Carriage and Transmission of mcr-1 in Salmonella Typhimurium and Its Monophasic 1,4,[5],12:i:- Variants from Diarrheal Outpatients: a 10-Year Genomic Epidemiology in Guangdong, Southern China.

The banning of colistin as a feed additive for food-producing animals in mainland China in 2017 caused the decline in the prevalence of Escherichia coli-mobilized colistin resistance (mcr-1) in China. Salmonella Typhimurium and its monophasic 1,4,[5],12:i:- variants are also the main species associated with the spread of mcr-1; however, the evidence of the prevalence and transmission of mcr-1 among Salmonella is lacking. Herein, the 5,354 Salmonella isolates recovered from fecal samples of diarrheal patients in Guangdong, Southern China, from 2009 to 2019 were screened for colistin resistance and mcr-1, and mcr-1-positive isolates were characterized based on whole-genome sequencing (WGS) data. Relatively high prevalence rates of colistin resistance and mcr-1 (4.05%/4.50%) were identified, and more importantly, the prevalence trends of colistin-resistant and mcr-1-positive Salmonella isolates had a similar dynamic profile, i.e., both were first detected in 2012 and rapidly increased during 2013 to 2016, followed by a sharp decrease since 2017. WGS and phylogenetic analysis indicate that, whether before or after the ban, the persistence and cross-hospital transmission of mcr-1 are primarily determined by IncHI2 plasmids with similar backbones and sequence type 34 (ST34) Salmonella in specific clades that are associated with a high prevalence of IncHI2 plasmids and clinically important antimicrobial resistance genes, including blaCTX-M-14-fosA3-oqxAB-floR genotypes. Our work reveals the difference in the prevalence rate of mcr-1 in clinical Salmonella before and after the Chinese colistin ban, whereas mcr-1 transmission was closely linked to multidrug-resistant IncHI2 plasmid and ST34 Salmonella across diverse hospitals over 10 years. Continued surveillance is required to explore the factors related to a sharp decrease in mcr-1 after the recent ban and determine whether the ban has affected the carriage of mcr-1 in Salmonella circulating in the health care system. IMPORTANCE Colistin is one of the last-line antibiotics for the clinical treatment of Enterobacteriaceae. However, the emergence of the mobilized colistin resistance (mcr-1) gene has spread throughout the entire human health system and largely threatens the usage of colistin in the clinical setting. In this study, we investigated the existence of mcr-1 in clinical Salmonella from a 10-year continuous surveillance and genomic study. Overall, the colistin resistance rate and mcr-1 carriage of Salmonella in tertiary hospitals in Guangdong (2009 to 2019) were relatively high and, importantly, rapidly increased from 2013 to 2016 and significantly decreased after the Chinese colistin withdrawal. However, before or after the ban, the MDR IncHI2 plasmid with a similar backbone and ST34 Salmonella were the main vectors involved in the spread of mcr-1. Interestingly, these Chinese mcr-1-carrying Salmonella obtain phylogenetically and phylogeographically distinct patterns compared with those from other continents and are frequently associated with clinically important ARGs including the extended-spectrum ß-lactamases. Our data confirmed that the national stewardship intervention seems to be successful in blocking antibiotic resistance determinants and that continued surveillance of colistin resistance in clinical settings, farm animals, and related products is necessary.

High Genetic Plasticity in Multidrug-Resistant Sequence Type 3-IncHI2 Plasmids Revealed by Sequence Comparison and Phylogenetic Analysis.

We report a novel fusion plasmid, pP2-3T, cointegrating sequence type 3 (ST3)-IncHI2 with an IncFII plasmid backbone mediating multidrug resistance (MDR) and virulence. Phylogenetic analysis and comparative genomics revealed that pP2-3T and other MDR ST3-IncHI2 plasmids clustered together, representing a unique IncHI2 lineage that exhibited high conservation in backbones of plasmids but possessed highly genetic plasticity in various regions by acquiring numerous antibiotic resistance genes and fusing with other plasmids. Surveillance studies should be performed to monitor multiresistance IncHI2 plasmids among Enterobacteriaceae.

Intragenomic polymorphism and intergenomic recombination in the ribosomal RNA genes of strains belonging to a yeast species Pichia membranifaciens.

A concerted evolution model has been proposed to explain the observed lack of sequence variation among the multiple ribosomal RNA (rRNA) gene copies in many different eukaryotic species. Recent studies on the level of intragenomic variations in the rRNA gene repeats of fungi resulted in controversial conclusions. In this study, we clearly showed that significant polymorphisms of the internal transcribed spacers (ITS1 and ITS2) of ribosomal DNA (rDNA) exist within the genome of a strain of the yeast species Pichia membranifaciens. More interestingly, we showed that the intragenomic ITS sequence polymorphisms were formed by intergenomic rDNA recombination among different P. membranifaciens strains with significantly different ITS sequences. Intergenomic rDNA recombination was also responsible for the diversification of rDNA sequences in different strains of the species. After the events bring together different rDNA types in individual genomes of the P. membranifaciens strains compared, rDNA sequence heterogeneity has remained in the genome of one but eliminated by homogenisation in the genomes of other strains. Our findings show new clue for further investigation on the mechanism of concerted evolution of rRNA genes in eukaryotes.

Candida tibetensis sp. nov. and Candida linzhiensis sp. nov., novel anamorphic, ascomycetous yeast species from Tibet.

Three anamorphic, ascomycetous yeast strains isolated from plant samples collected in Linzhi District, Tibet, China, were revealed as representing two novel species by 26S rRNA gene D1/D2 domain sequence and physiological property comparisons. The names Candida tibetensis sp. nov. and Candida linzhiensis sp. nov. are proposed for these novel species, with XZ 41-6T (=AS 2.3072T=CBS 10298T) and XZ 92-1T (=AS 2.3073T=CBS 10299T) as the respective type strains. D1/D2 sequence analysis showed that C. tibetensis and C. linzhiensis are closely related to Candida caryicola and Candida sequanensis, respectively.

Genetic diversity of the Pichia membranifaciens strains revealed from rRNA gene sequencing and electrophoretic karyotyping, and the proposal of Candida californica comb. nov.

The genetic diversity of the types or authentic strains of 20 facultative synonyms of Pichia membranifaciens (E.C. Hansen) E.C. Hansen was revealed on the basis of large-subunit (26S) rDNA D1/D2 domain and internal transcribed spacer region sequencing and electrophoretic karyotyping. At least five separate species were recognized among the strains studied. Fourteen strains were confirmed to belong to P. membranifaciens. Strain CBS 241, an authentic strain of Zygosaccharomyces chevalieri Guilliermond var. fermentati Saito, should be assigned to Pichia manshurica Santa María. Strain CBS 243, an authentic strain of Zygopichia chiantigiana Castelli, is conspecific with CBS 2287, the type strain of Pichia fluxuum (Phaff & Knapp) Kreger-van Rij. Strain CBS 1367, the type of Zygosaccharomyces bisporus Anderson, belongs to Pichia kluyveri Bedford var. kluyveri. Strain CBS 989, the type of Cryptococcus californicus Anderson & Skinner, represents a distinct species, for which a new combination, Candida californica comb. nov., is proposed. The taxonomic status of strains CBS 189, the type of Pichia calliphorae Klöcker, and CBS 214, the type of Pichia derossii Castelli, remain to be studied further. Their D1/D2 sequences and chromosomal DNA banding patterns were similar to those of P. membranifaciens, but their internal transcribed spacer sequences differed significantly.

Kazachstania aquatica sp. nov. and Kazachstania solicola sp. nov., novel ascomycetous yeast species.

The unidentified strains AS 2.0706(T), preserved in the China General Microbiological Culture Collection Center (CGMCC), Academia Sinica, Beijing, China, and CBS 6904(T), preserved in the Centraalbureau voor Schimmelcultures (CBS), Utrecht, The Netherlands, were shown to represent two novel ascomycetous yeast species of the genus Kazachstania by 18S rDNA, internal transcribed spacer (ITS) region (including 5.8S rDNA) and 26S rDNA D1/D2 domain sequence analysis and electrophoretic karyotype comparison. The names Kazachstania aquatica sp. nov. and Kazachstania solicola sp. nov. are proposed for strains AS 2.0706(T) and CBS 6904(T), respectively. Phylogenetically, the two novel species are closely related to Kazachstania aerobia, Kazachstania servazzii and Kazachstania unispora.

Kazachstania aerobia sp. nov., an ascomycetous yeast species from aerobically deteriorating corn silage.

In an investigation of the yeast biota involved in silage deterioration, a considerable number of strains belonging to Saccharomyces and related genera were isolated from aerobically deteriorating corn silage in Tochigi, Japan. Analysis of sequences of the internal transcribed spacer and the large-subunit rRNA gene D1/D2 domain and electrophoretic karyotyping indicated that two of the strains, NS 14(T) and NS 26, represent a novel species with close phylogenetic relationships to Kazachstania servazzii and Kazachstania unispora. It is proposed that the novel species be named Kazachstania aerobia sp. nov., with NS 14(T) (=AS 2.2384(T)=CBS 9918(T)) as the type strain.