Population Structure and Multidrug Resistance of Non-O1/Non-O139 Vibrio cholerae in Freshwater Rivers in Zhejiang, China

Metagenomic assembled genomes profile potential pathogens and antibiotic-resistant pathogens in an urban river

The microbiological safety of urban rivers that flow through cities is crucial to local public health. However, detailed insights into the key characteristics of pathogens in urban rivers remain limited due to the lack of efficient high-throughput analysis tools. In this study, a comprehensive profiling of potential pathogens, antibiotic-resistant pathogens (ARPs), and multidrug-resistant pathogens (MDRPs) in the Hai River, which runs through the central city of Tianjin, was conducted using metagenomic assembled genome (MAG) analysis. Of the 436 recovered MAGs assigned to 430 species, 110 MAGs were identified as potential pathogens due to the presence of virulence factors (VFs), whereas 19 MAGs containing both antibiotic resistance genes (ARGs) and VFs, were classified as potential ARPs, predominantly belonging to the genera Kluyvera, Enterobacter, and Klebsiella. Notably, nine species of MDRPs, including Enterobacter kobei, Klebsiella pneumoniae, Morganella morganii, Kluyvera intermedia, Aeromonas salmonicida, Rahnella aceris, Hafnia paralvei, the unidentified species Sep. D_bin46, and Vibrio cholerae, exhibited resistance to multidrug, beta-lactam, polymyxin, bacitracin, tetracycline, other peptide antibiotics, macrolide-lincosamide-streptogramin, aminoglycoside, and chloramphenicol. The unknown pathogen Sep. D_bin46, classified under Aeromonas, showed resistance to both carbapenems and polymyxins. The strong co-occurrence of ARGs, VFs, and mobile genetic elements suggests a significant risk of ARGs and VFs transfers among MDRPs with last-resort ARGs (r > 0.8; p < 0.05). Interestingly, the sampling location significantly influenced the presence of pathogens, ARPs, and MDRPs carrying last-resort ARGs in the water. Notably, their abundance was lower downstream of the Hai River compared to upstream. This observation suggests that urban environmental sanitation facilities may be more effective in reducing contaminants as the river flows from upstream to downstream. Nevertheless, the presence of pathogens, ARPs, and MDRPs with last-resort ARGs in the water underscores the ongoing microbiological risks associated with urban surface water.

Characterization of Vibrio cholerae from the Jukskei River in Johannesburg, South Africa

The current study aimed to isolate and characterize Vibrio cholerae isolated from the Jukskei River, one of the largest Rivers in Johannesburg, South Africa. Water samples collected from the Jukskei River were subjected to culture-based methods for the detection and isolation of V. cholerae. Twenty-four V. cholerae were isolated, confirmed using real-time PCR, and sequenced using the MInION portable nanopore-sequencing device. Reference-based genome assemblies were constructed from the raw reads using the EPI2ME software followed by bioinformatics analysis using the Centre for Genomic Epidemiology website. All the V. cholerae isolates isolated from the Jukskei River were classified as non-O1/non-O139 and none of the isolates harbored the cholera toxin gene, ctxA. All 24 V. cholerae isolates belonged to sequence type 741, virulent genes including toxR, vspD, als, hlyA, makA, and rtxA as well as the Vibrio pathogenicity island 2 were detected amongst the isolates. Antimicrobial resistance genes (parC, varG, and gyrA) were detected in 83% of isolates. Although V. cholerae non-O1/non-O139 are not associated with epidemic cholera they can still cause mild to life-threatening illnesses. Therefore, increased surveillance should be considered to better understand the public health risks to the local community.

Whole Genome Sequencing of a Non-O1/O139-Group Vibrio cholerae Isolated from a Patient with a Bloodstream Infection

Background

Diarrhea caused by non-O1/O139-group V. cholerae (NOVC) tends to be mild and can be readily overlooked. In this report, a NOVC strain designated XXM was isolated from the blood of a 68-year-old male undergoing surgical treatment for a bile duct malignancy in October 2023.

Methods

XXM was identified through a matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Virulence genes were detected using a V. cholerae ctxA/ctxB virulence gene dual real-time fluorescent PCR kit. AST-GN13 and AST-GN334 cards were used to test the resistance against 16 antibiotics with a Vitek2 compact system. The genomic and phylogenetic characteristics of XXM were established through whole genome sequencing (WGS).

Results

Serum agglutination tests revealed the isolate to be a non-O1/non-O139 strain. The strain was sensitive to all 16 tested antibiotics and did not carry the ctxA/ctxB gene. MLST analyses identified the XXM strain as ST1538. WGS analyses identified 8 classes of virulence genes with different functions. A total of 3.541 bacterial genes, including 3.482 from V. cholerae, were annoted using the Non-Redundant Protein Sequence (NR) database. Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses annotated 32 genes including 17 key proteins involved in the V. cholerae biofilm pathway. Comparative analyses using the Pathogen Host Interactions Database (PHI) identified the YbeY gene. Evolutionary genealogy of genes: Non-supervised Orthologous Groups (eggNOG) was used to annotate 3280 genes in 21 categories. Phylogenetic analyses revealed that strain XXM was closely related to V. cholerae strain Man9.

Conclusion

The XXM carries multiple virulence genes, and this genomic analysis of the XXM in comparison with other NOVC strains provides important information for an improved understanding of the pathogenicity of NOVC in clinical samples.

Genomic evidence of two-staged transmission of the early seventh cholera pandemic

The seventh cholera pandemic started in 1961 in Indonesia and spread across the world in three waves in the decades that followed. Here, we utilised genomic evidence to detail the first wave of the seventh pandemic. Genomes of 22 seventh pandemic Vibrio cholerae isolates from 1961 to 1979 were completely sequenced. Together with 152 publicly available genomes from the same period, they fell into seven phylogenetic clusters (CL1-CL7). By multilevel genome typing (MGT), all were assigned to MGT2 ST1 (Wave 1) except three isolates in CL7 which were typed as MGT2 ST2 (Wave 2). The Wave 1 seventh pandemic expanded in two stages, with Stage 1 (CL1-CL5) spread across Asia and Stage 2 (CL6 and CL7) spread to the Middle East and Africa. Three non-synonymous mutations, one each, in three regulatory genes, csrD (global regulator), acfB (chemotaxis), and luxO (quorum sensing) may have critically contributed to its pandemicity. The three MGT2 ST2 isolates in CL7 were the progenitors of Wave 2 and evolved from within Wave 1 with acquisition of a novel IncA/C plasmid. Our findings provide new insight into the evolution and transmission of the early seventh pandemic, which may aid future cholera prevention and control.

Epidemiological and genetic characterization of multidrug-resistant non-O1 and non-O139 Vibrio cholerae from food in southern China

This study reports a comprehensive epidemiological and genetic analysis of V. cholerae strains, specifically non-O1/non-O139 serogroups, isolated from animal-derived food samples in Guangdong province from 2015 to 2019. A total of 21 V. cholerae strains were obtained, which exhibited high resistance rates for nalidixic acid (57.14 %, 12/21), ampicillin (33.33 %, 7/21), and ciprofloxacin (19.05 %, 4/21). The quinolone resistance-related gene, qnrVC, was prevalent in 80.95 % (17/21) of the isolates. Additionally, chromosomally mediated quinolone-resistance mutations, including mutations in GyrA at position 83 (S83I) and ParC at position 85 (S85L), were detected in 47.62 % of the isolates. The combination of target mutation and qnrVC genes was shown to mediate resistance or intermediate resistance to ciprofloxacin in V. cholerae. Furthermore, an IncC-type conjugative plasmid carrying thirteen antibiotic resistance genes, including genes conferring resistance to two clinically important antibiotics, cephalosporins and fluoroquinolones, was identified in the shrimp-derived strain Vc516. While none of our food isolates harbored the toxigenic CTX- and TCP-encoding genes, they did possess genes encoding toxins such as HlyA and Autoinducer-2. Notably, some V. cholerae strains from this study exhibited a close genetic relationship with clinical strains, suggesting their potential to cause human infections. Taken together, this study provides a comprehensive view of the epidemiological features and genetic basis of antimicrobial resistance and virulence potential of V. cholerae strains isolated from food in southern China, thereby advancing our understanding of this important pathogen.

Emergence and genomic insights of non-pandemic O1 Vibrio cholerae in Zhejiang, China

IMPORTANCE

It is well recognized that only Vibrio cholerae O1 causes cholera pandemics. However, not all O1 strains cause pandemic-level disease. In this study, we analyzed non-pandemic O1 V. cholerae isolates from the 1960s to the 1990s from China and found that they fell into three lineages, one of which shared the most recent common ancestor with pandemic O1 strains. Each of these non-pandemic O1 lineages has unique properties that contribute to their capacity to cause cholera. The findings of this study enhanced our understanding of the emergence and evolution of both pandemic and non-pandemic O1 V. cholerae.

Antibiotic resistance and virulence genes profiling of Vibrio cholerae and Vibrio mimicus isolates from some seafood collected at the aquatic environment and wet markets in Eastern Cape Province, South Africa

The current study determines the density of Vibrio spp. and isolates V. cholerae and Vibrio mimicus from fish-anatomical-sites, prawn, crab and mussel samples recovered from fish markets, freshwater and brackish water. Virulence and antibiotic resistance profiling of isolates were carried out using standard molecular and microbiology techniques. Vibrio spp. was detected in more than 90% of samples [134/144] and its density was significantly more in fish than in other samples. Vibrio. cholerae and V. mimicus were isolated in at least one sample of each sample type with higher isolation frequency in fish samples. All the V. cholerae isolates belong to non-O1/non-O139 serogroup. One or more V. cholerae isolates exhibited intermediate or resistance against each of the eighteen panels of antibiotics used but 100% of the V. mimicus were susceptible to amikacin, gentamycin and chloramphenicol. Vibrio cholerae exhibited relatively high resistance against polymyxin, ampicillin and amoxicillin/clavulanate while V. mimicus isolates exhibited relatively high resistance against nitrofurantoin, ampicillin and polymixin. The multiple-antibiotic-resistance-index [MARI] for isolates ranges between 0 and 0.67 and 48% of the isolates have MARI that is >0.2 while 55% of the isolates exhibit MultiDrug Resistance Phenotypes. The percentage detection of acc, ant, drf18, sul1, mcr-1, blasvh, blaoxa, blatem, blaoxa48, gyrA, gyrB and parC resistance-associated genes were 2%, 9%, 14%, 7%, 2%, 25%, 7%, 2%, 2%, 32%, 25% and 27% respectively while that for virulence-associated genes in increasing other was ace [2%], tcp [11%], vpi [16%], ompU [34%], toxR [43%], rtxC [70%], rtxA [73%] and hyla [77%]. The study confirmed the potential of environmental non-O1/non-O139 V. cholerae and V. mimicus to cause cholera-like infection and other vibriosis which could be difficult to manage with commonly recommended antibiotics. Thus, regular monitoring of the environment to create necessary awareness for this kind of pathogens is important in the interest of public health.

Genomic Epidemiology of Vibrio cholerae O139, Zhejiang Province, China, 1994-2018

Cholera caused by Vibrio cholerae O139 was first reported in Bangladesh and India in 1992. To determine the genomic epidemiology and origins of O139 in China, we sequenced 104 O139 isolates collected from Zhejiang Province, China, during 1994-2018 and compared them with 57 O139 genomes from other countries in Asia. Most Zhejiang isolates fell into 3 clusters (C1-C3), which probably originated in India (C1) and Thailand (C2 and C3) during the early 1990s. Different clusters harbored different antimicrobial resistance genes and IncA/C plasmids. The integrative and conjugative elements carried by Zhejiang isolates were of a new type, differing from ICEVchInd4 and SXTMO10 by single-nucleotide polymorphisms and presence of genes. Quinolone resistance-conferring mutations S85L in parC and S83I in gyrA occurred in 71.2% of the Zhejiang isolates. The ctxB copy number differed among the 3 clusters. Our findings provided new insights for prevention and control of O139 cholera .

Antimicrobial Resistance and Molecular Characterization of Citrobacter spp. Causing Extraintestinal Infections

Objectives

This prospective study was carried out to investigate molecular characteristics and antimicrobial susceptibility patterns of Citrobacter spp. from extraintestinal infections.

Methods

Forty-six clinical Citrobacter spp. isolates were isolated from hospital patients with extraintestinal infections and analyzed by multilocus sequence typing (MLST) using seven housekeeping genes. Antimicrobial susceptibility testing was performed by disk diffusion method according to the Clinical and Laboratory Standards Institute (CLSI) recommendations. Adhesion and cytotoxicity to HEp-2 cells were assessed.

Results

The 46 clinical Citrobacter spp. isolates were typed into 38 sequence types (STs), 9 of which belonged to four clonal complexes (CCs). None of the isolates shared the same ST or CCs with isolates from other countries or from other parts of China. Over half of the isolates were multidrug-resistant (MDR), with 17/26 C. freundii, 5/6 C. braakii, and 3/14 C. koseri isolates being MDR. Moreover, four isolates were carbapenem resistant with resistance to imipenem or meropenem. Among eight quinolone resistant C. freundii, all had a mutation in codon 59 (Thr59Ile) in quinolone resistance determining region of the gyrA gene. Only a small proportion of the isolates were found to be highly cytotoxic and adhesive with no correlation to sample sources.

Conclusions

There was a diverse range of Citrobacter isolates causing extraintestinal infections and a high prevalence of MDR.