M20] (n = 26), Icterohaemorrhagiae [CHU Réunion] (n = 7), Icterohaemorrhagiae [R1] (n = 1) and Copenhageni [Shibaura 9] (n = 1). Each colony was infected with leptospires having the same MST profile., Major Conclusions: This study demonstrated that MST could be used for the purpose of field studies, either on culture isolates or on DNA extracted from kidneys and urine, to distinguish among L. interrogans isolates in rats. MST could thus be used to monitor their distributions in urban rats from the same city, thereby providing new knowledge that could be applied to explore the circulation of L. interrogans infection in rat colonies. Because the strains are related to those previously found in humans, this application of MST could aid in the source tracking of human leptospirosis, and the findings would be relevant for public health purposes according to the One Health principle.

Indigenous bacteria in the alimentary tract are exposed to various bactericidal peptides and digestive enzymes, but the viability status and morphological changes of indigenous bacteria are unclear. Therefore, the present study aimed to ultrastructurally clarify the degeneration and viability status of indigenous bacteria in the rat intestine. The majority of indigenous bacteria in the ileal mucous layer possessed intact cytoplasm, but the cytoplasm of a few bacteria contained vacuoles. The vacuoles were more frequently found in bacteria of ileal chyme than in those of ileal mucous layer and were found in a large majority of bacteria in both the mucous layer and chyme throughout the large intestine. In the dividing bacteria of the mucous layer and chyme throughout the intestine, the ratio of area occupied by vacuoles was almost always less than 10%. Lysis or detachment of the cell wall in the indigenous bacteria was more frequently found in the large intestine than in the ileum, whereas bacterial remnants, such as cell walls, were distributed almost evenly throughout the intestine. In an experimental control of long-time-cultured Staphylococcus epidermidis on agar, similar vacuoles were also found, but cell-wall degeneration was never observed. From these findings, indigenous bacteria in the mucous layer were ultrastructurally confirmed to be the source of indigenous bacteria in the chyme. Furthermore, the results suggested that indigenous bacteria were more severely degenerated toward the large intestine and were probably degraded in the intestine.

Although rat feces are widely suspected to be a source of pathogenic bacteria, few investigators have studied fecal pathogens in rats. We investigated the prevalence and characteristics of Escherichia coli and Salmonella spp. in Norway and black rats (Rattus norvegicus and Rattus rattus, respectively) from an urban neighborhood of Vancouver, Canada, collected September 2011-August 2012. Colon content was cultured for E. coli and Salmonella spp. and screened for the seven most-common enteropathogenic Shiga toxin-producing E. coli (STEC) serotypes by PCR. Isolates were tested for antimicrobial resistance and Salmonella isolates were serotyped. We detected E. coli in 397/633 (62.7%) urban rats. Forty-one of 397 (6.5%) E. coli isolates were resistant to ≥ 1 antimicrobial while 17 (4.3%) were multidrug resistant (including two isolates demonstrating extended-spectrum β-lactamase resistance). Ten of 633 (1.6%) urban rats were carrying STEC serotypes including O145, O103, O26, and O45. Norway rats were more likely to be carrying E. coli compared to black rats, and there was geographic clustering of specific resistance patterns and STEC serotypes. Salmonella spp. were detected in 3/633 (0.5%) rats including serotypes Derby, Indiana, and Enteritidis. In contrast to zoonotic pathogens for which rats are the natural reservoir (e.g., Leptospira interrogans, Rickettsia typhi, Seoul virus), rats likely acquired E. coli and Salmonella spp. from their environment. The ability of rats to be a 'sponge' for environmental pathogens has received little consideration, and the ecology and public health significance of these organisms in rats requires further investigation.

Control eradication campaigns of bovine tuberculosis based on the «test and slaughter» approach were successful in many countries and regions; however, in some areas the infection persists and one of the main reasons is Mycobacterium bovis infection in wild life species. Argentina has applied the same approach since 1999, achieving progress in dairy cattle herds. Nonetheless, the wildlife role has never been investigated. The objective of this study was to determine if wildlife from the Santa Fe dairy area is infected with M. bovis. Wildlife species having a positive tuberculin skin test were captured in five dairy farms. Ninety five wildlife mammals were captured; M. bovis was recovered from 7 possums (Didelphys albiventris), from one fox (Lycolapex gimnocercus) and from one rat (Rattus norvegicus). None of the animals exhibited macroscopic lesions. The most frequently isolated M. bovis spoligotypes were types 34 (4 isolates) and 12 (3 isolates). Spoligotype 34 is the most frequently isolated type in Argentine cattle. The role of D. albiventris as spillover host of M. bovis is discussed in this study., (Copyright © 2015 Asociación Argentina de Microbiología. Publicado por Elsevier España, S.L.U. All rights reserved.)

Background: Leptospirosis is a widespread but underreported cause of morbidity and mortality. It has rarely been reported in either humans or animals in Madagascar., Methods: We conducted a cross-sectional survey of the inhabitants in Moramanga, Madagascar, in June 2011, to estimate the prevalence of human infection using the microscopic agglutination test (MAT). This activity was carried out as part of a workshop implemented by the Pasteur Institute of Madagascar, focusing on surveillance with a one week field study and targeting the health staff of the district level., Results: In total, we sampled 678 inhabitants from 263 households. The sex ratio (M/F) was 0.65 and the mean age 26.7 years. We obtained a value of 2.9% for the first recorded seroprevalence of this disease in the human community of Moramanga. Questionnaire responses revealed frequent contacts between humans and rodents in Moramanga. However, activities involving cattle were identified as a risk factor significantly associated with seropositivity (OR=3)., Conclusion: Leptospirosis remains a neglected disease in Madagascar. This study highlights the need to quantify the public health impact of this neglected disease in a more large scale, in all the country and to establish point-of-care laboratories in remote areas.

Several rodent-associated Bartonella species are human pathogens but little is known about their epidemiology. We trapped rodents and shrews around human habitations at two sites in Kenya (rural Asembo and urban Kibera) to determine the prevalence of Bartonella infection. Bartonella were detected by culture in five of seven host species. In Kibera, 60% of Rattus rattus were positive, as compared to 13% in Asembo. Bartonella were also detected in C. olivieri (7%), Lemniscomys striatus (50%), Mastomys natalensis (43%) and R. norvegicus (50%). Partial sequencing of the citrate synthase (gltA) gene of isolates showed that Kibera strains were similar to reference isolates from Rattus trapped in Asia, America, and Europe, but that most strains from Asembo were less similar. Host species and trapping location were associated with differences in infection status but there was no evidence of associations between host age or sex and infection status. Acute febrile illness occurs at high incidence in both Asembo and Kibera but the etiology of many of these illnesses is unknown. Bartonella similar to known human pathogens were detected in small mammals at both sites and investigation of the ecological determinants of host infection status and of the public health significance of Bartonella infections at these locations is warranted.

Mycoplasma haemomuris is causative of infectious anaemia or splenomegaly in rodents. We examined the nucleotide sequences of the non-ribosomal genes, rnpB and dnaK, in strains of the species M. haemomuris detected in small field mice and black rats. rnpB nucleotide sequences in strains of the species M. haemomuris isolated from small field mice and black rats had only 89 % sequence similarity, suggesting their separation into two distinct subgroups. dnaK had a nucleotide sequence similarity of 84 % between the subgroups. These results support the classification of M. haemomuris into two genetically distinct subgroups. Here we propose the establishment of these subgroups as 'Candidatus Mycoplasma haemomuris subsp. musculi', detected in small field mice (Apodemus argenteus), and 'Candidatus Mycoplasma haemomuris subsp. ratti', detected in black rats (Rattus rattus)., (© 2015 IUMS.)