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New Microbes and New Infections

A H L Bruning, H Aatola, H Toivola, N Ikonen, C Savolainen-Kopra, S Blomqvist, D Pajkrt, K C Wolthers, J O Koskinen
Human coronaviruses (CoVs) are increasingly recognized as important respiratory pathogens associated with a broad range of clinical diseases. We sought to increase the insight into clinically relevant CoV infections by monitoring antigen concentrations in six confirmed CoV-positive patients using a newly developed assay for rapid detection of CoV OC43 infections. Antigen positivity lasted 3 to 6 days in secondary infections and 13 days in primary infection. CoV infections are clinically diverse, are common, and cannot be diagnosed from clinical symptoms alone...
July 2018: New Microbes and New Infections
M A Washington, A E Jerse, N Rahman, M Pilligua-Lucas, E C Garges, N H Latif, T Akhvlediani
Antimicrobial resistance in Neisseria gonorrhoeae is a global health problem. Enhanced international collaborative surveillance and disease control are needed to reduce the global burden of this important pathogen. Currently the antimicrobial resistance properties and molecular mechanisms of multidrug-resistant N. gonorrhoeae in the Republic of Georgia represent a significant knowledge gap. Here we report the isolation of a strain of N. gonorrhoeae exhibiting resistance to cefixime and ciprofloxacin with reduced susceptibility to penicillin and tetracycline from a patient being treated at a Georgian medical centre...
July 2018: New Microbes and New Infections
A Melan, M S Aung, F Khanam, S K Paul, B K Riaz, S Tahmina, M I Kabir, M A Hossain, N Kobayashi
Chikungunya viruses from the 2017 outbreak in Dhaka, Bangladesh, were analysed phylogenetically. E1 sequences from 21 strains belonged to the Indian Ocean clade of the East/Central/South African (ECSA) genotype, forming a novel cluster with latest South Asian strains. They lacked the A226V substitution.
July 2018: New Microbes and New Infections
M Beye, S Bakour, E Le Dault, J Rathored, C Michelle, F Cadoret, D Raoult, P-E Fournier
Strain EL1T was isolated from a sinus sample of an 85-year-old man with chronic refractory sinusitis complicating ethmoidal adenocarcinoma. We studied its phenotypic and genomic characteristics. This is a Gram stain-positive, anaerobic and microaerophilic coccus. Cells are catalase negative, nonmotile and non-spore forming. The major fatty acids are saturated hexadecanoic acid (34%), unsaturated 9-octadecenoic acid (32%) and 9.12-octadecadienoic acid (21%). The 1.86 Mb long genome exhibits a 29.9% G+C content and contains 1750 protein-coding and 43 RNA genes...
May 2018: New Microbes and New Infections
E H Seck, A Diop, N Armstrong, J Delerce, P-E Fournier, D Raoult, S Khelaifia
Bacillus salis strain ES3T (= CSUR P1478 = DSM 100598) is the type strain of B. salis sp. nov. It is an aerobic, Gram-positive, moderately halophilic, motile and spore-forming bacterium. It was isolated from commercial table salt as part of a broad culturomics study aiming to maximize the culture conditions for the in-depth exploration of halophilic bacteria in salty food. Here we describe the phenotypic characteristics of this isolate, its complete genome sequence and annotation, together with a comparison with closely related bacteria...
May 2018: New Microbes and New Infections
I Lafri, W Benredjem, F Neffah-Baaziz, R Lalout, K Abdelouahed, B Gassen, S Bakhouch, M Chergui, M Karakellah, H Adjmi-Hamoudi, I Bitam
Argasid ticks include vectors of relapsing fevers caused by Borrelia spp. in humans, and they can transmit arboviruses and other bacterial pathogens. Knowledge about soft ticks ( Ixodida: Argasidae ) in Algeria is incomplete, and distribution data need to be updated. Here we report a series of entomologic investigations that we conducted in five different areas in Algeria between 2012 and 2015. Ticks were identified by entomologic keys and molecular tools (16S rRNA gene). Six distinct species belonging to two genera were identified, including Ornithodoros capensis s...
May 2018: New Microbes and New Infections
D A Raele, D Galante, N Pugliese, G La Salandra, M Lomuto, M Assunta Cafiero
The poultry red mite (PRM), Dermanyssus gallinae, is a nonburrowing haematophagous nest-dwelling ectoparasite of birds; occasionally it bites humans, inducing dermatitis. The possibility that this parasite may also be involved in transmission of pathogens is an additional concern. We investigated the presence of zoonotic agents in PRMs from bird nests and pets, and related them to urban outbreaks of dermatitis. A total of 98 PRMs from 12 outbreaks of PRM dermatitis that occurred in Italian cities from 2001 to 2017 were molecularly investigated for detection of Coxiella spp...
May 2018: New Microbes and New Infections
S N Shpynov, P-E Fournier, N N Pozdnichenko, A S Gumenuk, A A Skiba
The development of a formal order analysis (FOA) allowed constructing a classification of 49 genomes of Rickettsiaceae family representatives. Recently FOA has been extended with new tools-'Map of genes,' 'Matrix of similarity' and 'Locality-sensitive hashing'-for a more in-depth study of the structure of rickettsial genomes. The new classification confirmed and supplemented the previously constructed one by determining the position of Rickettsia africae str. ESF-5, R. heilongjiangensis 054, R. monacensis str...
May 2018: New Microbes and New Infections
S N Shpynov, I V Tarasevich, A A Skiba, N N Pozdnichenko, A S Gumenuk
The  Coxiella burnetii strain NL3262 was isolated during the Q fever outbreak in the Netherlands in 2007-2010. Formal-order analysis (FOA) was used to study the similarity of the genome (chromosome and plasmid) of this strain with the genomes from other strains. Chromosomes from ten C. burnetii strains and eight plasmids were studied with FOA tools such as 'Map of genes' and 'Matrix of similarity.' The 'Map of genes' tool showed that the chromosome of strain C. burnetii str. NL3262 distanced itself by the index of average remoteness ( g ) of 1...
May 2018: New Microbes and New Infections
C Ndiaye, H Bassène, F Cadoret, D Raoult, J C Lagier, C Sokhna
We report the main characteristics of ' Citricoccus massiliensis 'strain Marseille-P4330, a new species within the genus Citricoccus. This strain was isolated from the skin of a healthy human man living in Dielmo, Senegal, Western Africa.
May 2018: New Microbes and New Infections
C Al-Bayssari, G Dubourg, T Cimmino, L Okdah, N Mathlouthi, T T Nguyen, C Andrieu, J Rathored, P-E Fournier, D Raoult, J-M Rolain
Paenibacillus ihuae strain GD6 (=CSUR P892 = DSMZ 45751T ) is the new type strain collected from the stool of a 69-year-old Frenchman admitted to an intensive care unit and receiving a 10-day course of imipenem at the time of stool collection. This is a Gram-positive, facultative anaerobic, rod-shaped bacterium. We describe here the features of this organism, together with its complete genome sequence and annotation. The genome size is 6 719 043 bp with 49.6% G+C content and contains 6211 protein-coding and 65 sRNA genes, including four 5S rRNA genes, one 16S rRNA gene and one 23S rRNA gene...
May 2018: New Microbes and New Infections
C-C Chao, B O Ingram, W Lurchachaiwong, W-M Ching
Scrub typhus is an acute zoonosis caused by the obligate intracellular Gram-negative bacterium Orientia tsutsugamushi. To better understand the host response elicited by natural infection by chigger feeding, ICR mice were infected by Leptotrombidium chiangraiensis (Lc1) chiggers, and the metabolic profiles of their serum were examined over several time points after initiation of feeding. ICR mice were infected by either naive Lc1 chiggers (i.e. not infected by O. tsutsugamushi, NLc1) or O. tsutsugamushi -infected Lc1 chiggers (OLc1)...
May 2018: New Microbes and New Infections
Mohamed Amine Ouidri
A study was performed of Staphylococcus aureus and methicillin-resistant S. aureus (MRSA) strains isolated from nasal preoperative samples. Of 663 samples assessed, staphylococcus was detected in 143 (21.57%). The disc diffusion method (cefoxitin 30 μg), a screening test (oxacillin 6 μg/mL) and a search for Protein Binding Additional Penicillin 2 (PLP2a) allowed the detection and confirmation of resistance to methicillin for 36 strains, a rate of 5.43% of the total population studied. Eight MRSA carriers received care in the trauma service, 14 in cardiology, five in ear, nose and throat, four in neurosurgery and paediatrics, and one in SCI...
May 2018: New Microbes and New Infections
U Garza-Ramos, H Barrios-Camacho, S Moreno-Domínguez, J Toribio-Jiménez, D Jardón-Pineda, J Cuevas-Peña, A Sánchez-Pérez, J Duran-Bedolla, J Olguín-Rodriguez, A Román-Román
Klebsiella spp. isolates from community-acquired infections were characterized. A total of 39 Klebsiella spp. isolates were obtained from outpatients at four rural hospitals in Mexico (2013-2014). The biochemical tests identified all as being K. pneumoniae . The molecular multiplex-PCR test identified 36 (92.4%) K. pneumoniae isolates and one (2.5%) K. variicola isolate, and phylogenetic analysis of the rpoB gene identified two isolates (5.1%) belonging to K. quasipneumoniae subsp. quasipneumoniae and K...
May 2018: New Microbes and New Infections
S Ndongo, F Bittar, M Beye, C Robert, F Di Pinto, P-E Fournier, D Raoult, J-C Lagier
'Cellulomonas timonensis' sp. nov. strain sn7T is a new species within the Cellulomonas genus. We present the main phenotypic characteristics and provide a complete annotation of its genome sequence. This facultative anaerobic bacterium, isolated from the stool of 38-year-old obese Frenchman, is Gram-positive, has motile rods and is sporulating. The genome is 4 057 828 bp long with 72.42% G + C content. Of the 3732 predicted genes, 3667 were protein-coding genes and 65 were RNAs.
May 2018: New Microbes and New Infections
P-E Fournier
No abstract text is available yet for this article.
May 2018: New Microbes and New Infections
M Vouga, C Kebbi-Beghdadi, J Liénard, L Baskin, D Baud, G Greub
Waddlia   chondrophila and Simkania negevensis are emerging Chlamydia- related bacteria. Similar to the pathogenic organisms Chlamydia pneumoniae and Chlamydia trachomatis, these emerging bacteria are implicated in human genital infections and respiratory diseases. We used a screening strategy based on a newly developed S. negevensis -specific quantitative real-time PCR (qPCR) and a pan- Chlamydiales qPCR. We could not detect S. negevensis in 458 respiratory, genitourinary, cardiac and hepatic samples tested...
May 2018: New Microbes and New Infections
S Ndongo, J-C Lagier, D Raoult, P-E Fournier
We report the main characteristics of Gorillibacterium timonense strain SN4T sp. nov. and Vitreoscilla massiliensis strain SN6T sp. nov., two new bacterial species isolated from stool specimens of obese Amazonian patients.
May 2018: New Microbes and New Infections
N Dione, I I Ngom, C Valles, F Cadoret, P E Fournier, D Raoult, J C Lagier
We report here the main characteristics of 'Collinsella provencensis' strain Marseille-P3740 (CSUR P3740), 'Parabacteroides bouchesdurhonensis' strain Marseille-P3763 (CSUR P3763) and 'Sutterella seckii' strain Marseille-P3660 (CSUR P3660), which were isolated using culturomics from the human gut microbiota of healthy individuals living in Marseille.
May 2018: New Microbes and New Infections
A Torri, S Bertini, P Schiavone, F Congestrì, M Matteucci, M Sparacino, G Testa, M F Pedna, V Sambri
Shewanella algae are Gram-negative, nonfermentative, motile bacilli, classified in the genus Shewanella in 1985. These environmental bacteria are occasionally identified in human infections, with a relatively strong association with exposure to seawater during warm seasons. This report describes a case series of 17 patients with infection correlated to S. algae in the coastal area of Romagna, Italy, from 2013 to 2016. The types of infection included otitis, pneumonia, sepsis and soft tissue (wound). Exposure to the marine environment during hot months was confirmed in 12 of 17 patients...
May 2018: New Microbes and New Infections
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