Human- and infrastructure-associated bacteria in greywater.

Greywater, the wastewater from sinks, showers and laundry, is an understudied environment for bacterial communities. Most greywater studies focus on quantifying pathogens, often via proxies used in other wastewater, like faecal indicator bacteria; there is a need to identify more greywater-appropriate surrogates, like Staphylococcus sp. Sequencing-based studies have revealed distinct communities in different types of greywater as well as in different parts of greywater infrastructure, including biofilms on pipes, holding tanks and filtration systems. The use of metagenomic sequencing provides high resolution on both the taxa and genes present, which may be of interest in cases like identifying pathogens and surrogates relevant to different matrices, monitoring antibiotic resistance genes and understanding metabolic processes occurring in the system. Here, we review what is known about bacterial communities in different types of greywater and its infrastructure. We suggest that wider adoption of environmental sequencing in greywater research is important because it can describe the entire bacterial community along with its metabolic capabilities, including pathways for removal of nutrients and organic materials. We briefly describe a metagenomic dataset comparing different types of greywater samples in a college dormitory building to highlight the type of questions these methods can address. Metagenomic sequencing can help further the understanding of greywater treatment for reuse because it allows for identification of new pathogens or genes of concern.

Characterization of the relative importance of human- and infrastructure-associated bacteria in grey water: a case study.

AIMS: Development of efficacious grey water (GW) treatment systems would benefit from detailed knowledge of the bacterial composition of GW. Thus, the aim of this study was to characterize the bacterial composition from (i) various points throughout a GW recycling system that collects shower and sink handwash (SH) water into an equalization tank (ET) prior to treatment and (ii) laundry (LA) water effluent of a commercial-scale washer. METHODS AND RESULTS: Bacterial composition was analysed by high-throughput pyrosequencing of the 16S rRNA gene. LA was dominated by skin-associated bacteria, with Corynebacterium, Staphylococcus, Micrococcus, Propionibacterium and Lactobacillus collectively accounting for nearly 50% of the total sequences. SH contained a more evenly distributed community than LA, with some overlap (e.g. Propionibacterium), but also contained distinct genera common to wastewater infrastructure (e.g. Zoogloea). The ET contained many of these same wastewater infrastructure-associated bacteria, but was dominated by genera adapted for anaerobic conditions. CONCLUSIONS: The data indicate that a relatively consistent set of skin-associated genera are the dominant human-associated bacteria in GW, but infrastructure-associated bacteria from the GW collection system and ET used for transient storage will be the most common bacteria entering GW treatment and reuse systems. SIGNIFICANCE AND IMPACT OF THE STUDY: This study is the first to use high-throughput sequencing to identify the bacterial composition of various GW sources.

Development and evaluation of an off-the-slide genotyping technique for identifying Giardia cysts and Cryptosporidium oocysts directly from US EPA Method 1623 slides.

AIMS: This study developed and systematically evaluated performance and limit of detection of an off-the-slide genotyping procedure for both Cryptosporidium oocysts and Giardia cysts. METHODS AND RESULTS: Slide standards containing flow-sorted (oo)cysts were used to evaluate the off-the-slide genotyping procedure by microscopy and PCR. Results show approximately 20% of cysts and oocysts are lost during staining. Although transfer efficiency from the slide to the PCR tube could not be determined by microscopy, it was observed that the transfer process aided in the physical lysis of the (oo)cysts likely releasing DNA. PCR detection rates for a single event on a slide were 44% for Giardia and 27% for Cryptosporidium, and a minimum of five cysts and 20 oocysts are required to achieve a 90% PCR detection rate. A Poisson distribution analysis estimated the relative PCR target densities and limits of detection, it showed that 18 Cryptosporidium and five Giardia replicates are required for a 95% probability of detecting a single (oo)cyst on a slide. CONCLUSIONS: This study successfully developed and evaluated recovery rates and limits of detection of an off-the-slide genotyping procedure for both Cryptosporidium and Giardia (oo)cysts from the same slide. SIGNIFICANCE AND IMPACT OF THE STUDY: This off-the-slide genotyping technique is a simple and low cost tool that expands the applications of US EPA Method 1623 results by identifying the genotypes and assemblages of the enumerated Cryptosporidium and Giardia. This additional information will be useful for microbial risk assessment models and watershed management decisions.

SARS-CoV-2 monitoring at three sewersheds of different scales and complexity demonstrates distinctive relationships between wastewater measurements and COVID-19 case data.

Wastewater monitoring of SARS-CoV-2 presents a means of tracking COVID-19 community infection dynamics on a broader geographic scale. However, accounting for environmental and sample-processing losses may be necessary for wastewater measurements to readily inform our understanding of infection prevalence. Here, we present measurements of the SARS-CoV-2 N1 and N2 gene targets from weekly wastewater samples at three sites in Hamilton County, Ohio, during an increase and subsequent decline of COVID-19 infections. The concentration of N1 or N2 RNA in wastewater, measured over the course of six months, ranged from below the detection limit to over 104 gene copies/l, and correlated with case data at two wastewater treatment plants, but not at a sub-sewershed-level sampling site. We also evaluated the utility of a broader range of variables than has been reported consistently in previous work, in improving correlations of SARS-CoV-2 concentrations with case data. These include a spiked matrix recovery control (OC43), flow-normalization, and assessment of fecal loading using endogenous fecal markers (HF183, PMMoV, crAssphage). We found that adjusting for recovery, flow, and fecal indicators increased these correlations for samples from a larger sewershed (serving ~488,000 people) with greater industrial and stormwater inputs, but raw N1/N2 concentrations corresponded better with case data at a smaller, residential-oriented sewershed. Our results indicate that the optimal adjustment factors for correlating wastewater and clinical case data moving forward may not be generalizable to all sewersheds.

Twenty-first century molecular methods for analyzing antimicrobial resistance in surface waters to support One Health assessments.

Antimicrobial resistance (AMR) in the environment is a growing global health concern, especially the dissemination of AMR into surface waters due to human and agricultural inputs. Within recent years, research has focused on trying to understand the impact of AMR in surface waters on human, agricultural and ecological health (One Health). While surface water quality assessments and surveillance of AMR have historically utilized culture-based methods, culturing bacteria has limitations due to difficulty in isolating environmental bacteria and the need for a priori information about the bacteria for selective isolation. The use of molecular techniques to analyze AMR at the genetic level has helped to overcome the difficulties with culture-based techniques since they do not require advance knowledge of the bacterial population and can analyze uncultivable environmental bacteria. The aim of this review is to provide an overview of common contemporary molecular methods available for analyzing AMR in surface waters, which include high throughput real-time polymerase chain reaction (HT-qPCR), metagenomics, and whole genome sequencing. This review will also feature how these methods may provide information on human and animal health risks. HT-qPCR works at the nanoliter scale, requires only a small amount of DNA, and can analyze numerous gene targets simultaneously, but may lack in analytical sensitivity and the ability to optimize individual assays compared to conventional qPCR. Metagenomics offers more detailed genomic information and taxonomic resolution than PCR by sequencing all the microbial genomes within a sample. Its open format allows for the discovery of new antibiotic resistance genes; however, the quantity of DNA necessary for this technique can be a limiting factor for surface water samples that typically have low numbers of bacteria per sample volume. Whole genome sequencing provides the complete genomic profile of a single environmental isolate and can identify all genetic elements that may confer AMR. However, a main disadvantage of this technique is that it only provides information about one bacterial isolate and is challenging to utilize for community analysis. While these contemporary techniques can quickly provide a vast array of information about AMR in surface waters, one technique does not fully characterize AMR nor its potential risks to human, animal, or ecological health. Rather, a combination of techniques (including both molecular- and culture-based) are necessary to fully understand AMR in surface waters from a One Health perspective.

Source of Pneumocystis carinii in recurrent episodes of pneumonia in AIDS patients.

OBJECTIVE: To investigate the hypothesis that P.carinii special form hominis (P.c. hominis) reinfections occur in AIDS patients. DESIGN: Polymerase chain reaction (PCR) was used to identify patients who had different P.c. hominis mitochondrial DNA (mtrRNA) genotypes in the two disease episodes (genotype switching). P.c. hominis from these patients were analysed with an allele-specific PCR (ASP) assay to determine whether the genotype found in a second disease episode were present in the first disease episode. To assess the possible contributions of other factors to genotype switching, data on the sampling method and drugs used to treat each patient were compiled. METHODS: Bronchoalveolar lavage fluid (BALF) was subjected to PCR using primers that amplified a 346 base-pair region of the mtrRNA locus known to be polymorphic at site 85 of the amplicon. Samples from patients in whom the P.c. hominis mtrRNA sequence had changed at site 85 in the two disease episodes were studied by ASP in which primers designed to prime synthesis from the allele of the mtrRNA sequence found in second episodes of disease were used in PCR of P.c. hominis DNA from first episodes of P. carinii pneumonia. RESULTS: In four of five patients who produced P.c. hominis with different mtrRNA genotypes during first and second episodes, ASP did not detect the second-episode genotype in first-episode BALF. There was no evidence that either sampling methods or drug-resistance contributed to genotype switching. CONCLUSIONS: P.c. hominis reinfections occur in AIDS patients.

Isolation and characterization of mouse nasal lymphocytes.

A method for isolation of mouse nasal lymphocytes is described. Lymphocyte-enriched suspensions are examined for their morphologic, surface immune staining and mitogenic characteristics. This method will allow testing of immune function in the upper respiratory tract of the mouse.

Identification of porcine Pneumocystis carinii as a genetically distinct organism by DNA amplification.

DNA was amplified from lung samples from three piglets infected with Pneumocystis carinii, using oligonucleotide primers designed to the P. carinii mitochondrial large subunit ribosomal RNA gene. The nucleotide sequence of the amplification product was determined and indicated lack of sequence variation among these pig-derived P. carinii samples at this locus. The data showed that porcine P. carinii was genetically distinct from P. carinii isolated from other mammalian host species.

Influenza-specific ELISA IgA and IgG predict severity of influenza disease in subjects prescreened with hemagglutination inhibition.

Four influenza A challenge studies were performed over a period of three years using the same dose of one virus pool. The first three studies were conducted two influenza seasons apart from the last study. In all four studies only subjects with screening hemagglutination inhibition (HAI) antibody titers less than or equal to 1:8 in sera were accepted as study subjects. The rate of infection after influenza challenge was 96% (25 of 26) in the first three studies, and only 73% (8 of 11) in the last study (P less than 0.04). The rate of influenza illness in the first three studies was 62% (16 of 26), and only 9% (1 of 11) in the last study (all subjects: P = 0.003; infected subjects: P = 0.01). Even though screening HAI titers were comparable between groups, prechallenge serum influenza-specific IgG titers correlated inversely with respiratory symptoms (P = 0.04). Prechallenge nasal wash influenza-specific IgA titers were lower in subjects who developed influenza illness (P = 0.03). Prechallenge influenza-specific nasal wash ELISA-IgA titers and serum ELISA-IgG titers predicted influenza severity in patients prescreened by HAI during influenza challenge studies.

Sequences of Pneumocystis carinii f. sp. hominis strains associated with recurrent pneumonia vary at multiple loci.

The sequences of the internal transcribed spacer (ITS) of Pneumocystis carinii f. sp. hominis strains from 7 of 15 AIDS patients were found to vary during discrete episodes of P. carinii pneumonia. Changes in the ITS sequence correlated with changes in the mitochondrial large-subunit rRNA sequence. The coincidence of changes in the sequences of the ITS, which is located in the nucleus, with changes in a mitochondrial gene excludes mutation as the cause of the genetic differences between P. carinii f. sp. hominis strains isolated during different episodes of P. carinii pneumonia and supports the hypothesis that recurrent P. carinii pneumonia is caused by reinfection rather than by reactivation of latent organisms. Thus, limiting the exposure of immunocompromised patients to P. carinii f. sp. hominis should help prevent P. carinii pneumonia.

Genetics of surface antigen expression in Pneumocystis carinii.

This article reviews the molecular genetic data pertaining to the major surface glycoprotein (MSG) gene family of Pneumocystis carinii and its role in surface variation and compares this fungal system to antigenic variation systems in the protozoan Trypanosoma brucei and the bacteria Borrelia spp.

Rapid recovery in mice after combined nasal/oral immunization with killed respiratory syncytial virus.

Based on the concept of a common mucosal immune system, the murine gastrointestinal tract was inoculated (oral) with three doses (5, 20, and 40 micrograms) of UV-inactivated respiratory syncytial virus (RSV) in order to elicit a virus-specific immune response in the respiratory tract. Only the 40 micrograms dose induced significant (P less than 0.01) anti-RSV-IgG rises in serum and lung wash compared to controls. To improve the immune response, mice were immunized intranasally under light anesthesia with the same 40 micrograms dosage regimen of killed RSV so that each dose passed through the nose and was swallowed. This combined nasal/oral immunization stimulated anti-RSV-IgG in serum, lung wash and nasal wash (P less than 0.001) and anti-RSV-IgA in lung and nasal wash (P less than 0.001) that were comparable to levels after infection with live RSV. Three days after challenge with live RSV, mice given combined nasal/oral immunization showed suppressed nasal virus shedding (P = 0.025). Nasal virus shedding correlated inversely with concentrations of anti-RSV-Ig in nasal secretions but did not correlate with concentrations in serum.

Similar subclass antibody responses after intranasal immunization with UV-inactivated RSV mixed with cholera toxin or live RSV.

To determine the effect of cholera toxin as a mucosal adjuvant on the class and subclass antibody response to RSV, mice were immunized intranasally with different doses of live RSV or UV-inactivated RSV mixed with cholera toxin. A single 10(6) pfu dose of live RSV and a single 50 micrograms dose of UV-inactivated RSV mixed with cholera toxin produced comparable serum IgG and respiratory secretion IgG and IgA antibody titers. Subclass antibody titers to whole RSV were also comparable between these two immunizing regimens. A predominance of IgG2a subclass to whole RSV was found for both regimens. The quantity of serum total IgG antibody to glycoprotein F or glycoprotein G did not differ between these regimens. The serum IgG subclass antibody response to both glycoprotein F and G was also not significantly different between regimens. Cholera toxin as a mucosal adjuvant can stimulate class and subclass antibody responses to UV-inactivated RSV that are similar in quantity and distribution to those after live RSV infection.

Comparison of class and subclass antibody response to live and UV-inactivated RSV administered intranasally in mice.

To determine the effect of viral dose and replication on the subclass antibody response to RSV, mice were immunized intranasally with different doses of live RSV (10(4)-10(6) pfu) and compared to mice given an immunizing regimen of UV-inactivated RSV. Mice given the 10(6) pfu dose of live RSV and mice given the 40 micrograms dose of UV-inactivated RSV had comparable class specific antibody responses to whole RSV in serum and respiratory secretions. Serum from these two groups of mice were then compared for IgG subclass response to whole RSV. A predominance of IgG2a subclass antibody was found for both immunizing regimens, and no significant differences in subclass proportions were noted between regimens. These two regimens were then compared for serum total IgG response to RSV surface glycoproteins F and G. The serum IgG response to these glycoproteins was lower after immunization with UV-inactivated RSV than after live-RSV immunization (F: P = 0.03; G: P less than 0.05), even though the serum IgG response of the two groups to whole RSV was comparable. The IgG subclass response to surface glycoproteins was evaluated for live RSV immunization. The proportions of subclass antibody responses to glycoprotein F were comparable to the subclass response proportions to whole RSV and were not characteristic of a T-dependent response pattern. The subclass profile for glycoprotein G was not comparable to that of whole RSV but was suggestive of a T-independent response pattern.

Time between inoculations and karyotype forms of Pneumocystis carinii f. sp. Carinii influence outcome of experimental coinfections in rats.

The prevalence of Pneumocystis carinii pneumonia (PCP) in humans caused by more than a single genotype has been reported to range from 10 to 67%, depending on the method used for detection (3, 19). Most coinfections were associated with primary rather than recurrent disease. To better understand the factors influencing the development of coinfections, the time periods between inoculations and the genotype of the infecting organisms were evaluated in the chronically immunosuppressed-inoculated rat model of PCP. P. carinii f. sp. carinii infecting rats differentiated by karyotypic profiles exhibit the same low level of genetic divergence manifested by organisms infecting humans. P. carinii f. sp. carinii karyotype forms 1, 2, and 6 were inoculated into immunosuppressed rats, individually and in dual combinations, spaced 0, 10, and 20 days apart. Infections comprised of both organism forms resulted from admixtures inoculated at the same time. In contrast, coinfections did not develop in most rats, where a 10- or 20-day gap was inserted between inoculations; only the first organism form inoculated was detected by pulsed-field gel electrophoresis in the resultant infection. Organism burdens were reduced with combinations of forms 1 and 2 spaced 20 days apart but not in rats inoculated with forms 1 and 6. A role for the host response in the elimination of the second population and in reduction of the organism burden was suggested by the lack of direct killing of forms 1 and 2 in an in vitro ATP assay, by reduction of the burden by autoclaved organisms, and by the specific reactions of forms 1 and 2 but not forms 1 and 6. These studies showed that the time between inoculations was critical in establishing coinfections and P. carinii f. sp. carinii karyotype profiles were associated with differences in biological responses. This model provides a useful method for the study of P. carinii coinfections and their transmission in humans.

Genetic variation among Pneumocystis carinii hominis isolates in recurrent pneumocystosis.

Pneumocystis carinii hominis is a ubiquitous organism that causes pneumonia in immunocompromised persons. Paired P. carinii hominis isolates from human immunodeficiency virus-infected persons who had two episodes of pneumocystosis were examined for genetic heterogeneity. Genetic variation was detected by sequence comparison of a portion of the mitochondrial ribosomal RNA gene. In 5 of 10 patients experiencing two episodes of pneumocystosis, genetically distinct isolates were associated with each episode. These included 4 of 6 patients whose second episode of pneumocytosis occurred > 6 months after their initial bout. The genetic data support the hypothesis that some recurrent episodes of P. carinii hominis pneumonia are caused by reinfection rather than by reactivation of latent infection.

Differential effect of amantadine hydrochloride on the systemic and local immune response to influenza A.

Anti-influenza serum and nasal antibody titers were followed during a double-blind, placebo-controlled, randomized study assessing the prophylactic efficacy of 50, 100, and 200 mg/day of amantadine hydrochloride against experimental challenge with influenza A/Beth/1/85. The geometric mean titers (GMT) of serum hemagglutination inhibition antibody (P = .05) as well as serum influenza-specific IgG (P = .004) were significantly lower for all amantadine groups when compared to placebo. There were no significant differences in the GMT of either type of serum antibody titer comparing any of the three amantadine groups. Viral titers were also lower in the amantadine groups compared to the placebo group and not significantly different among the three amantadine groups. Nasal antibody titers in the 100-mg and 200-mg amantadine groups were significantly lower than placebo titers (P = .002). Nasal antibody titers in the 50-mg amantadine group did not differ significantly from titers in the placebo group (P = .892). Possible reasons for the differential effect of amantadine on the serum and nasal antibody response are discussed.

Expression and complexity of the PRT1 multigene family of Pneumocystis carinii.

Pneumocystis carinii has a multigene family, PRT1, that encodes proteins with homology to KEX2-like proteases. PRT1 genes cluster with MSG genes near the telomeres and, like MSG, PRT1 proteins seem to be surface-expressed. The clustering of PRT1 and MSG genes suggested that expression of the two multigene families might be coordinated. Studying gene expression in P. carinii has been hampered by the lack of a culture system, and by lack of clonality in P. carinii populations in naturally infected rats, the host of this fungus. Heterogeneity can be reduced, however, by low-dose intratracheal inoculation, which can produce P. carinii populations dominated by organisms derived from a single progenitor. To study PRT1 expression, nude rats were inoculated with approximately 10 P. carinii each. The clonality of the P. carinii populations from inoculated rats was assessed by analysis of the UCS locus, a site in the genome that is known to be very heterogeneous in naturally infected rats, but nearly homogeneous in rats infected by low-dose intratracheal inoculation. Each of the populations had the same MSG gene at the UCS locus in at least 80 % of the organisms. To investigate PRT1 gene expression, RNA was amplified using primers that amplify numerous PRT1 genes. Seventy-four cloned cDNAs were sequenced, including at least 12 clones from each population of P. carinii. Many differently expressed PRT1 sequences were identified in each population, and a total of 45 different sequences were detected. However, the same PRT1 sequence was present in 15 of 74 plasmids and was found in 3 of the 5 P. carinii populations, suggesting that some PRT1 genes may be either more commonly expressed or expressed at a higher level. These data show that many members of the PRT1 gene family can be expressed in populations of P. carinii derived from few progenitors and suggest that the regulation of this family is different from that governing expression of the MSG gene family.