Emerging Fatal Ib/CC12 Hypervirulent Multiresistant Streptococcus agalactiae in Young Infants With Bloodstream Infection in China

Streptococcus agalactiae [also known as group B Streptococcus (GBS)] is a tremendous threat to young infants. Eighty pediatric GBS infection cases were enrolled from a teaching hospital in Shanghai between 2009 and 2020; among them, 72.5% (58/80) were diagnosed with bloodstream infection (BSI). Sequence types (STs) and serotypes of associated GBS strains were identified, and most of the Ib/clonal complex (CC)12 (86.7%, 13/15) strains caused BSIs, which was significantly higher than that of the genetically related clone Ib/CC10 (20%, 2/10; p < 0.05). Ib/CC12 BSI (30.8%) mortality was significantly higher than that of non-Ib/CC12 BSI (2.2%; p < 0.05). Virulence genes associated with adhesion, invasion, and immune evasion were detected using polymerase chain reaction. The fbsA and gbsPC1 positive rates of Ib/CC12 strains was higher than that of non-Ib/CC12 strains, whereas cpsIaJ, cpsJ, cpsI, and cpsG positive rates were lower than those of non-Ib/CC12 (p < 0.05). In in vitro studies, the Ib/CC12 strains had strong invasiveness in RAW264.7 cells, but less invasiveness in human umbilical vein endothelial cells, human brain microvascular endothelial cells, and human mammary epithelial cells when compared to other two clones. In the in vivo model, the Ib/CC12 GBS invaded the circulation system more rapidly after intraperitoneal injection, was more difficult to eradicate by phagocytes, and caused significantly higher mortality than Ib/CC10 and III/ST17 (p < 0.05). Genome analysis showed that the Ib/CC12 strains had two clustered regularly interspaced short palindromic repeat-Cas systems and carried more antibiotic resistant genes, which conferred resistance to macrolides, clindamycin, aminoglycosides, and tetracycline. The Ib/CC12 strains had 45 unique annotated genes compared to that of Ib/CC10, including the pathogen-related toxin/antitoxin system, PezA/T. In conclusion, Ib/CC12 is an emerging hypervirulent multiresistant GBS clone that causes invasive and fatal infections in pediatric patients. The prevention and control of Ib/CC12 GBS infection should be emphasized.

Prototype endogenous avian retroviruses of the genus Gallus

Ancient endogenous retroviruses (ERVs), designated endogenous avian retrovirus (EAVs), are present in all Gallus spp. including the chicken, and resemble the modern avian sarcoma and leukosis viruses (ASLVs). The EAVs comprise several distinct retroviruses, including EAV-0, EAV-E51 and EAV-HP, as well as a putative member previously named the avian retrotransposon of chickens (ART-CH). Thus far, only the EAV-HP elements have been well characterized. Here, we determined sequences of representative EAV-0 and EAV-E51 proviruses by cloning and data mining of the 2011 assembly of the Gallus gallus genome. Although the EAV-0 elements are primarily deleted in the env region, we identified two complete EAV-0 env genes within the G. gallus genome and prototype elements sharing identity with an EAV-E51-related clone previously designated EAV-E33. Prototype EAV-0, EAV-E51 and EAV-E33 gag, pol and env gene sequences used for phylogenetic analysis of deduced proteins showed that the EAVs formed three distinct clades, with EAV-0 sharing the last common ancestor with the ASLVs. The EAV-E51 clade showed the greatest level of divergence compared with other EAVs or ASLVs, suggesting that these ERVs represented exogenous retroviruses that evolved and integrated into the germline over a long period of time. Moreover, the degree of divergence between the chicken and red jungle fowl EAV-E51 sequences suggested that they were more ancient than the other EAVs and may have diverged through mutations that accumulated post-integration. Finally, we showed that the ART-CH elements were chimeric defective ERVs comprising portions of EAV-E51 and EAV-HP rather than authentic retrotransposons.

Identification of Mn(II)-Oxidizing Bacteria from a Low-pH Contaminated Former Uranium Mine

ABSTRACTBiological Mn oxidation is responsible for producing highly reactive and abundant Mn oxide phases in the environment that can mitigate metal contamination. However, little is known about Mn oxidation in low-pH environments, where metal contamination often is a problem as the result of mining activities. We isolated two Mn(II)-oxidizing bacteria (MOB) at pH 5.5 (Duganellaisolate AB_14 andAlbidiferaxisolate TB-2) and nine strains at pH 7 from a former uranium mining site. Isolate TB-2 may contribute to Mn oxidation in the acidic Mn-rich subsoil, as a closely related clone represented 16% of the total community. All isolates oxidized Mn over a small pH range, and isolates from low-pH samples only oxidized Mn below pH 6. Two strains with different pH optima differed in their Fe requirements for Mn oxidation, suggesting that Mn oxidation by the strain found at neutral pH was linked to Fe oxidation. Isolates tolerated Ni, Cu, and Cd and produced Mn oxides with similarities to todorokite and birnessite, with the latter being present in subsurface layers where metal enrichment was associated with Mn oxides. This demonstrates that MOB can be involved in the formation of biogenic Mn oxides in both moderately acidic and neutral pH environments.

Uncovering a Microbial Enigma: Isolation and Characterization of the Streamer-Generating, Iron-Oxidizing, Acidophilic Bacterium “Ferrovum myxofaciens”

ABSTRACTA betaproteobacterium, shown by molecular techniques to have widespread global distribution in extremely acidic (pH 2 to 4) ferruginous mine waters and also to be a major component of “acid streamer” growths in mine-impacted water bodies, has proven to be recalcitrant to enrichment and isolation. A modified “overlay” solid medium was devised and used to isolate this bacterium from a number of mine water samples. The physiological and phylogenetic characteristics of a pure culture of an isolate from an abandoned copper mine (“Ferrovum myxofaciens” strain P3G) have been elucidated. “F. myxofaciens” is an extremely acidophilic, psychrotolerant obligate autotroph that appears to use only ferrous iron as an electron donor and oxygen as an electron acceptor. It appears to use the Calvin-Benson-Bassham pathway to fix CO2and is diazotrophic. It also produces copious amounts of extracellular polymeric materials that cause cells to attach to each other (and to form small streamer-like growthin vitro) and to different solid surfaces. “F. myxofaciens” can catalyze the oxidative dissolution of pyrite and, like many other acidophiles, is tolerant of many (cationic) transition metals. “F. myxofaciens” and related clone sequences form a monophyletic group within theBetaproteobacteriadistantly related to classified orders, with genera of the familyNitrosomonadaceae(lithoautotrophic, ammonium-oxidizing neutrophiles) as the closest relatives. On the basis of the phylogenetic and phenotypic differences of “F. myxofaciens” and otherBetaproteobacteria, a new family, “Ferrovaceae,” and order, “Ferrovales,” within the classBetaproteobacteriaare proposed. “F. myxofaciens” is the first extreme acidophile to be described in the classBetaproteobacteria.

Ecophysiology of Fe-Cycling Bacteria in Acidic Sediments

ABSTRACT Using a combination of cultivation-dependent and -independent methods, this study aimed to elucidate the diversity of microorganisms involved in iron cycling and to resolve their in situ functional links in sediments of an acidic lignite mine lake. Using six different media with pH values ranging from 2.5 to 4.3, 117 isolates were obtained that grouped into 38 different strains, including 27 putative new species with respect to the closest characterized strains. Among the isolated strains, 22 strains were able to oxidize Fe(II), 34 were able to reduce Fe(III) in schwertmannite, the dominant iron oxide in this lake, and 21 could do both. All isolates falling into the Gammaproteobacteria (an unknown Dyella-like genus and Acidithiobacillus-related strains) were obtained from the top acidic sediment zones (pH 2.8). Firmicutes strains (related to Bacillus and Alicyclobacillus) were only isolated from deep, moderately acidic sediment zones (pH 4 to 5). Of the Alphaproteobacteria, Acidocella-related strains were only isolated from acidic zones, whereas Acidiphilium-related strains were isolated from all sediment depths. Bacterial clone libraries generally supported and complemented these patterns. Geobacter-related clone sequences were only obtained from deep sediment zones, and Geobacter-specific quantitative PCR yielded 8 × 105 gene copy numbers. Isolates related to the Acidobacterium, Acidocella, and Alicyclobacillus genera and to the unknown Dyella-like genus showed a broad pH tolerance, ranging from 2.5 to 5.0, and preferred schwertmannite to goethite for Fe(III) reduction. This study highlighted the variety of acidophilic microorganisms that are responsible for iron cycling in acidic environments, extending the results of recent laboratory-based studies that showed this trait to be widespread among acidophiles.

Phenotypic and Molecular Analysis of Penicillin-Nonsusceptible Streptococcus pneumoniae Isolates in Poland

ABSTRACT β-Lactams are the drugs of choice for the treatment of infections caused by the important bacterial pathogen Streptococcus pneumoniae. The recent growth of resistance of this organism to penicillin observed worldwide is of the highest concern. In this study, using 887 surveillance pneumococcal isolates recovered in Poland from 1998 to 2002, we observed the increase in penicillin nonsusceptibility from 8.7% to 20.3%. All of the 109 penicillin-nonsusceptible S. pneumoniae (PNSP) isolates identified, together with 22 archival PNSP isolates from 1995 to 1997, were subsequently analyzed by susceptibility testing, serotyping, profiling of pbp genes, pulsed-field gel electrophoresis, and multilocus sequence typing (MLST). Four predominant serotypes, serotypes 6B, 9V, 14, and 23F, characterized 85.5% of the isolates. MLST revealed the presence of 34 sequence types, 15 of which were novel types. Representatives of seven multiresistant international clones (Spain23F-1, Spain6B-2, Spain9V-3, Taiwan23F-15, Poland23F-16, Poland6B-20, and Sweden15A-25) or their closely related variants comprised the majority of the study isolates. The spread of Spain9V-3 and its related clone of serotype 14/ST143 has remarkably contributed to the recent increase in penicillin resistance in pneumococci in the country.

Antimicrobial Susceptibilities and Epidemiological Analysis of Salmonella Enteritidis Isolates in Korea by Phage Typing and Pulsed-Field Gel Electrophoresis

A total of 81 isolates of Salmonella Enteritidis were analyzed by antibiotic susceptibility, phage typing, and pulsed-field gel electrophoresis (PFGE). Thirty-two isolates came from broiler carcasses and pig feces, and 49 isolates were from humans in Seoul and suburbs of Seoul, Korea. Antibiotic resistance was most prevalent among human isolates. Of human isolates, 89.8% were resistant to more than two antibiotics, while 64.7% of poultry isolates and 13.3% of pig isolates showed multiple resistance to more than two antibiotics. The most common phage type (PT) was PT1, followed by PT30 or 33, PT21 and PT20a. The isolates showed six PFGE patterns with XbaI or SpeI digestion, and five PFGE patterns with NotI digestion. But a single pattern, PFGE X1, S1, or N1, was predominant and the rest of the PFGE patterns differed by only one or two bands. Results indicated the spread of a genetically related clone of Salmonella Enteritidis in foods and humans in Korea and that phage typing as well as PFGE may offer an improved level of discrimination for the epidemiological investigation of Salmonella Enteritidis.